if you're studying for the AP Bio exam and you're feeling nervous or anxious that makes so much sense the AP Bio exam is tough but don't worry in this video we're going to go through the entire course every unit every topic you'll learn everything that you need to know so that you can crush it on the AP Bio exam my name is Glenn woken Feld also known as Mr W and I love teaching b i o l o g y to help you study I put together a checklist it includes everything that you need to get ready for to study for this test you can download it at AP bios. checklist unit one focuses on the chemistry and properties of water and hydrogen bonding The Elements of Life and the four biomolecule families that all living things are made of carbohydrates lipids proteins and the nucleic acids DNA and RNA first thing to note is that water is a polar molecule there's unequal electron sharing between oxygen and hydrogen and so there's a partial negative region over here there's partial positive regions over here note that hydrogen bonds are intermolecular bonds they're between molecules not within molecules like Cove valent bonds or ionic bonds or anything like that what's happening is that the oxygen is partially negative the hydrogen is partially positive and the hydrogen bond is a weak Bond that forms between those two areas hydrogen bonds are much weaker much much weaker than calent bonds ionic bonds any of those inra molecular bonds using the diagram below as an example describe how hydrogen bonds can form between molecules besides water the key idea is that hydrogen bonds are everywhere they're not just within water they're essential in biology in general so in this example there are two hydrogen bonds and here's one oxygen to hydrogen over here here's another one between nitrogen and hydrogen this is between the nitrogenous based adenine and thyine and these are the hydrogen bonds that hold together DNA hydrogen bonds again are essential they're um key to the structure of DNA RNA proteins you'll meet them again and again throughout your biology course and they're important to know for the AP Bio exam as well so now let's look at some of the consequences so describe cohesion adhesion and surface tension and explain how these Key properties of water result from hydrogen bonding cohesion that's hydrogen bonds between water molecules so this is cohesion right here and it's responsible for many of water's very peculiar properties it's a very small molecule but it has a very high heat of vaporization takes a lot of energy to get water to evaporate a high specific heat it can hold a lot of heat and it has high surface tension which we'll talk about below adhesion is water sticking to other stuff so like for example here you see hydrogen bonds between water molecule and the um cellulose walls that make up the conductive tubes of plants which are also called xylm a phenomenal thing is called transpiration which is uh how water gets pulled up to the top of trees and that's all based on water's ability to cohere to other water molecules and to adhere to the sides of the conductive tubes of plants as water evaporates from the top and finally surface tension here we see a paper clip that's resting on a net of water molecules and of course that's ridiculously out of scale you can see how that's keeping this paper clip from sinking down and here it's the force exerted by water molecules on the surface of a body of water creates a kind of web or net upon the surface in terms of hydrogen ions hydroxide ions and pH describe the difference between an acidic and a basic solution first thing to note is that um acidic Solutions are solutions that have more hydrogen ions that here's a hydrogen ion over here than hydroxide ion that's represented by o over here so if you dissolve this in water you wind up having lots of hydrogen ions and that pushes the PH down all right um the pH is below seven in bases there are more hydroxide ions than hydrogen ions so if you dissolve sodium hydroxide in water you wind up with a lot more hydroxide ions and that pushes the pH in this direction pH is above seven and one thing that I want to emphasize is that you don't really need to know about pH for the AP exam directly there won't be a question about it but it might be part of an frq or a multiple choice questions so it's an essential underlying concept Elements of Life topic 1.2 of a biology so what do you need to know about the Elements of Life carbon hydrogen nitrogen oxygen phosphorus and sulfur sometimes referred to as chops carbon is the central element in all of the molecules that make up living things hydrogen often used in energy exchange uh we have molecules like NAD and nadh which show up in cellular respiration NAD plus is the low energy form nadh is the high energy form you see stuff like that over and over again and also hydrogen as an ion as a hydrogen ion a proton is often pumped around to create energy gradients it's very important in the synthesis of ATP it's the basis of acidity and alkalinity which we just talked about but the main thing is to know about these atoms in context phosphorus is in phosphate groups which is found in ATP that's the kind of interconnected cross topic knowledge that you want to have for success in AP Bio now we're on to topic 1.3 monomers and polymers and functional groups so what are monomers what are polymers the basic idea is that three of the four groups of biomolecules carbohydrates proteins nucleic acids are built from smaller building blocks that are called monomers so here's a glucose monomer over here uh living things build macro molecules the big molecules proteins nucleic acids polysaccharides and that have specific three-dimensional shapes and shape determines function um by combining these monomers into polymers and a great analogy if you hadn't already thought of it is that the monomers are like Legos you can combine them in any way to create other structures and these big structures the Millennium Falcon that you might have built as a kid or something like that those are the polymers and um here's a note about structural formulas if you see something like this might wonder like what's going on at these angles every unspecified angle vertex has a carbon atom and um that that's why this is a C6 h206 because there's carbons here here here here here carbon is so Central that it's just understood how do you put monomers together to make polymers it's a process that's called dehydration synthesis everything in biology is run by enzymes as we'll see in unit three and what enzymes do is they pull a hydroxy group over here off one monomer and it pulls a hydrogen off the other one so here's the hydroxy here's the hydrogen that water is pulled out right because this is H2O the water gets removed and that creates a bond that's right over here so here we see that between two amino acids and same thing so two monomers becoming a larger molecule dehydration synthesis easy to remember synthesis is how you build things and dehydration when you're dehydrated you lack water so dehydration synthesis is pulling out a water water now what about hydrolysis hydrolysis is the opposite of dehydration synthesis um in biology the suffix lice is very important and it involves breaking so what happens in hydrolysis is that an enzyme which isn't shown inserts a water molecule in between the two monomers making up the polymer and what that does is it breaks them apart here we have lactose which is a disaccharide I'll review that in a minute it's a sugar that's made of two simple sugars that are bonded together you add a water molecule and you get galactose and glucose what do you need to know about functional groups in one sense not a lot they're not going to directly appear on the AP Bio exam but in another sense they're very important in terms of you decoding what's happening with the molecules in biology which means the molecules that might appear on the AP Bio exam or in your course so let's go through a couple phosphate groups number one over here they're key for energy exchange ATP adenosine Tri phosphate phosphates are also found in DNA and they're what energize DNA monomers as they're put together this methyl group over here at number two it's used to silence DNA it makes molecules nonpolar or hydrophobic there are a couple of polar functional groups to know about there's the hydroxy group at five the carbonal group at seven and they make molecules hydrophilic or water soluble the carboxy group that's at number three and the amino group that's at number four those are essential in amino acids which obviously have an amino group over here have a carboxy group um the S hydral group over here at number six is very important in terms of protein structure it uh creates a stabilizing bond that holds proteins in a specific three-dimensional shape and the acetal group at 8 is used to activate DNA through a process called acetalation so it's kind of the opposite in terms of function from the methyl group that we talked about carbohydrates and lipids so what are the four types of macro molecules that make up living organisms what can you identify from this diagram so what you have here are carbohydrates represented by this disaccharide over here we have a lipid represented by a phospholipid a key molecu membrane we have a protein represented by hemoglobin and a nucleic acid represented by DNA so those are the big four what do you need to know about carbohydrates carbohydrates the monomer or monosaccharides those are simple sugars and some of those are all important in biology like for example glucose which is essentially the fuel of Life disaccharides are going to show up Less in the course but you might have a question that's about lactose and lactose intolerance well really doesn't make sense unless you know that lactose is a disaccharide composed of two linked monosaccharides and then you have polysaccharides molecules that are used for energy storage like starch which is in Plants glycogen which is in you and other animals and then polysaccharides that play important structural roles like cellulose which makes up the cell walls of plants while humans and other animals can't digest cellulose for food energy a few animals such as ruminants and termites can EXP Lane most animals can't hydroly the bonds that connect glucose monomers in cellulose so here's cellulose it's a polysaccharide it's a bunch of linked glucoses but it's linked in a way so that you don't have the enzymes that can break this Bond freeing up the glucose monomer so essentially you could eat lettuce celery these are high cellulose Foods all day you'd never get enough calories to really power your life processes you do have the en enzymes that can break this bond in starch so over here and over here and over here and that enables you to convert starch into glucose and that enables you to use that glucose to power cellular respiration there are a couple of animals such as termites and ruminants ruminants include uh cows sheep goats deer other animals other mammals and what they did is they involved symbiotic relationships with microorganisms that can hydrolize this Bond and thereby break this excuse me break this Bond over here break this Bond over here break this Bond over here and that releases these glucose monomers making food energy available let's end our review of carbohydrates by looking at an issue in relatively recent human evolution related to carbohydrates and that's about the biology of lactose tolerance and intolerance so here's what you need to know lactose is the sugar in milk here it is it's a disaccharide lactase is the enzyme that hydes lactose into monosaccharides and here you see that reaction happening most mammals only produce lactase during infancy while they're suckling because that's the only time that most mammals ever drink milk so that makes sense from an evolutionary point of view because uh when you're an adult you uh don't produce lactases why should you produce an enzy enzyme for something that you don't eat but what happened in human evolution is that some human groups that were pastoralist herders these are people who um were associated with cows and sheep and goats and so on and so forth they had access to all these milk products from the cows and the sheeps and the goats and some of them developed a mutation that enable them to continue to produce the lactase enzyme into adulthood and opened up a whole niche of food exploitation that wasn't otherwise available now this didn't happen all over the world this happened in a couple of hotspots here's one in Africa here's one in Europe and here's one in uh Saudi Arabia current Saudi Arabia and here's one that is in the Indian subcontinent and in those areas lactase persistence production of lactase into adulthood became widespread but in large areas of the world that never happened and there are many humans the majority of humans who are lactose intolerant as adults but if that's true of you as it is of me then we have products like lactate lactate is essentially lactase the enzyme that you can use as an additive to food and it'll break lactose down into lactose and uh glucose and you can buy lactate milk and so on and so forth and that's how that problem if it's even a problem is solved now let's move on to lipids let's talk about lipids and what are their functions so here we have four different lipids and what makes a lipid a lipid first of all lipids or molecules that are wholly or partly nonpolar so uh for example like you see all these hydrocarbons over here those are all completely non-polar they don't dissolve in water they're hydrophobic they also are characterized by the fact that unlike the carbohydrates that we've met and the proteins and the nucleic acids that we will meet they're not composed of repeating monomers they might have subunits but they don't have those subunits repeated hundreds or dozens of times so what are their functions well over here we have um a fat a triglyceride and that's used for energy storage that's true in both animals and plants in animals those fats are usually solid in Plants those fats are usually liquid we call them oils here's a wax waxes are used for waterproofing this molecule is phospholipid it makes up cell membranes we'll talk about that later and then we have a steroid hormone like estrogen or testosterone that's used for signaling so what's the relationship between phospholipid structure and membrane structure well here's what you need to know phospholipids have a hydrophobic non-polar tail that's this over here and they have a hydrophilic or polar head and those two parts are connected by a molecule of glycerol and the key thing is that when you mix this kind of molecule in water they spontaneously form an orientation where the heads will interact with water and the Tails will avoid water hydrophilic over here hydrophobic over here and so if you can think about that arranged in a kind of spherical way you wind up having a structure that is a bylayer two layers of phospholipids and that's the structural framework of cell membranes we'll talk much more about that when we do unit 2 at learn biology.com we understand why students struggle with AP Bio it's a hard course the material is complex the amount of vocabulary is ridiculous and the pace is withering it's natural to feel overwhelmed and inadequate to get an A or a 45 you need an easier way to study and that's why we created learn biology.com it's got quizzes it's got flash cards it's got interactive tutorials about every topic in the AP Bio curriculum it's got a comprehensive AP Bio exam review system use learn biology.com and you'll gain the skills and confidence to Ace your course and to crush it on the AP Bio exam here's your plan go to learn Das biology.com we've got free trials from June through March for both teachers and students sign up you won't believe how much you'll learn let's review proteins so the monomer is an amino acid and it has a central carbon over here and connected to that carbon is an amine group over here that makes this basic in its structure but over here on the other side it's got a carboxy group and that makes it acidic so therefore it's an amino acid there's a hydrogen atom attached to the central carbon and then there's a variable group or an R Group and there are 20 variations and that's true of all life all life is built of the same 20 amino acids that our group is also called a side chain and it can be polar non-polar acidic or basic there are four levels of protein structure this is a super important topic we're going to do an overview and then we're going to walk through all four of these levels primary structure is what's shown over here in a it's a linear sequence of amino acids it's genetically determined the secondary structure which is shown here and here those are interactions that involve What's called the polypeptide backbone when you um do a dehydration synthesis and connect one amino acid to the next to the next to the next that chain of carbon carbon nitrogen carbon carbon nitrogen that's the polypeptide backbone the next level is called tertiary structure and those are interactions between those R groups and then finally there's quaternary fourth level structure and that involves interactions between multiple folded tertiary peptides okay let's talk about primary structure in this diagram A1 A2 A3 those all represent different amino acids so the sequence of amino acids that make up a polypeptide that's what you call multiple amino acids linked together that's the primary structure proteins aren't really built by enzymes in the way that everything else is built by ribosomes the amino acid here's one here's another one they're connected to one another by peptide bonds so I was saying before nitrogen carbon carbon nitrogen carbon carbon that's the polypeptide backbone all of those amino acids link together that's primary structure what's secondary structure well here you have a nice diagram that shows you what that polypeptide backbone is and the secondary structure emerges as interactions between the carbonal groups over here and the um Amino or amine groups over here within the polypeptide backbone now what happens is that interactions between these amine groups and these carbonal groups they form hydrogen bonds and they stabilize certain shapes one of the shapes to know about is called an alpha Helix and that's kind of a cork screw over here so you can see that there's a Hy hydrogen bond that's stabilizing this hydrogen bond hydrogen bond so that forms that shape now the other thing that happens is if the parts of the polypeptide chain are either parallel to one another like this or anti-parallel to one another like this then carbonal and amino groups can again interact and form hydrogen bonds and that can lead to a form called a pleated sheet and that's what we see over here tertiary protein involves interactions between the side chains or the r groups and there are a couple to know about first of all there are hydrogen bonds shown at number two there are ionic bonds that are shown at number five over here there are Cove valent bonds which are shown at number three that was uh between two sulf hydral groups another one of the functional groups and this is a coent bond that's very important in really tightly holding that protein into a specific shape and then finally you have what's called hydrophobic clustering where nonpolar side chains will cluster together avoiding water down here you see myoglobin which is a oxygen storing Protein that's found within muscle tissue that's a tertiary protein folded into a specific shape and you can see like over here there's a whole bunch of alpha helices that are in that structure aary structure involves multiple polypeptides that interact with one another to create the final form of the protein so those interactions might be hydrogen bonds they might be ionic bonds they might be hydrophobic interaction in this diagram actually you can see all four of the levels so here's the primary structure here's an alpha Helix secondary structure this hair pin turn is actually um part of the tertiary structure over here and then you have multiple polypeptides interacting this molecule looks a lot like hemoglobin this is kind of cool in light of our recent history the spike Protein that's on the outside of SARS K2 and in fact all the SARS viruses is also a quaternary protein that's made of multiple folded polypeptide chains an application of what we learned about proteins is this question describe the structure and function of hemoglobin and explain the molecular cause of sickle cell disease so CLE cell disease is an inherited blood disorder it was one of the first molecular um genetic diseases that was really well understood the molecule that is in question here is hemoglobin and hemoglobin its function is to transport oxygen in our red blood cells the structure it's a quaternary protein it's made of four polypeptide chain sickle cell disease is caused by a recessive mutation we'll cover that in unit five but the key idea is that there's a mutation that causes the amino acid veiling over here to substitute for glutamic acid and that's an important mutation because glutamic acid is acidic whereas veine is nonpolar the result of that is that when blood becomes deoxygenated those mutated hemoglobin molecules they form hydrophobic bonds with one another well why because they have a hydrophobic amino acid sticking on the outside and that causes them to do this they cause uh fibers to develop within the cells and that causes the cells to become spiked like this they're mutant cells and those cells will then Clump up within smaller arteries and that causes these pain crises it causes tissue damage it's a debilitating disease there are a few other things to know about CLE cell anemia the first is that during the 30 years that I've been a biology educator CLE cell disease has been transformed from a childhood disease with certain early mortality to a disease that can be managed with good medical care so that people can live into their 50s 60s and even Beyond CLE cell disease is also a target for gene therapy something that we'll talk about in unit 6 and finally there's a really interesting evolutionary thing where CLE cell disease evolved because having one copy of the gene is actually a benefit that gives you resistance to the tropical mosquito born disease malaria something that we'll talk about in unit 7 and now for our last Topic in this unit one review nucleic acids DNA and RNA note that we'll give an overview now and we come back to nucleic acids when we cover gene expression in unit six so we'll start by describing the biological importance of the nucleic acids these are the molecules of genetic information DNA is the molecule of heredity it's what passes from generation to generation it's the molecule that cells pass on as they divide and replicate within a multicellular organism RNA has other functions RNA is the hereditary molecule in some viruses never in cells and rna's key role is information transfer as in messenger RNA So within a cell here is DNA the repository of genetic information it has its information transcribed into RNA and then that RNA goes into the cytoplasm where a ribosome will translate that RNA message into protein RNA is a very versatile molecule it's not in the form of a double helix the way DNA is it can take many many forms and it can act as an enzyme catalyzing reactions um ribosomes are essentially catalytic RNA there are also other molecules called spom micro rnas that play a whole variety of functions and I finally want to say that this typically isn't put into this unit but ATP is a nucleotide monomer it's one of the monomers of RNA and it's the energy molecule of life it's how cells get work done what is the monomer of nucleotides what's its structure how are these monomers different in DNA and RNA the monomers are called nucleotides we just looked at ATP all of these molecules have a f carbon sugar that's shown at number two they have a phosphate group that's shown over here at number one and then there's one of four nitrogenous bases so the nitrogenous base doesn't have to have this structure note that the phosphate group is connected to a number five carbon whereas the nitrogenous Bas is connected to the number one carbon when you learn about DNA replication you'll talk about things like DNA is replicated in a five to re orientation and now you know that's about the five carbon over here and the three carbon over here in DNA the sugar is deoxy ribos and there are four bases adenine thyine cytosine and guanine in RNA the sugar is ribos and the bases are adenine uracil cytosine and Guan so now let's talk about the structure of DNA DNA consists of two nucleotide strands so easier to see in this flattened out version here's one here's the other within each strand the nucleotides are connected by sugar phosphate bonds so here's a sugar here's a phosphate here's a sugar here's a phosphate but the strands connect to one another by hydrogen bonds so here you see G connecting with C A connecting with t and those are rules to memorize adenine a always bonds with t c bonds with G they have comp complement shape their molecular dimensions are such so that they fit nicely within the Helix that's more of a story for unit six um and note that these two strands fit together in an anti-parallel orientation in order for the nucleotides to form hydrogen bonds with one another they each need to be upside down relative to the other and that's what anti-parallel is all about we'll talk about this again more in unit 6 but just to lay this down for right now DNA is directional notice that in a chain of nucleotides these are RNA nucleotides you can tell because there's uriell the nucleotide sugar binds with a phosphate then there's a sugar there's a phosphate there's a sugar there's a phosphate well the enzymes that build DNA it's called DNA polymerase and these enzymes like all enzymes have an active site they only can work in certain orientations and they work by completely by feel and they can only add new nucleotides at the three prime end of a growing nucleotide strand so that's what directionality is all about all of these nucleic acids are built in the five Prime to thre Prime Direction your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio [Music] exam cells and introduction describe the basic structure and fundamental parts of cells cells are the basic unit of life they're the basic unit of structure and function in every organism in terms of their own structure they have a membrane which separates the cytoplasm all the living material inside the cell from the cell exterior they always have genetic information in the form of DNA the double helix and there are systems that maintain and replicate the cell as a whole and the cell's genetic information its DNA one of the most important systems is a system by which the genes in DNA get transcribed into messenger RNA another nucleic acid and that messenger RNA is red by a particle called a ribosome and translated into proteins proteins are all important they're the Workhorse of the cell and one of the most important proteins are enzymes enzymes control the cell's metabolism other proteins might be embedded in the cell's membrane and others might even be exported from the cell compare and contrast procaryotic and eukaryotic cells among living organisms There's a Great Divide between the procario and the ukar here's what it's all about procaryotic cells are small and relatively simple they have no nucleus their chromosome is circularized and what that means is that there's a loop the beginning and the end meet up they contain extra chromosomal pieces of DNA that are called plasmids and they're found in two of life's three domains the archa and the bacteria eukaryotic cells are larger and more complex they're found in the domain that has their name the ukaria they have a nucleus they have multiple linear chromosomes so here they're shown over here and you can see the chromosomes here they have a beginning and an end and those chromosomes have DNA that's associated with proteins which is different from the simpler DNA packaging that is found in the procaryotes ukari have mitochondria and the presence of that organel is the defining feature of the ukar and they have many membranebound organel membrane bound means surrounded by a membrane AP biotopic 2.3 cell size an essential topic use the relationship between surface area and volume to explain why cells are small cells need to have enough membrane surface area to allow for diffusion of substances and molecules in and out everything that gets into cell gets there through the membrane and it might be counterintuitive but a small cell has much more surface area relative to its volume than a large cell does let's look at the math if you have a cell that's one micrometer one micron on the side that's its length then its surface area if it's cubic would be 1 * 1 * 6 think of the formula for surface area for a cube its volume is 1 * 1 * 1 and therefore its surface area to volume ratio is 6 to one six units of surface area to every one unit of volume now if you have a larger Cube one that's 10 micromet then its surface area is 600 wow that seems like a lot but its volume is 1,000 because volume's a cubic function and it's going going up much faster so if you look at the surface area to volume ratio it's 6 to 1 as an object gets larger its amount of surface area relative to its volume decreases and in this example the larger cell surface area to volume ratio is 1/10th that of the smaller cell and a large cell can't efficiently use diffusion to get the nutrients it needs in and to get waste carbon dioxide and metabol Wast out why do organisms need to increase surface area in certain tissues how do they do that the why is in order to increase the surface for diffusion of molecules or heat how you can have thin sheets of tissue like these thin sheets that make up the gills of a fish that have been dissected out that's for increasing the intake of oxygen and the diffusion out of carbon dioxide or if you think about the ear of elephants those are big flat sheets of tissue that enable the elephant which has very little surface area relative to its volume and lives in a hot place to get heat out of its body you can also have highly folded surfaces like the internal membrane of the mitochondria or the structures that are called Villi that make up your intestine and there's actually folds within folds explain in terms of surface area why there are no small mous siiz marine mammals and why some marine mammals like the whales the largest organisms to have ever evolved are really huge mammals are warm-blooded ocean water is cold increased size decreases the surface area to volume ratio so there's less Heat lost to the environment think about a mouse it's small it has a lot of surface area relative to its volume it would be over here on the graph it couldn't survive because it would experience so much heat stress in the water the smallest marine mammals are the otter and they have a thick coat of fur that helps them maintain their body temperature whales have evolve to be larger and larger for a variety of reasons but one of which is that by being big they lose relatively less heat to the environment than a smaller animal would it's all about the surface area to volume ratio cellular compartmentalization and the endomembrane system how UK carotic cells are organized what is cell compartmentalization what are its advantages compartmentalization means internal division of a space into sections think about the overhead luggage compartment in an airplane what are the advantages the first is that it allows a cell to have regions with an internal chemistry that are distinct from the cytoplasm a great example of that is the lome shown at G over here and number seven over here lomes contain hydrolytic enzymes those are enzymes that break things down those can't be released into the cytoplasm where they would break down the cytoplasm so they are compartmentalized they're kept in a membranebound space in addition compartmentalization provides a lot of internal surface area and that's important for membranebound enzym that are found in the Smoothie r or the GGI that can only do their job when they're embedded in a membrane compartmentalization makes that possible and that's also true of the ribosomes that are found in the rough ER compare compartmentalization in procaryotic and eukaryotic cells procaryotic cells have few compartments though there are internal regions with specialized structures and functions here's a procaryotic cell you can see that its internal structure is much simpler than that of a carotic cell but one notable compartment is called aoid and it's this over here in a cyanobacterium ciona bacterium evolved into chloroplasts we'll talk about that in a moment and they have these internal compartments called thids that are essential for the function of photosynthesis eukariotic cells are highly compartmentalized there are many internal membranes that divide the cell into regions with distinct structures distinct chemistry and functions and examples include lomes the endoplasmic reticulum the GOI complex and vacu like this large vacu in a plant cell what is the endomembrane system it's a dynamic connected system of internal membranes and compartments it includes the nuclear membrane the ruff r the Smoothie R the GGI lomes and all the little vesicles that interconnect them membrane and material flow from one compartment to the next so the membrane that's part of the ruar might become the same membrane the same phospholipids that are part of the Smoothie R and those might become parts of vesicles which flow into the GGI so those phospholipid molecules are the same it's Dynamic there's constant exchange Explain the origin of mitochondria cellular compartmentalization and chloroplast what we're explaining is the origin of the ukar when did this happen about 1.8 billion years ago before that there was nothing on Earth but procaryotes how did this happen it arose as a mutualistic endosymbiosis symbiosis means living together two species living closely associated with one another endosymbiosis is when one of those species lives inside the other we normally think of that as parasitism that's a negative of endosymbiosis but there's also positive endosymbiosis that's a mutualistic relationship and that is what gave rise to the ukar so what happened is that here we have representatives of the two procaryotic domains and an Aral cell took up a bacterial cell now I want to emphasize that there are many scenarios and many diagrams that represent how this happens and this one is the one that makes most sense to me so so the bacterial cell entered inside the archal cell and it evolved into a mitochondrian that mitochondrian still kind of the bacteria secreted vesicles and those vesicles became the nuclear membrane shown over here and it started to develop structures that are part of the endomembrane system like the endoplasmic reticulum which is shown over there so that's how we have UK carots then later a second endosymbiotic event led to chloroplasts which were free living CA bacteria entering into a eukaryotic cell and that set the stage for algae and plants what's the evidence that chloroplast and mitochondria were once Free Living bacterial cells that arose through endosymbiosis what's the evidence for this idea like bacteria both of these organel mitochondria and Chlor plast have their own circular DNA they replicate themselves through binary fision that's how procaryotes replicate themselves they use their own ribosomes to produce some of their own proteins these ribosomes resemble bacterial ribosomes in terms of their R RNA sequence and structure and they have two membranes the outer one so the outer bacterial membrane let's consider it over here is a vestage of an endocytotic vesicle at learn biology.com we understand why students struggle with AP Bio it's a hard course the material is complex the vocabulary is ridiculous and the pace is withering it's natural to feel overwhelmed and inadequate to get an A or a four or a five you need an easier way to study and that's why we created learn biology.com it has quizzes it has flashcards it has Interactive tutorials about every topic in the AP Bio curriculum it has a comprehensive AP Bio exam review system use learn Das biology.com and you'll gain the skills and confidence that you'll need to Ace your biology course and to crush it on the AP Bio exam so here's your plan go to learnbiology dcom we've got free trials from June through March for both teachers and students you won't believe how much you'll learn you carry out Excel parts and functions describe the structure and function of the nucleus the nucleus is function is to store and protect genetic information in the form of DNA that DNA is wrapped around proteins to form chromosomes this representation here is only present during mitosis or meiosis when cells are dividing otherwise the DNA is more diffuse and spread out it's still in chromosomes but we call the form chromatin the nucleis is is this dark part in the center of the nucleus and it assembles ribosomes the entire nucleus is surrounded by a membrane that separates the chromosomes from the cytoplasm and the nuclear membrane has pores that allow molecules to enter and leave the nucleus important among those are messenger RNA which leaves the nucleus goes into the cytoplasm where it's transcribed into proteins and various transcription factors that come into the nucleus to turn genes on or to turn them off describe the structure and function of ribosomes ribosomes are particles composed of ribosomal RNA and protein they consist of a large subunit and a small subunit their function is to read a genetic message encoded in a sequence of messenger RNA and to translate that message into a sequence of amino acids that make up the primary structure of a protein the details of trans translation protein synthesis will occur in unit 6 what are two locations within a eukaryotic cell where ribosomes can be found ribosomes can be free or Bound free ribosomes shown at three float freely within the cytoplasm which is number five bound ribosomes shown at four are connected to the membrane of the rough ER all ribosomes start out as free though through a process called protein targeting they migrate to the ER to become bound they do that if the proteins that the ribosomes are creating are destined to be put inside a vesicle so they can go to the GGI or the membrane or a lome describe the structure and function of mitochondria mitochondria are shown here in the context of an animal cell here's a larger image the function is converting food energy into ATP that's the molecule that cells use to get work done the key structures there's a chromosome that consists of DNA there are also ribosomes which aren't shown in this diagram evidence of endosymbiosis there's an inner membrane it's highly folded that increases surface area and that's because there are many membrane embedded enzymes and proteins one of which is shown at five that are involved in the process of ATP synthesis the mitochondria as a former independent cell has its own cytoplasm it's called The Matrix it has enzymes for the kreb cycle and enzymes that perform other functions there's an intermembrane space which is an important cellular compartment that enables the mitochondrian to produce ATP we'll see how that works in unit three and there's an outer membrane that is a vestage of endosymbiosis describe the endoplasmic reticulum the ER and list its two forms the ER is an interconnected series of channels found between the nuclear membrane over here and the GGI body in UK carotic cell so here's the ER and it consists of two forms there's the rough ER and the smooth ER describe the structure and function of the rough and smooth well the rough is studded with ribosomes that's what all these little dots are over here and using those ribosomes the Ruff synthesizes proteins for inclusion in lomes in other organel in the membrane or for export from the cell the smoothie is on the outer side of the ER Network always towards the G and it lacks ribosomes but that doesn't mean that there's nothing in that membrane it has many membrane embedded enzymes and the functions of the Smoothie are vary by tissue so it can include synthesis of lipids converting toxins into soluble forms that can be excreted from the body carbohydrate breakdown and synthesis describe the structure and function of the G complex the go is a series of membranebound flattened sacks and you'll remember that flattening increases surface area the Gogi receives vesicles From the Rough and smooth R and chemically modifies their contents so here's the ru here's the smooth here's the GGI and here's a vesicle bringing something from the ER system to the GGI the GGI packages those modified proteins into vesicles shown at six that are sent to organel like lomes over here at seven to the cell membrane or exported from the cell describe the structure and function of lomes here's a lome over here here's a lome over here and one thing that I rarely say but I'll let you know that you will almost certainly never have to identify aosome on a diagram on the AP Bio exam it's just a big vesicle lomes are membranebound organel that contain hydrolytic enzymes they're only found in animal cells they carry out intracellular digestion so like for example here you see a particle it actually looks like a cell that's being engulfed by the membrane it'll be packaged into a vesicle and that vesicle will be sent to a lome where hydrolytic enzymes will break this down the lome also recycles worn out damaged or excess organel and molecules and it plays a key role in a process called apotosis the P silent that's program cell death and we'll talk about that later in the course the cytoskeleton is a dynamic network of protein fibers and those fibers make up the bones the skeleton of the cell in the same way as our skeleton our bones working with muscles enables us to move the cytoskeleton is a dynamic Network that enables the cell to move both internally so it enables cells to move materials and organel within themselves and it also enables the cell to move their membrane so that they can do things like endocytosis where cells can engulf things by moving their membrane or also moving their entire bodies this is an organism called an amoeba and it moves by extending um parts of the membrane over the surface enabling it to crawl how does it do that through the cytoskeleton what are centrosomes and centrioles centrosomes are the organel they contain two centrioles and the function is creating spindle fibers that's what these are over here that separate chromosomes during mitosis and meiosis the parts that we've talked about so far have all been represented within animal cells but most of those parts are also found in plant cells the one exception is the lome unique to animal cells let's describe the function of the central vacu this large structure right here it's only in plants cells its functions include water storage storing and releasing macromolecules sequestering waste products and maintaining turar pressure we'll talk about this in the context of Osmosis the movement of water but as water flows into a cell it creates outward pressure that keeps plant cells full firm upright they're not wilting describe the evolutionary origin and function of chloroplasts here are chloroplast over here here's a single chloroplast chloroplasts are the endosymbiotic descendants of Free Living photosynthetic bacteria and that's why they have their own DNA their own ribosome that's why they have two membranes their function is creating carbohydrates through photosynthesis we're going to leave their detailed structure and how they work for unit 3 when we discuss photosynthesis describe the chemical composition and the function of the plants cell wall the cell wall is composed primarily of cellulose which is a polysaccharide it's that polysaccharide that we can't digest but which ruminants cows goats can digest because they have these symbiotic relationships that enable them to break that down and release food energy the major function of the cell wall is it acts as a pressure vessel that prevents overexpansion in response to inward flow of water osmotic pressure so here we see as water flows into a plant cell the central vacu will expand and it'll look like this the cell will be full of water and that water will push against the cell wall keeping the plant cell full and firm avoiding wilting so that's a good thing for the plant and the cell wall is the primary component of wood and the water conducting tubes in plant stems membrane structure and function what is the function of the cell membrane the cell membrane separates the high organized contents of the cell from the cell's environment cells are open systems they need to let things like food in they need to let things like waste out the membrane is how that's controlled that's because the membrane is a selectively permeable boundary it allows the passage of some substances and particles through but not others that selectivity is really the key to life describe the structure of phospholipids and their role in cell membranes phospholipid structure there's a hydrophobic non-polar tail region here's the structural formula here's a representation there's a hydrophilic polar head notice that the head has this phosphate group over here with its negative charge the whole thing is held together by this three carbon molecule called glycerol in solution when phospholipids are mixed with water the heads of the phospholipids bond with water molecules while the Tails form a waterfree zone so interaction interacting with water interacting with water waterf free zone over here that creates a by layer that's the basic framework of the membrane to which proteins and other molecules are added we'll see that further on and the phospholipid bilayer is stabilized by weak bonds Vander wal's bonds that occur between the Tails describe the fluid mosaic model of of cell membranes this model posits that the membrane is composed of phospholipids plus proteins plus cholesterol in motion so why is it called fluid mosaic well it's fluid because the components are moving around laterally within the plane of the phospholipid bilayer which you can see here it's a mosaic because it's composed of a variety of pieces in the same way as a mosaic tile is composed of different tiles with different colors that get put together to form the art within the phospholipid bilayer you have phospholipids that are at four and nine you have proteins that are at 1 3 five and six and you have molecules like cholesterol which are shown at seven and then inside and outside the phospholipid bilayer you might have additional molecules attached to proteins or phospholipids and those might be glycoproteins which are not shown but at eight you have a glyco lipid glyco means it's a carbohydrate and it's attached to these fatty acids right over here describe how proteins fit into the cell membrane there are three ways that proteins can fit in and if you think about hydrophobic hydrophilic what binds with what it makes a lot of sense so there are transmembrane proteins that's shown over here and over here here notice that beautiful Alpha Helix that you should remember from our unit one review there's a hydrophobic four that fits into the nonpolar inner portion of the membrane so these would be hydrophobic amino acids over here and over here and there'd be hydrophilic regions that extend into the cytoplasm and the membrane exterior there are integral proteins such as the one at five and these proteins would have a non-polar region that extends into the hydrophobic membrane middle and a single Hydro philic region that juts into the cytoplasm as this one does or into the cell exterior then finally you have peripheral proteins like this one that's shown at three and they attach to phospholipid heads that are either on the cytoplasmic side of the membrane or in the cell exterior these terms transmembrane integral peripheral they're not important in and of themselves but you should be able to understand the concept of how things fit into the membrane membrane transport how things get across the cell membrane diffusion is the tendency of molecules to spread out from where they're more concentrated to where they're less concentrated so here you have some substance more concentrated over here less concentrated over here here's ink going into a beaker more concentrated and then less concentrated this happens spontaneously it's based on the kinetic energy of the molecules and a good way to Envision this is to think of molecules as flowing down a concentration gradient from higher concentration to lower concentration explain how cells control what diffuses across their membranes diffusion is called passive transport and that's because it requires no cellular energy there are two forms the first is simple diffusion across the phospho lipid bilayer that's what's shown up here there are two things that can do simple diffusion the first are any small nonpolar molecules such as oxygen nitrogen carbon dioxide the second are non-polar substances such as steroid hormones or fats facilitated diffusion is for polar molecules and ions that can't diffuse across the phospholipid bilayer so they require protein channels and these are transmembrane proteins they go all the way through that only let specific molecules or ions s pass so over here you see one for glucose over here you see one for amino acids those are both polar molecules and here you see one for an ion such as calcium there'd be others for ions such as sodium or potassium compare and contrast active and passive transport as you do explain what powers each process passive transport is what we just discussed it's when molecules or ions flow down a diffusion gradient here more concent ated to less concentrated and that's what it's all about it's diffusion from high concentration to low concentration it relies on the kinetic energy of the diffusing molecules or ions it doesn't require cellon energy as you can see here molecules are flowing down their concentration gradient that's different from active transport where we're pumping a molecular ion up its concentration gradient from lower concentration to higher concentration over here lower concentration to higher concentration that requires an energy expenditure on the part of the cell usually that's ATP that's being converted into ADP and phosphate to power the pumping process but also the flow of electrons can power the pumping of protons and that's important in the creation of ATP itself compare and contrast endocytosis and exocytosis these are both forms of bulk transport in endocytosis the membrane pinches in to surround a particle or some extracellular fluid creating a cavity that can become a vesicle in exocytosis a vesicle containing something fuses with the membrane and then that contents is dumped outside the cell both of these processes require energy on the part of the cell and they both require the involv of the cytoskeleton which is changing the shape of the membrane what is membrane potential how do cells create membrane potential how is membrane potential used membrane potential is an electrical charge across a membrane that creates a voltage difference how is it created through cells expending energy to pump ions across their membranes a key example and this is a preview of a topic that we'll get into in unit three is how mitochondria pump protons from the mitochondrial Matrix to the intermembrane space that gives the intermembrane space a positive charge relative to The Matrix that has all these protons inside of it and that creates an electrochemical gradient a voltage difference and that pulls protons through this channel it's called ATP synthes back into the Matrix and that powers the creation of ATP some other examples chloroplasts do pretty much exactly the same thing and there's also a 70 molt charge across the membranes of nerve cells that makes nerve impulses possible and that's how I am able to think and teach biology and how you are able to learn it is biology mind-blowing or what I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam tonicity and osmo regulation that's the college board's term I wish that was just called osmosis and its consequences so let's start by defining what osmosis is it's the diffusion of water water diffuses like everything else and that means that water's going to move from higher to lower concentration water is the solvent of life so we have to pay attention to how it moves water flows down its diffusion gradient just like everything else from hypotonic to hypertonic those are essential terms to know hypotonic means relatively more water and relatively less solute and these terms are not absolute they're always relative to another solution so in this diagram this side is hypotonic it has a higher percentage of water molecules it has a lower percentage of solute molecules this side is hyperonic that means that it has relatively less water a lower percentage of water molecules and a higher percentage of solute molecules but that's this compared to this now what is that going to do that's going to have water move down its concentration gradient which means it'll move from here to here after osmosis takes place it'll look like this over here this level will go down this level will go up the water actually is getting pushed up on this side that's called osmotic pressure it has enormous consequence and the thing for you to memorize is that water diffuses from hypotonic to hypertonic here's a fabulous and fun example a student places a gummy bear in a cup of water overnight the next day the gummy bear has expanded explain well the gummy bear is mostly sugar the water in the cup is 100% water water always flows from hypotonic to hypertonic so water's going to flow from the hypotonic solution in the cup into the gummy bear the gummy bear will expand because of osmotic pressure osmosis in implants use the principles of Osmosis to explain each of the images Below on the left side the cell is hypotonic to the environment water leaves the cell the membrane peels away from the wall that's also known as plasmolysis the vacu shrinks and the plant wilts how could the environment be hypertonic to the cell how could the cell be hypotonic to its environment this environment has to have for example a lot of solutes dissolved in it so that it has a lower water concentration than is in the cytoplasm that'll cause water to go from the hypotonic cell to the hypertonic environment in the middle the cell is isotonic to its environment that's a new term isotonic means that the solute concentration and the water concentration are the same on both sides of the membrane so water enters and leaves leaves and enters at the same rate and on the right side the cell is hypertonic to its environment so water flows into the cell that osmotic pressure in the case of plants is called turer pressure it causes the vacu to expand it pushes the membrane against the cell wall and this is a good situation for plants to be in it makes them full firm happy they're not wilted osmosis and animal cells use the principles of Osmosis to explain each of the images below cell number one the cell is hypotonic to its environment water leaves the cell water always flows from hypotonic to hypertonic so the cell shrivels up in Situation Number Two the cell is isotonic to its environment water enters and leaves the Cell at the same rate this is an important condition for animal cells because they have a membrane but not a wall cells that are kept in a tissue culture need to be kept in an isotonic solution and in situation three the cell is hypertonic to its environment and therefore water is flowing into the cells and because there's no cell wall the membrane can't really stop the inward force and the cell will ultimately burst explain the function of the contractile vacle in freshwater protus such as paramia a protest is a ukar that's not a plant an animal or a fungus protest in freshwater are hypertonic to their freshwater environment that means that the cytoplasm has more solutes dissolved in it than the lake or stream that they're swimming in and as a result water moves into these cells by osmosis flowing from hypotonic to hypertonic to osmo regulate that's a new term osmo regulate means to regulate your osmotic balance the contractile vacu that's this organel over here fills with water and then contracts to expel water from the cell if the environment becomes more hypertonic then the cell can adapt by decreasing its rate of contractile vacu contraction and do the reverse in more hypotonic environments describe the structure of leaf stomata stomata are pores that are on the underside of a leaf if you took a leaf and you did a microscopic cross section you'd see layers of cells the top layer and the bottom layer are responsible for waterproofing the leaf and they're covered with wax but nevertheless the leaf needs to be open to its environment in order to exchange gases and other material um each stom which is singular stomata is plural is formed by two guard cells so here's one guard cell here's the other guard cell and when there's sufficient water these guard cells Buckle outward like that and that creates a pore that allows carbon dioxide to enter the leaf for photosynthesis but also allows water vapor to escape these stomata can be regulated they can close in response to environmental cues including water stress and then open when water is abundant explain how guard cells are regulated in order to open and close the stomata when water is available cells adjacent to the stomata pump potassium ions into the Gard cells so we're talking about these cells and these cells the ones that are adjacent to the guard cell and they're represented like this over here the pumping of potassium makes these Garn cells hypertonic to the adjacent cells water follows by osmosis causing the guard cells to buckle and open up when water is scarce the pumping stops potassium ions flow out of the guard cells and water follows by osmosis causing the stomata to close down to revert back to this form what is water potential water potential is a concept that's really closely related to osmosis and osmotic pressure but it's more quantitative the symbol for water potential is this Greek letter Sai so water potential is a measurement of water's tendency to move from where it is to where it's not adding solute decreases a body of waterers water potential adding pressure increases water potential and water will flow from areas of higher water potential to areas of lower potential so if you look at this device over here it's called a Ube and um these two parts are separated by a membrane that's permeable to water but not to the solute so here we are we're adding solute to this side of the Ube that makes this side hypotonic but that's another way that you can say it has higher water potential and water's going to move from higher water potential to lower water potential that's going to force up the level of water over here that's going to lower it over here could you have explained this entire thing with just hypotonic and hypertonic well I just did but you'll see that water potential is more quantitative and it allows for other factors to be included such as pressure EXP explain the formula for water potential here it is over here in plain English it's water potential equals solute potential plus pressure potential so s is water potential S Subs is solute potential and remember that adding solute to water decreases its water potential s p is pressure potential and adding pressure like if you pressed on a syringe that increases water potential so let's look at these two examples over here so we added solute to this side of the Ube pressure potential is zero there's nothing pressing down on either side but adding solute lowered the solute potential over here to 0.23 megap pascals and that's the unit that's used for pressure so the total water potential over here is minus 0.23 megapascals the water potential over here is just zero there's no pressure there's no solute so water moves from higher water potential to lower water potential that's why it's moving from this side of the Ube to this side in this example we have a potato cell or potato tissue that's been placed in water and so again there's no pressure on either side it's just an open container but the cell has a 1.0 megap Pascal solute potential so the total water potential is 1.0 this is just water so the water potential is zero over here water moves from the beaker into the cell which has a lower water potential that's causing water to flow into the cell it's causing the cell to expand all of these things related to the cell wall in a typical lab in AP biology you put potato tissue into water or Solutions of various concentration and you can see what happens and you can actually quantify it based on water potential that's what water potential is used for your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio exam [Music] topics 3.1 to 3.3 enzymes to help you study I've put together a checklist that you can download at AP bios. checklist describe the Key properties of enzymes enzymes are usually proteins there are some rnas that act like enzymes that catalyze reactions in cells they lower the activation energy of the reactions that they catalyze and inreasing the rate of those reactions so in this diagram you see a reaction that's catalyzed by an enzyme number two and a reaction that's not catalyzed at number one and the difference is that the activation energy for the enzyme catalyzed reaction is much less than the non-enzyme catalyzed reaction enzymes are highly specific because their active site complements the shape and charge of their substrate which is the substance that an enzyme acts upon here's an active sight here's the substrate this is the enzyme as a whole it would be a large protein here's the enzyme interacting with the substrate and here we have the products enzymes are both highly specific and have a narrow set of conditions where they can function at or near their Optimum explain enzymes are proteins with secondary tertiary and quaternary level structures that involve hydrogen bonds ionic bonds and hydrophobic clustering changing pH temperature or ion concentration interferes with these bonds changing the shape of the active site keeping the enzyme from binding with its substrate enzymes therefore have a pH ionic or temperature Optimum at which the shape of their active site best fits their substrate environmental change can cause denaturation a change in the shape of the enzyme that lowers or completely negates enzyme function describe how enzyme activity is affected by changes in the pH of its environment most enzymes have a pH optimum where they operate at Peak efficiency here's the optimum right here as pH moves above or below the optimum enzyme performance drops and this is the rate of enzyme activity and you can see that as the pH drops it goes down as the pH increases it goes down why it's for all the reasons we talked about in the previous slide it's that enzymes or proteins if you change the pH you disrupt the bonds that hold that protein in its specific shape the result is denaturation and less good fit between the enzyme and its substrate describe how enzyme activity is affected by changes in the temperature of the enzyme's environment up to a certain point enzyme activity increases with temperature and that's because there's more kinetic energy that increases molecular motion and it increases the chance that the enzyme will bond with its substrate and therefore be able to catalyze the reaction but at a certain temperature Beyond two in the graph the enzyme will denature it'll change its shape reducing the enzymes catalytic abilities because it'll no longer be able to bind with its substrate what's the difference between reversible and irreversible enzyme denaturation reversible denaturation is where the restoration of optimal conditions restores the enzyme's function as it regains its optimal shape if you can imagine that an enzyme has an optimal shape at seven you move it up a little bit the enzyme starts to denat but then if you restore the pH the enzyme shape might go back to its previous form thereby going back to its optimal rate of efficiency but irreversible denaturation is where the enzyme shape is permanently changed and its catalytic ability is destroyed and this isn't exactly with enzymes but if you think about what happens when you cook an egg the egg white goes from clear to a solid and it'll never go back even once you cool it back down that's irreversible denaturation of a protein imagine the same for an enzyme explain how enzyme activity is affected by substrate concentration with low substrate concentrations the probability of the enzyme meeting its substrate is low and the product is produced at a very low rate as substrate concentration increases the collision and the reaction rate will also Al increase but at a certain point you get to a saturation point and at that point all the enzymes have their active sites interacting with substrates so there's a peak in the rate and you don't go any higher compare and contrast competitive and non-competitive inhibition in competitive inhibition a foreign molecule one that's not part of the cell or the organism that's not the enzyme substrate so this is number four over here blocks the enzymes active site and that keeps the substrate from binding here's the substrate and that inhibits the rate of the reaction it's inhibiting by competing for the active site in non-competitive inhibition which is shown over here a foreign molecule not one that's part of the organism binds away from the active site at a region that's called the allosteric site over here so here's the aleric site here's the aleric site that's occupied by this foreign molecule binding at the alisic site causes a ripple effect throughout the protein that causes a change in the shape of the active site therefore the substrate can no longer bind the active site and that diminishes or blocks enzyme activity topic 3.4 Cell Energy I'm Mr W from learn biology.com where we believe that successful learning requires interaction and feedback and we're so sure of that that a subscription to our website comes with a money back guarantee what is a metabolic pathway a metabolic pathway is a linked series of enzyme catalyzed chemical reactions occurring within a cell so here you can see that these are all separate reactions but they're linked together above 1 2 and three are all enzymes a is the initial reactants B and C are what we call intermediates and D is the final product examples of metabolic reactions that you'll come to know well include glycolysis the kreb cycle the Calvin cycle all of which we'll deal with in this unit and these reactions can be linear so glycolysis is a linear reaction you have a beginning point and an end point or they can be cyclical like the kreb cycle and the Calvin cycle so for example in the kreb cycle this compound over here aalo acetate it's the beginning comp compound gets modified and it also comes back and it's the ending compound a similar thing happens in the Calvin cycle what are autot tropes compare and contrast photo autot tropes with chemo autot tropes autot tropes are organisms that can produce their own food we are not autot troes but plants and certain bacteria and ARA are so photo autotrophs include plants and cyanobacteria they use the energy in light to create organic compounds that they need to survive through photosynthesis whereas chemo aotrs include some bacteria some archa ARA is that third domain the energy for their life processes comes from a process called chemosynthesis and that involves oxidizing inorganic substances including iron sulfur or hydrogen sulfide what are heterotopy and matter they need to live grow and reproduce het tropes capture the energy present in organic compounds produced by other organisms they can be ecological consumers decomposers or parasites and they get their energy in matter by metabolizing the organic compounds and organisms that they eat or absorb or in the dead remains of other organisms here's a heterotroph and here's another heterotroph what's the difference between an exonic reaction and an endergonic reaction exonic reactions release energy and increase entropy so here's an extonic reaction over here and the energy of the reactants is less than the energy of the products and you can't see this but like for example if you burn a piece of paper or a piece of wood you start with cellulose over here and you wind up with many unorganized atoms of carbon dioxide and water so that's an increase in entropy because you've decreased organization cellular respiration most hydrolysis reactions are extonic reactions endergonic reactions require energy and decrease entropy and examples include photosynthesis or almost any dehydration synthesis reaction describe the structure and function of ATP explain how ATP can be used to store and release energy the structure of ATP involves a five carbon sugar that's called a ribos a nitrogenous base that's called adenine and three phosphate groups the function of ATP is to power work within cells every cell makes its own ATP there's no sharing of ATP between cells and to store energy what happens is that cells take energy from food during cellular respiration or light during photosynthesis and use that to combine ADP and a phosphate group into ATP and to release energy for work cells remove a phosphate group from ATP they break off this terminal phosphate group and that creates ATP and phosphate and that makes energy available to do cellular work what is energy coupling energy coupling is the linking of an exonic reaction to an endr onic reaction and that linking drives the endergonic reaction forward here's an example cellular respiration which is exonic drives the formation of ATP from ATP and phosphate so this exonic reaction is driving this endergonic one and example number two is the exonic conversion of ADP and P is coupled to endergonic processes such as active transport we discussed that in our unit 2 review video that takes energy so ATP to ADP and phosphate makes this uronic reaction possible or muscle contraction also andronic reaction it's made possible by the breakdown of ATP to ADP and phosphate at learn Dash biology.com we understand why students struggle with AP Bio it's a hard course the material is complex the vocabulary is ridiculous and the pace is withering it's natural to feel overwhelmed and inadequate to get an A or a four or five you need an easier way to study and that's why we created learnbiology it has quizzes it has flashcards it has interactive tutorials about every topic in the AP Bio curriculum it has a comprehensive AP Bio exam review system use learn biology.com and you'll gain the skills and confidence that you'll need to Ace your biology course and to crush it on the AP Bio exam so here's your plan go to learn Das biology.com we've got free trials from June through March for both teachers and students you won't believe how much you'll learn photosynthesis the big picture what happens during photosynthesis what's its chemical equation is it endergonic or exonic in photosynthesis using light energy here's the sun photo autot tropes like plants combine carbon dioxide and water to create carbohydrates that's what the plant is made of oxygen is released as a waste product it's the source of biomass and the base of almost every food chain the formula is 6 CO2 six carbon dioxides plus 6 H2O six Waters with light energy to power the reaction are combined into glucose C6 h206 and six oxygens this is an endergonic reaction for two reasons it takes two low energy inputs carbon dioxide and water and converts them into a high energy product glucose it reduces entropy that means it increases organization and you can sort of count that out so there are 12 molecules on this side of the equation and there are seven on this side so we've taken something that was disorganized made it into something more organized a highly unorganized carbon dioxide it's diffuse it's a gas and it's made into solid matter and that's a huge decrease in entropy when did photosynthesis first evolve what are some of the consequences of photosynthesis in terms of when BAS based on fossil and chemical evidence about 3.5 billion years ago that's relatively soon after the emergence of Life at 3.8 billion years ago its consequences were vast first of all when the earth first formed there was no oxygen in the atmosphere its photosynthesis which splits apart water to release oxygen that created the oxygen-rich atmosphere and that made our aerobic metabolism possible and it also created an ozone layer that's a protective layer in the atmosphere that Shields us from ultraviolet radiation and that made life on land possible so we owe everything to photosynthesis what are the two phases of photosynthesis and what does each accomplish we start with the light reactions that's on this side of this diagram and it converts light energy into chemical energy and that chemical energy is in the form of ATP and nadph you already know about ATP nadph is like nadh it's an electron carrier the Calvin cyle is the second phase of photosynthesis and it converts the chemical energy that's in nadph and ATP into carbohydrate and it does that by using carbon dioxide as an input and it fixes that low energy gas into high energy sugars describe the role of chlorophyll in photosynthesis explain the absorption spectrum of chlorophyll and other pigments chlorophyll is the pigment that absorbs light energy in photos synthesis and here you can see its structural formula it's got a hydrocarbon tail that enables it to fit into the phospholipid by layer of the thids and it's really this structure over here this nitrogen ring with the magnesium in the center that enables chlorophyll to help plants convert light energy into electrical energy as we'll see in a little bit an absorption Spectrum shows the amount of light absorbed at different light wavelengths by a pigment by a substance that absorbs light energy and chlorophyll has two forms they're different based on this functional group here's Chlorophyll B here's chlorophyll a and you can see that they both absorb most energy in the blue part of the spectrum and in the red part of the spectrum but very little in the green part of the spectrum and that's why leaves are green because leaves are reflecting green light whereas they're absorbing other light wavelengths there are other pigments that are also involved in photosynthesis one's called a carotenoid and they absorb other wavelengths what is the action spectrum of photosynthesis the action Spectrum which looks a little bit different from the absorption spectrum that we just looked at shows how various light wavelengths drive photosynthesis and blue and red Drive the most photosynthesis and green drives very little this was determined by the anglan experiment Thomas Angelman in the 1800s did a cool experiment where he grew a filament of algae under light from a prism that divided the light up into its various wavelengths and aerobic bacteria grew around the filament best in the blue and the red part of the spectrum and they were able to do that because that's where the most oxygen was being produced you can in the lab and I actually hope that you did recreate this experiment with the famous photosynthesis spin Leaf disc experiment where these discs of spinach leaves will rise based on the amount of oxygen that they produced and you can set different variables like the intensity of the light or the uh wavelength of the light connect the structure of chloroplast to the reactions of photosynthesis so chloroplasts where do you find them so here they are this is a crosssection of a leaf these are cells within the top part of the leaf and these are chloroplasts there many per cell there's only a couple shown here and in terms of the structure of the chloroplast itself it has an outer membrane and an inner membrane the outer membrane is a vestage of The evolutionary origins of chloroplast there's DNA which is a vestage of the fact that the suwan is an independent living cell there's also ribosomes they're there for the same reason and then there are thids shown at number five over here those are membrane bound sacks and they contain the me membrane bound photos systems and chlorophyll for the light reactions of photosynthesis they're organized into these Stacks called Grana and surrounding them is the stroma which is essentially the cytoplasm of the chloroplast it contains DNA it contains ribosomes and it's where the Calvin cycle occurs so that's where carbohydrates are actually created the light reactions of photosynthesis topic 3.5 of AP biology what do the light reactions produce where do these reactions occur what are the inputs and the outputs the light reactions convert the energy in light into the chemical energy of nadph and ATP nadph is an electron carrier it's like nadh in cellular respiration ATP is the molecule that cells use to build things it's the Workhorse of the cell where does it occur it occurs in the phids oxygen is the waste product as well as NPH and ATP and the inputs are light and water the outputs of the Calvin cycle are the inputs of the light reaction so nadp plus and ADP and P are the inputs those get fed into the light reactions ATP and nadph go out what are the key structures involved in the light reactions so we have a chloroplast over here and then at n we have a Grana and a single phid membrane so this whole thing here is a thilo covid membrane within the phid membrane there are photosystems those are complex Assemblies of proteins and they have embedded chlorophyll molecules those little green dots are chlorophylls and those photosystems those are the things that actually convert light energy shown here at a and shown here at D into a flow of electrons this whole array is kind of like a solar panel that's converting light energy into electricity they're also splitting water molecules and that happens in photosystem too let's just get this out of the way right now in the organization of the photosystems in the thilo covid membrane photosystem 2 comes before photos system one for years biology students have been memorizing that and you have to memorize it too so this is the electron path way through which electrons flow and at one point those electrons flow through proton pumps they're labeled as cytochromes but there's other stuff going on too and what these do is they pump protons from the stroma into the phylloid space and over here is an enzyme called ATP synthes and as the protons that are trapped here diffused through this they generate ATP this is where nadph is created this is an overview we're going to go through the details right now describe how the light reactions of photosynthesis create ATP photo exitation of chlorophyll in photosystem 2 leads to a flow of electrons along an electron transport chain in the thilo covid membrane that electron transport chain that's an electrical current and it Powers a device in this case the device is is a proton pump that's embedded in the thilo covid membrane and that pumps protons from the stroma into the thilo covid space so here's the stroma here's the thid space we're pumping from the stroma into the phylloid space and that creates a chemiosmotic gradient chemiosmotic what does that mean well there are all these protons that are over here and there are very few over here it took energy to do that and that gradient is a diffusion gradient and it's also an electrical gradient and that causes these protons to want to diffuse from the thilo covid space back to the stroma they can't do it through any part of the phylloid membrane except through this channel that's called ATP synthes the ATP synthes channel is also an enzyme and as protons diffuse through the kinetic energy of those protons is used to power an endergonic reaction of taking ADP and phosphate and making it into ATP now note that there's also this water splitting complex that's part of photosystem 2 and what it does is it takes water molecule splits them apart to create oxygen that's a waste product but also to create protons and those protons accumulate in the thid space that enhances the gradient and it Powers additional at P production describe how the light reactions create reducing power nadph that can be used in the Calvin cycle so we're going to start over here we're looking at photosystem one photo excitation of chlorophylls in photosystem one is how the process starts that creates a flow of electrons that's flowing through the electron transport chain of photosystem one and over here those electrons flow to this enzyme it's called nadp+ reductase and that reduces nadp+ into nadph reduction that's a thing from chemistry reduction is gain of electrons so that NP plus is going to gain electrons and uh hydrogen making it into nadph and why because During the Calvin cycle that nadph provides the electrons and hydrogens that reduce carbon dioxide into carbohydrates use the Z scheme to summarize the light reactions so the Z scheme is a graphical representation of everything that happens in the light reactions this axis over here the Y AIS shows electron energy so what happens light drives electron boosting from photosystem 2 remember photosystem 2 comes first and so that electron goes to a much higher energy level and at the same time water is split apart into protons and oxygen gas then there's electron flow through the electron transport chain of photosystem 2 and that goes through proton pumps that power the synthesis of ATP from ADP and phosphate those electrons arrive at photosystem one they're relatively low energy at this point you can see that by their position on the graph but light comes in and it stimulates chlorophyll and another electron gets boosted to a high energy level into what's called a primary electron acceptor that's in the phyo covid membrane and that passes it off to the electron transport chain of photo system one it flows to the enzyme nadp+ reductase and nadp+ reductase creates nadph from nadp plus and a proton so we have the two products of the light reactions a TP and NPH beautifully explained by the Z scheme photosynthesis part three we've covered the big picture and the light reactions and now we're going to talk about the Calvin cycle what are the three phases of the Calvin cycle so let's remember the Calvin cycle takes the products of the light reactions and carbon dioxide and uses it to create sugars so that occurs in three phases and the first phase is called the carbon fixation phase carbon dioxide gas is brought essentially into the biosphere that is followed by the energy investment and harvest phase where matter is actually pulled out and that matter becomes part of the plant and ultimately part of you and then finally there's the Regeneration of the starting C compound this is a cyclical reaction this compound rubp ribulose buus phosphate is at the end and it's at the start now we'll go into each phase describe what happens during the carbon fixation phase of the Calvin cycle the fixation phase begins as carbon dioxide is combined with rubp that is a reaction that's catalyzed by the enzyme rubisco fun fact that might be the most abundant protein on Earth it creates a sixc carbon product which isn't shown so think about this rebp has five carbons each of these black dots represents a carbon atom CO2 has one carbon You' think that would create a six carbon product but immediately that six carbon product dissociates into two three carbon molecues so that's how we end the carbon fixation phase describe what happens during the energy investment and harvest phase of the Calvin cycle we ended the carbon fixation phase with this three carbon molecule and that three carbon product is reduced and phosphorilated so here's a phosphorilation in other words at P contributes a phosphate to this molecule this had one phosphate group this one has two over here so that's a phosphorilation and reduced so nadph donates an electron to this molecule so at the end we have this molecule g3p glycer aldhy 3 phosphate it's also called peal phosphoglyceride those are both interchangeable names and the key thing is that this has a lot more energy than this why because it was given that energy from ATP and nadph this molecule can now be harvested taken out of the Calvin cycle and used to build plants this is the origin of the biomass in almost any ecosystem it's the origin of your biomass because that's ultimately where it came from describe what happens during the last phase of the Calvin cycle before we do that I want to talk about a way to think about the entire Calvin cycle that's really really going to make you think about it in a more sophisticated way and that way pays attention to the number of carbon atoms that are present at each stage of the cycle so we talked about how during carbon fixation rebp is combined with CO2 but a more proper way and correct way to think about it is that it's three RPS rubp is a five carbon compound so that's a total of 15 carbon atoms get combined with three carbon dioxides 15 + 3 is 18 and we've talked about how the three six carbon compounds immediately dissociate into two three carbon compounds so what we have over here at the end of carbon fixation is six three carbon molecules and that's a total of 18 carbons makes sense 5 * 3 is 15 + 3 is 18 and we've got 18 carbon atoms over here now in the energy investment and harvest phase during energy investment we're just going to phosphorate and we're going to reduce we're adding energy but we're not adding carbon so what we wind up with over here is six molecules of g3p glyer alide 3 phosphate 6 * 3 is 18 we had 18 over here we have 18 over here but what we're going to do in the Harvest phase is we're going to pull one of those g3ps out so 18 minus 3 we're left with 15 carbon atoms 5 * three now during the next phase these 5 g3ps are rearranged by a variety of enzymes that's why I have multiple and uh arrows over here and they're rearranged into three five carbon rubb PS and along the way a phosphorilation occurs and that's again energy from the light reactions that's invested over here and rebp is one of the substrates of carbon fixation along with carbon dioxide but now we've accounted for all of our carbons we start with these 15 over here 15 carbons and after the whole process is done we again have 15 carbons and if you can explain that you're set up for an A and A five on the AP bioex exam and that is now an appropriate time for me to say congratulations because you've hung through one of the most difficult parts of this review we're going to do cellular respiration next you're a hero keep with it you're going to get a five on the AP Bio exam I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP bi bi exam cellular respiration the big picture what's the chemical equation for cellular respiration is it endic or exonic where in UK carotic cells does it occur equation C6 h206 or glucose plus 6 oxyg yields six carbon dioxides six water molecules plus energy in the form of ATP it's an exonic reaction it releases energy and it creates disorder it takes an organized molecule like glucose and creates much less organization over here and it occurs in various phases the first phase is glycolysis that occurs in the cytoplasm then the link reaction brings the product of glycolysis into the mitochondrian and in The Matrix we have the kreb cycle and then finally the phase which produces the most ATP is oxidative phosphorilation and that occurs based on enzymes and proteins along the mitochondrial membrane using the intermembrane space to create a CH osmotic gradient briefly describe what happens in each phase of cellular respiration here we've got the whole process let's break it down the process begins with glycolysis so energy in glucose generates ATP and nadh nadh like nadph that we met in photosynthesis it's an electron carrier and the end product is a three carbon molecule called pyruvic acid or pyruvate one glucose a six carbon molecule becomes two pyruvates which are each three carbon molecules in the link reaction what happens is that that pyruvate enters into the mitochondrial Matrix and enzymes along the way convert it to a molecule called aetl COA with two carbons the carbon that's removed is released that's oneir of the carbon that you exhale and that conversion is uh Powers the reduction of an NAD plus to nadh and that's later going to be used in the electron transport chain in the kreb cycle over here what enzymes do is they oxidize these two carbons in a cetal COA and that powers the production of three nadh's one fadh2 that's another mobile electron carrier like nadh and it creates one ATP that releas es two carbon dioxides and that's the other 2/3 of the carbon dioxide that you exhale and note that for every glucose that ENT cellular respiration the kreb cycle runs twice as does the link reaction and then finally you have the electron transport chain the ETC and what that does is it takes these reduced products these reduced mobile electron carriers and it oxidizes them and that creates electron flow that powers through chemiosmosis the production of ATP from ADP and phosphate that's where most of the ATP during cellular respiration is produced cellular respiration Parts two and three glycolysis the link reaction and the Krebs cycle what happens during glycolysis include phases inputs and outputs in your answer I've got a great song about glycolysis that goes like glycolysis come on sugar come on sugar for the breakdown it occurs in the cytoplasm it doesn't require oxygen it's anerobic and it has three parts to it investment cleavage and energy harvest in terms of investment what happens is that enzymes phosphorate glucose so glucose is a starting compound enzymes which aren't shown here but are implied by the arrows take a phosphate from ATP and plant it onto intermediate compounds by the end of that process you have fructose 16 bisphosphate and that goes into the next phase where enzymes take fructose 16 bisphosphate loaded with energy and cleave it apart into two molecules of g3p g3p is the same molecule that gets harvested from the Calvin cycle of photosynthesis in the Harvest phase enzymes again indicated by these arrows do two things they take g3p and they oxidize it that means it's going to lose energy lose El electrons and those electrons go to NAD plus it's a mobile electron carrier which gets reduced to nadh and that's later going to be used in the electron transport chain in addition there are other enzymes that take ADP and phosphate and phosphorated to ATP they're using the chemical energy in g3p to bring that about we're getting gross energy yield of four atps and that leads us to the next idea what's the net yield of glycolysis we get two atps why two even though there are four over here it's because two were invested at the start of the process so we net two and we also get two nadhs one produced over here from this g3p one produced over here and we wind up with two molecules of pyruvate or pyruvic acid that's still loaded with energy and that's going to power the next phases of cellular respiration what happens between glycolysis and the kreb cycle the answer is the link reaction what we have ended glycolysis with is pyruvic acid and that's transported across the inner and outer mitochondrial membranes that's something that's represented by B in this diagram into the mitochondrial Matrix as that happens enzymes remove a CO2 from this pyic acid you see this carboxy group over here it's basically a CO2 and that is oneir of the CO2 that you and any other animal that does cell respiration plants too for that matter wind up releasing other enzymes oxidized the resulting two carbon molecules so we had three carbons now we're at something with two carbons it's actually called an acetal group and the oxidation of that acetal group oxidation is loss of electrons where do those electrons go they go to NAD plus a mobile electron carrier we just met it in glycolysis and that NAD plus gets reduced to nadh and that has electron energy that can get used in the electron transport chain finally enzymes take that acetal group and they attach it to a carer molecule called co-enzyme a and the result is acetal COA that's the starting point for the kreb cycle describe the kreb cycle the kreb cycle which I have a great song about occurs in the mitochondrial Matrix and it's a cyclical series of reactions that generate nadh adh2 and ATP it starts with enzymes all of these are enzymes over here enzymes taking this two carbon acetyl group from acetyl COA and transferring it from oxaloacetate also known as ayic acid to citric acid which is also known as citrate the alternative names of the kreb cycle are the citric acid cycle or the tricarboxylic ACI acid cycle TCA cycle and that's for this carboxy group over here this carboxy group over here this carboxilic acid over here so three carboxilic acids TCA cycle what happens next is that enzyme after enzyme oxidizes citric acid and oxidation is loss of electrons those electrons get transferred to the mobile electron carriers nad+ which becomes reduced nadh that happens over here here over here and over here and there's also a reduction of fad another mobile electron carrier to fadh2 along the way other enzymes over here power a substrate level phosphorilation of ADP and phosphate into ATP there's actually a complication involving GTP but you don't need to worry about that for an AP bio class for each acetal COA that enters the Cycle One ATP three nadh and one fadh2 are generated and that's probably worth memorizing and CO2 is released as a byproduct there's one over here over here that's the other 2/3 of the CO2 that you exhale and oxaloacetate is the starting and ending compound that's the KB cycle cellular respiration part four the electron transport chain and ox oxidative phosphorilation this is such a beautiful and important process let's go through it in the previous phases of cellular respiration glycolysis the link reaction crebs we've been creating nadh and fadh2 those are mobile electron carriers they've been accumulating in the mitochondrial Matrix and they diffuse over to the inner membrane where they're oxidized oxidation is loss of electrons those electrons now flow through an electron transport chain that's this yellow arrow over here and that's a series of membrane embedded proteins that are in the mitochondrial inner membrane so it's as if there's an electrical current that's flowing along the mitochondrial membrane through these various proteins notice that nadh comes in first it has a little bit more energy in its electrons than fadh2 which drops its electrons off a little bit further on down the chain some of these electron transport proteins are proton pumps and they pump protons from The Matrix to the intermembrane space pumping is active transport that requires energy where's the energy from it's from this flow of electrons notice that there's less protons over here and more over here again active transport requires energy and that creates an electrochemical gradient there's more protons over here fewer over here there's more positive charges over here there's fewer positive charges over here it's also a pH gradient because the pH is much lower in the intermembrane space than it is in The Matrix all those protons are trapped oxygen acts as the final electron acceptor and what it's doing is it's so electr negative that it's pulling electrons down this electron transport chain and as it does because it absorbs electrons and protons that are available in The Matrix and that increases the gradient this is why you need oxygen to do aerobic respiration because it's the final electron acceptor in the electron transport chain now all of these protons have been accumulated here they can't diffuse through any part of the inner membrane except through one channel that's called ATP synthes it's the same that we discussed when we discussed photosynthesis it's a channel and it's an enzyme as protons diffuse through so that's diffusion it's facilitated diffusion their kinetic energy is used to create ATP from ADP and phosphate that's how the electron transport chain generates ATP cellular respiration can be used to generate heat instead of ATP explain in newborn humans and other mammals and hibernating mammals there are cells that are called Brown fat cells they're extremely dense with mitochondria that's where the heat is generated when body heat is needed hormones induce a protein Channel called thermogenin or UCP it's also called the uncoupling channel to form in the inner mitochondrial membrane so here it is over here now notice in normal cellular respiration protons that are trapped have to diffuse through ATP synthes which creates ATP but now there's an additional channel so protons diffuse back to the Matrix from the intermembrane space without passing through ATP synthes but all of this activity in the electron transport chain here called the respiratory chain still has to happen and think about the fact that when electrons move through a wire that generates heat through resistance well basically you can think of the electron transport chain as a wire the electrons that are moving through it generate heat but in this case they generate heat without generating ATP and that's how cellular respiration can be used to generate heat instead of ATP how is ATP generation in mitochondria and chloroplast similar in unit 3 we've talked about these two great metabolic reactions photosynthesis and the electron transport chain of cellular respiration and there are deep similarities to the way that they work and this kind of cross topic thinking is essential to your success in the AP Bio exam both of these processes use an electron transport chain to pump protons to an enclosed space creating a proton gradient and in photosynthesis here's the electron transport chain we're pumping protons from the stroma to the thilo covid space in cellular respiration we're pumping protons from The Matrix to the inter membrane space and both use a subsequent process of chemiosmosis the fusion of protons through an ATP synthes channel to generate ATP and that's not a coincidence as we'll see in unit 7 where we'll talk about Evolution the similarities that are present between mitochondria and chloroplast indicate that at some point in very ancient history they had a common an ancestor ATP synthes evolved once and then it became shared by the ancestors of chloroplast and mitochondria it's an incredible ride seeing biology and seeing evolution in process cellular respiration part five anerobic respiration and fermentation compare aerobic and anerobic respiration aerobic respiration oxygen is required it involves essentially the whole shebang of respiration that we've talked about glycolysis plus the link reaction plus the CB Cycle Plus the electron transport chain generate a lot of ATP 32 atps approximately for every molecule of glucose that enters the cycle most of the ATP is generated over here in the mitochondria there's a small amount that's generated through glycolysis anerobic respiration occurs when oxygen is lacking or insufficient or I should add when the organism doesn't have the enzymes to do aerobic respiration glycolysis is really the key part of Anor robic respiration so it involves glycolysis followed by fermentation and it generates a total of Two atps And it occurs entirely in the cytoplasm the mitochondria are not involved what is fermentation and why does it occur fermentation is glycolysis that's followed by reactions that regenerate NAD plus so here we have one form of fermentation it's called alcohol fermentation here we have lactic acid fermentation but the key thing is that they produce nad+ that's kind of the opposite of what glycolysis does why does fermentation happen it's because if you're an aerobic organism but you need to uh keep on moving and there's not enough oxygen available because you're working so hard then you can continue to get two atps per every glucose and that sure isn't as good as 32 or more that you get from aerobic respiration but at that moment you just can't do it glycolysis however can only create those two atps if NAD plus is available it's a substrate for one of the reactions of glycolysis so two ATP are better than none and that's why animals like us that do lactic acid fermentation perform it when oxygen is on available compare and contrast alcohol and lactic acid fermentation alcohol fermentation really what we're talking about is ethanol fermentation because there are other alcohol fermentations occurs in yeast when you're baking bread and you use yeast you're doing an alcohol fermentation enzymes remove a carbon dioxide from pyruvic acid remember that's the molecule that ends glycolysis that produces acid alahh and acid aldah is then by other enzymes reduced to ethanol well reduction is gain of electrons something has to lose electrons and nadh is oxidized to nad+ that allows glycosis to continue interesting and fun fact this CO2 that makes with the bubbles and beer which come about through an alcohol fermentation that also makes up the bubbles that uh cause bread to be spongy and have its so spongy form now lactic acid fermentation occurs in muscle tissue under Anor robic conditions it's a little bit simpler than alcohol fermentation what happens is that pyruvate is reduced to lactic acid and again um as that reduction occurs something has to be oxidized and nadh is oxidized to nad+ that allows glycolysis to continue There are all kinds of Anor robic sports like weightlifting or doing push-ups or things like that and you're doing them at a level where muscle tissue can't really get enough oxygen so during that time they're doing lactic acid fermentation you feel that lactic acid build up and then eventually you have to stop exercising until you can recover aerobically I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn dm.com and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam topics 4.1 to 4.4 part one cell signaling the big picture to help you study I've put together a checklist that you can download at AP bios. checklist cells are constantly communicating with one another it's a basic feature of Life cells are never really on their own they're always in populations or they're in multicellular organism so there's direct cellto cell communication that you see here where there's some kind of Junction between two adjacent cells and molecules can pass between those two cells and that enables one cell to change the behavior of the other there's also communication that happens through signals so here you have a cell that's producing a molecule it's secreting that molecule into the bloodstream or into the extracellular fluid and that message is going to be picked up by a Target cell these signals are known as lians and there are basically two kinds if the ligg the signal is traveling a long distance through the bloodstream from a gland to another part of the body that's called a hormone when cells are in relatively close proximity to one another they produce local regulators and that's for short distance cellto cell communication describe direct contact Communication in plant and animal cells plant cells can be connected by plasmo dimata these are bridges involving the cell wall and the membrane these Bridges allow signaling molecules water and other substances to diffuse from cell to cell animal cells have Gap Junctions these are built of protein channels that connect adjacent cells they allow a variety of substances including signaling molecules to move from the cytoplasm of one cell to the next what are ligans ligans are signaling MO molecules many ligans are hormones and we'll discuss some in depth in this review what they do is they bind with receptors based on complimentary shape and here I've represented that very simply with a kind of circle and an arc but because this is biology you know that the shapes will be extraordinarily complex like enzymes and substrates binding leads to a cellular response and the mechanism by which that happens is going to be most of what we're going to talk about in this video what is Quorum sensing this is a kind of cell communication that's seen in bofilm formation in bacteria and if this seems out of context these are films that can form for example on your teeth leading to the buildup of plaque what happens is that bacteria so here's a single cell be like one of these over here what they do is they release signaling molecules shown over here at number two and those bind to cytoplasmic receptors so those are receptors that are actually inside the cell they're on the membrane surface when the signal exceeds a certain intensity so when there's a lot of cells around that's a quorum and those signals will be binding with the receptors and that will activate genes and that Gene activation will lead to the expression of for example in this case it looks like what these cells are doing is they're producing a bofilm a polysaccharide that forms that bofilm what's the takeaway twofold the first is that all cells communicate even bacteria and the second is that you should brush your teeth so that you don't get a buildup of bofilm leading to plaque cell signaling involves three phases list them the three phases are reception of a Lian that's what's happening over here there signal transduction where the initial message gets changed into another kind of message that can go into the cytoplasm that often involves amplification of the signal and finally there's a cellular response we're now going to expand on the material in the previous slide what happens during the reception phase of cell signaling the signal molecule also called a Lian as we've talked about before binds with a receptor molecule here you can see a receptor that has a more realistic depiction and you can see how it's embedded in the phospholipid by layer of the cell membrane that binding is based on complimentary shape what happens during the transduction and response phases of cell signaling the receptor during the transduction phase interacts with membrane proteins to produce a second messenger so something will be happening between here and other proteins in the membrane to bring about this second messenger the second messenger with other relay molecules will bring that message to the cytoplasm activating enzymes or the nucleus where we'll have the activation of genes how is the mechanism of steroid non-polar hormones different from that of water soluble hormones the hormones we've talked about so far the cell communication mechanisms we've talked about have all involved water soluble hormones but what if the hormone is nonpolar a steroid hormone like estrogen or testosterone in that case these hormones which are nonpolar can diffuse through the phospholipid bilayer and once they're there they can bind with a cytoplasmic receptor that forms a receptor hormone complex and that is capable of diffusing into the nucleus where it acts as a transcription Factor something we'll talk about in AP Bio unit 6 but all you need to know for now is that that can activate genes so the DNA gets made into RNA the RNA goes into the cytoplasm it gets read by a ribosome and gets made into a protein water soluble hormones they're capable of binding with receptors they interact with uh second messengers and they bring about a cellular response and in general these responses are slower but more longer lasting these responses are quicker topics 4.1 to 4.4 part two now that we've had an overview of cell communication we're going to look in depth at an illustrative example epinephrine and G protein coupled receptor systems before we delve into this I want to let you know that I have a song that's a WAP about cell communication which covers of this material cellular communication Works through phases the context for what we're about to review or learn is the fight or flight response and that has effects throughout our bodies one of the effects is the effect on the adrenal glands which produce a hormone that's called epinephrine or adrenaline and that acts upon the liver to get it to produce glucose that goes into the blood as part of the fight or flight response epinephrine is also known as adrenaline it's a polar water soluble hormone you can see these hydroxy groups over here and over here here's an amino group this is not going to be able to diffuse into the cytoplasm it's going to bind at the membrane note that epinephrine's effects are widespread but tissue specific so epinephrine is going to get released from the adrenal glands into the bloodstream it's going to go everywhere it's going to touch every cell your body but only tissues with receptors are going to respond that response will differ based on tissue types so all of these are adaptations that are part of the phlight response so over here we'll decrease digestion because when you're trying to fight off some Mortal threat you don't need to be digesting at that moment you want to increase your heart rate so that you can deliver more food and oxygen to your cells pupil dilation more light you're going to have better senses conversion of glycogen to glucose that gives your cells your muscle tissue more energy to fight or flee and bronchial dilation allows you to get more oxygen into your lungs so you can deliver more oxygen to the cells of the body epinephrine interacts with cells in the liver and it induces changes that causes those liver cells to take stored glycogen that's a polysaccharide and to hydroly it into the monomers of polysaccharide glucose that GL glucose then diffuses into the bloodstream and there it goes to the muscles of the body and to other organs as well and that provides energy to fight or flee as part of the fight or flight response the question for us is how does epinephrine get liver cells to bring about this response so we're now looking at the off State before epinephrine is released and In This Moment the receptor is Unbound there's no epinephrine in the system there's a nearby membrane protein that's called a g protein a g protein is not a receptor it's a membrane embedded protein and it can oscillate between two states now it's off it's inactive nearby the G protein is a membrane embedded enzyme not a receptor but an enzyme that's called adenol cyclas that is actually the correct pronunciation and it's also in the off State and as a result it's not activating the second messenger what happens when epinephrine enters the system first thing that happens is that epinephrine binds with a G protein coupled receptor so here's epinephrine and here it's binding with the receptor this is a complicated protein and we've talked about allosteric shifts in relationship to enzymes where when something binds at an allosteric site it can then change the active sight well the same mechanism is at work here epinephrine's binding over here and that change kind of ripples through this protein and it induces a change over here now right at this moment the nearby G protein is still dormant it's still bound to GDP GDP is a relative of ADP and it's the low energy form it can oscillate between this low energy form and a high energy form that we're going to see in a minute and that happens when the G protein becomes activated what's the effect on the G protein of epinephrine binding with the receptor well the G protein is then able to interact with the receptor we noted before that the receptor has changed on its cytoplasmic side and that enables the G protein to interact with that part of the receptor and that causes the G protein to discharge GDP that's the low energy form and to bind with GTP that's the high energy form and again notice that this has three phosphates over here just like ATP this only has two phosphates over here like a DP the result is that the G protein now becomes activated so what happens to the G protein once it's bound with GTP it drifts in the membrane It ultimately binds with a denil cyclas this membrane embedded enzyme that activates a denal cyclas and a denal cycles's substrate is ATP and it converts it into a molecule called cyclic which is the second messenger in these G protein coupled receptor systems note that ATP is trip phosphorilated this only has one phosphate and the stands for adenosine mono mono Asin one phosphate what have we done we've taken our initial messenger and we've transduced it creating the second messenger so let's review what we've talked about so far we've talked about reception we have the ligand which is epinephrine it binds with the G protein coupled receptor the receptor changes shape on its cytoplasmic side it interacts with the G protein causing it to discharge ggp which is what it's bound to when it's dormant and binded with GTP which is what it binds with when it's active the G protein then in turn can activate a denal little cyclas which takes its substrate ATP and converts it into cyclic the second messenger what we're going to look at next is the cellular response the second messenger cyclic is going to activate a chain of relay molecules these are called kinases or canes and this activation involves one KY activating the next kise activating the next I've only put three in this chain but there can be many many more and that's called a phosphorilation Cascade how does that phosphorilation Cascade work the kinases are activated by phosphorilation by gaining a phosphate and once they're activated what they do is they activate the next kise in the chain so here we have protein kise one that acts upon protein kise 2 by phosphor it so now protein kise 2 is active phosphor ated what does it do it activates protein KY 3 by phosphor lating it I've only shown three but there can be many more in this chain and we get this Domino like effect of one kise activating the next and activating the next once we get to a denal cyclas then each step involves multiple activations denal cycl will activate many cyclics each of these cyclics will start different phosphorilation chains and the result is signal amplification we had one epinephrine enter the system but by the end and I couldn't of course depict that here but you'll have the activation of millions of enzymes to bring about a massive cellular response in the case of liver cells and the way that they're acted upon by epinephrine the response is activation of the terminal enzyme which is glycogen phosphor and what glycogen phosphor does is it converts glycogen again a polysaccharide into glucose a monosaccharide that glucose diffuses into the blood giving you energy for the fight or flight response we've seen how epinephrine working through this G protein coupled receptor system can mobilize this massive cellular response this is incredibly quick and it has to be because it's part of the fight or flight response but after the threat has been escaped from or dealt with the system also needs to be shut down and that needs to happen quickly as well to explain that I'm going to show you this excerpt from my cell communication wrap enjoy back to the LI of the receptor it only stays for a moment before it diffuses away so when the thread is gone the Cascade gets shut down with no adrenal secretion the receptor's Unbound G protein drops the phosphate and bound to GDP it goes back to sleep stops its activity bound to GDP it no longer stimulates adental little cycl which no longer creates cyclic so the second message stops kise phosphorilation quickly drops as other enzymes protein phosphatases clip off phosphates turn off kinases glycogen phosphor stops hydroling glycogen so blood glucose normalizes liver cells return to their resting state I love how G proteins let cells communicate I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam topic 4.5 feedback and homeostasis what is homeostasis what are feedback mechanisms and how do they connect to homeostasis homeostasis is the tendency of a living system to maintain its internal conditions at a relatively constant optimal level your body temperature for example stays around 37° C 98.6 fahit despite fluctuations in the external temperature the changes in your body to maintain that temperature that's a great example of homeostasis feedback is when the output of a system is also an input so here we have some system here's the thing that's coming out and feedback is when it feeds back into the system so so the output is also an input and feedback can do two things one is connected to homeostasis it can allow organisms to maintain homeostasis as they respond to internal and external changes just as I told you with temperature or it can accelerate internal changes and drive a process towards a conclusion this is generally connected with what's called negative feedback and this is connected with what's called positive feedback let's talk about set points what is a set point how are set points used in negative feedback first a word about the method here we're going to talk about this in relationship to your home heating and cooling system it's much easier to understand this before we look at the biological examples so a set point is where you set the thermostat it's the value around which a homeostatic process fluctuates so above the set point for the thermostat is 68° F in Nega feedback the output of the system feeds back to the system in a way that decreases the system's output so here we have the set point here's a measurement of the temperature the set point is above the temperature that'll send a signal to turn on the furnace that'll generate heat heat feeds back to the system there's a thermostat over here with the thermometer that will increase the temperature and then when we get to 68° fah the set point the system will turn off negative feedback promotes homeostasis returning a system to its set point how can antagonistic negative feedback loops be paired to promote homeostasis so same goal keep the temperature at 68° well here we have a negative feedback system that responds when conditions are above the set point so temperature 70 the set point is 68 what will you do you'll have a signal that turns on and air conditioner that will put out cool it's a real word and that will feed back to the system and eventually it'll get the system to turn itself off there's been Cooling and we've therefore lowered the temperature but we still have a heating system and if the temperature goes below the set point then that system would turn on it would release heat that would feed back to the system and that would wind up turning the system off so we have paired antagonists systems one for cooling one for heating now we're going to look at some biology let's talk about how feedback Works in blood sugar homeostasis it's important to your body to maintain your blood sugar levels your blood glucose levels the main hormone that controls that is insulin and it's a negative feedback system in response to high blood glucose levels after eating a sugary or a starchy meal your pancreas will release the hormone insulin just represented here as a triangle in the liver insulin will bind at a receptor over here and that will unleash a signaling Cascade and that talks to a glucose transporter that's a channel that allows for facilitated diffusion if glucose is in higher concentration outside than inside the cell it'll diffuse into liver cells and the glucose will get converted into glycogen which is a storage polysaccharide or it'll get converted into fat blood glucose levels down homeostasis restored but as with our home heating and cooling system insulin is paired with another hormone so let's explain how insulin and glucagon maintain blood glucose homeostasis our blood glucose has a set point about 90 milligram per deciliter above the set point the pancreas will release insulin eat a big meal insulin gets released and your liver fat and muscle cells which aren't shown will absorb glucose and stored away as glycogen below the set point that's when you've gone a little while without eating what'll happen is that the pancreas will release a second hormone called glucagon and that will induce the liver to convert its stores of glycogen into glucose glucose goes into the blood homeostasis is restored an important AP bios skill is explaining what happens when systems get disrupted and here we're going to explain how blood glucose homeostasis breaks down in type 2 diabetes that's also called adult onset diabetes but increasingly it's happening in teens and even children due to the Obesity epidemic in the United States we're going to look at normal metabolism first which we just discussed here we see insulin in response to a high blood glucose level is binding with the insulin receptor the 's a signaling Cascade that causes the glucose channel to open there's glucose absorption into the cells blood glucose level Falls homeostasis restored in people with type 2 diabetes what happens is that the cells become insulin resistant there's glucose in the blood there's insulin released from the pancreas but The Binding of insulin does not lead to the signaling Cascade and because of that the glucose Channel remains closed because of that blood glucose level stays high and that damages organs and tissues breakdown of homeostasis leading to type 2 diabetes we just discussed adult onset type 2 diabetes how does that compare with type 1 diabetes type one is also known as juvenile diabetes it's an autoimmune disorder and basically what happens is that cells of your immune system attack the pancreas cells that produce insulin therefore those cells can no longer secrete insulin and therefore even in response to a high blood glucose level insulin is not secreted that can only be treated by insulin injections type 2 diabetes we've just discussed also called adult onset and that involves insulin resistance where the receptor is become insensitive to the insulin signal all of the biological feedback loops that we've talked about so far relating to blood sugar have involved negative feedback loops what about positive feedback loops how does positive feedback work explain how positive feedback works during childbirth so in positive feedback the output of a system feeds back into the system increasing the systems activity and output it doesn't involve quieting that leads to homeostasis it involves acceleration it drives a biological process such as child birth to a conclusion after which the system shuts down in child birth the growth gr of a baby activates uterine stretch receptors the uterus among other things is a big muscle when that muscle is stretched out it sends messages to the brain the brain releases oxytocin a hormone that oxytocin then circulates in the blood when it's picked up by receptors and uterine cells that leads to more contraction that increased contraction leads to more oxytocin release and ultimately that continues until the baby is born explain how feedback leads to fruit ripening if you were to pause the video and take a look at this diagram I'll bet you that you could figure it out this is a positive feedback system ripening in Fruit leads to the release of a hormone that is a gas it's called ethylene ethylene receptors in nearby fruit pick up the ethylene and that induces additional ripening and more Ethylene production that increased concentration of ethylene accelerates the ripening process and all the fruit leading to more ethylene So eventually all the fruit ripens in Fruit shipping you can prevent that by pumping carbon dioxide into the storage container where the fruit are and that suppresses the ethylene and that's how you can ship fruit long distances at learn biology.com we understand why students struggle with AP Bio it's a hard course the material is complex the vocabulary is ridiculous and the pace is withering it's natural to feel overwhelmed and inadequate to get an A or a four or a five you need an easier way to study and that's why we created learn biology.com it has quizzes it has flashcards it has interactive tutorials about every topic in the AP Bio curriculum it has a comprehensive AP Bio exam review system use learn biology.com and you'll gain the skill skills and confidence that you'll need to Ace your biology course and to crush it on the AP Bio exam so here's your plan go to learn biology.com we've got free trials from June through March for both teachers and students you won't believe how much you'll learn topic 4.6 the cell cycle on a big picture level what does mitosis do list three of its key functions in living things note for this question that mitosis and as it often is is synonymous with eukaryotic cell division mitosis duplicates the chromosomes of a eukariotic cell transmitting that cell's entire genome to its daughter cell so here you have the parent cell it's got two chromosomes here those chromosomes have been duplicated now they're being pulled apart and now you have daughter cells each with two chromosomes and each one is going to be an exact clone of its parent cell in a multicellular organism like you and me mitosis is how an organism grows and repairs itself remember that you started life as all multicellular beings do as a single cell in a unicellular UK carot like a parium or an amoeba mitosis is how reproduction occurs describe what happens during the cell cycle the cell cycle as you can see in this diagram can be divided into two main phases so the outside AR orange part of the circle that's interphase this yellow part over here that's mitosis or mphase represented by the letter M during interphase you can subdivide three basic phases but the cell doesn't appear to be dividing during interphase the first is G1 and during G1 the cell increases in size G1 stands for growth Phase 1 during s which stands for synthesis you have DNA replication or chromosome duplication and during G2 growth Phase 2 you have the growth of the structures that are required for cell division during mphase you have mitosis separation of the chromosomes followed by cyto canis so at the end you have two daughter cells that are clones of the parent cell describe the phases of mitosis we begin with interphase during which the cell grows and replicates its DNA during that time it doesn't look look as if it's dividing but DNA replication for example has occurred during prophase chromosomes which are spread out as what's called chromatin during interphase they condense into these x-like structures the nuclear membrane disintegrates and spindle apparatus which is these fibers over here you can see the entire apparatus in the next phase start to grow from each centrosome during metaphase the spindle fibers Gra onto the chromosomes and they pull and push them to the cell equator if you can sort of Imagine a line running down from top to bottom that would be the cell equator I talked about this x like formation that the chromosomes are in that's because each chromosome is doubled and consists of two clones called sister chromatids during anaphase the spindle pulls the sister chromatids apart and starts dragging them to the opposite ends of the cell at the same time there are what are called non- kineticore microtubules a kineticore is like a handle on the chromosomes that these spindle fibers use to pull the chromosomes apart but there are other fibers that basically push on one another and that causes the cell to elongate during Tila phase a new nuclear membrane starts to grow around each set of chromosomes the chromosomes spread out into their interphase formation so you can't really see them anymore and a nucleolus reappears in each cell it disappeared during interphase the nucleis makes ribosomes and ribosome production shuts down during most of mitosis finally during cyto canis the cell splits apart into two daughter cells I have a great song about mitosis and I'll put the link below mitosis chromos ride in a pro meta an phase divide UK carot SC from one cell to two my to how cells explain the importance of the g0 phase of the cell cycle basic idea here is that not all cells go through the entire cell cycle so if you have highly specialized cells like a nerve cell or a muscle cell they'll leave the cell cycle and they'll enter into g0 after which they won't divide certain stimuli however can induce cells in g0 to reenter the cell cycle but for the most part the nerve cell that you have the nerve cells that you're going to have which is why a traumatic spinal cord injury is something that you can't recover from topic 4.7 regulation of the cell cycle I'm Mr W from learn biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription describe the role that checkpoints play in regulating the cell cycle cell cycle checkpoints are moments when the cell checks its internal conditions and decides whether to progress to the next phase of the cell cycle if certain molecules are in the right concentration then the cell continues through the cell cycle and if not the cell moves into g0 or might initiate what's called apotosis we'll explain that in a moment which is called programmed cell death the primary checkpoints to know about for AP Bio are the G1 checkpoint over here the G2 checkpoint and the M checkpoint what is apotosis I've talked about that several times note that the second p is silent apotosis is programmed cell death it's part of a signaling Cascade that involves the mitochondria and the nucleus it's highly regulated which is very different from cell death that results from traumatic cell injury cells are broken down into cytoplasmic fragments that are called blbs you can see some of those over here and over here and blbs are consumed by cells of the immune system preventing cellular debris and enzymes from damaging nearby cells what are cyclins and cyclin dependent kinases cyclin and cyclin dependent kinases are important internal Regulators of the cell cycle the cell cycle is regulated by outside signals but also by internal conditions cyclines are molecules whose concent ation Rises and Falls throughout the cell cycle so like for example you can see that cycl e Rises right before the S phase cyclon a Rises right before G2 the cell has mechanisms to read the level of these cycl concentrations kinases which we discussed previously in the context of cell communication those are molecules that activate other molecules often by phosphor them they're not shown and and cyclin dependent kinases or cdks are kinases that respond to rising and falling levels of cycl levels now we're going to put that all together and see what some of the mechanisms are that regulate cell division explain how the interactions between cyclin and cycl dependent kinases control the cell cycle so cdks here they are over here are present at a constant level throughout the cell cycle by contrast the level of cyclin as we saw in the previous slide rise and fall when cycl levels are high the cyclin bind with cdks to form a complex called maturation promoting Factor but a good way to remember that is just think of it as mitosis promoting Factor because once you have mpf that allows the cell to pass through the G2 checkpoint and actually divide during mphase however the cycl is broken down and that allows the process to repeat in each daughter cell when it grows to the appropriate size and gets ready for cell division we talked about the cell cycle now let's talk about disregulation of the cell cycle what's the connection between cell division and cancer what are the two types of genetic mutations that are connected to cancer cancer is a disease of unregulated cell division as opposed to cells staying in place doing what they're supposed to do they become Rogue players pursuing their own destiny at the cost of the organism mutations in genes that are called protooncogenes increase cell division by creating too many growth factors growth factors are things that stimulate cell division within a cell itself or within other cells and there are other kinds of genes that are called tumor suppressor genes and what they do is they remove cell division Inhibitors the kind of checkpoints that we've seen in previous slides so a normal cells you have the brakes those are tumor suppressors and you have the accelerator those are growth factors but they act at appropriate times when cells become cancerous it can be for one of two or actually both reasons you can have mutated tumor suppressors that can't prevent cell division even when cell division shouldn't be happening and you have growth factors that promote cell division at unneeded moments describe how a mutation in the Ross Proto anre Gene can induce a non-cancerous cell to become cancerous what we're going to do now is really cool because we're going to connect what we've learned about the cell cycle and its control to what we learned about previously relating to cell communication so Ross is a g protein over here and as a protooncogene it only becomes active when an outside growth signal binds with Ross's coupled receptors so here we have binding that activates Ross it picks up GTP that sets off a phosphorilation Cascade and that leads to cell division so this is in a healthy normal system Ross only gets activated when there's a li when Ross becomes cancerous when it mutates from a protooncogene to an enco gen then it becomes constitutively active and constitutively means it's part of its nature to be active normal Ross is only active it only binds GTP when the receptor binds a liant but this Ross which is an enco Gene is constitutively active it's binding GTP even in the absence of a growth signal and because it's always active the growth factor over here is overproduced and that results in too much cell division this is connected with about 30% of human cancers describe how a mutation in a tumor suppressor genes such as p-53 can contribute to the development of cancer p-53 is a tumor suppressor Gene when cells experience DNA damage a signaling Cascade activates p53 so here we have DNA damage it's detected there's a signaling Cascade and now p53 is activated if the damage can be repaired then what p53 will do is it'll halt the cell cycle while DNA repair enzymes fix the damage so we're going to fix up the DNA that's what's happening over here if the damage is too great then p-53 will initiate a whole signaling Cascade that'll cause the cell to initiate apotosis so either we have repaired DNA that occurs while the cell cycle is halted or the cell will self-destruct Cancer's been prevented if mutations lead p53 to become nonfunctional then the cell will continue to divide even with damaged DNA so here we have DNA damage it's been detected but p-53 can't do anything about it therefore there is no stop signal the cell will continue to divide and that'll increase the chance of the cell acquiring further mutations that can lead it to become cancerous again disregulation of a signaling Cascade disregulation of a cell cycle repair mechanism leading to cancer your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio [Music] exam meiosis the big picture what is meiosis why is it important meiosis is how sexually reproducing ukar that includes animals plants fungi protests transmit genes from one generation to the next it creates variation between parents and their offspring and creates variation Among The Offspring Describe the life cycle of sexually reproducing ukari in ukar adults have specialized tissues testes and ovaries for creating gtes gametes are sperm and egg cells and they do that through this process that we'll be exploring called meiosis the sperm fertilizes the egg and that produces a zygote or a fertilized egg that zygote then divides and develops the tissues differentiate to produce an adult organism in relation to meiosis compare haid and diploid cells these are super important terms for understanding meiosis parents have two sets of chromosomes in all of their body cells with the exception of their gametes those chromosomes are paired so like for example here's chromosome one there are two of them here's chromosome 2 there are two of them one was inherited from one parent one was inherited from the other those pairs are said to be homologous and that's a term that we'll explain in the next slide when parents pass on their chromosomes to the Next Generation they can't pass all of them on if they did then the chromosome number would double in every generation so what happens in meiosis is a having of the number of chromosomes and the half number of chromosomes kind of rhymes with the word half or it begins with the same prefix it's called haid so notice that there are four chromosomes down here there are only two over here what's the difference the difference is what happened during meiosis which is division of cells that involves reduction reduction division define homologous chromosomes homologous chromosomes are the matching chromosomes that you inherited from your parents so for example here's chromosome 3 one of them came from your mom one of them came from your dad here's chromosome four it's the same thing here's chromosome 5 all the way on down the line they are not identical how could they be your Mom and Dad aren't identical so the chromosomes that they passed on to you wouldn't be identical they do have the same genes in the same order but the AL the specific code that is in the location where those genes are found that might be different let's use the analogy of a gene as a recipe well the one that you you inherited from your mom if that were a recipe for tomato sauce maybe that one has a lot more garlic and the one that you inherited from your dad that might have a lot more basil in it well let's now think more biologically if C refers to a specific protein then the DNA that's coding for a specific sequence of amino acids might be slightly different in what you inherit from your mom and your dad and that might even be to the extent where the amino acid sequence of that protein differs so the genes are the same but the alals might be different that's what homologous means more essential meiosis genetics vocabulary compare and contrast germ cells gametes and somatic cells germ cells are the diploid cells that are found in the testes and the ovaries that undergo meiosis they produce gamt and after meiosis we have sperm and egg cells that are haid in a human being the diploid number is 46 that's 23 pairs of chromosomes in the haid gtes the chromosomes aren't paired anymore so there are just 23 chromosomes in the sperm 23 in the egg now the sperm goes ahead and fertilizes the Egg and that egg or zygote will divide develop the cells will differentiate and what you'll wind up with are somatic cells those are the cells of the body the diploid cells that make up the body tissues somatic cells are diploid germ cells are diploid gamt are hloy what happens during meiosis meiosis is reduction division why reduction division it's cell division that reduces chromosome number cells go from diploid with two sets of chromosomes to haid with one set of chromosomes the first step is DNA replication which we see over here at number one it creates doubled chromosomes consisting of two sister chromatids what's going on even though meiosis is reduction division it starts in exactly the same way that mitosis starts with a round of DNA or chromosome replication so if you look at this cell over here there are four chromosomes if you look over here there are still four chromosomes but each one is doubled consisting of two sister chrom omds in step two we have meiosis 1 and what meiosis 1 does is it separates the homologous pairs so this chromosome is homologous to this one this one this one and they're going to be separated so now each of the resulting gametes only has one member of each homologous pair that means it's now a haid cell but each chromosome is still doubled and that's why we have meiosis 2 what meiosis 2 does is it separates the sister chromatids the result is four unique haid gametes compare mitosis and meiosis mitosis consists of one round of cell division that separates the sister chromatids the cells begin as diploid and they end as diploid the daughter cells over here are clones of the parent cell it's used for growth and repair meiosis can of two cell divisions meiosis one over here separates homologous pairs so here we have the doubled chromosomes homologous pairs they get separated in meiosis 1 meiosis 2 separates sister chromatids we go from diploid to haid it's used to create gtes for reproduction it introduces variation the daughter cells are unique how meiosis creates variation I'm Mr W from learn biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription what are the two ways that meiosis generates diversity they're shown here the first is independent assortment the second is crossing over and genetic recombination we'll explain both of those now explain what independent assortment is and how it generates genetic diversity note that the phases of mitosis and meiosis have the same names the same designations but because there are two cell divisions in meiosis we have to give them a kind of suffix so in meiosis there's interphase one followed by prophase 1 metaphase 1 Etc then there's a cyto canis interphase 2 followed by a prophase 2 metaphase 2 anaphase 2 Etc the reason why that's important is because the events that we're going to talk about happen in between prophase 1 and metaphase 1 that's where independent assortment really takes place what happens is that during prophase one homologous pairs pair up and if you think about that it's quite poignant and extraordinary in the adult organism who's undergoing meiosis the chromosomal parents wind up finding each other and what I mean by that is that in the germ cells of an organism do meiosis the mother and the father's chromosome number one will find one another and I'm not kidding they actually embrace and chromosome 2 does that chromosome three does that all those chromosomes find one another and embrace one another during metaphase 1 they're pulled by spindle fibers just as happens in mitosis to the cell equator right so here we have that but the way that each pair gets dragged to the middle is independent of every other pair so In This Very simplified system it's possible that the paternal chromosomes might be on the left side and the maternal ones might be on the right side it's equally possible that you could have this Arrangement versus this Arrangement whereas you have paternal chromosome one on the left maternal chromosome one on the right whereas maternal chromosome 2 is on the left and paternal chromosome 2 is on the right it's as random as flipping a coin and that Randomness is essential what happens is that with two homologous pairs four different chromosome arrangements are possible that's two squared in the gamet in other words what we're going to do now during anaphase is we're going to pull these homologous pairs apart so one possible Arrangement is like this and then in the gamut we have paternal chromosome 1 paternal chromosome 2 and in this gamy we have maternal chromosome 1 maternal chromosome 2 and if the chromosomes are organized like this then this gami can have paternal chromosome 1 paternal chromosome 2 and this gami can have maternal chromosome one and paternal chromosome 2 now you can play around with this you can make a cutout little pieces or you can label coins M1 P1 M2 P2 and you can try different combinations but you won't get more than four in a system that has four chromosomes as its diploid number with three homologous pairs then the math takes you to two cubed that's eight possible arrangements and with 23 pairs like we have in Homo sapiens you have 2 to the 23rd possible Arrangements that's 8 million 388,000 so the same egg it's 1 over 2 23rd the same sperm it's 1 over 2 23rd you multiply those two together and that's 1 in 70 trillion you ever wonder why you're different from your siblings this is only one of the reasons why that's why myosis is so phenomenal so this is independent assortment what every chromosome does is independent of every other chromosome pair and that creates tremendous diversity in The Offspring independent assortment is a phenomenal engine for creating diversity but there's yet another one in meiosis that's crossing over what is crossing over and how does it create variation when those homologous pairs pair up during prophase one they don't only Embrace they Embrace in such an intense way that they actually exchange parts so this Embrace is called synapsis and at a point called a kayma segments of DNA will move from one homologue to the other the result is that you start like this this array of four sister chromatids is called a tetraat four tetrad and so this is what it's like before crossing over and then after crossing over it's like this well you'll notice this isn't really a maternal chromosome anymore it's a maternal chromosome with a paternal piece and the same thing for this one so crossing over creates what's called recombinant chromosomes and these have unique and novel sequences of DNA how does sexual reproduction create diversity one engine for diversity is independent assortment and how it randomly arrays different combinations of chromosomes in the gametes the other engine is crossing over and genetic recombination which creates uniquely recombinant chromosomes and then finally there's fertilization where the sperm and egg from different individuals combine in a fertilized egg and that is the third generator and that's why sexual reproduction creates diversity it explains you it explains me biology is it amazing or what meiosis the whole shebang let's walk through the entire process we begin with interphase and the thing to remember about interphase of myosis is that it does exactly what interphase of mitosis does it replicates the chromosomes duplicates the DNA that's why when we get to prophase one each chromosome consists of two sister chromatids what else happens during prophase 1 the homologous pairs pair up the mat etal and paternal chromosomes find one another and they Embrace they do this thing called synapsis and crossing over where they actually exchange pieces of DNA so that's happening during prophase during metaphase the spindle fibers pull these homologous pairs to the center of the cell and remember that each pair is pulled independently from every other that's the source of one of the main sources of variation in meiosis independent assortment the way that these maternal and paternal chromosomes get arrayed is completely independent it's two to the number of pairs if you want to mathematically calculate the number of chromosomal Arrangements in the gametes during anaphase 1 the homologous pairs are pulled apart during tase 1 a new nucleus forms there's a cyto canis one and an interphase 2 that's not shown in this diagram that moves us to prophase 2 where the chromosomes once again condense note that whereas there were four chromosomes in prophase 1 there's only two in this cell in prophase 2 we've gone from diploid over here to haploid over here that's the main transition or one of the main transitions that occurs in meiosis 1 during meiosis 2 during metaphase the doubled chromosomes get pulled to the cell equator and then they get pulled apart during anaphase 2 then there's a telophase where a new nuclear membrane forms and then there's another cyto canis the result four haid gametes each consisting of single chromosomes we've gone from diploid to haid from double chromosomes to single chromosomes and each of these haid gametes is unique it's genetically unique and that's what happens during meiosis at learn biology.com we understand why students struggle with AP Bio it's a hard course the material is complex the vocabulary is ridiculous and the pace is withering it's natural to feel overwhelmed and inadequate to get an A or a four or a five you need an easier way study and that's why we created learn biology.com it has quizzes it has flashcards it has interactive tutorials about every topic in the AP Bio curriculum it has a comprehensive AP Bio exam review system use learn Das biology.com and you'll gain the skills and confidence that you'll need to Ace your biology course and to crush it on the AP Bio exam so here's your plan go to learnbiology dcom we've got free trials from June through March for both teachers and students you won't believe how much you'll learn topic 5.6 part one chromosomal inheritance sex determination how is sex determined in mammals we've seen this image before it's a cotype it shows all of the homologous pairs paired up chromosomes 1 through 22 are called autosomes they're paired homologous pairs they're the same in chromosomal males and chromosomal females but the last pair are called the sex chromosomes females have two X chromosomes males have an X chromosome and a y chromosome unlike the autosomes chromosome pairs 1 through 22 in humans the X and the Y are quite different from one another for one thing unlike those homologous pairs they don't cross over and swap pieces of DNA the x is a normal chromosome it has a variety of alals related to various nonsex relating functions that includes immune function Vision blood clotting and so on the Y has a region that's called Sr y it's indicated by this yellow bar over here and that initiates the development of the testes during early embryonic development and later on production of testosterone which winds up differentiating the body into its male form during fertilization it's the sperm that determines the chromosomal sex of the zygote which becomes the embrio which becomes the baby which becomes the person the males which have their 22 autosomes and then in X and A Y chromosome during meiosis will pass on either an X chromosome or a y chromosome because even though they're not truly homologous they will get separated just like how the other homologous pairs get separated the egg has two X chromosomes so every single egg cell is going to have the X chromosome if the egg is fertilized by a x carrying sperm then the zygote will have two X chromosomes and it'll develop into a female if the sperm that's carrying the Y chromosome does the fertilization then the resulting zygote will be XY and it'll develop into a male that's chromosomal sex determination in all of the mammals the fact that half of the eggs will be fertilized by an X carrying sperm and half will be fertilized by a y carrying sperm explains the fact that among the births in any mammal population the initial ratio of males to females will be 5050 Birds also have a chromosomal system of sex determination but it's different it's kind of a flipped version of the one in mammals in Birds it's the egg that determines the chromosomal sex of The Offspring that's because the females have what we call a z chromosome and a w chromosome and during meiosis half of the eggs will wind up being Z and half will be W the females will pass on either that Z or W chromosome the males have two Z chromosomes so when they form their sperm all of the sperm carry Z fertilization of a z carrying egg will lead to a male who z z fertilization of a w carrying egg will lead to a female who is ZW that's chromosomal sex determination in birds as in mammals because half of the eggs will be Z eggs and half of the eggs will be W eggs the result is that among the initial births that happen in any bird population half of those birds will be male and half of those birds will be female among certain reptiles sex is determined by the temperature at which the embryos develop some reptiles lay their eggs in a nest that's dug in the sand and as you might imagine it's warmer on the top closer to the Sun and cooler down below these animals develop based on a pivot point that's represented by tpiv over here so in sea turtles the eggs that develop above the Pivot Point become female here's the proportion of males over here so if you're above the pivot point if you're in the warmer area you'll develop into a female if you're in the cooler area over here below the Pivot Point you'll develop into a male and then at the pivot point it's pretty much random 50/50 in another kind of reptile called a tuara it's the opposite so basically if you develop above the pivot point then you have a higher chance of being a male if you're below the pivot point then the proportion of males goes down you have a higher chance of being a female and in crocodiles there are two pivot Points a low temperature one and a high temperature one in the coolest and the warmest temperatures the eggs develop into females in other words the proportion male weigh down but at intermediate temperatures over here the eggs develop into males how is sex determined in ants bees and wasps this is completely mind-blowing it's a system that's called Hao diploid sex determination or Hao diploidy the males are hloy they develop from unfertilized eggs so here's a male here hloy the females which includes the queen and all of the workers they're all diploid and they develop from fertilized eggs so the mother in a bee Colony just to use that example is the queen she undergoes normal meiosis when she creates her eggs but the father is a haid male also called a drone and he can't really do meiosis because he's haid he's not diploid so essentially he passes on 100% of his chromosomes in the sperm that he creates the consequence is that all the bees in a hive with the exception of the drones all of the worker bees are sisters but they're more closely related to one another than any two mammal sisters are just think about it mammal sisters inherit half of their mom's genes half of their dad's genes so they're 50% related to one another whereas these sisters inherit half of their mom's genes and 100% of their dad's genes so they're 75% related to one another they're more closely related to one another than they would be to their own offspring so that is thought to be an explanation of why the workers cooperate with one another to help the queen create more offspring keep the hive going to find food all of these incredible foraging behaviors that you find in ants wasps and other social insects but it's not a complete explanation because like for example the termites are also social but they don't have this Hao Hao deploy system so biology amazing this is as much as you need to know about Hao diploid for the AP Bio exam topic 5.6 part two chromosomal inheritance non-disjunction and chromosomal variation what is nondisjunction what are its consequences nondisjunction is kind of a cool word so a junction is where things come together a disjunction would be things coming apart a non-disjunction means things failing to separate it's when the homologous pairs or the cister chromatids don't separate during meiosis there's a couple of variations in meiosis one the homologues don't separate and as a result so you see that over here this blue uh chromosome over here these homologues didn't separate they stayed together so the result is that in meiosis 2 uh we're going to have three chromatids on this side three over here one over here one over here so 50% of the gametes are n haid plus one extra and 50% are n minus one so and the haid number missing a chromosome if non-disjunction occurs during mosis 2 it involves the sister chromatids not separating in meiosis 2 the sister chromatids don't pull apart so the result is that 25% of the gametes are n + 1 25% are n minus one in other words the haid number but missing one and then 50% of the gtes will be normal so that's what nondisjunction is and how it can happen in meiosis 1 or meiosis 2 we saw in the last slide how non-disjunction during meiosis 1 or meiosis 2 can result in gamt that have an abnormal number of chromosomes if the eggs are n + one they have the haid number plus one more then the zygote will have an extra chromosome then what we have is a triom and what that means Tri three and instead of a homologous pair with two we have three the most famous example of that is Down syndrome which is a triom of the 21st chromosome which has various developmental consequences and developmental delays if the eggs are n minus1 like over here or over here and the sperm again are carrying a normal number of chromosomes so that's not necessarily the case you can have non-disjunction that occurs during the formation of sperm as well but then the zygotes will have a missing chromosome so they'll have all of the homologous pairs but one will be short and the result of that is a monosomy and most of those aren't really survivable except in the case of the sex chromosomes so uh one to know is called turna syndrome where instead of females having two X chromosomes they have one and there's a significant of variation that could happen in the sex chromosomes there can be men who are born with an extra X chromosome there can be men who are born with an X and two Y chromosomes so those are all chromosomal variations that come about through non-disjunction followed by fertilization I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam topic 5.3 melan genetics genes are the basic unit of heredity they are what gets passed from parents to offspring they determine traits or characteristics you can also think of genes from a molecular genetics perspective and you can think of them as a sequence of DNA nucleotides that code for for RNA and ultimately code for protein and those proteins ultimately determine the characteristics of the organism describe mle's principle of segregation in your answer cover the difference between the terms homozygous and heterozygous just a historical note Gregor mendal is considered the father or grandfather of genetics in the 1800s he figured out many of these basic principles that we're talking about right now every individual has two copies of each gene those copies are located on the chromosomes that are organized into homologous pairs the alals are alternative versions of those genes that might have different DNA sequences that will produce proteins that have different amino acid sequences homozygous means that the two alals are identical for example in this parent over here both of the alals are designated with a capital letter A they are the name this person is a homozygote for this particular Gene in a heterozygote the alals can be different in this individual over here one of the alals is capital A one of the alals is small a the principle of segregation shows What's Happening Here when individuals create gtes their sex cells they pass on only one of their two alals so the alals are together in the parent but they become segregated or separated during gamet formation here that's happening in the formation of sperm here that's happening in the formation of eggs if you feel that that corresponds to the events of meiosis you're on to something and we'll talk about that later Define the terms dominant and recessive dominant alals are always observed in the phenotype of The Offspring they're represented by a capital letter so for example the capital letter A so here's an individual whose homozygous dominant and they express the dominant characteristic dark black fur in these heterozygotes there's also a recessive alil but because the dominant Al is present then the characteristics of the organism is determined by the dominant alil a recessive alil only shows up in a homozygote so this mouse over here is homozygous recessive and therefore it has the recessive appearance that homozygous alil recedes into the background when it's paired with a dominant alil and these are represented in the melan system by a lowercase letter in this case lowercase a what's the difference between genotype and phenotype phenotype is your appearance it's the observable characteristics in an organism an example is brown eyes genotype is the genes that you've inherited the type of genes that you have it's your underlying DNA in my case my eye color is brown that's a dominant phenotype though eye color is actually complex there are many alals involved in determining eye color actually I think it's about three but I'm a heterozygote so my genotype would be like capital B little B how do I know that because my wife has blue eyes and both of my kids have blue eyes and that would only be be possible if I were a heterozygote because if I was a homozygote then I could only pass on the Big B Al and then both of my children would have been heterozygotes explain what a monohybrid cross is and what the results of such a cross will be in your response create a punet square to demonstrate your understanding this which we've seen before is a Punit Square it uses the rules of probability to quickly predict The Offspring of genetic crosses a hybrid cross is a cross between two heterozygotes so these are P's which was one of mle's steady organisms and this P has purple flowers the genotype is capital P Little P capital P Little P why because it's a heterozygote and this is a monohybrid cross so they're hybrid for one characteristic now the result will be Offspring in a 3:1 ratio so how do you do these punet squares well you start by identifying the genotype of the parents well in the problem it's given to you it's a monohybrid cross big p Little P crossed with big p Little P so you can think of this as a germ cell it's going to go through meiosis the homologous pairs are going to separate principle of segregation so some of the gametes will have big p some will have little p and that's true for each parent here big p Little P flowers are her fiic so it doesn't really make sense to talk about father and mother in this case what you do is then the um gtes will fertilize one another you know if this were a pollen the equivalent of sperm it would fertilize the egg assuming this is the female and this is the male over here but in other words this combines with this and we have this organism is capital P capital P it's got the dominant phenotype it's homozygous dominant this organism gets a big PE and a little p it's a heterozygote and it still has the dominant phenotype same with this one over here this one gets two little piece one from each parent and as a result it shows the recessive phenotype and that recessive phenotype is white flowers we have three individuals with the dominant phenotype one with the recessive phenotype a quarter of The Offspring are homozygous dominant half of The Offspring two quarters are heterozygous they still have the dominant phenotype and one quarter will be homozygous recessive and they'll show the recessive phenotype that's how you do a punet square for a monoh hybrid cross in genetics what are the P F1 and F2 Generations this is a common notation that's used in genetics and you as an AP biology student need to understand it the P generation is the parental generation and in general they're true breeding homozygotes now now notice that we've jumped in complexity in this example we're not dealing with just one gene we're dealing with two so there's a gene for tallness and there's the gene for flower color and the um alternatives are tall versus short and purple flowers versus white flowers when you breed the P generation together those offspring are called f1s it's the first filial generation and in this case they're heterozygotes they're double heterozygotes because they're Big T Little T that's a heterozygote and big p Little P so double heterozygotes now let's go from the f1s to the f2s you breed together the F1 generation these double heterozygotes and you get the f2s so the F1 that's the first filial generation and the F2 it's the second generation it's the grandchildren of the key generation and crossing the dihybrid f1s why are they di hybrid because they're double heterozygotes they're hybrid they're mixed for two characteristics that's called a DI hybrid cross we're going to take that apart in just a moment Define mle's principle of Independent Assortment independent assortment it's what we talked about in the context of meiosis this is essentially the same process mendal was able to Intuit this just looking at the trans transmission of traits from one generation to the next genes carrying different traits are segregated and passed on independently from one another so in an organism that's di hybrid Big T Little T big p Little P the way that the T Gene pair gets passed on is independent from the way that the P Gene pair gets passed on and therefore in a double heterozygote a dihybrid big T Little T big p Little P four unique gametes can be created here they are Big T big p Big T Little P Little T big p Little T Little P how can you figure this out for yourself it's very very simple if you use the foil algorithm that's for factoring binomials you should know it from algebra if you don't just remember it first Outside Inside last so you think about this and you think about the gene pairs so you take the first one big T big p you take the outside one big T Little P that's over here then you take the inside one little T big p that's over here and then the last one little T Little P so four gametes can come from a DI hybrid organism this is limited to genes that are found on different chromosomes the game completely changes when those genes are on the same chromosome and we'll deal with that later explain what a DI hybrid cross is and what the results of such a cross will be it's a cross between two double heterozygotes a couple of slides ago we were looking at the production of the f2s when there was a DI hybrid cross we're crossing Big T Little T big p Little P with the same you're going to use the foil algorithm to figure out the gametes and we just described that in the last slide you just bring these alals down and over and combine them you do that for all 16 squares of this di hybrid cross and what do you wind up with you wind up with a 9-3 to 3:1 ratio in The Offspring and that is actually something that's worth memorizing what's the connection between mle's laws of inheritance and what happens during meiosis we've just articulated mle's two laws the principle of segregation and the principle of Independent Assortment the principle of segregation according to mendle says that parents have two alals for each trait but pass on only one to their offspring which inherit their two alals from two separate parents in meiosis there's a diploid parent that produces haid gtes the diploid phase corresponds to the two alals in each parent the haid phase corresponds to the one alil that the parent passes on to their offspring in zygotes that diploid condition is restored and that's not shown in this diagram over here independent assortment according to mendal is what happens to one gene pair is independent of every other Gene pair at least in the ones that mendal studied in meiosis chromosomes assort independently during metaphase 1 of meiosis What is the rule of multiplication demonstrate your understanding by explaining how to predict the probability of genotype little a little a little B little B little C little C resulting from a trihybrid cross between big a little a big b little B Big C little c times the same don't make a huge Punit Square to try and solve problems like this what you want to do instead is use one of the laws of probability the rule of multiplication here's what it is the probability of independent events occurring together is the product of their IND idual probabilities here's how to think about this it's like three independent Punit squares because what each gene does is independent of every other Gene what a is going to do is independent of B is independent of C so three independent ponent squares one for a one for B and one for C but you don't have to create three Punit squares you just have to use the rule of multiplication in a cross between big a little a and big a little a the probability of little a little a is 1 out of four it's the same for b 1 out of four and it's the same for c 1 out of four these are independent events so you use the rule of multiplication it's 1/4 * 1/4 * 1/4 or 1 out of 64 topics 5.4 and 5.5 non-mendelian genetics and environment phenotype interaction non-mendelian genetics is about genetic principles that were discovered after mle's original contributions one of the most important of these involves linked genes what are linked genes describe their inheritance pattern and explain which melan rule linked genes don't follow link genes are genes that are on the same chromosome so fruit flies as opposed to peas were the widely used experimental organism to discover the principles of non mandelian genetics and here you can see one chromosome from a fruit fly and there's a whole variety of genes sequences of DNA that code for specific traits that are located on the same chromosome one has to do with this kind of bristled appendages on the head One controls body color One controls one type of eye color One controls Wing length these genes are mostly inherited together which is different from the independent assortment that we saw with melan genetics because they're on the same chromosome these genes don't independently assort so like for example above genes T and A in this cell over here they're Linked In This cell over here they're not linked these would independently assort and these wouldn't so what happens in crosses involving link Gene note first of all that we have a different symbol system over here you can see that right over here we have B+ B+ vg+ vg+ in this system in non-mendelian genetics a plus sign indicates the wild type or the dominant Al if you have a symbol that can be more than one letter without a plus side that indicates the recessive in this P cross what we're doing is we're crossing normal body normal winged fly B+ B+ vg+ vg+ with a black bed vestigial Wing fly those are both recessive traits and note that all the F1 offspring are dihybrid they're B+ B vg+ VG and they have both dominant phenotypes this is what you'd expect in a melan tradeit for the f1s we have a gray body and normal winged fly which has all of the dominant characteristics now over here what we're doing is we're representing this chromosome Al B+ vg+ and B VG notice that B+ and vg+ they're on the same chromosome and B VG are on the same chromosome too these genes are linked what if they were perfectly linked and they never separated what would you expect to happen the method here is a little bit different than the method in a melan cross we're not doing a dihybrid cross we're doing what's called a test cross and a test cross a DI hybrid so B+ VG plus VG is being crossed with a double recessive and the way that it's done is the double recessive is the male the female is the double hybrid the double recessive I've represented this over here here's a representation of the female on one of her chromosomes she'll have B+ and vg+ on the other chromosome she'll have B and VG the male is a double mutant and he has B VG on both of his chromosomes when the female produces gtes then half of her gametes will have B+ and vg+ and half of her gametes will have B and VG now that's assuming perfect linkage in the male all of the sperm have to have B and VG here's a punet square these are the eggs that's going here the other eggs are going here the other half of the eggs and all the sperm are going over here you put them together and what you'd expect is that half of The Offspring would be B+ B vg+ VG the other half of the offspring would be b b VG VG this organism these offspring would have normal body and normal wings that's 50% of The Offspring and the other 50% of The Offspring would have black body and vestigial wings but that is not what happens and what I'm doing here is I'm letting you know what you would expect if they were perfect linkage what actually happens in a cross involving linkage note that the numbers won't always be the same but the general concepts apply what we see is that the majority of The Offspring have parental phenotypes what does that mean well the mom's phenotype was gray body with normal wings and many of these flies have that phenotype gray body normal Wings the father's phenotype is black body with btig Wings many of The Offspring have that phenotype but a significant number of Offspring Have recombinant phenotypes what are Rec combinant phenotypes they take one of the phenotypes of the mom and they combine it with one of the phenotypes of the dad that's what's happening over here in these flies that have a gray body like the mother and vestigial wings like the father or you can have a black body like the father with normal wings like the mother those are Rec combinant phenotypes why do we have most of The Offspring having parental phenotypes but a significant minority having recombinant phenotypes it's because linkage is not perfect genes that are linked don't always stay together why not because during meosis there's recombination and crossing over so linked genes because of that process can separate we'll see the details of this in the next slide what happens in crosses involving link genes why are there recombinant in diagrams A and B we have a dihybrid female and her germ cells in C we have meiosis 1 with crossing over we have homologous pairs they're going to get together they're going to swap genes and the production of recombinate chromosomes but notice that some of the sister chromatids are recombinant and some aren't so now what we're going to do is we're going to complete meiosis we're going to go through gamet formation and when we do that note that of the eggs that the female produces two of them at letter H they're recombinant what do I mean by that well they have B+ and they have VG in other words this chromosome is B+ vg+ this chromosome was B VG well the recombinant ones are the ones where those those alal swapped places so this is a recombinant B+ VG this is a recombinant b vg+ but these two at letter I those are parental right they're just like the parents B plus VG plus bvg now over here we have the male parent who's a homozygote and his gamet he can only produce one kind of gamt he's homozygous he can only produce a gam that has B and VG here's what happens with The Offspring offspring n and p have recombinant phenotypes in other words they have in this case graybody vestigial wings that's recombinant neither of the parent look like that and this is black body normal Wings again recombinant neither of the parent look like that but o and Q are parental phenotypes o is graybody normal wings and Q is black body the stigi wings why are there so many more more parentals than there are recombinant phenotypes it's because crossing over happens but it happens at a rate that's dependent on the distance of these alals on the chromosome and so the closer to alals are the less they'll tend to cross over and this frequency which is I believe 177% that represents the distance between the be and the VG on the fruit flies chromosomes what's the relationship between the percentage of recombination and the distance between any two linked genes the further apart any genes are on the chromosome the higher the percentage of recombinant gametes in the chromosome map above genes A and E will recombine the most because they're the furthest apart in other words there can be crossing over over here over here over here and all of those will get e to jump over here and Big E to jump over here that's going to look like recombination that's going to actually almost look like independent assortment because they're so far away but genes B and C they'll recombine the least because the only way that they can cross over is if there's a kayma right over here at this specific spot that would enable little CA to jump over here Big C to jump over here or B could do the same the percentage of recombination can be used to calculate the map distance between two alals so over here this is a chromosome map and it's saying here that the distance between this long bristled appendages called long Arista and gray body that's 48.5 well those are units that reflect the frequency of recombination over here between gray body and red eyes that's a little bit under that's nine recombination units and really what this amounts to is the frequency of recombinant so doing all of these mapping experiments or doing all of these breeding experiments with fruit flies the researchers at Columbia University in the 1900s Thomas Hunt Morgan and his crew were able to create maps of chromosomes and this was establishing that genes are on chromosomes and was part of the pathway that ultimately led to the double helix and all that other great stuff note that these are not physical maps so that the numbers don't add up but this should get you far enough to have a basic understanding again on learnes biology.com I have a whole tutorial about linkage and recombination with practice problems that will get you all the way there your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio exam what are link genes sexlink genes are located on the X chromosome males because the genes are located on the X chromosome can't be heterozygous they either have the alil or they don't so the whole heterozygous homozygous thing doesn't apply to males but females can be heterozygous as shown in this case it's X big h x little H A heterozygote or they could be homozygous dominant that would be X big b h x Big H or they could be homozygous recessive X little h x little H using hemophilia as an example how can males inherit a recessive sexlink trait hemophilia is a blood clotting disorder and essentially hemophiliacs can't clot their blood it's much more common in males than it is in females because the alil for hemophilia the mutated alal that leads to ineffective blood clotting is on the X chromosome Sun's in parit their exlink alal from their mothers so we'll look at the punet square first this punet square is from learn biology.com these boxes are things that you would drag the alal into here we have a hemophiliac X little Hy it's recessive xlink condition how did this uh young man inherit that EX-L alil from his mom mom is a heterozygote xbig h exate she's not a hemophiliac but she carries the alil it's commonly known as a carrier the dad in this case is unaffected X big h y but it doesn't matter because dads don't pass on their X chromosomes to their sons they pass on their Y chromosomes that's why they're Sons to begin with so the mom has to be a heterozygote as shown here or she could be homozygous recessive though that's quite rare we'll look at that in the next slide here's a pedigree that shows uh the same thing basically a cross between a heterozygous female and a normal male and note that in this case the mom passed on her her normal chromosome and the dad passed on his normal chromosome it's the only ex chromosome that he has to pass on in the case of these two sons the mom passed on her defective ex chromosome with the hemophilia alal so we have two sons who are X little h y they're both hemophilia this daughter over here is a carrier she received the normal ex chromosome from her dad and an ex chromosome with the mutant hemophilia alil from her mom and here we have a son who inherited the normal X chromosome from the mom she had one of two to give he got lucky and the Y chromosome from the dad so he's a normal young male examples of excellent processive conditions in humans hemophilia which we just talked about also a very common one is red green color blindness in fruit flies which have a similar sex determination system to humans it's just the X chromosome and the Y chromosome just like mammals the AL for white eyes is a mutation that's on the X chromosome and fruit flies and in fact this was the first a that was ever located on a specific chromosome can a female inherit a recessive sexlink trait absolutely but it's uncommon here's what has to happen the male parent must have the sexlink recessive trait so here we have a wide-eyed fruit fly X little Wy the female must be a heterozygote in this case or have the trait so it could be a wide-eyed female here the female is X Big W X Little W and when we create the pent Square we can see that among the female Offspring 50% of The Offspring are carriers they have to be carriers they get the normal Al for red eyes in this case from their mom they get the recessive Al for white eyes from their dad and in this case they get the recessive alal from both parents so 50% are carriers and 50% of the females have the trade among the male offspring 50% of the males are normal why because the mom's a heterozygote she passes on her her normal ex chromosome with the redey alil to half of her sons but there's also the 50% chance that she'll pass on the recessive mutated Alo and that's why this Offspring over here will be white-eyed but the key thing that we were looking for was how can a female wind up inheriting recessive sexling condition she can if the dad has the condition and the mom is is a heterozygote what is non-nuclear inheritance I'm Mr W from learn biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription it's inheritance of genes that are not on a nuclear chromosome but on the chromosome of a mitochondrian or a chloroplast a nuclear chromosome is one of the auto or a sex chromosome that are found inside the nucleus of a eukaryotic cell these genes that are on mitochondria or chloroplast are only passed on to The Offspring through the female gamat why let's look at the example of sperm sperm have mitochondria the mitochondria power the flagellum that enables the sperm to swim towards the ovam but when there's fertilization only the head of the sperm penetrates through the egg membrane or is allowed in through the egg membrane and all of the mitochondria are left outside so all of the mitochondria that get passed on to The Offspring are mitochondria that were passed on through the female germ cell The Inheritance pattern of these mitochondrial or chloroplast genes doesn't follow mandelian patterns you can see that in this pedigree over here where the mom passes on on the mitochondrial Gene to all of her Offspring male and female but the male who inherits the mitochondrial Gene doesn't pass it on to any of his offspring the male is essentially a mitochondrial dead end if we're talking about mitochondria where the female passes on her mitochondria to all of her Offspring in the case of mitochondrial inheritance in eukaryotes all of one's mitochondria are inherited from one's mother and in Plants they also have mitochondria so the same rule applies but they also have chloroplasts and only the Ule not the pollen passes on chloroplast and mitochondria to The Offspring so it's the same thing it's female line inheritance of alals when it relates to genes that are on an organel such as the mitochondria or a chloroplast what is incomplete dominance this is when the pheno type of the heterozygote is different from and usually intermediate between either of the homozygous phenotypes neither alil is dominant so in this case we have to use a different notation system this is carnations and C Big R with a superscript represents the red flower color alil C Big W with a superscript represents the white flower color or so here's our P generation cbig r cbig r cross with C Big W cbig W the F1 generation they're all hybrids cbig r c Big W but they're pink it's because two doses of gene expression in other words this is DNA that's coding for protein and you need that much protein in order to produce that vibrant red color if you just have one then it's not enough to push the phenotype all the way to red and you wind up with this intermediate phenotype one dose can produce sufficient pigment to create the red color let's see what happens when you do your F1 cross to produce the F2 Generation so we have a pink carnation cbig r c bigw crossed with another pink carnation cbig r cbig w what do you get in The Offspring you get one Offspring that's red because it's cbig r cbig r one offspring that is white because it's cbig w cbig w and two that have the intermediate phenotype pink because they're going to be cbig r c bigw cbig r cig W explain how the same genotype can result in different phenotypes under different environmental conditions this is also known as an environment genotype interaction and what happens is that factors in the environment influence gene expression and that leads to variation in the subsequent phenotype and basically what it's saying is something that's fairly well known that genes don't determine everything genes interact with the environment and note that this is the norm not the exception here are two examples to know about if you have uh hydranges in your yard you can determine the color of the hydranges because the flower color is determined not by gen but by the acidity of the soil in a more acidic soil shown over here you'll get this beautiful purple color in more alkaline soil you'll get reddish color and there's actually mixes that you can add to the water that you give to your hydranges that will adjust the alkalinity or acidity of the soil example number two is dark fur regions in mammals and they develop in cooler body regions away from the core this is a Himalayan rabbit but if you can picture a Siamese cat it's pretty much the same thing so this is a cool region this is a cool region this is a cooler region and all the cells have the same genes but the cells that are being exposed to cooler temperatures Express different pigment alals than those that are in the warmer regions of the body there are many other examples height and weight in humans is caused by an interaction between the genes that someone inherits in the environment that they're in the way that your skin color can change in relationship to the amount of sun that you're exposed to to that is genes being expressed in relationship to environmental cues we talked earlier about how sex is determined by temperature in certain reptiles another example of environment genotype interaction topic 6.1 DNA and RNA structure describe the structure of DNA DNA is a double stranded helical molecule composed of nucleotide monomers in this flattened out representation of DNA here's one strand here's the other strand in this helical representation you can see one strand another strand because there's two strands it's a double helix the monomers are nucleotides they consist of a five carbon sugar called deoxy ribos hence deoxy ribonucleic acid a phosphate group and one of four nitrogenous bases so it doesn't have to have this exact structure it can vary over here in terms of the nitrogen base each strand consists of coal bonded deoxy rivos sugars and phosphate groups which comprise DNA's sugar phosphate backbone within the Helix bases with complimentary shapes bind through hydrogen bonds thyine is complimentary to adenine guanine is complimentary to cytosine in the case of adenine and thyine you can see the hydrogen bonds that form between the oxygen over here the hydrogen over here hydrogen over here nitrogen over here the bonding follows base pairing rules that you have to commit to memory adenine binds only with thyine a binds with t guanine binds only with cytosine G binds with C for the nucleotides to bind they have to be oriented upside down relative to one another making the two strands anti-parallel this strand has its five Prime end over here it's three prime end down here and this strand is the opposite anti-parallel like this explain how DNA's structure allows it to serve as the molecule of heredity we'll start with information storage the four bases can occur in any order I've represented them over here as a TG over and over again to show the structure but there could be three A's in a row followed by two C's followed by a t followed by whatever the sequence isn't determined by DNA's chemistry that allows the sequence to be an informational code that specifies sequences of RNA and protein replicability the specific base pairing a GC that we talked about previously allows each strand to serve as a template for the synthesis of a complimentary strand during DNA replication which we'll talk about in a moment that also ensures High Fidelity transmission of genetic information from parent cells to daughter cells CS DNA is highly stable its double helical structure protects the sequence of bases that are inside but while it's stable it's also capable of mutation mutability is the fourth characteristic there's a low level of mutation where bases can change from one to another either spontaneously or caused by mutation causing factors in the environment and that allows for change in this code which allows for evolution compare and contrast the functions of DNA and RNA DNA is the molecule of heredity in all organisms anything that is cell-based life which is all life has DNA as its molecule of heredity as the stuff that genes are made of RNA is the hereditary molecule in some but not all viruses viruses that you might know about that are RNA based include HIV and SARS a form of which just caused the covid-19 pandemic in all organisms RNA is involved in information transfer related to protein synthesis how DNA becomes RNA and how RNA becomes proteins and that includes forms of RNA such as mRNA TRNA and rrna in ukar RNA is also involved in the regulation of gene expression and this preview some topics that we'll talk about later in this unit that includes splicing out introns non-coding DNA from pre-mrna to create mRNA and regulating protein synthesis compare and contrast how genetic information is stored in procaryotes and ukar procaryotes store their DNA in looped circular chromosomes in other words the beginning and the end is connected it's sometimes ascribed as circular but Loop is really more accurate the genomes of bacteria and ARA range from about 100,000 base pairs to 10 million base pairs and their DNA is naked it's not wrapped around a protein scaffold in ukar the DNA is organized into multiple linear chromosomes so there's one end and there's another end and the DNA is wrapped around these proteins that are called histones eukaryotic gen genomes are much larger than procaryotic genomes the human genome is one example consists of 3.2 billion base pairs but there are some plant genomes that consist of 150 billion base pairs what are plasmids what's their function how are they used in genetic engineering plasmas are small extra chromosomal Loops of DNA commonly found in bacteria less commonly in archa rarely in UK carots here's the main bacter iial chromosome these Loops also made of DNA are the plasmas they're involved in horizontal Gene transfer between bacterial cells through a process called conjugation these transfer genes because they're transferring DNA that codes for protein from one cell to another they're often for antibiotic resistance plasmans are commonly used in genetic engineering for replicating DNA and for expressing engineered genes within bacterial cells both horizontal Gene transfer and genetic engineering are going to be covered later in unit 6 topic 6.2 DNA replication your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your bi ology course and crush the AP Bio exam on a big picture level describe how DNA replication occurs and what the term semiconservative means during DNA replication a team of enzymes using each strand of the double helix as a template synthesizes New Daughter strand here's the original strand enzymes pull that strand apart and that results in in two daughter strands that are each single strands these single strands serve as a template and what that means is that nucleotides that are available in the nucleus following the Bas pairing rules will bind with the exposed strand a will bind with t c will bind with G Etc the result is that each daughter DNA double helix consists of one conserved strand from the parent molecule and another strand that was synthesized a new in these daughter molecules one of the strands is this strand here we go the other strand is this strand whereas these strands over here are new semiconservative one strand is conserved the other strand is new you can see that represented here with a kind of color coding where the parent strand has both strands colored red and you can see in the daughter strands one strand is red conserved one strand is orange new that method of replication is known as semiconservative replication describe how DNA replication starts in the model of DNA replication that we're about to talk about there's a lot of simplification compared to how the process actually works in nature but don't worry this is exactly what you need to know for AP biology the process begins with an enzyme called helicase over here at B finds a sequence called the origin of replication that basically says start replicating here and separates the double stranded DNA as you know that means breaking the hydrogen bonds that are holding the two strands together this exposes two single strands and it creates a structure that's called a replication fork describe the roles of DNA polymerase primas and primers in replication let's get oriented here before we start this is a replication fork this is DNA helicase that's opening up the paron Strand exposing the nucleotides in the two daughter strands DNA polymerase is this enzyme shown over here and over here it's the key enzyme involved in creating new DNA the parent DNA is shown in dark blue the new DNA that's coming in is represented in light blue the nucleotides bind based on base pairing rules DNA polymerase doesn't know which nucleotide should fit the knowledge is basically in the template strand so if there's a c over here then a g will bind if there's an a over here then a t will bind what DNA polymerase does is it binds new nucleotides to the three prime end of a growing Strand and that's a sugar phosphate Bond DNA polymerase has a limitation it can only add nucleotides to an existing strand so think of it as an enzyme and it has an active site it's substrate is the pre-existing Strand and the new nucleotide that came in so to start the process DNA polymerase needs an RNA primer a couple of bases of RNA that DNA polymerase can start connecting DNA nucleotides to here's the primer shown over here here it's shown and it's represented by number four there's another enzyme that can come to an open replication fork and start laying down that primer and that's represented here at five it's called primase primas lays down the primer what role does single strand binding proteins play during replication the single strand binding proteins are shown at eight and what they do is they keep the double helix from rewinding so that all of these other enzymes can get into place and Carry Out replication how is DNA replication at the leading strand different from replication at the lagging strand in each replication fork there's going to be a leading Strand and a lagging strand in the leading strand which is shown over here at J DNA replication is relatively continuous because DNA polymerase at G is following the opening replication fork that's being created by helicase over here in the lagging strand which is shown at L DNA polymerase synthesizes in the opposite direction from the opening replication fork so what you have to imagine is that DNA helicase opens up the Helix a little bit DNA polymerase gets in and starts synthesizing and then it opens up a little bit more well DNA polymerase can't go in this direction it can only go in the 5 to3 Direction so that means another DNA polymerase comes in and synthesizes this over here and yet another and each time there's a primer what that means is that on the lagging strand DNA replication is discontinuous and it's built from short sequences that are called okasaki fragments named after the researchers who discovered that this is how the process works describe the roles of DNA polymerase 1 and ligase during DNA replication DNA polymerase 1 shown over here at K removes the RNA primers here's one over here here's a whole bunch over here and it replaces the RNA with DNA another enzyme called DNA ligase is required to finish the process and create the complete daughter strands what it does is it seals the gaps between fragments with sugar phosphate bonds topic 6.3 transcription explain the overall flow of genetic information within cells this is the central dogma of molecular genetics which is DNA makes RNA makes protein information flows from a sequence of DNA triplets to a sequence of mRNA codons to a sequence of amino acids what is a gene if you've been following this series we looked at this slide in unit five but now let's look at it again in the context of molecular genetics a gene is the basic unit of heredity passed from parent Offspring it determines a trait in terms of molecular genetics it's a sequence of DNA nucleotides that codes for RNA which codes for protein list the principal forms of RNA and describe the function of each one mRNA or messenger RNA is a linear molecule and it brings instructions from DNA to ribosomes R RNA ribosomal RNA makes up the catalytic part of ribosomes and binds amino acids together during protein synthesis ribosomes are these particles that are composed of our RNA and protein we'll look at them in depth later but they're essentially enzymes and they're the enzymes that bind amino acids together during protein synthesis trnas Transfer RNA bring specific Amino acid to the ribosomes again for protein synthesis small rnas are a large group of rnas of different shapes and sizes and they're involved in eukaryotic Gene regulation what happens during transcription transcription is the creation of RNA which we see over here in Blue from DNA every Gene begins with a promoter region that indicates that that's where the gene starts and during transcription an enzyme called RNA polymerase binds with the Promoter on DNA then it transcribes the sequence of DNA bases on DNA's template strand into a sequence of RNA RNA polymerase like all of the enzymes involved in working with DNA reads the DNA in the thre Prime to five Prime Direction and synthesizes new RNA in the five Prime to thre Prime Direction and when the RNA polymerase reaches a Terminator region which is at the end of the gene it dissociates from the DNA ending transcription Define and describe template strand minus strand non-coding strand or anti-sense strand in relationship to RNA transcription the template strand it's this one over here in blue it's also called The noncoding Strand The anti-sense Strand and the minus strand that's what gets transcribed from DNA into RNA the complementary strand to the template strand is called the coding strand why because you can see that it has the same sequence of nucleotides as the Mr will here's the coding strand G gtta AA here's the RNA that's being produced GG uuu U substitutes for T in RNA AA so GG uu a a g g TT AA it's the same why is it the same because it was created in response to this template strand over here that's why the coding strand is called the sense strand or the positive strand what are some unique features of procaryotic transcription procaryotes don't have a nucleus there's no separation between the genetic material and the cytoplasm as a result in procaryotes transcribed RNA which is shown here at D can immediately be translated by ribosomes into protein and that's what you see as these strands over here often multiple ribosomes read the same RNA strand these multiple ribosomes are sometimes called polysomes and you can see them in a more zoomed in version over here the genetic code and translation SL protein synthesis what is the genetic code how do you read a genetic code chart use the code to translate Aug gu a a GU into protein the genetic code is the code used by living things to translate nucleotide sequences into amino acid sequences we've talked about how DNA makes RNA makes protein DNA to RNA is transcription now we're going to get from RNA to protein in the genetic code groups of three RNA nucleotides so like for example Aug gu they're called a codon and they code for one amino acid codon code one the code is nearly Universal nearly every living thing uses it in exactly this way there are some minor exceptions specific every codon can determine one amino acid but it's redundant there are synonymous codons Aug gu a a guu codes for methionine veine lysine veine how did I do that here's how you use the code a u this is the first nucleotide in the RNA codon this is the second nucleotide and the RNA codeon and this is the third so you work from the inside out a u g codes from methionine g u c codes for veiling a a g codes for lysine and g u u codes for veiling so we can see how gu and gu are synonymous and that's an important relationship often the first two nucleotides are more important than the third one and ones that have the same two first nucleotides are often synonymous use the genetic code dictionary below to code out c g Au GCA guu cgu the code that we looked at on the previous slide is a circular code I actually think it's easier to use though you'll frequently see codes like this that are tabular in this code the first base is represented on this column the second nucleotide base is represented over here and the third is going to be one of these four let's demonstrate how that's used c u c is the first code on c u and here's C that codes for Lucine G Au G is the first base a is the second base U codes for asparagine GCA g c a codes for alanine GU c g u c codes for veiling and CG c g u codes for arginine here you see all of the amino acids and their corresponding codons ref presented here what's the big picture of translation who are the key players mRNA shown over here at G2 it contains the codons this group over here Aug or this Aug or the ccg that specify the order of amino acids here are amino acids shown over here the ribosome connects amino acids to create a poly ribosome is represented as K and what it does is it'll connect for example this amino acid Proline to this growing chain of amino acids a chain of amino acids is also referred to as a polypeptide remember that's the first level of protein structure the linear sequence of amino acids trnas are shown over here at letter O here's a TRNA and trna's bring amino acids such as this one over here to this ribosome mRNA complex trnas have an anti-codon such as this over here g g g letter H and an immuno acid binding site over here in the next slides we'll put the entire process together step by step what is the role of the ribosome in Translation what are the key parts of ribosomes to know ribosomes are general purpose protein factories they can take any mRNA which is what brings it information and converted into any sequence of amino acids they're the enzymes that string together amino acids to form polypeptides and they do that following the instructions in mRNA they have a large and a small subunit and they have three TRNA binding sites the E is the exit site that's where the TRNA that's given up its amino acid will leave from the pite holds the polypeptide and the new amino acid comes into the asite describe how translation protein synthesis begins processed mRNA that means mRNA that's ready to be translated that doesn't have any introns in it leaves the nucleus it'll leave through a nuclear pore the small ribosomal subunit will bind with the MRNA and make make its way over to the start codon which is a ug that's where translation begins that small subunit then Waits quote unquote for a TRNA with a matching anti-codon to bind with the star codon so this TRNA has the anti-codon UAC which complements Aug this first TRNA is carrying the first amino acid methionine then the large subunit binds with the small subunit the ribosome is now complete and that first TRNA with methionine is located in the ribosome's P site that's the middle binding site describe the elongation phase of translation the next TRNA comes to the asite and it Bears a new amino acid here it is the ribosome then catalyzes a peptide bond between the p and asite amino acids so here's a peptide Bond that's forming between methionine and veine then the ribosome translocates it moves over one more codon so that means that a dipeptide is now hanging off the pite amino acid the a side is empty and there's a TRNA in the E side but it's not connected to the polypeptide it's not connected to any amino acid now what happens is that the TRNA that's in the eite exits the new TRNA enters at the asite the aot's empty over here a new TRNA comes in the ribosome is going to catalyze a bond between that new amino acid and the existing dipeptide so there's going to be a tripeptide that's temporarily at the asite but the process is going to continue there'll be another round of translocation followed by exit followed by another TRNA that's charged with an amino acid coming in followed by another peptide bond happening and that continues along the entire length of the MRNA describe the termination phase of translation the ribosome gets to a stop codon the stop codons and the genetic code have no corresponding TRNA instead what they do is they code for a release Factor That's A protein that can bind with the stop codon and induce certain changes in the the MRNA TRNA ribosome complex and those changes cause the ribosome to dissociate and that polypeptide to be released the only thing that needs to happen now is for this polypeptide to fold up into a functional protein translation is done I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam topics 6.5 to 6.6 regulation of gene expression part one operons let's start with a little context eoli is a bacterial cell that lives in our colons that coli is related to colon and it also lives in the colons of many other animals the colon is the large intestine eoli has about 4,000 genes this is a chromosome map of eoli chromosome and it shows a small portion of these 4,000 genes which code for a variety of proteins the overall Genome of eoli consists of about 4 million base pairs a TS C's and G's and this leads to a question of reg ation which is what's the control system for turning its genes on and off let's start by responding to this very general question what is an operon one definition is that an operon is a cluster of genes transcribed as a single RNA here we have a portion of DNA that's labeled structural genes and it's all transcribed as one RNA transcript but then that RNA is processed C so that it's producing a variety of enzymes a cluster of genes transcribed as a single RNA but our focus in AP biology is that an operon is a mostly procaryotic system of Gene regulation that has control elements that allow for Gene regulation describe the structure of an operon here we see a string of DNA and it's an operon it consists of structural genes and those are genes that code for protein there's an operator which is where a repressor protein binds and that enables this system to be regulated there's a promoter where RNA polymerase binds and there's a regulatory Gene that produces the regulatory protein that regulatory protein is generally A repressor protein that binds at the operator how does the trip operon work the trip operon is a system that codes for a series of enzymes that make tryptophan that's what the structural genes do these enzymes work as part of a metabolic pathway that codes for tryptophan which is one of the 20 amino acids but it's also a regulatory system that only turns on production of these enzymes at certain moments if there's no tryptophan in the environment then the regulatory protein over here which is produced by the regulatory Gene and that's pretty much always on that can't bind with the operator look at the shape of this regulatory protein over here and notice that this part won't bind with this and really what we're talking about is a protein with a complex shape that can actually bind with a sequence of DNA because that's what the operator is it's DNA that means that RNA polymerase can bind at the promoter and it can roll down the length of the Gene and transcribe the structural genes creating these enzymes when tryptophan is in eiz environment that tryptophan the amino acid will diffuse into the cell what will happen when tryptophan is in the cell's environment then what'll happen is it'll bind with the repressor protein and when it does that will cause the repressor protein to change shape shape think of this like an enzyme that's doing an allosteric shift binding over here causes a chain over here how and why this is a protein that has Alpha helices and pleated sheets and it's very Dynamic so The Binding over here causes a change over here that enables this regulatory protein a repressor to bind with the operator when it does it blocks RNA polymerase that means that RNA polymerase can no longer transcribe these structural genes to make enzymes that synthesize tryptophan that makes a lot of sense the basic rule is if tryptophan is present don't make it it's an adaptation for saving energy trip is therefore called a repressible operon and tryptophan is the co- repressor this protein when it binds with tryptophan blocks the operator repressing the system transcription becomes impossible that's the trip operon how does the lack operon work we just looked at the trip operon which controls the synthesis of enzymes for synthesizing tryptophan what about this Lac operon Lac operon is an inducible operon as opposed to trip which was a repressible one and it codes for enzyme that digest lactose a disaccharide so here's lactose you can see it's composed of two sugar monomers and the enzymes that digest lactose will break it down into glucose and galactose what happens when lactose is in the environment remember these bacteria live inside our guts so if you had ecoli in your gut and you drank a glass of milk the sugar in the milk which is lactose would then be in the environment of eoli that lactose will diffuse into eoli once lactose is inside ecoli it binds with the repressor protein here's lactose it's binding with the repressor protein and notice the effect in this case the lactose causes the repressor protein to change shape so it can't bind with the operator that keeps the operator free and when RNA polymerase binds at the promoter it can roll down the length of the operon it can transcribe the structural genes and those structural genes produce enzymes that break down lactose into monosaccharides and also increase the permeability of ecoli cell membrane so that more lactose can enter when lactose is absent however there's no lactose available to bind with the repressor the compressor's default shape lets it bind with the operator RNA polymerase therefore after binding with the promoter can transcribe the structural genes the rule is if lactose is absent don't make genes to digest it again think of this as a metabolic adaptation this saves energy don't make enzymes to digest something when the thing that you're digesting isn't around Lac is therefore an inducible operon it can be induced to be turned on what turns it on lactose lactose is the inducer the Lac operon is a negative feedback system explain think about how the Lac operon works lactose turns the system on turning the system on removes lactose from the system why because turning the system on allowing RNA polymerase to transcribe these genes allows for the production of enzymes and proteins that enhance lactose digestion that enhance lactose digestion will make all of this lactose go away when all of this lactose goes away there'll be no more lactose to bind with the repressor which will then bind with the operator the result is that the system turns off and that's negative feedback where the output of the system has the effect of quiet or repressing the system you can say the same thing about the trip operon it's also a negative feedback system why the absence of tryptophan starts transcription when tryptophan is not in the environment then the regulatory protein can't bind with the operator that enables RNA polymerase to transcribe these structural genes producing these enzymes that are part of the metabolic Pathway to produce tryptophan that produces tryptophan and the production of tryptophan puts tryptophan at high enough concentration in the cell so that it binds with the repressor protein changing its shape allowing the repressor protein to bind at the operator shutting down transcription that turns the system off that's also negative feedback both trip and lack negative feedback systems even though lack is an uble system and trip is a repressible system the graph below shows the growth of an ecoli culture that's fed with both glucose and lactose X and Y show the glucose and lactose concentration so note how the glucose concentration is going down over here and notice that the lactose concentration maintains itself and then goes down over here the red line shows the growth of the bacteria over 9 hours there are two lags in growth one is at B over here between a and c and the other one is here at D what's happening eoli prefers to metabolize glucose why because glucose is a monosaccharide lactose is a disaccharide and as you know glucose is the fuel that goes right into the gly olysis process that begins cellular respiration now up to point a eoli eats glucose and grows rapidly but then the glucose starts to run out as the glucose starts to run out there's a lag in growth during activation of the Lac operon and lactose digesting enzymes from C to D the Lac operon is churning out those enzymes that break down lactose into glucose and galactose but at a certain point lactose runs out and then there's another lag which might be a permanent lag until another food source is introduced into the culture the key idea is that glucose is easier to digest than lactose glucose will be metabolized it'll be digested first followed by lactose there was a graph like this that was an F frq on one of the previous tests and this is why you have to understand operons in order to succeed in AP biology regulation of gene expression part two eukaryotic Gene regulation hi Mr W from learn Das biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription Gene regulation in multi cellular ukar key issues organisms like you and me and lizards and redwood trees and Jellyfish any multicellular ukar is composed of trillions of cells organized into specialized tissues we have 46 chromosomes three billion base pairs in each hloy genome and 20,000 genes Gene regulation is a big and complex issue here are some more parts of that issue every single cell has the same DNA but cells need to know which genes to express as they develop and Gene regulation as we just saw with procaryotes and operons is also influenced by factors in the environment how did genes get turned on and off note that most eukaryotic DNA is noncoding so what's the difference between the coding DNA and the non-coding DNA and genes contain introns we've mentioned these before now we'll really look at them in depth in eukaryotic cells what determines which genes are expressed let's start with this fact in any cell in a multicellular organism most of the DNA is not expressed you have cells that make up the lens of your eye those cells Express a single single protein that means that 19,900 something other proteins are not being expressed all those genes are turned off those genes that are turned off are tightly packaged around proteins that are called histones that's what these diss over here represent there's an additional chemical modification which is called methylation it's the addition of a methyl group that carbon attached to three hydrogen and that prevents transcription in the few genes within any cell that are turned on there's a process called acetalation that loosens up the DNA and that makes it possible for RNA polymerase to come in find the promoter and transcribe the genes what is epigenetics we just talked about how in most cells most of the DNA is not transcribed it's silenced it's turned off only a small number of genes are turned on what's the difference that is all defined by this newly emerging topic that's called epigenetics epigenetics are changes in DNA expression that evolve reversible chemical modifications of DNA or modifications in DNA packaging chemical modifications of DNA methylation modification and DNA packaging wrapping around these proteins that are called histones but the genes themselves the sequence of nucleotides is not changed it's a level above the genetic level that's why it's called Epi genetics it's responsible for the differentiation of tissues during development why are skin cells expressing skin proteins where fingernail cells are expressing fingernail proteins and muscle cells expressing muscle proteins those are all about epigenetics because all of those cells contain the same genes somewhat astonishingly sometimes these changes can be transmitted from one generation to the next that's a newly emerging field of study and that's intergenerational transmission of epigenetic modifications of the genome what's the connection between epigenetics cell differentiation and gene expression the key idea one that needs to be memorized is that all cells in the same organism are genomically equivalent every cell in your body except for your gametes has the same DNA all cells are descended from the zygo that's shown at number one in this diagram all cells have the same DNA that's shown at three and four cells differentiate because they express different genes and that relates to the epigenetic modifications that we just talked about in the previous slide describe on a big picture level how transcription is regulated in ukar and eukariotic cells previously we talked about operons which is how genes can be turned on and off in response to environmental changes UK carots have to be able to do that too some of that relates to acetalation methylation histones the things we've talked about but some of this is on a more immediate regulatory level so let's look at the regulatory processes that occur in ukar ukar possess regulatory DNA sequences that interact with regulatory proteins to control transcription I know that this diagram looks horrifyingly complex but you really only need to know it on a basic level so you can understand questions that might come your way on unit tests or on the AP Bio exam some of these regulatory sequences include promoters we've talked about those in the context of transcription so there are promoters shown at letter e there are also enhancers that are shown at letter a and what they do is they increase the probability that a gene will be transcribed they enhance that possibility interactions between activator proteins they're shown at B DNA bending proteins that's at F mediator proteins at G and general transcription factors H enable RNA polymerase shown at letter i to bind making transcription possible all you really need to know is that this kind of system is one that's used for eukariotic Gene regulation you'd never be asked to differentiate between these mediator proteins at G and these General transcription factors you just need to know the big picture this is what you carotic Gene regulation can look like how can gene expression be coordinated in different body tissues during development as we've discussed different tissues Express different genes but those different tissues can also share common regulatory sequences that enable the transcription of genes with in those various tissues to be coordinated an example of that is that the tissue in a male Lion's neck skin talking about this over here and their muscle tissue Express different genes one's expressing the hair that makes up the Mane and the other is expressing the tissue in the muscle but both of those tissues share a common testosterone receptor Gene that testosterone receptor Gene gets expressed as a cytoplasmic receptor and therefore when testosterone gets released into the body it binds with the testosterone receptor this becomes a transcription factor that go goes into the nucleus and activates genes the genes that are activated are going to be different depending on whether those cells are in the Lion's neck or in the Lion's muscle tissue but that leads a single hormone in this case to be able to induce changes in different tissues it's coordination of gene expression in different body tissues what are introns exons what's required to make translatable mRNA in UK carots introns are intervening sequences of DNA within genes they're transcribed into premrna here's an intron in DNA here's an intron in pre-mrna exons are DNA that becomes RNA that ultimately becomes mRNA that gets expressed into protein it gets translated into protein and that is just a bit of the processing of premrna that has to happen in ukar here's the process of transcription relatively straightforward but then what we need to have happen is all of these introns need to be cut out and then the MRNA needs some modification so that it can survive in the cytoplasm and be translated by a ribosome into protein we'll see that in a couple of slides describe some of the post transcriptional modification that has to happen to premrna and ukar before it can be translated into protein in eukariotic cells premrna is what's transcribed from a protein cating Gene so this is DNA over here you can tell because it's a double helix and this is premrna right over here at number two before it can be translated into protein that premrna has to be processed in several ways it has to get an addition at its five Prime end of a GTP cap and a thre Prime poly a tail poly a tail it just means it's adenine adenine adenine adenine all over again as we've discussed previously introns those intervening sequences that don't code for protein need to be excised they need to be cut out and then the fragments that consist of the exons need to be spliced together then you wind up with mRNA that can be translated into protein what is the function of the five Prime GTP cap and the three prime polyat tail that's added to mRNA during eukaryotic RNA processing that five Prime GTP cap which is shown over here at G protects the MRNA from breakdown by enzymes in the cytoplasm and it also assists the MRNA in leaving the nucleus and binding with a ribosome the three prime polyat tail shown over here that makes the MRNA more stable and it delays its enzymatic breakdown by enzymes that are in the cytoplasm explain how the organization of eukaryotic genetic material into introns and exons can increase phenotypic variation as we've discussed before exons are expressed sequences they're transl into amino acid sequences introns are intervening sequences that are spliced out of mRNA before translation here we have DNA and here we have premrna and what we've got to do is we've got to cut out these introns but in ukar there's a process called alternative splicing through alternative splicing exons can be spliced together in alternative ways allowing for the production of mult mble protein versions from the same premrna transcript so for example in this mRNA and in this protein what we've done is we've dropped out a couple of the exons there's Exxon 1 3 4 and six here's another version of the same protein Exxon 1 2 5 and six and here's yet another one Exxon 1 2 4 five and six the basic idea is that each of these exons codes for what's called a functional domain a piece of the protein that can actually do something you put those functional domains together and you get proteins with slightly different functions they're all within the same close family they're all from the same gene but they're different manifestations of those genes and they provide for additional phenotypic variation that's found in carots but it doesn't happen in procaryotes who don't have the intron Exon organization of their coding genes explain the role of small rnas in eukariotic gene regulation small rnas are exactly what they sound like they're segments of RNA that don't consist of a huge number of nucleotides yet they play important regulatory roles in the cell one of these is micro r micr rnas are particularly small and they play a role in what's called posttranscriptional control of gene expression that's exactly what it sounds like it's after transcription a key process that micrornas are involved in is called RNA silencing here's how it works here's DNA that DNA will contain a gene that codes for a micro RNA not all genes code for proteins some of them just code for RNA in the same way as premna needs to be processed before it matures there is processing of the Prem microrna to make it into mature microrna in the same way as ribosomal RNA will connect with protein this microrna will connect with a protein that's called an RNA silencing complex protein together that RNA plus the RNA silencing complex protein will do one of two things if the microrna completely matches 100% part of a sequence within an mRNA then that complex will cause the MRNA to be degraded and destroyed if on the other hand there's a partial match then this complex will cause a pause in Translation in either case what have we done we've changed expression of a gene through microrna topic 6.7 part one mutation what is a mutation what's a point mutation a mutation is a random change in DNA or an entire chromosome a point mutation is a change in a single nucleotide you see that here with the nucleotide C mutating to the nucleotide T distinguish between silent mutations non-sense mutations and missense mutations silent mutations are mutations that result in the same amino acid being coded for the DNA changes but the amino acid and the protein doesn't why because the genetic code is redundant with many codons coding for the same amino acid a nonsense mutation is a mutation that inserts a stop codon instead of an amino acid and a missense mutation changes the amino acid from one to another we see a silent mutation over here the original DNA is lysine the DNA that's now being coded for despite this mutation is lysine here's a nonsense mutation where instead of Lysine we have a stop cat on and here we have missense mutations one is coding for arginine instead of Lysine and one is coding for threonine the effect of U sense mutation depends on the chemistry of the substitution this isn't a term that you need to know but a conservative missense mutation is one where the chemistry is of less significance so lysine is a basic amino acid it has this amino group over here at the end and so does Arginine so that might not change the structure of the protein very much it might not change it in a functional way that is really observable in a phenotype it's not clear but it might not be a big deal on the other hand substituting threonine which is a non-polar amino acid for lysine would be a big deal this is non-polar this is basic that's a very significant change in chemistry and that will impact the function of the protein what are frame shift mutations to review this concept I've put together a sentence composed of threel words there are no spaces but we have these little dividers here if we were to do a mutation where we did a substitution of E4 a over here then note that most of the words still make sense we have the Kat what's a cat well you could probably surmise that that was intended to be cat and that it's just a typo but if we deleted one of the letters like hitting the delete key on your keyboard then what we get is if we drop this a over here then essentially we've significantly changed the meaning we have one word that makes sense and so far as it's a word but it doesn't make sense in the context over here that is called a frame shift mutation because codons are read in groups of three if you delete or insert you change the reading frame now let's look at some nucleotides here is a series of codons that code for four amino acids and then a stop codon and note that this example shows RNA to show the consequences the mutation would have been in the DNA if we have a frame shift mutation then what we've done is we've done a deletion or an insertion that changes the reading frame just like we did over here and that will cause extensive missense or nonsense deleting this U over here causes these two amino acids to be wrong that missense or what can happen is you can have the insertion of a stop cat on and then the entire protein doesn't get coded for after this first amino acid that is the impact of a frame shift mutation CLE cell disease is caused by a single substitution mutation explain how one such substitution can cause CLE cell disease CLE cell disease is one of the first genetic diseases that was understood well on a molecular level it's important to know about the disease involves changes in the protein hemoglobin hemoglobin shown over here is a quaternary protein that carries oxygen in red blood cells so here's hemoglobin in red blood cells and here the red blood cells are carrying oxygen delivering it to the tissues of the body the mutation that causes CLE cell disease is a missense mutation that causes veine which is nonpolar to substitute for glutamic acid that causes a significant change in the chemistry of hemoglobin it causes hemoglobin molecules to stick together so notice how over here they're separate within the red blood cell but the mutated form they'll form very weak bonds and that happens under low oxygen conditions that just means when you exercise or walk up a flight of stairs anything like that that causes the cells to become sickled or spiked and they get stuck in red blood cells and that causes extensive tissue damage this is a recessive mutation you need to be homozygous in order to express the phenotype that there is a phenotype that is caused by being a heterozygote that's called CLE cell trait in any case this is how a single substitute tion mutation can be responsible for a significant genetic disease mutations can be positive negative or neutral explain the big idea is that a mutation's effect always depends on the environment it's contextual a positive mutation improves a phenotype in a way that increases evolutionary Fitness Fitness is about survival and reproduction if it increases both of those things then it's a positive mutation here's an example this is a kind of fish that's called a three spine stickleback there are populations that live in oceans there are populations that live in fresh water note this pelvic spine over here it's an adaptation that promotes survival in Marine environments because it protects against certain kinds of predators there are populations of sticklebacks that became strand in freshwater lakes in those populations the Predators were absent there was a mutation that emerged that resulted in the loss of that pelvic spine not only because it doesn't make sense to produce a structure that has no survival benefit but there are predators that actually can prey on sticklebacks with the pelvic spine so losing the pelvic spine positive mutation we just talked about CLE cell anemia that's uh most cases a mutation that reduces Fitness why because it causes diseased red blood cells and it causes tissue damage as we just explained however in the context in which the mutation for Cle cell anemia evolved in some ways it's a positive mutation why because having one dose of the CLE cell alal in other words being a heterozygote gives you resistance to malaria so that makes it a positive mutation in a malaria ridden area in that context it's positive a neutral mutation has no effect on the phenotype and that's because it might happen in non-coding or non-regulatory DNA or it might result in a silent mutation where the amino acid doesn't change how are mutations important to Evolution mutations provide the raw material upon which natural selection acts note that I'm using the same illustration as in the previous slide and I'm doing that on purpose mutation makes evolution a creative process that results in adaptation without mutation natural selection could only call harmful variant from a population but with mutation new variants can arise that increase a population's Fitness what's the difference between germline and somatic mutations germline mutations are mutations in the cells that make gametes and all other cells here's sperm here's an egg if there were a mutation in either one then that mutation would be present in every cell in the embryo that means it would be present in every cell in the organism and it would be present in the gametes that that organism produced germine mutations can be inherited they're subject to Natural Selection and what's an example any inherited genetic disease such as CLE cell anemia which we have discussed or every adaptation a somatic mutation it emerges in some tissue during the course of development or during the course of adult life it only affects the organism it's not passed on to the Future and an example are the somatic mutations that can cause cancer there are some inherited cancer mutations but you can also have a mutation that's caused by some environmental exposure ultraviolet radiation for example that can cause skin cancer and that becomes a somatic mutation that can cause a cancer are you asking yourself how am I going to get a four or a five on the AP Bio exam it's a good question because it's a hard test but we have a plan for your success go to learn biology.com sign up for a free trial and complete our interactive tutorials and interactive AP Bio exam reviews we guarantee you a four or a five on the AP Bio exam see you on learn biology.com topic 6.7 part two horizontal Gene transfer contrast horizontal Gene transfer with vertical Gene transfer in vertical Gene transfer parents transmit all or half of their genome to their offspring that's what's happening here here's a bacterium it's reproducing and in this generation all of the genes have been transmitted and in the Next Generation all of the genes have been transmitted you inherited your genes from your parents through vertical Gene transfer horizontal Gene transfer is quite different in horizontal Gene transfer one organism transfers genes to another organism that is not its offspring that's what we see happening down here this bacterium over here is transferring genes on this Loop of DNA to this second bacterium in unicellular recipients as is shown here the newly acquired genes become part of the recipient's genome and when this bacterium reproduces it'll pass on the newly acquired genes to its Offspring in a multicellular recipient there's only long lasting results intergenerational results if the genes are transferred into the germ line describe bacterial conjugation if you want to build your vocabulary or use your vocabulary to enhance your understanding of biology conjugation is another word for sex here's how it works it's unlike any kind of sex that human beings or other animals have bacteria have in addition to their main chromosome main chromosome over here they have a loop of DNA that's called a plasmid plasmids can express genes for a membrane extension that's called a pyus that's shown over here at C when the pilus contacts a second cell the plasmid can be copied and transmitted to that recipient and the recipient now has all of the genes that are on the plasmid we have horizontal Gene transfer conjugation plays a key role in the spread of anti I biotic resistant genes through bacterial populations describe bacterial transformation in bacterial transformation bacteria pick up DNA fragments shown over here at one from the environment and those DNA fragments enter into the cell and then become incorporated into the genome that's what's shown over here this DNA can include plasmids so here's a circularized piece of DNA a plasmid that's being incorporated into the cell in genetic engineering transformation using plasmas is used to introduce foreign genes including human genes into bacterial cells describe how horizontal Gene transfer can occur through viral transduction transduction is a kind of horizontal Gene transfer that occurs through viruses it occurs through mistakes in the viral replication cycle during viral infections the virus breaks apart the host's genome here's a virus it's injecting its DNA into its victim this cell over here and one of the first things that happens is that the cell that was infected has its DNA broken apart what the virus then does is it uses the cell's molecular Machinery to create new viral genes and to produce new viral proteins and those become assembled into new viral particles but during a mistake in the proc process sometimes DNA fragments from the host over here are mistakenly incorporated into a virus so this virus over here is leaving the cell carrying genes from the host it should just be carrying its own genes when that virus infects a cell in another organism another bacterial cell in this case it can bring in the other organism's DNA so here's the DNA from the original host and notice that DNA is being injected into this new host that DNA will recombine with the DNA that's in the new host and this can happen to animals as well and if the virus infects a germline cell then new genes can be incorporated into the gene pool of the recipient what is viral recombination this is a kind of horizontal Gene transfer that occurs within virus in this case two different viruses different strains of different viruses infect the same host so this virus and this virus they're variants of one another and here you see them infecting a new host and here you see both of these viruses inside a cell from the host as they carry out their replication cycle there's DNA from the host there's DNA from the viruses and the DNA from the vir viruses can get mixed up so the genes of the viruses can recombine and the result is instant emergence of new viral strains sometimes if animal immune systems can't recognize the new strain this can lead to pandemic viral outbreaks this is what happens when every couple of years there's a strain of the flu that's new and that's novel and which infects many people sometimes with disastrous results this kind of viral recombination is what causes it topic 6.8 biotechnology explain what recombinant DNA is and how it can be artificially created recombinant DNA is DNA that's been combined from more than one source during meiosis you would create recombinant DNA as you combine the DNA that you inherited from your parents in the form of new gametes but this is artificial recombinant DNA it's DNA from more than one source shown over here that might have bacterial DNA with a snippet of human DNA with more bacterial DNA so DNA artificially combined more than one source it's been recombined the main tool in creating recombinant DNA is something called a restriction enzyme shown over here at letter C what these restriction enzymes do is they find sequences of DNA they're called restriction sites so here's one at B and they cut the DNA here's the DNA with sticky ends and you can see these sticky ends over here those sticky ends are exposed single strands of nucleotides you see that over here in this diagram that shows the DNA double helix and those single strands are able to form hydrogen bonds with complementary bases the result of using a restriction as enzym shown over here shown over here are restriction fragments so here's a fragment over here here's another fragment over here if you cut a second piece of DNA for example a piece of human DNA with the same restriction enzymes what you'll wind up having are complimentary sticky ends because of complimentarity the ends of the two pieces will form hydrogen bonds that's what you see happening over here and then you need to use another enzyme it's called DNA ligase and that creates sugar phosphate bonds connecting the strands creating recombinant DNA using restriction enzymes and DNA liase you can create a recombinant plasmid with a human gene explain how note for this question assume that intrs have already been removed from the human DNA the first step is to extract a plasmid from a bacterial cell and then cut open that plasm with restriction enzyme leaving sticky ends the way that we just described in the previous slide use the same restriction enzyme to cut out a Target human gene and therefore the ends will be complementary because they've been cut with the same restriction enzymes the human gene will combine with the plasmid forming hydrogen bonds between their complimentary sticky ends then you have to use DNA liase we referred to that in the previous slide it's not shown here to find the human DNA and plasma DNA together creating a recombinant plasmid that contains a human gene then you'd insert the plasmid into a bacterial cell that's using the technique of transformation which we previously referred to when we talked about horizontal Gene transfer this genetically engineered recombinant bacteria this over here and its descendants over here will produce the human protein and produce the plasmid in every reproduction cycle this is how genetically engineered insulin has been created that means bacterial cells that produce a human Protein that's widely used in order for the genes for human proteins such as insulin to be expressed in bacteria introns need to be removed explain why and how to review introns are non-coding sequences of DNA within eukaryotic genes that have to be spliced out before the gene RNA can be translated into protein here's human DNA there are exons that are expressed sequences and they're separated from one another by introns these intervening sequences the consequence of the presence of introns is that to transfer a human gene to a bacterium to create a gene product you have to use DNA from which the introns have been removed the bacteria would just translate everything including the introns and that would lead to a nonfunctional protein how do you remove the introns you have to do it before transforming the bacterial cells and you can do it in two ways the first method involves determining the amino acid sequence for the protein biochemists can look at a protein like insulin and figure out what the linear sequence of amino acids is once you do that you use your genetic code chart to reverse engineered DNA that codes for that amino acid sequence another method is shown here you find cells that produce the desired protein you extract mRNA from those cells that codes for this protein that mRNA already has had its introns removed and then you use the enzyme reverse transcriptase that's an enzyme that's in retroviruses which are virus es that are RNA based but can create a DNA copy of themselves that gets incorporated into the human cell that they've infected HIV is an example of one such virus you use reverse transcriptase which is shown here at B to create cdna compliment DNA from the RNA and then you insert that compliment DNA into the plasmid and that's how you do your successful genetic engineering what is gel electroforesis how is it used to analyze DNA gel electris is a technique that's widely used it's used to sort molecules by size and or electrical charge it's the basis of a technique that's called restriction fragment analysis also called DNA fingerprinting widely used in forensics it involves placing molecules in a porous gel here's the gel over here at number five that is in a a device an apparatus a box that can produce an electrical current so you'd run an electrical current generated over here through the gel because DNA's phosphate groups shown over here are negatively charged DNA fragments will move away from the negatively charged side of the electroforesis chamber so you put the DNA over here like repels like negative charge negative charge and that's going to push the DNA in this direction the small fragments will be impeded by the gel less than the large fragments so over time the smaller fragments will move more than the larger fragments enabling the fragments to be sorted by size by the end of the process you'd have here DNA with one large fragment here DNA with two fragments and here DNA that's been cut into three fragments how would it be cut by restriction enzymes so you use a combination of these techniques to get results like this as you're analyzing DNA material related to biotechnology often shows up on the AP Bio exam in this form here's a simple restriction mapping problem a 20 kilobase plasmid KB kilobase has several restriction sites the image on the right shows the results of electroforesis following various combinations of restriction enzymes which lane shows the gel that would result if the plasmid were digested with the Restriction enzyme bamh1 your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn Das biology.com to find out how you can master your biology course and crush the AP Bio exam this line over here indicates a restriction site that's been labeled with bam H1 so there's a restriction site over here for bam H1 a second one over here and a third the entire plasmid is 20 kilobases and the map is telling you that this is a 3 Kil base difference so if you cut the plasmid with bam H1 you'd wind up with three fragments here's one here's a second one would start here go all the way down to here and here's a third one that would start here go all the way up to here the first one would be 3 kilobases in size the second one would be 11 kilobases in size how did I do that 3 kilobases + 8 = 11 and the last one is 6 kilobases in size and what that means is that you'd have to look over here at the gel and you'd see oh this fragment is 11 kilobases this fragment is six kilobases and this one is three perfect that means B would be your answer if this were on a multiple choice test what is PCR what is it used for PCR stands for polymerase Chain Reaction the polymerase is DNA polymerase it's a cell-free technique for cloning DNA in other words you can clone DNA in a test tube you don't need a cell in order to do it it requires the DNA sample that you want to clone it's shown over here at a it requires primers those are short strands of single stranded DNA that bind to sequences at the start of the DNA that you want to amplify so here is a primer and here you see the primer binding to the Target DNA if requires heat resistant DNA polymerase shown over here at G that would be a large protein why does it need to be heat resistant because the process involves repeated cycles of Heating and Cooling and you need a DNA polymerase that won't be denatured by the heating process where do you find it from bacteria and ARA that live in hot springs and you also need free nucleotides that are going to be used for DNA synthesis because what we're doing is we're making lots of DNA from a sample that we want to amplify how does it work and involves repeated cycles of heating the DNA to separate it into different strands so here's the DNA you heat it you break those hydrogen bonds and now you've separated it into single strands that's step one over here then you cool the DNA enough so that primers can bind to it and so that DNA polymerase can synthesize new DNA that's shown at two and it's shown at three the DNA polymerase will read the template Strand and it'll seal uh sugar phosphate bonds between the nucleotides that bind with the template strand so here you are uh you're seeing DNA poates creating new DNA and every Heating and Cooling cycle will double the amount of DNA so we started with one piece of DNA now we have two pieces of DNA that's an exact copy of the original DNA do it again you have four pieces of DNA do it again and you'll have eight pieces of DNA after 10 Cycles you have a thousand times more DNA than you started with and after 30 Cycles you've Amplified your DNA a billionfold this is widely used in any kind of science that needs to work with DNA it's widely used in forensics where little DNA samples from a crime scene for example are Amplified so that they can be analyzed for for electroforesis DNA fingerprinting Etc what is DNA sequencing what are some of its uses DNA sequencing you just need to know what it is you don't really need to know how it's done though if you're interested in seeing how it's done you can do that at learn biology.com DNA sequencing involves taking a sample of DNA anything from a small fragment to the entire Genome of an organism and figuring out the specific sequence of a t c NG nucleotides that make it up it allows biologists to determine what proteins an organism can produce it's used to infer evolutionary relationships and it's used by cancer biologists to sequence tumors to see what genetic mutations are causing the cells to become cancerous during the covid-19 pandemic sequencing was used to analyze the emergence of new SARS kv2 variants and of course it was used in order to create the vaccine in forensic sequencing is being used along with DNA fingerprinting to identify and exonerate suspects and resolve paternity disputes welcome to AP Bio unit 7 Evolution to help you study I've put together a checklist that you can download at AP bios. checklist topics 7.1 to 7.3 natural artificial and sexual selection in terms of understanding the process of Evolution the most important idea to understand is natural selection developed by Charles Darwin in the 1800s Darwin himself built the idea of natural selection upon the foundation of artificial selection so that's where we're going to start artificial selection is also known as selective breeding and in this process breeders Envision a desired trait in an animal or a plant for many generations the breeder select organisms with that trait and the process over time over many generations creates a carefully guarded gene pool with individuals that only have genes for the desired trait here are two examples the plants that are in the barasa Olas family include cauliflower broccoli brussels sprouts Etc they're all the same species The ancestral plant Brasa olari has been bred for specific traits for flower clusters in terms of cauliflower for flower buds in terms of broccoli for lateral buds in terms of Brussels sprouts for kale in terms of leaves but all of these are varieties of the same species that have been bred for specific traits the same is also true of dogs dogs and wolves are all members of the same species canis lupus and all the breeds varieties of dogs the German Shepherds and the schn and the doxins those are all varieties that have been bred for specific human purposes for protection for hunting or for just looking cute and being really cuddly so how does natural selection work in any population there's variation the kind that matters is inherited variation that's in the genes and that comes about through recombination and mutation in any population the reproduction rate the number of individuals who were born exceeds the survival rate and that's even true of slow breeding populations sometimes that's summarized by the phrase many are born but few survive the survivors have a beneficial trait that gave them some type of Advantage as the generations proceed mutation continues to create new variants and if you repeat steps 1 through four you wind up with adaptation adaptations can include things like the incredible structure of the wing of a bat or the incredible behavioral adaptation which is sonar which is of course combined with structures like the ears of a bat which can hear high frequency sounds they can be camouflage mutations like this satanic leaf gecko or they can be on a molecular level like the way that enzymes fit with substrates you've learned a lot of biology and whenever you see things and you find yourself thinking how could that work how could that be so perfectly put together it was put together by natural natural selection in addition to artificial selection and natural selection a third type of selection to know about is sexual selection sexual selection is selection for traits that directly increase reproductive success they create an evolutionary Dynamic that results in sexual dimorphism where there are different phenotypes in males and females one type to know about is called intersexual selection and that's where members of One sex typically the females choose mates of the other sex that are typically males so here's a photograph that I took relatively near to my home this is a female turkey there's a bunch of male turkeys who are displaying to her and they're essentially saying through their movements and through their extension of their tail feathers I'm really attractive you should mate with me and that means that there's been selection for these tail feathers and for features like these Waddles and for the M's Behavior peacocks are a bird species where that's been carried to extraordinary lengths and that typically leads to colorful and highly adorned males and choosy females the other kind of selection is called intrasexual selection and that's where competition between males for control of a harm of females or control of a breeding territory leads to a dynamic where the males are aggressive and often really big and strong and that's what we see over here with these elephant seals that live off the coast of Northern California and they're about twice the size of females they're huge aggressive testosterone filled animals selection can change the distribution of phenotypes in a population in a variety of ways in any population most characteristics can be represented by a bell curve of continuous variation if you took all the students in your school and you organized them by height most of the people are average height there are a few people who are short and a few people who are tall that's a bell curve of distribution directional selection which is shown over here selects again against one of these Extremes in other words here's the original population you're selecting against this extreme over here and so you're pushing the population in this direction in stabilizing selection you are selecting against the two extremes an example of stabilizing selection is birth weight in babies babies that are too small have lower survival babies that are too big have lower survival the babies who survive most are the ones who are of average size the third type is called disruptive selection if you can imagine a scenario where the average phenotype is maladaptive then there' be selection for the two extremes it would kind of split the population into two an important type of directional selection to know about is adaptive melanism adaptive melanism is the darkening of the body within a population in response to the darkening of the environment it occurs within a population as its gene pool evolves in responds to Natural Selection so so it's not like getting a tan which happens in an individual this is something that happens over evolutionary time as genes for light coloration are selected against and genes for darker coloration are selected for the selective pressure that results in adaptive melanism is typically predation what's shown here in this example is the rock pocket Mouse which lives in the southwest of the United States and what's been documented on a genetic level is that populations of these mice live on a dark colored substrate have evolved a mutation that results in more melanin production and that mutation spreads throughout the population and results in subpopulations that have the dark coloration we've been talking about various types of selection natural selection is often summarized as survival of the fittest what does it mean to be fit how is evolutionary Fitness measured evolutionary Fitness is not about strength or speed it's the number of Offspring and offspring of offspring that survive to reproduce and the reason why I have this Montage of penguin life is just to indicate that it is something that emerges at every level of the life cycle when the penguins are feeding when they're doing their March Inland when they're breeding when they're juveniles huddling together there's Fitness at every single stage and fitness throughout the life cycle is what enables genes to be passed on to the next Generation to end this this discussion of all types of selection we're going to look at this question explain how the peppered moth demonstrates an evolutionary change in response to environmental change the key point about the peppered moth is that it provides science with a directly observed example of directional selection and adaptive melanism in response to an observed change in the environment the peppered moth comes in two forms there's a peppered form mostly light colored and a dark form and before the Industrial Revolution the Industrial Revolution began with the invention of the steam engine the burning of coal the predominant phenotype was peppered was this one over here so in any population of moths almost all of them were peppered there'd be a few dark moths why is this because that was a form of adaptive coloration the moths were camouflaged as they rested on light colored tree trunks which were often covered by these whitish colored lyans that's the situ situation before the Industrial Revolution with the Industrial Revolution soot from factories was put into the air it landed on the trees it killed the lyans and darkened the tree trunks and what that did is that it created a selective Advantage for the dark colored moths if you were to do a census of the moths um at the beginning of Industrial Revolution most of them were white only a few were black but as the Industrial Revolution proceeded the mean phenotype shifted from light to dark until in the depths of the Industrial Revolution the majority of the moths were dark colored the interesting thing is that this process was also historically reversed about 1960 s from pollution declined with the development of laws like the Clean Air Act that happened around the world the lyans returned the trunks became lighter the mean phenotype of the peppered moth shifted from dark colored to light colored I have a song about the peppered moth and there's also fascinating stuff related to the history of this because it was embroiled in some controversy but the work of Michael magerus which was done in the early 2000s which replicated some work done by BD kettlewell which was done in the late 1800s or early 1900s established this as a clearly observed case of adaptive melanism phenotypic shift in response to an environmental change your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio [Music] exam topics 7.4 to 7.5 population genetics and Hardy Weinberg what is population genetics population genetics is a study of how genes are distributed in populations and how they change over time key thing that we measure in population genetics is alal frequency in this population over here we have 20 individuals and we're tracking the frequency of the AL big a and little a and we can see that the frequency of little a is 0.5 it makes up 50% of the AL in this gene pool what is a gene pool it is simply all of the alals of all of the genes in a population and in that context Evolution means a change in the genetic makeup of a population over time it's the change of alal frequencies within a gene pool before we get more into the details of population genetics I want to address the biggest misconception I've seen among my students at to population genetics that's the wrong idea that's why it's crossed out that the dominant Al has to be more common than the recessive alal these are different dimensions of biological analysis and alal frequency whether an Al is common or rare has nothing to do on dominance or recessiveness it's based on the advantage or harm and Al confers to its Associated phenotype or random historical factors and here's an example the AL for the condition called acondroplasia is exceedingly rare but it's a dominant Al population genetics is one of the more mathematical parts of the AP curriculum and it's built around two equations p + Q = 1 and P ^2 + 2 PQ + Q ^2 = 1 in this system P represents the frequency of the dominant alal and Q represents the frequency of the recessive alal if if you load p + Q into a punet square the whole thing makes a lot more sense p+ Q = 1 means that for a gene with two alals the frequency of the dominant Al and the frequency of the recessive Al equals all the alals p + Q = 1 P ^2 + 2pq + q^2 = 1 what does that mean well first of all here's p and here's P if you do the punet square kind of thing this would be p^ squ the frequency of homozygous dominance p^2 plus the frequency of heterozygotes PQ plus PQ = 2 PQ plus the frequency of recessive individuals q^ sared is all the individuals in a population and you can see that right here here's how you might see this in a sample problem you've identified you've been told that 49% of the mice in a population have the recessive trait of white fur figure out the frequency of PQ p^2 2 PQ and Q ^2 so here's our original setup what we're going to do is q^2 is this value over here so we're just going to put .49 over here from there what we're going to do is we're going to work to figure out that the square root of 049 is 7 then we know that this plus this equals 1 so therefore this the value P has to be3 then we know that 2 PQ has to be42 why3 * 7 is 21 * 2 is42 and p^2 is 093 * 3 is 9 if you set up punet Square cross multiplication tables you'll get this right every time the Hardy warberg principle is that the frequencies of alals in gene pools will stay constant unless one of the more following conditions is not met this Hardy Weinberg population is a fictional population that's used to understand what causes evolutionary change in real populations the first is that the population is infinitely large there are no harmful or beneficial Le there's random mating there's no immigration or immigration and there's no net mutation of one AAL to another if any of these five conditions is violated then alal frequencies can change and these are the factors that can cause evolution what are these factors small populations leading to a phenomenon called genetic drift natural selection where certain alals are beneficial and others are harmful sexual selection which is the opposite of random mating gene flow where genes move into a population or out of a population and directional mutation where one of has a tendency to mutate into another alil so what's genetic drift and we'll also look at one variant of genetic drift called a population bottleneck genetic drift is random change in alal frequencies in a population gene pool usually associated with small population size a population bottleneck can cause genetic drift a biotic living or abiotic non-living factor wipes out a large percentage of the individuals in a population leaving only a few survivors the survivors alals might not be representative of the alal frequencies in the former larger population and some alals might Disappear Completely the reason why I have a picture of a cheetah here is that cheetahs are extraordinarily genetically uniform it's as if all cheetahs are practically identical twins or at least very close siblings based on genetic analysis it looks like the Cheetahs underwent some enormous population bottleneck maybe a viral infection or something like that that wiped out almost all of the Cheetahs down to only a few individuals they repopulated from those few individuals but as a result many Al were lost and they're highly genetically uniform note that in a population bottleneck the survivors didn't have any advantage it's not natural selection they were just lucky another form of genetic drift is the founder effect and this is where a small number of individuals from a large population founds a new population but because of insufficient sampling because it's only a few individuals who leave the larger population the alal frequencies of the gene pool of the founders who found the new population might be different from those in their parent population in this graphic over here here's the original population and the squares and circles represent different Al the Founders go off to colonize three islands in this situation over here the blue alil is completely lost and now the red alil is at 100% here there's a representation of the diversity of the former population and in this case the r alal is lost and the frequency of the blue alil is now at 100% what is gene flow and what's its effect on evolving Gene pools gene flow is the movement of alals from one population to another and that can involve the movement of individuals like we see here this beetle is moving from population 2 to population one but it can also involve the movement of gametes and that's easier to imagine in the case of plants where pollen is flying from one field to another what's the effect of gene flow it can change alal frequencies especially in the recipient population and it can diminish differences between adjacent populations mutation is one of the conditions that violates the Hardy Weinberg equilibrium so what's its importance to Evolution mutation is the ultimate source of genetic variation within and between populations and if it's directional if alal big a tends to mutate to little a then it can change alal frequencies within a population here's a population genetics illustrative example CLE cell disease is caused by a recessive alil in the gene for hemoglobin it can significantly decrease the quality of life and lifespan yet the alil is in high frequency in certain populations explain CLE cell disease is caused by a point mutation in the gene for hemoglobin it results in the substitution of veine a non-polar amino acid for glutamic acid an acidic amino acid it occurs only in children who are recessive for the alil but heterozygotes can experience a small amount of sickling not enough to generate pain crisis and tissue damage under most circumstances the red blood cells in heterozygotes despite the fact that they don't normally sickle are hostile environments for the plasmodium parasite that causes malaria this is a parasite that's carried by mosquitoes and then lives inside red blood cells so what we have is a phenomenon that's called heterozygote Advantage where big S big S homozygous dominant is selected against why because of malaria big S little s heterozygosity is selected 4 why because it doesn't have the symptoms of cyel anemia but it provides protection against the malaria parasite and small s small s is selected against because you have CLE cell disease what this map shows is the high correlation between the frequency of the little s alil and the intensity of malaria in various parts of Africa and this same model heterozygote Advantage might apply to genetic disease like cystic fibrosis and tasac I'm Mr W from learn biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription topic 7.6 to 7.8 evidence of evolution there is abundant evidence to support the theory of evolution for AP Bio the most important type of evidence to know about is the idea of homologous traits homologous features homologous traits are traits that share a common underlying structure and a common embryological origin they show descent with modification from a common ancestor here's the Forum of a human dog bird and whale the bones that make up their for liims have been given the same name by anatomist who recognize that they were the same bones you can also see that they develop from the same piece of tissue embryologically it's because these structures evolved from a common ancestry who had these structures and then natural selection Evolution LED these structures to evolve differently in different lineages homologous features result from an evolutionary pattern that's called adaptive radiation adaptive radiation occurs when one parent species produces several descendants Each of which has unique adaptations and fills a different ecological Niche these are some of the finches that live on the Galapagos Islands they are all the descendants of an ancestral Finch that was blown over there from Ecuador a small population of finches and that evolved in different directions what's the connection these are descendants of the same species and their beaks are actually homologous features they descended from a common ancestor they became modified in each of the descendant species in different ways a vestigial structure is a special kind of homology that provides further evidence for evolution a vestigial structure has no apparent function but it was inherited from an ancestor from whom that structure had a function for example whales have no hind limbs but they have a pelvis over here onto which to attach those limbs why do they have that their ancestors possessed Hine limbs which were lost as whales adapted to their aquatic lifestyle we have a coxic a tailbone this is homologous to the Tails of cats and dogs and other vertebrates other mammals we lost it in the course of our primate Evolution into one of the great apes what can be confusing when you're looking at common features to draw evolutionary connections are the difference between homology and analogy analogous features have a similar function but when you look deeply there's a different underl l in structure they arise through a different kind of evolution not adaptive radiation but convergent evolution and an example is shown here we have sharks we have iosaur an extinct kind of reptile and we have Dolphins they all have a hydrodynamic form and that's a convergent solution to the challenge of swimming here's a tricky question are the wings of birds and bats analogous or homologous think about the answer then see M the wings of birds and bats are a convergent solution to the challenge of flying they did not evolve from a common ancestor bats evolved from some ancestral mammal that was probably like a rodent and birds are dinosaurs and they evolve from small land living Dinosaurs the function of the Birdwing the function of the Batwing is similar but the underlying structure the organization of the bones is different the wings are an analogous structure but if you look at this question a little bit differently you get a different answer the four limbs of birds and bats are homologous they're the same bones inherited from a common ancestor so another example of why on the AP Bio exam or in your AP Bio course you need to carefully read The Prompt and think before you answer what are molecular homologies how do they serve as evidence for evolution molecular homologies are homologous features but at the molecular level they're molecules that by their structure and monomer sequence indicate common ancestry all vertebrates for example have hemoglobin that has the same structure two alpha chains two beta chains many of the amino acids are the same but as you might expect the closer an animal is to us morphologically the closer its hemoglobin is to us in terms of amino acid sequence so there's only one different difference in amino acid sequence between us and gorillas between rees's monkeys and humans there are eight differences mice which are also mammals but not primates there are 27 differences chickens which are yet more distantly related to us have 45 differences and frogs which are the most distantly related have the greatest amount of difference 62 differences pseudo genes are yet another category of evidence for evolution and they're really extraordinary a pseudogene is a non functional Gene that's a variant of a functional Gene in a related species an example is the glow pseudogene that humans have as well as most of our primate cousins here's the glow pseudogene it has a series of mutations that keep it from working perhaps the mutations in a broken promoter or perhaps the mutation is in the structural genes but rodents have a functional version of this Gene it enables them to produce the enzymes to synthesize vitamin C but primates can't do it why do we have the remnants of this Gene it's a molecular vestigial feature these pseudogenes only exist because of descent withd modification we and rodents share a common ancestor over here that common ancestor had the glow Gene and it was able to produce the enzymes to synthesize vitamin C we primates lost the ability to do that a mutation emerged broke the gene but because we lived in a fruit environment that mutation wasn't selected against what's really fascinating is that we're not the only mammals that have that pseudogene it's also found in guinea pigs and it's also found in bats but if you look at the sequence of those pseudogenes they have different mutations from our pseudogenes so this pseudogene this pseudogene and our pseudogene those are all convergent features they're analogous not homologous biology so amazing homologies can take us all the way back to the origin of life there are a couple of features that show that all living things are related what are they DNA used as a genetic material ATP used for energy coupling the same genetic code that's universally used ribosomes used for protein synthesis shared metabolic pathway like glycolysis the KB cycle the electron transport chain and ATP synthesis through CH osmosis this shows that all living things are cousins we all share a common ancestor going back to the origin of Life the homologies that we just discussed go back 3.8 billion years or so to the origin of life there are also more recent ones still ancient that go back 1.8 billion years that indicate that all UK carots are cousins these include the presence of a nucleus mitochondria or organells that are derived from mitochondria the endomembrane system genes that possess introns linear chromosomes as opposed to the circular chromosomes of procaryotes and sexual reproduction involving gamt production and fusion of gtes to form a diploid zygo these are features shared by all ukar they indicate common ancestry we're cousins to all the ukar Nots we're cousins to all life but we're closer cousins to those in our domain ukaria describe how embryological development provides evidence for evolution early embryos of vertebrates look similar here's a fish a reptile a bird and a human during development the embryo differentiates and that leads to the adoption of the body form of the adults of the lineage so bird and human embryos quite similar but we all know what adult birds look like and we all know what adult humans look like the similarity of the embryonic form indicates common ancestry there was a common vertebrate ancestor that gave rise to the lineage of fish reptiles birds and humans descent with modification leads to the elaboration of form in different lineage the different body forms of fish reptiles birds and humans but the embryo iic similarity along with fossil evidence shows that all of these organisms are descendants of a common ancestor an additional line of evidence for evolution related to embryos is as follows embryos often show vestigial features such as the tail in humans the Fingal Gill slit in humans that indicate descent with modification from a common ancestor so again embryonic development on entirely separate line of evidence for evolution diverse species share common genes for animal development describe how this provides evidence for evolution this is a mind-blowing example of homology an animal separated by hundreds of million years of evolution shared genes control certain developmental processes here's an example there's a gene that's called isas that's a master switch that turns on eye development in arthropods and vertebrates the genes can be transplanted leading to successful development what do I mean by that here's a mutated version of Tropa that doesn't develop an eye it has a mutant version of the eyeless Gene you can find mice that have similar mutations that also don't develop eyes but if you can take the gene from uh eye developing dropa and implanted it into the eyeless form it'll develop eyes but the amazing thing is that if you take the gene from an eye developing dropa and put it into an eyess version of a mouse that Mouse will develop an eye in other words this doesn't control the eye the eyes are quite different but it basically says build an eye in a fruit fly it'll build a compound eye that's common to insects and in a mammal it'll build the kind of eye that we have but there's a master switch that's common to all animals that have eyes that could control eye development another example of that is homeotic genes these are genes that basically say uh that you should have a head up here and you should have a tail down there and you should have these appendages over here and these are common across all animals as diverse as arthropods and vertebrates and these shared genes again are homologies and they indicate that all animals shared a common ancestor that goes back to the origin of the animal clay made about 600 million years ago what is biogeography how does biogeography provide evidence for evolution biogeography is the study of the geographic distribution of species and varieties if you enjoy looking at birds as I do you know that there are certain species that are found on the west coast of North America and there are others that are found on the East Coast that in of itself is biogeography the pattern of distribution on the surface of the Earth fits the idea that populations first evolve in one area then spread to adjacent areas where subsequent Evolution occurs in other words the pattern of evolution is not only seen through time it's also seen through space and a great example of biogeography is the fact that the marsupial mammals are mostly but not completely limited to Australia why because Australia is a kind of isolated island continent the only placental mammals that were ever able to get to Australia were the bats which could fly there and a few rodents that were able to reach Australia on floating vegetation mats but other larger land living non-flying placental mammals couldn't get to Australia and hence it's the marsupiales that are the predominant mammals in Australia a fascinating thing connected with the evolution of marial is parallel Evolution where because placental mammals never made it to Australia all of the niches that are filled by placental mammals in North America and Eurasia and Africa are filled by marsupial and those similarities are all convergent so the marsupial mole and the Eastern mole convergent similarities based on the common Niche they're both digging in the soil the sugar glider and the flying squirrel and even top predators the now extinct Tasmanian wolf and the wolf that we find in North America and Eurasia biogeography another entire line of evidence for evolution as we've seen you can find evidence for evolution in the structure of animals in their genes in their distribution over the face of the Earth but you can also find evidence for evolution in time that's what fossils are all about what are fossils how are they eviden for evolution fossils are petrified remains of living things evolution is change over time and fossils demonstrate this change as you go back in time you find different arrays of living things through transitional forms fossils show Descent of modification in a variety of lineages now this example over here is an artistic rendition but it provides the point which is that as you go back in time you don't find modern whales you find the ancestors of whales who have features that indicate that whales evolve from animals that once were mammals that lived on land that over time adapt it to an aquatic lifestyle what is relative dating of fossils how does it work it's based on the idea of superposition and the idea is that in rocks that are sedimentary that are laid down layer by layer the younger material is on top of the older layer so this would be younger over here and this would be older down there the deeper layers are older than the fossils in layers closer to the surface that's superposition I but because the Earth is complex and because there are earthquakes and volcanic eruptions there's faulting uplift and inversions that can complicate this analysis but based on the position of fossils within sedimentary strata you can determine which fossils are older than others in addition to relative dating determining which fossil is older than others based on their position in sedimentary strata there's also absolute dating describe how absolute dating of fossils works it's based on the decay of radioactive isotopes that are in fossilized remains or nearby volcanic strata that are interspersed with sedimentary strata the key idea is the idea of Half-Life that's the time it takes for half of a sample of radioactive isotopes to Decay from one element to another so an example carbon 14 decays to nitrogen 14 carbon 14 is radioactive unstable it's the case to nitrogen 14 the halflife is 5,730 years if a sample has 50% carbon 14 and 50% nitrogen 14 then for example if this was a piece of bone then that bone would be 5,730 years old it's one halflife if 1/4 of the carbon 14 is left then it would be two half lives 11,400 60 years other Isotopes have longer half- lives you can find carbon 14 directly in organic remains but you can also find as I said before radioactive elements that are in volcanic strata and you can use that to date older fossils so that's how we know how long ago the dinosaurs became extinct when the first vertebrates emerged when the first fish emerg so on and so forth that's an absolute dating of fossils Evolution can be observed in structures that we see in modern organisms but there's plenty of evidence that Evolution continues to this day a great example of that is shown in this slide how is evolution of resistance to DDT and mosquitoes evidence of continuing Evolution let's talk about what's happening in this slide here's a mosquito this is showing the percent of mortality of um mosquitoes to a 4% solution of DDT exposed to them for one hour DDT is a pesticide kills mosquitoes why do we want to kill mosquitoes mosquitoes can spread a parasite that causes the bloodborne disease malaria and malaria is a devastating disease that causes illness in hundreds of millions of people around the world what happens is that when you spray the pesticide at First It's very effective and it kills most of the mosquitoes but never all of them there's always some mosquitoes that have some inborn resistance that survive the initial use of DDT those mosquitoes pass on their genes for resistance the other ones have been wiped out so the mosquitoes that survive have resistance and they pass them on over time within a matter of months you have only about 50% of the mosquitoes are killed why because mosquitoes have a very short generation time so this process is occurring quite rapidly and then after about 16 18 months very few of the mosquitoes are being killed this is observed genetic change there's some Gene that's producing some protein and that Gene is increasing in frequency throughout the population caused by human selection for DDT resistant mosquitoes this is not the only example of the rise of resistance there are parallel instances of evolution of resistance that have been observed in the evolution of antibiotic resistance in bacteria resistance to herbicides and weeds resistance to chemotherapy drugs by cancer cells it's a phenominally important example of evolution that we can observe in this day I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn-y. comom and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam speciation and Extinction what is the biological species concept and what are some of its limitations the biological species concept defines a species as a group of organisms that can naturally interbreed to produce viable meaning healthy fertile meaning able to reproduce Offspring and which is reproductively isolated from other such groups here is an example of one species there are different breeds of dogs but the dogs don't care left to their own devices they'll interbreed and they'll produce viable fertile offspring these two species of ducks by contrast don't interbreed or at least they interbreed to such a small degree that their Gene pools are separate the concept is not perfect and it falters in a couple of cases the first is in the case of closely related species which can often hybridize they can often in breed but not so much so the gene pools maintain relative separateness extinct or asexual species how could you tell if they could produce fertile or viable Offspring and procaryotic species what are reproductive isolating mechanisms compare and contrast pre and postzygotic forms of isolation reproductive isolating mechanisms are processes behaviors or other traits that keep the gene pools of closely related species separate malards pintails they're both Ducks how do they maintain separate Gene pools there were two kinds of barriers the first are prezygotic isolating mechanisms and they prevent breeding altogether they prevent the formation of a zygote postzygotic barriers exist between species that are close enough to mate and form a zygote but formation of a zygote doesn't ultimately lead to the production of success successful individuals viable individuals who can survive and produce Offspring themselves let's look at prezygotic isolating mechanisms the first kind is behavioral different mating rituals or courtship behaviors would keep a female and a male from accepting one another as members of the same species and mating temporal means that they would breed during different times of the day or different seasons one species mates in the winter another mates in the summer they're not going to in breath mechanical structural barriers that prevent sperm or pollen from reaching an egg if the flower structure was very different then a pollinator wouldn't be able to bring pollen from one flower to another flower habitat one species lives in the forest another lives in a meadow one species lives in the Uplands another lives in the lowlands they won't meet each other in order to breed and finally GIC the egg won't allow fertilization because there's some molecular mismatch that would keep the sperm from being able to bind with the egg and induce the kind of changes that lead to fertilization list and describe three postzygotic isolating mechanisms postzygotic barriers can exist between species that are close enough to mate and form a zygote but nevertheless their Gene pools remain separate these can include hybrid inviability the hybrid organisms don't develop there might hybrid sterility the hybrid offspring are healthy but they can't reproduce that's what's going on between horses and dunkeys which can interbreed to produce mules but the mules themselves are sterile finally there's hybrid breakdown the hybrids are healthy and can reproduce but the Next Generation the f2s are inviable or infertile contrast allopatric and sympatric modes of speciation allopatric speciation in involves a geographic barrier it's what's shown over here in number one sympatric speciation occurs without a geographical barrier as shown over here in number two in allopatric speciation geographical isolation leads to genetic differentiation which leads to reproductive isolation in stage one a species is spread out over a geographical range there's gene flow between any subpopulations in stage two some kind of geographic barrier like this shown at B arises and it splits the species apart so there's no longer gene flow between these two isolated populations in stages 2 and three environmental differences result in different selective pressures which lead to genetic differentiation there's mutation happening and the environment is selecting which variants are going to be more favorable in each different environment and finally when that barrier disappears the two formerly subspecies have become so different that they can no longer interbreed they were geographically separated now they're reproductively isolated by any of the mechanisms that we've just discussed sympatric speciation can occur in animals and plants in Plants there can be sympatric speciation through polyploidy this can lead to changes in chromosome numbers causing instant one generation reproductive isolation between the newly emerged species and its parent species one example of Sy Patrick speciation in animals involves the hundreds of species of these fish that are called cichlids that live in Africa's Lake Victoria what is thought is that sexual selection ction has led to reproductive isolation between the subspecies that's been experimentally verified it's a very complex story and what I want to encourage you to do is go look at the case study on learn biology.com the link is below here's another mechanism of sympatric speciation in animals adaptation to specific microhabitats can also lead to reproductive isolation and speciation such as the evolution of a variety of life that inhabit different parts of birds this is kind of astonishing but there are lights that for example live only on the head of an albatross and there are different species that live on the wings there are other species of lice that only live on the heads of parrots While others live on the wings of parrots these are different species and they are in different parts of the bird and you might say well for uh little Lae well maybe that's like a mountain but that doesn't count as allopatric speciation there's no Geographic barrier all of these Li are just becoming extraordinarily specialized as they adapt to different parts of these birds and these specializations are getting passed on and that's leading to speciation over time so Sy Patric speciation in animals because of microhabitat adaptation what is adaptive radiation this is a concept that we dealt with earlier when we talked about the evolution of homologous features adaptive radiation occurs when one parent species produces several descendant species Each of which has unique adaptations and fills a different ecological niche the 14 species of Galapagos finches shown here all of which are descendants of a single South American species are an example this one species arrived at the Galapagos Island and then radiated into a whole variety of descendants Each of which has different features Each of which has a different ecological niche philogyny is a reflection of adaptive radiation each of the different branches show splitting from a common ancestor that's adaptive radiation on a very large scale finally homologous and vestigial traits which we talked about in the context of evidence for evolution are also a result of adaptive radiation it's about splitting from a common ancestor and subsequent descent with modification we're now going to Pivot away from speciation and just look at the evolution of variation and its importance so why is phenotypic variation important for evolution I'm Mr W from learn biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription phenotypic variation is essential for evolution it's the raw material upon which natural selection acts natural selection selects for organisms with phenotypes that confer a selective Advantage remember that the genotype is invisible to Natural Selection what natural selection sees what natural selection acts upon is the phenotype and the result is that individuals with advantageous phenotypes survive and reproduce at higher rates than organisms with less advantageous phenotypes now as those organisms reproduce they're passing along their genotype but that's somewhat of a secondary effect natural selection acts upon phenotypes and note that with no phenotypic variation there can be no natural selection and no adaptation and that's why loss of variation is so dangerous to a species and can often lead to Extinction so here are a couple of examples of the importance A phenotypic variation let's start with this one explain how variations in phospholipid structure can serve an Adaptive function in browsing mammals that Forge in snowy environments phospholipids we remember those from unit one they've got a glycerol with a hydrophilic head and a hydrophobic tail these are fatty acids over here and note that these fatty acids can be saturated or unsaturated and there can be a lot of variation in that in mammals that Browns in the snow there is a tendency for the phospholipid tails that are in the body core to be more saturated and those in the extremities to be more unsaturated why because as the temperature decreases these unsaturated fatty acid tailes keep the membrane fluid so that diffusion can continue to occur so that oxygen can continue to flow from the blood into the cells whereas the phospholipid tails in the body core are more saturated and that provides a correct level of fluidity in that part of the body so there tends to be a gradient of more saturated fatty acid taals in the core more unsaturated fatty acid taals in the extremities explain how variation in hemoglobin maximizes oxygen absorption in humans and other placental mammals at various life stages let's remember that hemoglobin is the protein that transports oxygen in red blood cells in almost all vertebrates before birth humans and other mammals produce fetal hemoglobin fetal hemoglobin is a variant and it has a higher affinity for oxygen than adult hemoglobin here's the difference all hemoglobins are the same in that they have these two alpha chains they're shown in red over here but adult hemoglobin has beta chains where fetal hemoglobin has gamma chains they're shown in yellow over here because of the higher affinity for oxygen the fetal hemoglobin will absorb it'll create a gradient that will cause oxygen to flow from maternal blood in the placenta over here into fetal blood so here's the gradient and that of course is highly adaptive because that's how the fetus gets oxygen while it's in the uterus but after birth what happens is that developmental genes kick in and slowly the beta form starts to be produced more and more until it's completely predominant in the adult whereas the gamma form starts to fall and fall and fall and you can see that that happens even before birth but the trans trans is pretty complete 42 weeks after birth has occurred explain how variation in chlorophyll types increases the efficiency of photosynthesis green plants have two main types of chlorophyll there's chlorophyll a over here and Chlorophyll B over here and the difference comes down to just a functional group chlorophyll a has a methyl group over here whereas Chlorophyll B has a carbon Al group Chlorophyll B absorbs more blue light and that's best in indirect light or in Shady environments or Shady situations and chlorophyll a absorbs more red light and it's best in direct light and therefore plants can do a couple of things one is that there are plants that are shade adapted and another plants that are direct light adapted and those will have different proportions of chlorophyll a and Chlorophyll B and then most plants have both and having both types of chlorophyll increases the amount of light energy that plants can use during photosynthesis over the course of a day or throughout the seasons now that we've looked at processes that increase biological variety speciation the development of variation now let's look at the flip side and equally important side of the evolution of life which is the idea of Extinction and the big idea is that Extinction is a normal part of the process of Life greater than 99% it might be 99.9% of the species that have ever lived have become extinct let's describe the process that a species goes through as it heads towards Extinction this is called an Extinction Vortex and it starts with a population decline so small isolated populations are the ones that are most vulnerable to Extinction that population decline can be caused by an adverse change in the physical environment climate change which has happened throughout the history of Earth or the arrival of a competitive species that reduces the species Fitness and reproductive rate that leads to genetic drift which we discussed in population genetics that results in a loss of genetic diversity that leads to less variability and that loss of variability leads to reduced Fitness there's more genetic uniformity and that reduces the ability to adapt to environmental change and the result is a smaller population that then goes through this process again and again it's a positive feedback loop it's not a positive thing but it's a positive feedback loop that feeds on itself it accelerates itself leading to Extinction what we just described is the typical normal process of Extinction that's quite different from mass extinction what is a mass extinction a mass extinction is a widespread rapid decrease in Earth's biodiversity often mass extinctions are caused by geological or even astronomical causes though biological causes are possible as well and there have been at least five major Extinction events during the last 600 million years and those are the numbered peaks in this diagram the most recent Peak which occurred 60 million years ago is the Cretaceous Extinction that's the one that wiped out the dinosaurs now you you might think that Extinction is all bad mass extinction in particular but there's a connection between mass extinction and adaptive radiation mass extinction leaves vacant a variety of ecological niches and that is an ecology term that we'll deal with in Unit 8 those are ways for a species to make a living and the result is a mass extinction such as that shown at two which wiped out all of this previous existing biological diversity is followed by extensive adaptive radiation in the species that survive and here's one the species at four and it made its way through for whatever reason this mass extinction over here and then it underwent an extensive adaptive radiation and an example of that is the diversification of placental mammals mammals like us that followed the Cretaceous Extinction that wiped out the dinosaurs and again just to connect this to our own lives if that mass extinction 65 million years ago hadn't happened we wouldn't be here talking about mass extinctions it's because our ancestors made it through that mass extinction and then radiated to produce the whales the hippopotamuses the primates the rodents and our group is the primates and here we are how is human activity affecting Extinction rates humans are the cause of what's been called the sixth Extinction here are the five great extinctions that have happened in the past humans are causing a decline in global biodiversity that could rival these previous five mass extinctions how are we doing that human activities that are causing Extinction include destruction and fragmentation of habitat over hunting over harvesting of animals and plants intentionally or unintentionally introducing invasive species into new habitats this is material that we'll look at more closely at the end of AP Bio Unit 8 are you asking yourself how am I going to get a four or a five on the AP Bio exam it's a good question because it's a hard test but we have a plan for your success go to learn biology.com sign up for a free trial and complete our interactive tutorials and interactive AP Bio exam reviews we guarantee you a four or five on the AP Bio exam see you on learn biology.com topic 7. 9 philogyny what is philogyny what is a philogenetic tree how are such trees built philogyny means evolutionary history a philogenetic tree also known as an evolutionary tree is a branching diagram that shows evolutionary relationships and philogenetic trees are built using morphological that means structural molecular or genetic evidence this is a philogenetic tree and one thing that I want to emphasize is that it is a claim that's based on evidence so the claim here is that hippos and whales are more closely related to one another than whales are to Deer why is that because based on the evidence which would be morphological molecular genetic hippos and whales have a more recent common ancestor than either does with deer we'll see the details in the subsequent slides Define the term CLA clade is an incred L important biology term that's not known to the general public but now you'll know it and you'll be able to explain it to people a CLA is a group of organisms that consists of a common ancestor and all of that ancestor's descendants in this diagram all of the species and all of the numbered groups are clayes so down here the large ground finch that's a seed eating Finch in the galopagos islands that's a CLA all members of a species have a common ancestor all humans have a common ancestor all human beings are a clay the large ground finch and the common Cactus Finch have a common ancestor that's this over here at e so those two species together constitute a CLA if you go back in time because there's implied time in any philogenetic tree then all of these four species the Woodpecker Finch the small tree Finch the common Cactus Finch and the large ground finch they comprise a clay that's group number five over here their common ancestor is this species that's over here at C Define shared derived character a shared derived character is a trait that identifies that distinguishes a clay and it evolved in the common ancestor of that clay and it sets it apart from other such clades so for example lungs and four limbs separate this clay all of these organisms that are CL ified as frogs lizards alligators Robins rats and gorillas that constitutes a clay and they all have this shared derived character going back in time the Shar dve feature vertebral column separates this clay that includes all the salmon through gorilla fur and mamory glands separates the clay that includes rats and gorillas from all the other organisms these are mammals and those are shared derived features of mammals what are nodes and sister groups a node is where two branches in a philogenetic tree diverge and nodes represent the common ancestor of the two diverging lineages so at left letters a through e those are all nodes nodes common ancestors so over here there was a common ancestor that led to the Divergence between this clay over here and this um species over here the green warbler Finch which is not part of the clay that includes all of these organisms that have a common ancestor at B Sister groups are The Descendants that split apart from the same node such as the common Cactus Finch over here and the large ground finch those can also be called sister species because that's the taxonomic level at which they're at so the Woodpecker Finch the small tree Finch that CLA that's a sister CLA to this CLA that's defined by letter E the comic Cactus Finch and the large ground finch what is an outgroup an outgroup is a more distantly related group of organisms that's used to determine the evolutionary relationships among the other organisms in the tree which is the ingroup in this philogenetic tree a is the outgroup for this CLA that's over here at number two it's a point of comparison for the ingroup and it's a species or it's some other taxonomic category that's not part of the clay to which all the other organisms in the philogenetic tree belong what's the biggest mistake to avoid in philogenetic analysis the misconception that many students naively have is that vertical closeness on a horizontal tree indicates evolutionary closeness but it doesn't for example the frog and the lizard they're next to one another but they're not particularly closely related the only thing that matters on a philogenetic Tree in terms of evolutionary relatedness is the recency of common ancestry so alligators and Robins they have their common ancestor over here rats and gorillas they have their common ancestor over here frogs are right next to lizards but their common ancestor the common ancestor the frog and the lizard is all the way back here and the basic idea is that nodes can rotate so this philogenetic tree over here is correctly drawn it's exactly equivalent to this one over here but you can see that in this one the lizard is no longer next to the Frog right so here's a lizard down here here's the Frog over here and here's a lizard over here and here's the Frog over here it's just about rotation and if you think about the art form called a mobile mobiles all rotate there it's a kind of kinetic sculpture and if you can think of philogenetic trees as one instantiation of a kinetic sculpture you'll have the right idea about this always look for recency of common ancestry when you're trying to figure out the evolutionary relationships described by a philogenetic tree Define ancestral feature an ancestral feature is a trait that members of a clay share but which is also shared by larger more inclusive clades it doesn't Define the clay so for CLA G which includes rats and gorillas that's the mammal clade an ancestral feature would be CLA Paws or nails and why is that because mammals they do have that trait but it's also found in this larger more inclusive clay that runs from lizards down to gorillas over here lungs and four limbs is another ancestral trait of rats and gorillas this mammal CLA it doesn't Define the clay but everyone in the clay has to have that because there's a larger more inclusive clay that has that feature what type of evidence is typically used to construct philogenetic trees of existing species before the 1960s morphological similarities was what biologists use to determine who was more closely related to whom and thereby construct a phylogenetic trees but more recently post 1960 remember Watson or Crick figured out the structure of DNA in 53 nucleotide sequences in DNA and RNA and amino acid sequences in proteins have become the gold standard in determining philogenetic relationship so a DNA analysis would indicate that the common Cactus Finch is more closely related to the large ground finch than to any of the other galopago species that's a hypothesis and you could confirm that through DNA sequencing what are molecular clocks here's how this works for any specific protein or nucleic acid the rate of change that's caused by accumulated mutations is constant over time and if you can calibrate the amount of change in a gene or protein to when species split apart which you can sometimes determine from the fossil record then you can do two things one is you can determine a rate of change in that Gene or protein and you can use that rate to determine when other species split apart what this graph says is it's looking at hemoglobin as a molecular clock based on some fossil evidence it's basically saying that 20 mutations accumulate every 100 million years so therefore if you're looking at the hemoglobin between two species and you notice 40 amino acid substitutions and you could infer that that occurred more like 23 million years ago this is widely used in evolutionary biology it's the basis for claims that for example humans in chimpanzees had a common ancestor about 6 million or so years ago based on the similar ity of DNA between hus and chimps topic 7.13 the origin of life this is one of the coolest topics in biology for AP biology you need to master a very specific body of knowledge the key question to address when trying to understand the origin of life is how did life emerge naturally and this connects to some biology that you've already learned in your AP biology course for example you've learned about the cell theory and theide aide that all cells come from pre-existing cells well at some point there had to be a first cell and in fact that moment really marks the emergence of Life how did a cell emerge with the absence of another cell to create it that's one of the Mysteries that we have to contend with in the origin of Life the other one has to do with chemistry the chemistry of life is largely controlled by complex proteins called enzymes enzymes can take simpler substances and make them into more complex substances through processes like dehydration synthesis well how do we get the complex substances that life is based on in the absence of enzymes what are the key steps required to explain the origin of Life the Earth is extremely ancient it's been around for 4.5 billion years and life is thought to have emerged about 3.8 billion years what steps allowed life to emerge the first thing is that Earth needed to become a habitable and more stable Planet the Earth formed from a nebula about 4.5 billion years ago that's beyond the scope of this course but what's important to know is that for the first several hundred million years of Earth's existence it was pummeled by asteroids and comets and all of that needed to come to an end before life could begin to emerge step number two is about chemistry leading to biology biology is based on cells and those cells in terms are based on complex molecules polymers the polymers are built from monomers so how did those monomers emerge that had to happen abiotically in the absence of enzymes monomers had to start to emerge we need to start to have amino acids nucleotides fatty acids Etc in today's Living World monomers get combined into polymers how could that happen in the absence of enzymes there needs to be some kind of abiotic process by which that could happen where we have the abiotic synthesis of polymers from monomers and the formation of vesicles those are going to become the little capsules into which cells will emerge in step four we need to combine those monomers and polymers into those little vesicles to create Proto cells these aren't quite living cells the way that we have them today but they have many of the characteristics of cells and finally we have the emergence of self-replicating cells that would be the last Universal common ancestor over here and that gives rise to the three great domains archa bacteria those two combine that's another story altoe to form the UK carots the Miller Yuri experiment which was carried out in the 1950s showed that in an abiotic setup up without life you could successfully synthesize amino acids in a simulated early Earth environment now as we'll see some of the details that were involved in the setup of the Miller Yuri experiment were wrong they don't correspond to our current understanding of the geology of the early Earth but it's an important proof of concept so what did Miller Yuri do they created this sterile apparatus with various Chambers and tubings and the whole thing was sealed off from the outside world and sterile this chamber over here at number two represented the early oceans it was heated by a bunson burner or some other heating device and then the steam circulated through these tubes over here this large area over here is a chamber that represented the early atmosphere and it was loaded with gases that were supposed to be present in the early atmosphere and that includes gases like methane ammonia hydrogen and water vapor those gases were chosen because in the 1950s that was the current understanding of what the early Earth's atmosphere would be there are two important points one is that that was chosen because that was the known atmosphere of some of the gas giant planets like Jupiter and it was thought that that might also be present on the Earth but the most important thing was that no oxygen was present because oxygen was was produced by photosynthesis it wasn't present in the atmosphere of the early Earth there were electrodes shown over here at number four by this plus and minus sign and what they did is they produced Sparks which simulated lightning the gases continued to circulate they circulated through this condenser over here and that caused whatever was formed in this chamber here to be caught within this trap this trap could be sampled without contaminating the apparatus and after a certain period of time Miller who was the actual experimentor was Stanley Miller Harold Yuri was his graduate thesis adviser sampled the liquid and they found the presence of amino acids well like I said that didn't necessarily establish that life could be produced in the absence of life but it did establish that some of the monomers of life could be produced in the absence of life as I said some of the details were wrong but this has proven to be the model for many subsequent experiments where there are inorganic catalysts and different mixes of gases that are changed and in subsequent experiments the nucleotide bases have been produced fatty acids have been produced many of the monomers of Life have been produced so what's the basic idea in the absence of life it's been experimentally established that some of the monomers that make up the chemistry of life could be produced to understand the origin of life you have to understand the origin of heredity it's widely thought that RNA not DNA was the first hereditary molecule why RNA does store genetic information in viruses so it has the capability of being a genetic molecule but Unlike DNA RNA can also act essentially as an enzyme RNA can have Catal cytic properties it does so in ribosomes where the catalytic part of a ribosome is what actually stitches together amino acids to create polypeptides and then proteins we have splies we have micrornas all of which are catalytic acting upon the world DNA with its double helical form is fantastic for storing genetic information RNA because it has both catalytic abilities and information storage capabilities is widely thought to have emerged as the first genetic molecule before there were cells it's thought that there might have been a phase in which there were self-replicating systems of RNA molecules that were subject to Natural Selection that would grow in complexity and that's called the RNA world that led up to the last Universal common ancestor of Life here's how that might have happened in the beginning what we had were inorganic precursor molecules it's what we talked about in the preceding slide with the uh discussion of the Miller Yuri experiment so at some point the sugars the phosphate and the nitrogenous bases that make up RNA would have to emerge those would combine through abiotic inorganic processes to form RNA monomers other abiotic non-enzymatic processes would lead to the next step and in that next next step we have RNA polymers that start to emerge they're shown at C rnas can fold up into complex shapes and that's what we start seeing over here at D and those complex shapes can start to have enzymatic properties one of those enzymatic properties could lead systems of rnas it doesn't have to be just one molecule but there could be a system of interacting molecules that could lead the system to replicate itself at some point those self-replicating RNA systems would become encapsulated within some kind of lipid bilayer and at that point at letter F we have a Proto cell further natural selection further Evolution would lead to the emergence of the last Universal common ancestor that's the population of organisms that gives rise to both ARA and bacteria and ultimately through a fusion of those two domains to to ukari nots and if you can look at this diagram you should pause and test yourself and identify all of the numbered items then you've learned a lot of cellular biology and you're well on the way to being set up for Success on the AP Bio exam just to run through at number one we have a lipid bilayer remember it doesn't have to be a phospholipid bilayer because ARA have a different kind of Bayer structure at two we have DNA being the genetic material that's found in all living things at three we have RNA which is used for information transfer and other things at four we have ribosomes which are translating messenger RNA into protein at five we have a membrane channel that's allowing matter and energy to flow in and waste to flow out at six we have complex proteins that are acting as enzymes which are combining monomers into polymers through dehydration synthesis and then pulling apart those polymers through hydris and at seven we had ATP synthes which is using a flow of protons across the ATP synthes channel to generate ATP that Universal energy molecule from ADP and phosphate that's the last Universal common ancestor and that's what you need to know about the origin of life for AP biology topic 8.1 one responses to the environment unlike the rest of Unit 8 topic 8.1 is somewhat difficult in terms of providing you with exact guidance about what to study that's because the objectives are very general and the College Board has provided these exclusion statements which tell you that you don't really need to know any specific body of knowledge in order to be able to handle this topic so what we're going to do is we're going to look at a couple of fascinating case studies and illustrative examp that'll give you practice at handling the kinds of data sets and images that the college board or your teacher might be throwing at you on the AP Bio exam or your upcoming test we're going to start by looking at Predator warnings Predator warnings also calleded alarm signals are calls or cries emitted by social animals in response to Predator danger these have been extensively studied in the belding's ground squirrel which lives in the Sierra NADA mountains of California building's ground squirrel has distinct warning calls for aerial Predators like Hawks and Eagles and for terrestrial threats from Bobcats coyotes and weasels here's warning call type one for an aerial predator and here's warning call type two for a terrestrial Predator note that these Predator warnings are not unique to the belding's ground squirrel African vervet monkeys which are primates like us have distinct calls for leopards snakes and Eagles Predator warnings are altruistic they're self-sacrificing they involve individual risk to the self to protect others when a squirrel emits a call about an aerial Predator it increases the chance that that Predator will attack the animal that calls out that's of course true for a terrestrial Predator as well and that leads us to the question why would an animal risk its own life to protect others altruism can be explained by kin selection and Inclusive fitness let's define both of these terms kin selection means that the value of a gene is not based on whether it promotes survival in a single individual but also in how it affects survival in the individual's relatives Inclusive fitness means that if an Al promotes sacrificing oneself for the benefit of one's close relatives who also share that Al then that Al might increase in frequency the idea of kin selection and Inclusive fitness was cleverly captured by the British biologist JBS halan a very important evolutionary thinker of the 1900s who famously said I would lay down my life for two brothers or eight cousins what did halane mean well here's me I obviously have 100% of my genes but my siblings have 50% of my genes so if I sacrifice myself and thereby allow my brother and sister to continue living and passing on my genes it's an even trade so it makes sense to sacrifice myself for two siblings I have a 12.5% relationship to each of my cousins and just think about the fact that you have a 25% % relationship to your aunt or Uncle so you'd have a 12.5% relationship to their children again it makes sense for me to lay down my life so that eight of my cousins would survive and continue to pass on my genes within our shared genan pool with those Concepts in mind let's take a look at a study by Paul Sherman about Predator warnings in belding's ground squirrels he carried out the study in the 19 7s to begin with notice this graph it shows the mean distance that males and females move from their natal burrow that means the burrow where they were born so everybody obviously starts out in the burrow where they were born but then the behavior of males and females is quite different females wander very little over the course of their lifespan these squirrels don't live very long so even when these squirrels are 26 months old which is quite old for a squirrel they're pretty close to the burrow where they were born less than 50 m the males by contrast move quite a bit so by the time they're 2 years old they're up to 280 or so meters away from the burrow where they were born Sherman's key move was to observe these ground squirrels and then to classify who was called based on two characteristics the age class whether they were juveniles one-year-olds or adult and then their sex I've labeled the age class but I haven't labeled the sex male or female here's how to read this the left side of this graph shows the distribution of each of these age classes and sexes in the population and again you know the age you know that these are adults but you don't know which one's male and you don't know which one's female and that's true for adults one-year-olds and juveniles the top graph shows the first squirrel to give the alarm call and the second shows all callers regardless of Precedence in other words it might have been the first call the second call the third call and these were calls to a predatory mammal so to a ground predator on the right side it shows what Sherman actually observed in terms of who was giving the call and what I'd like you to do is to predict which rows are for males and which rows are for females and I'd like you to inform your prediction by this graph over here and also what you've learned so far about kin selection and Inclusive fitness make a prediction and then I'll show you what the answer is here's what Sherman found females were overwhelmingly more likely to emit alarm calls than males were for example among adult females they're about 30% of the population but adult females emitted over 60% of the first call for a predatory mammal with males represent about 20% of the population but they don't even call 5% of the time so males are way under represented in terms of their taking the risk to call whereas the Fe females are way over represented and that's true of every age class and that's also true of callers in general not just the first call but callers regardless of Precedence so my challenge to you is how would you interpret this think about it and then you can see my answer Sherman's interpretation is that females are more altruistic than males but why would that be remember that a warning call attracts attention when females admit a call they're drawing attention to themselves and warning their close female relatives their sisters their daughters their female cousins the males don't call because the risk to themselves is not offset by a benefit to their close relatives so the conclusion is that Predator warnings in belding's ground squirrels are an example of kin selection and Inclusive fitness and what you should take away in addition to this concept is the way that we used claim evidence and reasoning to pull this together especially how you connect this piece of data to this piece of data to thereby conclude what we did about kin selection and Inclusive fitness the altruism that we just discussed in the belding's ground squirrel reaches its peak in a type of animal behavior and social organization that's called us sociality what is us sociality it's a social structure in which some individuals within a colony breed While others are non reproductive and just to State the obvious humans are highly social but we're not usocial who is usocial bees in bees there's a single queen who lays the eggs she's reproductive there are thousands of workers that take care of the larv they build and clean the nest they forage but they don't reproduce themselves in other words what they do is they work so that the queen can successfully reproduce and there are a couple of dozen of males and the males leave the nest to mate and then they die that's us sociality us sociality is not just found in the bees as we just discussed it's also found in ants and and wasps in termites in one species of shrimp and two species of mole rats that's a type of mammal and again what are we saying we're saying that in a termite Mound there are a couple of reproductive individuals and everybody else is non reproductive working for their benefit and that's true in a colony of naked mole rats as well there are individuals who get to reproduce and everybody else serves them and serves their reproductive interests us sociality can be partly explained in animals like bees and ants through the phenomenon of Hao diploidy and that's a kind of sex determination that we discussed back in unit five I'll review it now and I'll connect it to you sociality the idea of haplodiploid is that females are deployed in the same way as you are deployed with two sets of chromosom here we see the chromosomal situation of the diploid Queen and it's very simplified bees have 32 chromosomes as their diploid number I'm showing only six here the diploid Queen creates gtes by meiosis in the same way that humans and mammals do and as she does she passes on 50% of her genes to her daughters the daughters are the non reproducing females in males things are quite different males are a hloy they have only half the chromosomes in every cell of their body that the females do a haid male drone who's reproductive creates gametes by mitosis not by meiosis and what that means is that he's passing on 100% of his genes how do you get to be a male males veloped from unfertilized eggs that are laid by the queen and the drones as I just said pass on 100% of their genes to their daughters so how does haplodiploid connect to you sociality the sisters are 75% related to each other what do I mean by that well they inherit 50% of their mother's chromosomes and 100% of their their father's chromosomes so on average they're 75% related to one another that means that they're more related to one another to their fellow sisters than they would be to their own offspring that means that genetically it makes more sense in terms of the inclusion of their genes in the gene pool for workers to help their Queen create more sisters than it would be for the females to reproduce themselves because their own daughters would be 50% related to them so that is a genetic explanation for the altruism of the female workers within a beehive and just to emphasize something you sociality can exist without haplodiploidy termites are not haplodiploidy and they are usocial and that's true of the naked mole rat as well and again this is an important concept it's important for you to know about as an AP biology student but the most important thing for you to be able to do is to look at a diagram like this and use that as the basis for formulating a claim with some evidence and some reasoning about the connection between us sociality and Hao diploidy topic 8.1 is full of fascinating case studies we're going to stop presenting them here right now but what I want to encourage you to do is to go up to learn biology.com where you can learn about amazing things like why some VES a small type of rodent are monogamous While others are promiscuous you can learn about how ants learn how to make their way back to the nest after finding food in a straight line not an easy thing for them to do how Turtles can go out to sea forage there for years and then how they make their way back to their nest how and why animals school and how honeybees with their relatively small brains can communicate to one another through their dances about the location of food sources it's unbelievable stuff in and of its own right but the most important thing is that by looking at these case studies you'll get to be very good at looking at data sets illustrative examples visual representations that will be the kinds of things that you need to do on the AP Bio exam or your upcoming test on Unit 8 your success in AP biology starts here are you struggling with AP Bio with learn biology.com students get the skills and confidence to be a top student and earn fours and fives on the AP Bio exam guaranteed go to learn biology.com to find out how you can master your biology course and crush the AP Bio [Music] exam topic 8.2 part one metabolism and individual energy use let's start by answering the question what is metabolism metabolism is the sum total of the chemical processes that take place within an organism here we're showing a cell but it could be the inputs the processes and the out outp puts for an entire organism what is metabolic rate it's the amount of energy that an organism expends during a given amount of time basil metabolic rate is the amount of energy consumed by an organism at rest at a comfortable temperature they don't have to be sleeping as these lions are but it's resting metabolism how is metabolic rate measured to answer this we have to hearken back to unit three and think about the formula for cellular respir ation shown over here you can measure the input oxygen that could be happening here in this woman at rest who is hooked up to a kind of metabolism measuring machine you can measure carbon dioxide production this machine also might be measuring the amount of carbon dioxide she's emitting in a respirometer which is typically used in a lab back in unit 3 you're measuring consumption of oxygen and you can also measure the production of heat that leads us to a discussion of two major metabolic strategies that involved with being an ectotherm and that involved with being an endotherm endotherms are limited to mammals birds and a few other species endotherms generate their body heat internally metabolically as a result of heat that's generated through cellular respiration their body temperature is regulated around a set point so for example here we see an endotherm a wolf and despite the environmental temperature its internal temperature is going to stay the same ectotherms are different their body temperature conforms to the environmental temperature so when it's 20° out the snake's body temperature will be about 20° that's true as it gets colder and that's true as it gets warmer what are the advantages of being an endotherm you can be active regardless of the environmental temperature and that gives you flexibility throughout the seasons and whether it's day or night and it explains why the predominant animals in the coldest environments are endotherms mammals like polar bears and birds like penguins those are the animals that can survive on snow and ice so what are the advantages of being an ectotherm the energy requirements of ectotherms are much less ectotherms need about one tenth the food per gram of tissue than endotherms do as an example at 400 100 lb this American alligator needs the caloric equivalent of only a few slices of bread to meet its energy needs you as a mammal need the entire loaf to meet your energy needs that's how endotherms and ectotherms compare what's the relationship between temperature and metabolic rate in ectotherms metabolic rate increases with temperature as the temperature goes up the metabolic rate goes up in an ectothermic organism like a snake in an endothermic organism a mammal or a bird the relationship is more complex to begin with at cold temperatures the metabolic rate needs to be high why because a lot of energy needs to be consumed to create heat so that the animal can maintain its metabolic rate at that high constant set point as temperatures become more moderate the metabolic rate Falls and it can fall to the basil metabolic rate and as temperatures get high then the metabolism Rises as cooling mechanisms are deployed and those require some energy as well metabolism and size in endotherms as endothermic animals get bigger their rate of energy use their basil metabolic rate increases no surprise but an elephant consumes a lot more energy than than a mouse does and if you scale your axes your x- axis and your y AIS as is shown here that increase in energy use scales in a linear way if you look at energy use from a slightly different angle there's a fascinating relationship between size and metabolic rate that relates to the relative metabolic rate the relative metabolic rate is the metabolic rate per unit of body mass and it decreases as size increases so the smaller the mammal the more energy each gram of tissue requires and other words each gram of tissue in a shrew is burning much much more energy per the same unit of time than a gram of tissue in an elephant let's look at some specific examples here's an African elephant weighs in at 6 million G it consumes 70,000 calories a day it energy usage per gram is 0.011 now let's look at the other end of the scale a tiny shrew which weighs only 1.8 G it needs 144 calories a day and that's 80 calories per day per gram of tissue that difference in relative metabolic rate has vast consequences in the physiology of an organism we'll look again at the shrew 1.8 G weighing less than a dime its heart rate is 1,200 beats per minute it has 800 respirations 800 breaths per minute it starves to death if deprived of food in Just 4 hours and it has to eat 200% of its body weight every day an elephant by contrast its heartbeat is only 30 beats per minute it takes about four or five breaths per minute it can go many days without food and it eats about 4% of its body weight every day why are relative metabolic rates so different for large animals and small animals why is the metabolic engine of a mouse or a shrew revving at such a higher speed than that of a huge animal like an elephant it has to do a lot with surface area to volume ratios that's a lot of the explanation smaller animals they'd be over here that have a much larger surface area to volume ratio than do larger animals remember that volume is a cubic function whereas surface area is a square function so as an animal increases in size its volume increases much faster than its surface area and you can look back to my video about that in unit 2 if you need more instruction about that as a result smaller animals lose heat through their surface much more EAS easily than large animals do to replace that heat smaller animals need to perform more cellular respiration increasing their relative metabolic rate topic 8.2 part two energy flow through ecosystems what is an ecosystem it's a community the living populations in an area plus the abiotic non-living parts of the environment those abiotic Parts include the air the soil oil the water and the energy that's flowing through that ecosystem two essential concepts related to ecosystems are food chains and food webs a food chain is the passage of energy and matter from one organism to the next within an ecosystem on the left we see a terrestrial food chain where a plant is getting eaten by insects which is getting eaten by other insects which passes to a frog Etc on the right side we see something equivalent for an aquatic food chain on the right side we have a food web and a food web shows all the interconnected food chains in an ecosystem and the arrows flow from the organism that gets eaten to the organism that eats it and if these arrows look like they're flowing in the wrong direction they're not the small birds eat the fish and that passes energy and matter from the fish to the small birds and the same thing happens with mollusks and small birds and so on and so forth what are trophic levels the describe the trophic levels found in most ecosystems a trophic level is an organism's position in a food chain or food web you've seen this word root tro before in terms like hetero tro and autoro which we worked with in unit 3 producers autot tropes create energetic compounds almost always through photosynthesis the one notable exception are those ecosystems that are based on geothermal energy way under the sea near hydrothermal vents primary consumers or herbivores eat the producers secondary consumers or carnivores eat the primary consumers tertiary consumers eat secondary consumers and the level goes up to fourth level and fifth level consumers when organisms at any level die their remains are broken down by decomposers really important but not shown in this diagram of a food chain describe the pyramid of energy and explain the 10% rule the pyramid of energy shows the amount of harvestable chemical energy at each trophic level so this is saying that at the producers you could Harvest 10,000 kilo calories worth of chemical energy at the primary consumer level there's only 1,000 kilo calories and that relationship stands true for the other trophic levels as well each trophic level has 10% of the chemical potential energy of of the level beneath it we'll see why in the next slide what are the reasons for the 10% rule the first reason has to do with physics energy is lost to heat during any energy transformation that's the second law of Thermodynamics so when primary consumers are eating producers that's an energy transformation some of that energy is simply lost as heat the other reasons that we're going to discuss are more biological so any organism is using the fuel that it takes in as part of its metabolism that doesn't go to growth and therefore it's not available for the next trophic level there are limits to harvest deficiency in other words these caterpillars over here they're not going to eat every single bit of the leaves that they're eating and they're certainly not going to eat the stems or the roots so they're not harvesting everything and then in terms of what they do Harvest they don't assimilate everything a lot of the food that any organism eats goes through it and passes out as feces just note that the 10% rule is an average it's a rule of thumb that explains how energy is transferred from one trophic level to the next within ecosystems the pyramid of energy is only one way to represent what's happening in ecosystems there are other ecological pyramids as well one is the Pyramid of biomass and what that shows is how much living mass is passed from one trophic level to the next and that's usually Mass with water removed it's the dry weight of all of The Producers compared to the dry weight of all of the consumers some pyramids of biomass are indeed like pyramids but there are others like this one that's been famously studied in the English Channel that are not and if that seems counterintuitive the basic idea is that the producers grow at an enormous rate and they're consumed by the consumer so if you measure at any one moment the standing biomass of The Producers can be less than that of the consumers there's also a pyramid of numbers and some of those are pyramidal but if you think about a pyramid of numbers for a tree you'll have one tree that's being the source of food for thousands or millions of herbivores that are in turn being consumed by carnivore so the Pyramid of numbers not always pyramidal either a biog geochemical cycle is yet another way to represent what's going on in an ecosystem a biogeochemical cycle shows the movement of elements or compounds between the biotic living and the abiotic non-living parts of an ecosystem and the components include reservoirs that's locations where elements or compounds accumulate often in chemically different forms so for example one reservoir for the carbon cycle is carbon dioxide in the atmosphere another Reservoir would be all of the carbon that's found in plants fluxes or flows are ways in which these compounds or elements move from one reservoir to another so photosynthesis is a flux by which carbon dioxide in the atmosphere comes into plants consumption is a kind of flux by which the carbon that's trapped in Plants moves to animals if there's one biogeochemical cycle to be familiar with in your AP bio class that would be the carbon cycle and here's how it works the carbon cycle could start anywhere but let's start with carbon dioxide in the atmosphere that carbon dioxide gets pulled into plants through the process of photosynthesis and think back to the Calvin cycle back in unit three those plants themselves respire and that returns carbon dioxide to the atmosphere plants can also be consumed by animals animals respire and that returns carbon dioxide to the atmosphere when plants die when animals die their carbon moves to decomposers the decomposers do cellular respiration on those remains of plants and animals and respiration returns carbon dioxide to the atmosphere sometimes when plants die and to a much smaller degree when animals die too they become fossilized into fossil fuels things like coal and oil those get extracted through oil drilling and coal mining and then those power the machines of our civilization and so that becomes another major flux called combustion that of course is having impacts on our climate but that's more of a topic for an environmental science class than it is for AP biology topics 8.3 to 8.4 population growth what are the four factors that directly change population size if you had driven into my home City Berkeley California a couple of years ago you would have seen this sign listing the population at 11258 it's now a little bit bigger what could cause that to increase or decrease there's only four factors those are births which increase the population deaths which decrease it immigration which increases population size and and immigration which decreases it for AP Biology one of the most important Concepts to understand is exponential growth and its limits exponential growth is a pattern of population increase in which the population size doubles at a consistent rate over regular time intervals resulting in Rapid and accelerating increase why because the growth of the population is proportional to the amount already present in this growth growth curve over here the rate isn't changing it's continuing to be at 140% but when there are 1,000 individuals the number of individuals added over a period of time is going to be much higher than it was when there were 200 individuals the basic idea is that an exponential growth the bigger the population the bigger the increase exponential growth is based on a mathematical model and that's something you need to understand for AP Bio that you don't need to memorize it there's a formula sheet the formula is Delta n/ Delta t = r * n and in this formula n represents the population size T equals time R is the rate of increase so in plain English the change in population over time equals the rate of population growth times the population size in biological systems when does exponential growth occur it occurs when a population has ideal resources and nothing is slowing down its rate of growth this can be the arrival of an invasive species the early phase of a bacterial infection the early phase of an epidemic or pandemic so it's always ultimately limited because nature is finite but during this phase when the population has ideal growing conditions exponential growth can occur that's what occurred early during the Corona virus pandemic this shows one country Brazil 2020 and you can see this exponential growth curve as the virus entered the Brazilian population and spread from Individual to individual exponential growth exponential growth is related to the idea of biotic potential and that is the maximum rate at which a population can expand and you can see it represented by the letter r submax that represents biotic potential expon itial growth can't continue forever and ultimately it's limited by the environment's carrying capacity that's represented by the letter K it's this dotted red line over here and it's the maximum number of individuals that a particular environment can support it's caused by limiting factors factors that limit population growth as a population approaches as carrying capacity there's increased environmental resistance the environment starts pushing back against exponential growth as density dependent limiting factors slow and then stop a population's growth density dependent limiting factors are exactly what they sound like these are factors that increase in intensity as a population approaches K as the population grows its density the number of individuals in a particular area is going to go up that's when these density dependent limiting factors kick in they include competition between the individuals in the population for resources parasitism parasites that are parasitizing the individuals in the population and it gets easy for those parasites to spread from one individual to the next as the population increases it gets easier for predators to pick off members of the population as the population increases and it becomes more stressful for the individuals in that population and that tends to to lower their rate of increase to incorporate the effect of limiting factors and carrying capacity in our understanding of population growth we need a more sophisticated model that's the logistic growth model and it's represented by this formula over here it shows how a population's growth rate decreases as the population's number approaches its carrying capacity or K and it's represented by the formula Delta n over delta T equals the growth rate time n multiplied by this expression Kus n / k n is the population size T is time R is the rate of increase and K is the carrying capacity let's plug some numbers into this logistic growth formula and see how it actually works in this example k equals 1,000 that's our carrying capacity over here but let's say that our population is 10 if n is 10 if that's our population size then K - n / K is 1,000 that's K minus n that's our population divided by the carrying capacity 1,000 that's 990 / 1,000 that's 99 growth looks exponential because whatever our rate of growth would have been we're multiplying it times 99 will be in our exponential growth phase but if we increase the population to 900 then look what this does to this expression K minus n over K it's now 1, -900 / 1,00 K - n over K and that's 10 so whatever our rate of growth would have been over here we're now we're going to multiply it by10 and that's going to cause growth to quickly level off as we get to K as population is equal to the carrying capacity then population growth stops all together those density dependent limiting factors that are part of the logistic growth model that characterize carrying capacity can be extrinsic or intrinsic extrinsic factors come from outside the growing population and it includes things like predation parasitism competition intrinsic factors come from within in the physiology of the growing population and it's usually about stress caused by increased crowding and competition between individuals in the growing population and that lowers the birth rate limiting factors can also be density independent and these are factors that are unrelated to a population size they're not related to the population's increasing density so examples are things like hurricanes floods earthquakes human caused environmental disasters like an oil spill a toxic chemical release all of those have nothing to do with the population but for example there was a population of birds that was living within these trees well its population is going to be vastly reduced by the damage that's caused by the storm but that had nothing to do with whether there were a lot of individuals or just a few individuals it's outside the population's density it's density independent so to check your understanding take a look at this graph which shows the results of a student experiment where they're growing duckweed in a cup this graph is from learn biology.com it's part of an frq or a multiple choice question this is what duckweed looks like and the question is in this graph i' like you to identify carrying capacity I'd like you to identify the exponential growth phase and I'd like you to identify where you see density independent regulations so pause the video do that and then see my answer carrying capacity is over here at B you can see that there was an exponential growth phase and then it levels off that's got to be carrying capacity the exponential growth phase is over here at a when you have the J curve of growth and density independent regulation would be at letter C how do you know because here's the population it's growing just as it is over here but then at this point something abruptly stops population growth that didn't have to do with the density the density dependent regulation kicks in over here so that had to be independent of density density independent regulation what happens as a population reaches or surpasses its carrying capacity I'm going to show two scenarios there are probably more one is oscillation you have a cyclical overshoot of the carrying capacity and Decline and that's caused by reduction of resources and then recovery so here's a population that's grown Beyond its environments carrying capacity that caused somewhat of a degradation of resources and that reduces for example the food supply so the population Falls a little bit when it falls the carrying capacity recovers then the population Rises slightly overshoots and then Falls and that goes on and on that is different from what's shown on the right which shows a catastrophic overshoot the the line in blue represents the population of deer the line in green represents the shrubs that the deer used to forage and to supply themselves with food well in this case there's a catastrophic overshoot of the carrying capacity and that causes essentially a environmental collapse and the population of shrubs crashes and the populations of deer crashes and there's no subsequent recovery we have serious environmental degradation another population growth pattern to know about for your AP bio class is about Predator prey population Cycles here's an incredible data set that shows the population of lynxes a cat that's a predator in North America and hairs both of these animals live in Canada both have great data sets because their pelts were collected by trading companies that were active in Canada in the 1800s into the 1900s so we see this kind of oscillation what's going on it's partly explained by density dependent regulation of the hair population by lynxes the lynxes are the predators the hair is the prey as the population of hairs goes up that provides more food for the lynxes their population goes up they eat more of the hairs the hair population declines and then the lynx population declines but when the lynx population declines there's less predation on the hairs so their population increases but that's only a partial explanation what's also going on is that there's cyclical oscillation of the hair population by food availability so they're herbivores they're praying on plants that are available in this area and they're competing with one another so cyclical oscillation of the Hera population by food availability and intraspecific competition which in turn affects the links population everything is complex that's what makes biology so fantastic I want to acknowledge how difficult and complex some of these Concepts can be and I want to encourage you to go to learn dm.com and with a free trial you can do the tutorials and you can use our unit reviews and it's going to really help you to get on top of this material setting you up for Success on your unit test or the AP Bio exam topic 8.5 Community ecology part one symbiosis what is symbiosis symbiosis is an interaction when two species live together in close proximity and one species might be harmed by that interaction the other might gain or both species might benefit or one of the two species might be unaffected on learn Des biology we have a couple of interactive exercises that you can use to learn about all the different kinds of symbiosis that you need to know about for AP Biology one thing that I want to emphasize now is that there's a symbol system that's used to describe their relationship a kind of shorthand and a plus sign is used for the species that gains a minus sign is used for the species that loses and a zero is used if there's no effect so for example in competition it's a minus minus interaction in mutualism it's a plus plus interaction with that in mind we'll now go through the various types of symbioses that you need to know competition is a kind of symbiosis where two species require for the same resource and they're competing for that resource it's a minus minus interaction here we have the example of two Predators a leopard and a lion and they're competing for the same prey here we have the interaction between two trees that live in the forest of the North American Northwest and the Douglas fur tree and the coast Redwood compete for resources such as light water space and soil nutrients mutualism is an interaction where both species benefit from the interaction it's a plus plus a winwin interaction and here we have two examples one is between clown fish and anemones the clownfish lives amidst the tentacles of the anemon and evolution has led to a situation where the anemon doesn't sting the clown fish so the clownish gets safety that's its win what is the anemon get well the clown fish is a Messy eater so food falls out of its mouth into the tentacles of the anemon where they're digested and when the clown fish defecates the feces are also used by the anemone for food a wind win relationship not all of these symbioses that are mutualistic involve anemones but I couldn't resist sharing this other one this involves the giant green anemon that lives off the coast in the inter tidal zone of the Northwestern part of the United States and this anemon which is in the same CLA as jellyfish s stinging tentacles just as we saw over here kind of a predator it Harbors symbiotic algae that LE within its tissues well those algae get a safe place to live and they produce food that the anemone can digest so it's a wi for the anemone and it's a wi for the allergy that the anemone Harbors predation is a relationship where animal species one kills and eats animal species 2 it's obviously a plus for the predator and a minus relationship for the prey it's a win lose interaction here we we have a leopard killing a bush buck and here we have a king fisher killing a tadpole that's predation in herbivory an animal species eats a plant and that's a plus for the animal and it's a minus for the plant it's a win lose interaction here we have deer grazing on a tree and here we have a sawfly caterpillar eating a leaf commensalism is a relationship where species one benefits and species 2 two is unaffected so it's a plus sl0 relationship win no effect in this example over here we have a cattle Egret that likes to perch on top of the cattle the Egret gets a nice place to perch and the cattle is pretty much unaffected on the right we have moss growing on a tree trunk the Moss gets a nice place to live and grow and the tree is pretty much unaffected parasitism is a long-term relationship in which species one the parasite lives in or on species 2 which is the host and the host is harmed by that interaction so it's a plus minus win lose interaction here are two examples one involves viruses viruses are obligate intracellular parasites in order to reproduce themselves they need to infect cells and those can be your cells the cells of animals the cells of of plants the cells of bacteria the cells of protus so the virus is the parasite and you or another organism or another cell is the host here's another parasite this one is giardia that's a single cell decario that infects people when they take in contaminated water food Etc the Giardia reproduces inside our intestinal tracts it causes diarrhea other kinds of intestinal upset and then it leaves via the feces to contaminate other food water and spread to another person brood parasitism is a relationship in which bird species one lays its eggs in the nests of bird species 2 species two feeds and nurtures species one at the cost of its own young that's obviously a win lose plus minus relationship and here we see this little Reed warbler that's feeding this cuckoo that has parasitized its nest parasitoidism is yet another variation on parasitism it's mostly limited to insects and it's where species one lays its eggs in or on the eggs or larv of species 2 individuals in species 2 are eventually killed and that can take quite some time this is a plus minus relationship a win lose relationship and here we have parasitoid wasp cocoons and a lime butterfly caterpillar and the part of the story that you're not seeing is that a wasp came over to the caterpillar injected in its eggs the eggs developed inside the caterpillar and then emerged through these holes over here and then the larv formed cocoons around themselves when the cocoons have fully developed little wasp will emerge and they'll go ahead and they'll parasitize other caterpillars just in case you're thinking that this parasitism Niche is unique and unusual it's not there are more parasitic species than any other kind of animal Niche hi Mr W from learn Das biology.com where we believe that interaction and feedback is what leads to deep substantial learning we're so sure of that that we provide a money back guarantee that comes with your subscription topic 8.5 Community ecology part two competition and co-evolution before we get into competition and coevolution I want to define a term that I used in the last section and I've used throughout the series the term is ecological niche you can also say Niche and it's how an animal makes a living here we have a bunch of dinosaurs and other Mesozoic reptiles this one is an apex predator and a scavenger this flying reptile over here was an aerial predator and a scavenger this the Triceratops was a large herbivore here's an omnivorous forager this one's an omnivore this one's an herbivore or an omnivore this one's a small predator and here's an herbivore also an armored Grazer those are various dinosaur niches plants have niches as well so an oak is a sun tolerant tree a rododendron is a shade tolerant shrub a mangrove is a salt tolerant tree or shrub a cactus is a desert adapted plant a water lily is an air requiring aquatic plant that lives on the surface of lakes or ponds and Ivy is a climbing vine there are other plant niches as well but this should give you the idea an important idea related to competition is gauss's competitive exclusion principle this principle states that two competing species can't coexist in the same ecological niche gaus did experiments with various species of paramia so here are two species of paramia one of which lives on the bottom of lakes and ponds that's their natural habitat and the other is a Surface forager so it swims up higher and you can see that by the position they would take in a test tube when these two species were combined in the same test tube they were able to coexist just fine why because their ecological niches their ways of making a living were different but when GA took two species that had the same ecological niche both of them were surface foragers and when you combined them in the same test tube what he found was that species a outcompeted species B which became extinct what do we see we see two species in the same ecological niche can't coexist that's gauss's competitive exclusion principle over long periods of time competition can be a powerful evolutionary Force One possibility is that species become extinct the other possibility is that the competing species evolve through natural selection to do something that's called a re Source partitioning that's exploiting different parts of the resource that they were competing for the way that that happens is through specialization there's selection for different kinds of traits and that results in character displacement that simply means differences so that each species will dominate its sub Niche more effectively here we have the example of a variety of Shorebirds and you can see the character displacement the different length of the legs the different shape of the beaks and what that does is that it enables each bird to exploit a different part of the resource so that the avocets aren't really competing with the Ducks because they're foraging in this part of the shoreline habitat whereas the Ducks are foraging over here and the oyster catchers are actually on the sand and the clovers are higher up on the sand so again character displacements are the differences and what they wind up with is species that can effectively exploit the resource that they were formerly competing for to make this clear I want to offer an economic analogy character displacement and resource partitioning in the coffee Niche so here we have three companies that live in my part of the world and they've all evolved through competition slight differences Starbucks it's the mainstream everyday coughing experience with sugary specialty drinks and snacks seasonal offerings that's different from pets which appeals to Coffee purist really high quality beans dark roast more robust coffee taste and that's different again from Phil's Coffee which specializes in pour overs each cup brewed fresh to order customers are encouraged to customize their drinks so again we have three competing companies each is partitioning the resource for different parts of the um economic market for different customers and they've done that by evolving different characteristics if you can apply that to animals and plants you'll understand these Concepts well resource partitioning can lead to what are called ecomorphs and those are species that are morphologically adapted adapted through their form to specific niches so in the Caribbean islands you have lizards that have adapt to different parts of the forest canopy you have these very large lizards that are called Crown Giants smaller ones called trunk Crown ones that live on the trunk ones that live on the ground and ones that live in the grass well that's resource partitioning that is all about character displacement but what's really cool is that through convergent evolution ecomorphs from different regions different islands in this case can develop similar traits so you have crown giant lizards that can be found on Cuba Jamaica the island of Hispanola and Puerto Rico but they're not closely related to one another they evolve these traits independently through convergent evolution and that's true of the trunk Crown lizards the ones that live in the trunk the trunk ground and the grass Bush and this relates to a really cool case study from the Howard Hughes Medical Institute that most AP biology students experience and now you'll understand it better here's a really interesting data set that could show up on the AP Bio exam or in your course related to beak depth in the Galapagos finches here are three of the Galapagos Finch species that live on the Galapagos Islands which are off the coast of Ecuador the character that's been Quantified here is the beak depth the distance between here and here in the beak different size beaks are adaptations for exploiting different types of food here is what's going on on islands where these birds live together they're all inhabiting the same island note that there's no overlap in terms of the beak depth that's true of Island set a and Island set B an island set CA that involves floriana and San Christoval one one of the bird species G magaris is absent but note that there's no overlap between bird species G fenosa and the other bird species G foris but on these really small Islands quatro Hermanos over here and dhne mayor over here only one bird species is present and with only one bird species note the overlap in beak depth what I'd like you to do is TR try and explain that so pause the video and see if you can come up with an explanation on island set A and B over here there are three species that are coexisting and competition between those three is leading to Niche partitioning and adaptation to different types of food is leading to character displacement so there's no overlap in the beak depth we have the much larger beaks over here the mediumsized and the smaller size over here an island set c one of the species G magaris is missing but because there still competition between these two species G fenosa and G foris there is character displacement and there's no beak depth overlap on the smallest Islands DNE there's only one species and without competition with no competition between different species character displacement decreases the beak depths overlap so here we have a kind of natural historical validation of these ideas related to character displacement and resource partitioning another concept related to competition is the difference between a fundamental Niche and a realized Niche a fundamental Niche is the range of resources that a species could exploit in the absence of competition a realized Niche is the range of resources that a species actually does exploit in the competitive context in which it lives an interesting natural history study was done in the intertitle zone involving two species of barnacles that's a kind of crustation that lives on the rocks of the intertidal zone here's species a which lives closer to the high tide line here's species B which lives closer to the low tide line if species B is removed which you can do by scraping these Barnacles off the rock notice how species a expands into the low tide zone where species B was living but if species a is removed species B pretty much stays where it is so your task is for species A and B to compare their fundamental and realized niches pause the video do that and then go on for species a the fundamental Niche is much wider than its realized Niche how do we know that because when species B is removed species a is capable of colonizing this Zone over here that's much closer to the low tide zone species B by comparison has a fundamental Niche that's pretty much the same as it's realized n and how do we know that because when species a is removed species B is incapable of expanding into this Zone over here closer to the to the high tide line species B can out compete species a but it can't live in the area where species a is predominant that's the difference between a fundamental Niche and a realized Niche let's end this discussion of symbiosis by talking about evolutionary arms races these are positive feedback loops where adaptations in one species lead to counter adaptations in the second species and they're associated with predation parasitism and herbivory they result in extreme adaptations related to speed sensing camouflage defensive and offensive Weaponry that can be physical Weaponry or chemical Weaponry why is a cheetah capable of running 60 M an hour well it's because the cheetah speed has selected its prey for Speed and as the prey have evolved to become faster that's caused a counter adaptation in the Cheetahs which has caused them to become faster this obviously doesn't go on forever because there are physical and physiological limits but when you see an amazing adaptation it probably stems from an evolutionary arms race why is this insect so incredibly well camouflaged because there's some predator on the end which has incredible visual Acuity why is this crocodile or alligator so incredibly well camouflaged in the water where it's swimming because on the other end there's a prey organism which has acute hearing and acute vision and so the alligator has evolved counter adaptations and so it goes in the amazing pageant of life that we call b i o l o g y topic 8.5 Community ecology part three keystone species and trophic Cascades what are keystone species these are species whose action in a biological community structures the entire Community they're frequently but not always Predators who keep a particular hervo in check and their effect is to increase the overall biodiversity of a biological community using the example of sea stars in The intertitle Zone explain how keystone species promote biodiversity sea stars are predators and they pre on a variety of other animals in the inter tidal Zone here's the inter tidal Zone The Zone between the low tide and the high tide and here are some of the many animals that sea stars pre on including importantly muscles when sea stars are removed from the intertial Zone biodiversity can plummet that's because by preying on the muscles sea stars create ecological space physical space for other invertebrates to live in this community and that keeps biodiversity high so this is what this community looks like when sea stars are present when sea stars are experimentally removed which happened in a famous experiment by Robert Payne in the 1960s where he took sea stars and threw them into the ocean away from the inter tidal Zone where they were praying on muscles the muscles overgrew the entire intertial Zone and that caused species diversity to fall all the other species that were previously living in that zone couldn't live there anymore so that's the effect of the removal of a keystone species upon the diversity of a biological community another example of a trophic Cascade relates to the reintroduction of wolves into Yellowstone National Park that reintroduction happened in the 1990s previous to that wolves had become locally extinct in the Yellow Stone ecosystem mostly due to over hunting when wols were reintroduced they started to Prey Upon elk the elk in the Wolves absence had reduced the numbers of Aspen and Willows particularly along Riverbanks so the Aspen and Willows were able to regrow that provided habitat for beavers to use the Willows and Aspens to create beaver dams that created great aquatic habitat and that led to an increase in organisms like amphibians fish and song birds the wvs were also competitors with the coyot so their reintroduction led to a decrease in coyote numbers and that led to flourishing of some coyote prey including foxes rodents and antelopes the main thing for you as an AP biology student is to be able to interpret a diagram like this and to know the basic idea which is that the reintroduction of a keystone species increases biodiversity through a trophic Cascade effect to clear up a possible source of confusion note that the top predator is not always the keystone species this emerged from a famous study by James eses in the waters of Alaska in the 1990s and what eses discovered is that when orcas Chang their prey preference from Seals to Otter then otter were no longer able to control the population of urchins urchins over great is the kelp and that led to an overall decline in the kelp forest ecosystem you can see this in this data set and this kind of data set is something that could definitely appear on the AP Bio exam or on your teacher's next test and what this shows is that a reduction in otter by orcas these numbers show the various islands where SDS studied this decline led to an increase in the biomass of sea urchins here it is in the late 1980s here it is just before 1997 that led to more intense grazing by sea urchins upon kelp this is a measure of their grazing intensity and that led to kelp forest decline which you can see in the overall decrease in kelp forest density again what's important it's your ability to interpret these data sets and connect it to the idea of at trophic Cascade finally it's important to note that not all keystone species are top predators for example beavers are what are called ecosystem engineers and their dams create habitats for dozens of other species increasing biodiversity are you asking yourself how am I going to get a four or a five on the AP Bio exam it's a good question because it's a hard test but we have a plan for your success go to learn biology.com sign up for a free trial and complete our interactive tutorials and interactive AP Bio exam reviews we guarantee you a four or a five on the AP Bio exam see you on learn biology.com topic 8.5 Community ecology part four ecological succession what is ecological succession it's how a community under goes predictable changes following a disturbance such as a fire flood Landslide or Volcan iic eruption each array of species in each stage so these are the different stages of succession creates conditions that subsequently allow different plant and animal communities to thrive so as the community ages the plant and animal community here is going to be different over time and it culminates in a climax community that will endure in relative equilibrium until a disturbance restarts the process succession is classified as being either primary or secondary primary succession starts from bare rock and it follows in events such as a rock slide a volcanic eruption Glacier Retreat and the most important thing is that primary succession requires creation of soil which is the basis of plant communities here's a picture of my wife and myself in Maui and we're standing in a Volcan canic crater and you can see that there was a lava flow and plants are starting to come in that's primary succession on the right we have secondary succession the soil is still intact and it follows a fire a flood a clearing of forest Etc because the soil is already present the process can occur much more quickly how does ecological succession unfold it begins with pioneer species the those are shown over here at stage two and those are organisms like lyans and algae that can live on bare rock which was over here in stage one this is obviously a primary succession scenario and that begins the accumulation of biomass and the creation of soil after we have those pioneer species we have Sun tolerant mosses and herbs they're shown over here in stage three and they create soil you can see the soil starting to develop over here that sets the stage for sun tolerant grasses and ferns that are over here at stage four that's followed by the um introduction of small shrubs and then trees over here at stage five and those trees create a shady under story that's simply the area below the canopy of the trees and that creates a niche for sun tolerant shrubs in other words plants that really can't survive in full sun but are well adapt to live in partial Sun finally what we have is a self-perpetuating climax community and again that can endure until a disturbance resets the clock some of those communities like the redwood forest of the Pacific Northwest of California those can endure for tens of thousands of years what are the key trends associated with ecological succession no first of all that here we have succession not on a terrestrial ecosystem but in an aquatic ecosystem we have what's called Pond succession because successional processes occur there as well and the process runs sequentially a through F overall as the process unfolds abiotic conditions non living conditions are replaced by biotic conditions soil Mass increases you can see the creation of soil as this Pond begins to fill in over here overall biodiversity increases in other words there are more species over time the number of interspecific interactions increases as there are more species and the community over time becomes more stable and more resilient topic 8.6 biodiversity what is biodiversity what are its components biodiversity is the variety and variability of life within an area and it has several components that includes ecosystem diversity so if you think about an ecosystem like the one in Yellowstone National Park there are mountains there are meadows there are aquatic ecosystems so a variety of ecosystems in one area you can also talk about species diversity the number of different species within an ecosystem or you can talk about genetic diversity so if you're looking at that species how much genetic variability is there among the individuals that comprise that species and important idea related to biodiversity in AP Bio is that biodiversity increases resilience what's resilience it's the ability of a system to respond to change and to bounce back from difficulties here's an example here's a field of corn with one species and in fact in today's world this might be a genetically engineered Field of Corn where there's really only one individual that's cloned over and over again so we have low genetic diversity and low species diversity combined into one if there were some kind of fungal pathogen that were to enter the system or an insect herbivore that were to figure out how to uh eat this corn in the face of pesticides and herbicides and all the other things that we do to protect fields of of corn well this field would be extremely susceptible to damage in a grassland like this with many different species if there were a fungal pathogen that impacted one species there are many other species that are in the same system am I saying that we shouldn't be converting grasslands into fields of corn no of course we need corn for food and for other products but as we develop our planet we need to do that with an eye towards maintaining biodiversity ecosystem species and genetic at as high a level as possible because that promotes resilience we just made a connection between biodiversity and ecosystem resilience that's a benefit of biodiversity but there are several more one is that biodiversity is intrinsically beneficial that means it's a good thing in and of itself and to prove that just go out into nature and you can experience the joy of the diversity of different ecosystems the diversity of all the different species within those ecosystems and the variability of the organisms within the ecosystem so that is the intrinsic benefit of biodiversity in addition biodiversity provides many present and potential benefits to humanity one example is the Pacific U which is a shrub that lives in the forest and what was discovered years ago is that the U contains a compound that has anti-cancer properties and that's been developed into an important anti-cancer drug that's treating millions of people who knows what other compounds like that exist within the incredible biodiversity that exists in the rainforests or in coral reefs so on and so forth so we need to maintain biodiversity to gain those benefits if all those species become extinct those direct benefits won't be things that we'll be able to get and finally there are ecos system Services those are things that biodiversity provides to us for free that might otherwise have huge economic costs the oxygen in the atmosphere where's that from it's from photosynthesis provided for free by the producers of planet Earth the oceans when they're intact and healthy can absorb carbon dioxide that can mitigate climate change that is an important ecosystem service the bats that fly around eating insects that keeps insects under control another ecosystem service and there are thousands just like that the economic benefit of ecosystems that are intact and healthy is in calculable and that's the benefit of biodiversity within the AP Bio curriculum diversity comes up in two places in Unit Seven we looked a lot at the importance of variability within species and if you want to review that you can go back to my unit 7 video in Unit 8 what we focus on is mostly species diversity here are three communities Community a community B and Community C and what we're going to do is we're going to compare their diversity and we're going to do that based on two components the first is speci species richness the number of species in an area and the second is species evenness how evenly distributed the members of a species are so what we're going to do is we're going to rank these three plant communities from most diverse to least diverse and to do that we're going to do some counting and Analysis if you look at Community a it has three species one two and three and in terms of the number of individuals in each one they're very evenly distributed there are four individuals of species one four of species 2 and four of species 3 Community B has four species 1 2 3 and four and they're evenly distributed there are three individuals of each species in community C there are also four species but but they're not evenly distributed there are nine individuals of species 1 and there's one individual each of species 2 3 and four as we'll see in a moment we're ultimately going to use some math to determine which of these communities is the most diverse but we're going to start a little bit more intuitively Community B is the most diverse why because it's tied with Community C for the highest species richness both communities have four species and it's tied with a for highest species evenness in both A and B the species are completely evenly distributed but how would we compare Community a three species evenly distributed with Community C that has four species but they're not evenly distributed to properly compare the diversity of different communities we're going to need to use a formula that formula is the Simpson diversity index let me tell you what it is what all the symbols represent and then we'll use it to figure out the diversity of community a little n represents the total number of individuals of each species Big N represents the total number of individuals of the entire community and this symbol means the sum of so here's the diversity index let's compute it so for species one there are four individuals one 1 2 3 4 so we're going to plug four in over here then we have to figure out n the total number of individuals in the entire community and that is 1 2 3 4 5 6 7 8 9 10 11 12 that's the total number of individuals in the entire community so small n divided by Big N for species 1 is33 4 ID 12 is33 then we take that value and we Square It 33 squar is 0.111 for this community it happens to be the same for all three species so species 2 also has four individuals out of a total 12 in the entire community so the values are the same again n over n^2 is11 and that's true for species 3 as well you add those all together and that comes to 0.333 you subtract that from 1 1 minus 333 and the value is 0.67 that's your diversity index for Community a let's repeat the same steps for communities B and C for Community B There are four species and let's count how many members there are are species one there's 1 2 3 so small n equals 3 the total number of individuals again is 12 3 / 12 is25 the values are the same for species 2 3 and four there are three individuals for each of those species out of a total number of 12 individuals in the community so 25 is n small n / large n and then we're going to square it .25 squared is 0.063 the value is the same for each species in this community we add that up 0.063 plus 0.063 Etc we add that up and what we get as our sum is 0.250 1 minus 0.250 is 75 so we see that the diversity of community B is indeed higher than that of community a and that's because the species richness is higher even though the evenness of both is the same they're completely even our question was about comparing the diversity of community C with Community a so let's run the numbers for Community C like the other two communities it has a total of 12 individuals of which nine belong to species 1 so we're going to do little n / big n n / 12 we get 75 then we're going to square that and we get .5 63 so that's what this value is for species 1 now let's do the same for species 2 three and four because it's the same number for each of them there's one individual 1 / 12 is 0.08 that's little n divided by Big N we square that and we get .7 and that's the same for species three and four so we're going to add up all those values because of this expression over here and when we do that we get 0.583 we know that we have to subtract the sum from 1 so 1 -. 583 is 0.42 so we see that Community C even though it has four species has a lower diversity than Community a and that's because it had very low species evenness so we can see how by analyzing each of these communities using the Simpson diversity index that Community B has the highest diversity 0.75 and again think about why that is it has high species richness and high species evenness the next community in terms of diversity is community a which also had high evenness but its richness was a little bit below that of community B and Community C even though it had a higher species richness than Community a its evenness was so low that its diversity index wound up being lower than Community a that that's how you use the Simpson diversity index to determine the diversity of various communities topic 8.7 ecosystem disruption humans are causing biodiversity losses around the planet in unit 7 we talked about the five Great mass extinctions there's a sixth great mass extinction that's happening right now and humans are unfortunately the cause of it what we're doing is we're sending many species to the brink down the extinction Vortex By changes that are creating small isolated populations those populations are subject to genetic drift and inbreeding they lose genetic diversity they become less fit less adaptable that lowers their reproduction rate that increases their mortality rate that leads to smaller populations and so the cycle goes this is a positive feedback loop or a vicious cycle that's occurring around the planet right now we're going to talk about five things that humans are doing that are causing these biodiversity losses that are generating this six Extinction the first thing is habitat alteration and destruction there is nothing wrong with cities fields or golf courses but every time we build a city a field or a golf course we destroy the habitat of animals and plants that live there that's happening at a huge scale around planet Earth where a huge amount of the planet surface has now been in some way modified for human ends that's one of the causes of species Extinction another thing that humans have done is we've overexploited resources and that can be through overh harvesting or over hunting in the case of the Tasmanian wolf and the passenger pigeon these animals were hunted to to Extinction in the case of the American Bison to the brink of Extinction another major cause of biodiversity disruption has been habitat fragmentation and that's taking a large contiguous area and cutting it up by roads or by development into smaller areas what does that do it creates isolated disconnected populations that experience population bottlenecks and lose their adaptability and it also creates situations where there's too much Edge habitat Edge habitat is exactly what it sounds like it's the habitat on the edge of an area and when you fragment an area you create a lot of edge relative to the amount of habitat in the interior and those Edge habitats are Disturbed areas that have different conditions from the interior conditions and that makes it harder for the species that are trapped in the fragments to survive another another cause of ecosystem disruption is the introduction of invasive species invasive species have the following characteristics they're highly adaptable they tend to be generalists in terms of their niches they can figure out many ways to survive they're good at dispersing themselves they have high reproduction rates their effects include preing or parasitizing local species in the new area where they arrive and out competing local species and disrupting food chains and food webs again invasive species another main cause of habitat disruption a final cause of ecosystem disruption is deforestation obviously when you cut a forest you disrupt those ecosystems and Forest particularly tropical rainforest are some of the most diverse habitats ecosystems on the planet here are your next moves for AP Bio sucess please subscribe to learnbiology tocom and please watch this next video