AP Bio unit 1 is the foundation for all of the great biology that you'll be learning this year 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 to help you study for this unit one test or the AP Bio exam I've put together a checklist that you can download AT AP bios. checklist let's go water and hydrogen bonding 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 inter molcular bonds they're between molecules not within molecules like Co valent bonds or ionic bonds or anything like that so 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 intra molecular bonds using the diagram below as an example describe how hydrogen bonds can form between molecules besides water the 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 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 exer Ed 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 question so it's an essential underlying concept Elements of Life topic 1.2 of AP 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 Contex 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 that 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 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 Su hydral group over here at number six is very important in terms terms of protein structure it uh creates a stabilizing bond that holds proteins in a specific three-dimensional shape and the acetal group at8 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 phospho lipid and key molecu membranes 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 monosaccharides those are simple sugars and some of those are all important in biology like for example glucose which is essentially the fuel of 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 a 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 explain most animals can't hydrolize the bonds that connect glucose monomers and cellulous 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 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 lactase why should you produce an 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 enabled them to continue to produce the lactase enzyme into adulthood and that 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 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 Hydro phobic 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 water proofing this molecule is a 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 t 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 two at a 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 four or five 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 P Bio exam here's your plan go to learn 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 R 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 poly peptide 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 they're 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 poly peptide 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 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 pleaded 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 an 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 hotary 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 Al the 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 um 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 sickle 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 amuno acid veine over here to substitute for glutamic acid and that's an important mutation because glutamic acid is acidic whereas veine is nonpolar the 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 with in smaller arteries and that causes these pain crisis 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 sickle cell disease is also a Target for gene therapy something that we'll talk about in unit six 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 come back to nucleic acids when we cover gene expression in unit 6 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 micr Ras 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 a 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 five 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 bases connected to the number one carbon and when you learn about DNA replication you'll talk about things like DNA is replicated in a 5 to3 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 uracil cytosine and guanine 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 complimentary 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 six but just to lay this down for right now DNA is directional notice that in a chain of nucleotides these are AR nucleotides you can tell because there's uracil 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 polymer 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 three prime Direction you can learn a lot more about unit one by doing our unit one review on learned biology.com start with a free trial and you can learn a lot more about DNA by watching this song DNA fantastic