Transcript for:
Biology Module 2 Overview

hi everyone and welcome to miss estri biology and in this video I'm going through the entire module 2 for OC biology which is foundations in biology now this is a bumper video there is loads of content but if you do want to skip ahead then I've got the time card so you can see each subsection of the chapter and if you do need even more help either with remembering the information making notes then I actually have a full set of OC notes already made for you with all of the key terms included and highlight but now get yourself comfy get something to write with and let's get into it first thing you need to know is about the four different types of microscopes here's a very basic summary but we will go into each type in a little bit more detail so for our light or Optical microscopes they have a poor resolution and that is because of the wavelength of light and light is what is used to create the image you can use living samples though and that means that you can have a color you can use living samples though and you can get a color image transmission electron microscopes have a much higher magnification and resolution and in these microscopes the electrons pass through the specimen to create an image scanning electron microscopes very similar except the electrons are bouncing off the surface so you actually create a 3D image and then lastly the laser scanning conf focal microscopes these are high resolution and 3D and it uses laser light to create the image so we'll go through all of those in a little bit more detail but first let's see what we mean by this term resolution and magnification which was used in that summary the resolution is the minimum distance between two objects in which you can still view them as separate and in a light microscope or Optical microscope this is determined by the wavelength of the light whereas electron microscopes it's determined by the wavelength of an electron magnification refers to how many times larger the image is compared to the actual object that you are viewing so with the light microscopes or Optical microscopes there are four types of slide preparation that you need to be familiar with dry Mount wet Mount squash slide and smear Slide the dry mounts are when thin slices or even the whole organism or specimen of viewed and what you do is place that specimen on top of your glass slide with just a cover slip placed on top so this might be used if you're examining a really thin slice of plant tissue or you might have tried this before with your own hair wet mounts are more common and you would have done this potentially in lower school when you looked at maybe a swab of your cheek cells or onion cells and this is when the specimens are added to water or maybe a stain before you have the cover slip lowered on top with a mounted needle to prevent air bubbles forming and and if you were going to examine living aquatic organisms you would have to do that as a wet Mount now in a level you might be more familiar with a squash slide so these are wet mounts but then you would push down on the cover slip to ensure that you have a really thin layer of cell so that the light can pass through so when you did your root tip squash practical you would have taken a very thin slice from the tip of the root of an onion or garlic placed the stain on top squashed it by pressing down and that way you should get light passing through so you could visualize and see the chromosomes and then finally we have the smear slides these are created by placing a drop of the sample at one end of the slide and then using the edge of another slide held at an angle to smear the sample across that initial slide a cover slip is then placed on top and this is used when examining blood cells in a blood sample for example next we move on to this math skill the eyepiece Gra iule and calibrating it so inside a light microscope in the eyepiece there is actually a scale that you can insert on a glass dis and that is what the ipce graticule is and the point of it is that when you look through the microscope you can use that scale to measure the size of the object you're looking at but there are different lenses on your microscope which are going to be causing different magnifications so you might have times 10 * 40 * 100 and at each magnification the value of one of the divisions on your IP graticule will be different so you have to know how to calibrate it at every magnification to work out what one division on your ipce graticule is worth so this is how you would do that you would need to use something called a stage micrometer and this is a glass slide which entally has a ruler on it and you would place that on the stage of your microscope look through your eyepiece and then move your stage micrometer so that it is aligned right next to your eyepiece graticule so on this image the circle representing your field of view when you're looking down the microscope the bottom scale is the scale on your stage micrometer and that has been aligned against the eyepiece graticule which is already within the eyepiece of the microscope once you've then got them aligned step two is to count how many divisions on the eyepiece graticule fit into one of the divisions on the stage micrometer in this case we can see two divisions fit into one of the stage micrometers now on a stage micrometer each division is worth 10 micrometers that's why that value there says 10 it's one division but that one division is worth 10 micromet so we can then use that to work out at this magnification what is one division worth on the ipce graticule so if we know that one of these divisions is worth 10 and two divisions fit into one of those is 10 / 2 so we know that this magnification one of these divisions on the ipce graticule is worth 5 micromet so you can then measure your specimen to work out what is the actual size of your specimen something else that you can do in terms of calculations with the light microscopes but even with electron microscopes as well is the magnification calculation so you need to know that to work out the magnification it's the size of the image divided by the size of the real object and you might have to rearrange that formula to work out one of the other components of this equation and it's never usually that straightforward often you have to have changing of unit involved as well so we usually measure the size of an image in millimet and the size of the real object is usually in micrometers so to convert your millimet into micrometers you wouldd have to multiply by a th so there's normally that additional step as well so staining is the next thing you need to know about and some cell components are really difficult to see under the microscope unless you add a stain to make it a much more obvious color so it stands out and differential staining is a technique which involves many chemical stains being used to stain different parts of the cells different colors again just to make it visually more obvious what you're looking at so Crystal violet or methylin blue are two stains are commonly used and they are positively charged stains and that means they'll be attracted to anything that is negative so negatively charged components of the cell and they will stay in those parts of the cell you could then also add Negrin and Congo red which are negatively charged and therefore they actually can't enter the cells because the side Soul would repel it and that would create a stained background of different color and the unstained cells will then Stand Out observations of structures from under a microscope can be recorded in the form of scientific drawings and there are set rules that you need to know for how you create a scientific drawing because these are very different to your typical artistic shaded style drawings so number one it should always be in a pencil title the diagram to indicate what the specimen is you have to State what magnification was used for the microscope and that you have drawn the image at you should be labeling the key features as well so for a high power plan of this would be limited to just the nucleus cytoplasm and plasma membrane you also have to annotate cell components cells and sections of of tissues that are visible also and stating what colors and shapes they are so not necessarily their functions um so then point 6 is the bit where we're saying it's not like an artistic diagram so you don't do sketches so you should use solid lines that touch but there are no overlaps between those lines also there shouldn't be any coloring or shading in and then lastly the label lines should be horizontal drawn with a pencil and ruler and not have arrow heads on them so essentially the aim of a scientific drawing is to show the size location and proportion and annotating some of these structural details you could also be asked to do the scientific skill of scientific drawings and these are very different artistic drawings they have a complete set of rules and it includes when you are looking at your specimen under the microscope you would then try and draw it using first of all it has to be a pencil a really sharp pencil so you can be accurate you have to include a title of what you've drawn you have to State the magnification you or you could include a scale you should always annotate the cell components or the cells themselves or the section of tissue that is visible that you've drawn it shouldn't be sketchy lines it has to just be solid lines that don't overlap with no gaps and you mustn't do any coloring or shading so essentially the aim of these diagrams is to show the size location ation proportion they are not artistic so that's why we don't have any sketching shading or coloring it's all about the facts the size shape position and labeling the structures and although I've said this for microscopes when you come on to do dissections you could be asked to do scientific drawings of What You observe in your dissection as well so then we move on to the electron microscopes and a beam of electrons is used here to create the image and electrons have a very short wavelength and that is why electron microscopes have a higher resolution and because they've got a higher resolution small organel and internal structures can be visualized the image is created using an electromagnet so that magnet is used to focus the beam of electrons now you can't actually use living samples with electron microscopes and that's because the air would absorb the beam of electrons so your electron microscopes have to be used with a vacuum so your specimen has to be in a vacuum so that the air doesn't absorb the electrons the image is also in black and white so you do have to add a stain to add any color or you can do that artificially afterwards so transmission electron microscopes are one type of electron microscope and for these ones your specimen has to be very very thin you're using an extremely thin slice through your specimen there's stained and then placed in a vacuum an electron gun will then be used to release a beam of electrons the electromagnet will focus that beam and these transmit or pass through the specimen some parts of the specimen will absorb the electrons and that will make them look darker in the image and some parts won't and they look lighter so you get a 2D image because the electrons are passing through and these are really useful for being able to see the internal structures of cells scanning electron microscope in these ones the specimen doesn't have to be thin because the electrons don't pass through the specimen instead the electrons are beamed onto the surface and the electrons scatter in different ways so they reflect backwards in different ways depending on the Contours of your specimen and this is what produces a 3D image of the surface of the specimen so the next bit of spec then is knowing the organel you find in UK carotic and procaryotic cells you need to know the structure and function and here are the 13 organel that you need to know for eukariotic cells and eukariotic cells include animals plants and fungi so here's a cross-section of an animal cell showing some of those structures and here's a cross-section of the plant cell so you can see the location and general shape of these organel but we're going to go through each of them in detail starting with the nucleus the key structures are that you have a nuclear envelope which is this double membrane layer and the holes that we can see within it are the nuclear pores and that is what the MRNA can pass out of after transcription there's also nuclear plasm which is a granular jelly-like material in the middle the chromosomes are found inside of the nucleus and these are protein bound so wrapped around histone proteins and they are linear lastly we have the nucleolus which is this smaller sphere inside of the nucleus which is the site of RNA production and it makes ribosomes so the function then is first of all it's the site of DNA replication and transcription and transcription is the first stage of protein synthesis when mRNA is created it also contains the DNA for each cell and it's the site of ribosome synthesis fella are not actually found on all eukaryotic cells they're found on some so for example sperm cells and it's this whip-like tail structure and the function is for Mobility it is also sometimes as a sensory organel for chemical stimuli cyia again are not on all cells and these are hairlike projections that come out of the cell itself and they might be stationary silia or they might be mobile a mobile cyia move to help sweep substances along and that could be in the trachea for example they'll be moving in this wav like motion to help sweep the mucus up and out of your trachea to prevent lung infection stationary cyia are important in sensory organs such as your nose cental these are made up of micro tubules which we can see here in this image the micr tubu and they occur in pairs to form a centone so that's what we're looking at here we've got them as a pair forming that croone now these are involved in the spindle fiber formation which is a ential in organizing the position of chromosomes in mitosis and meiosis the cytoskeleton is a network of fibers found within the cytoplasm all over a cell and it consists of microfilaments microtubules and some intermediate fibers as well now the function of this is it provides mechanical strength to cells it helps to maintain the shape and stability of a cell and many organel are actually bound to that cytoskeleton to hold in a fixed Place microfilaments are responsible for cell movement and microtubules are responsible for creating scaffold like structures the intermediate fibers help to provide mechanical strength we then move on to looking at the endoplasmic reticulum in terms of the structures there's two types we have rough and then we have smooth endoplasmic reticulum both of them have folded membranes which are called cyan but the key difference is the rough have ribosomes attached to the outside whereas the smooth doesn't the difference in function then links to the fact that the rough has the ribosomes because the rough endoplasmic reticulum has the function of protein synthesis for proteins destined to leave the cell and the proteins are transported through the rough endoplasmic reticulum and into secretory vesicles the smooth endoplasmic reticulum is where lipids and carbohydrates are synthesized and stored next then we look at the goldia apparatus and the secrete vesicles this is the Gia apparatus and the secretary vesicles here which I've seen many students describe as looking a bit like a WiFi symbol and that's how they recognize it in comparison to the smooth endoplasmic reticulum but what it is is folded membranes making the cyy you then have secretory vesicles that pinch off from that cyy the function then is it's where we have the addition of carbohydrates to proteins to form glycoproteins you also have the production of secretory enzymes carbohydrates are secreted we have the transport modification and store of lipids we get lomes forming molecules are labeled with their destination and then finally the finished products are transported to the cell surface membrane which we can see here in those secretory vesicles where they fuse with the membrane and the contents are released liom so we just said lomes can be created by these GGI apparatus and lomes are vesicles um and they're bags or vesicles of digestive enzymes and they can contain lots of different enzymes some functions include the hydrolysis of bacteria so you have lomes fusing with phagosomes in phagocytosis that releases the digestive enzyme to hydroly and Destroy pathogens they're also involved in completely breaking down dead cells and then once they have hydrolized and digested whatever it is that they're breaking down the liome will then fuse with the cell membrane and that will release its contents to the outside of that cell mitochondria are double membrane bound organel so we have an outer membrane and the inner membrane is shown here in yellow it folds in to create the Christi the mitochondria is the site of the fluid Center in the middle is called the mitochondrial Matrix which is the site of some of the stages of aerobic respiration and they actually also contain their own ribosomes and Loops of DNA so that they can create the enzymes necessary for respiration inside of the organel itself so it's the site of aerobic respiration specifically therefore it's the site of ATP production and as I've already said it contains the DNA to code for the enzymes needed for respiration so the ribosomes it contains are the 70s ribosomes which are much smaller which are also the type that are found in proar cells so that leads us into ribosomes ribosomes are small they're very very small you can see like these tiny dots in the microscope images they're made up of two subunits of protein and RNA so those are the two molecules it contains there are ATS ribosomes which are the larger ribosomes found in the cytoplasm of eukariotic cells or 70s ribosomes which are much smaller found in procaryotic cells and also in mitochondria and chloroplast for ukar and the function is it's where protein synthesis occurs chloroplasts are found in plant cells which are eukaryotic organisms they also have a double membrane and then inside you have these foldings of even more membrane which are called the thids and these foldings stack up to look a bit like coins and we call those Stacks the Grana for plural or granum for singular and you also have this fluid which is shown in this beigy orange color which contains lots of enzymes needed for photosynthesis so this is the site of photosynthesis cell walls are found in plants and fungi of eukaryotic organisms not in animal cells and in Plants you have microf fibral of the cellulose polymer and fungi you have kiten instead so they're made up of two different molecules plants have cellulose for structural strength whereas fungi have kiten and that is still a polysaccharide but it also contains nitrogen the function of the cell wall though is to provide structural strength the plasma membrane is found in all cells and this would form the cell surface membrane it's made up of this phospholipid Bayer and within that by layer you have other molecules embedded such as channel proteins carrier proteins proteins on the outside which might act as receptors glycoproteins which might act as receptors you have cholesterol which affects the fluidity and therefore the permeability of the membrane as well and all of these structures together help to control what can enter and exit the cell or it could be the organel because you do have these membranes on the outside of some organel as well so some of those organel are involved in the production of proteins and you do get longans questions where it's in this topic but they want you to link together everything you've learned to say which organal are involv in the production and secretion of proteins so let's summarize that number one the polypeptide chains are synthesized on the rough endoplasmic reticulum or you could say the ribosomes because those are found on the outside those polypeptide chains move to the Cy in the re and they get packaged and and they get folded and packaged into vesicles to be sent to the GOI apparatus for further modification now they have to move move through the cytoskeleton to get to that GOI apparatus once they're inside the GOI apparatus the proteins are modified further and packaged into the vesicles and those secretory vesicles carry the proteins to the cell surface membrane the visle then fuses and releases the protein by exocytosis so looking at the procaryotic cells then in comparison to the eukaryotic cells here are the key differences first of all carotic cells are much smaller in size they don't contain any membrane bound organel both have ribosomes but procaryotic cells have the smaller 70s ribosomes whereas eukaryotic cells have the larger 80s ribosomes the DNA and a procaryotic cell is not contained within the nucleus and procaryotic cells do have cell walls but they're made up of peptidoglycan whereas in eukaryotic cells in Plants it'd be cellulose and in fungi it'd be kiteen now some procaryotic cells have additional features which are the plasmids a capsule around the cell and the fella so let's have a look at some of those key differences so we said there's known membrane bound organel so that means they don't have their circular DNA in a nucleus they don't have mitochondria chloroplast a goldia apparatus and endoplasmic reticulum they're much more basic organisms the ribosomes we said they do still have ribosomes but they're much smaller so they are the 70s ribosomes compared to the 8S ribosomes found in eukariotic cells they don't have a nucleus so instead of a nucleus they have their single circular DNA just free within the cytoplasm and is not attached to proteins and that is what this image here is showing now that is not the same thing as plasmids plasmids are additional Loops of DNA that some bacteria have they don't all have them and they only have a few genes on them and it's where you'd find the genes for antibiotic resistance and bacteria either don't have them at all or they might have them but they have them in varying numbers the cell wall of a procaryotic cell is made up of peptidoglycan which is a glyco protein in comparison eukaryotic cells animals don't have a cell wall but plants and fungi which are eukaryotes do and plants have a cell wall that's made up of microf fibral of the cellulose polymer and fungi have a cell wall made up of kiten which is a nitrogen containing polysaccharide the capsule which again only some bacteria would have this is a slimy layer made of protein on the very outside and the function is to prevent the bacteria from drying out or desiccating but it also helps to cover the antigens to make it harder for the host immune system to detect the bacteria the flagellum which some bacteria have and some might have multiple some might only have one some won't have any just like a fella in a eukariotic Cell it rotates and its function is to move the bacterium part of this chapter is 2.12 biological molecules biological molecules all contain carbon but below shows the elements that each molecule contains so in addition to carbon carbohydrates have hydrogen oxygen as do lipids but just in a different proportion proteins also have nitrogen and sometimes sulfur and nucleic acids also have nitrogen and a phosphorus ions also play a really important role and here is a long list of the ones that you need to know 2025 update here I have actually just edited some of the uses so just check through those carefully to be Mark scheme specific so if you're going to be making notes or flash cards definitely just double check that you're using the information from this slide so the catons which are the positive ions and then the annion which are the negative ions the best thing to do to learn this would be to turn all of these into a flash card so have cat I on calcium arms on one side and then have the information on the other side to show what the function of that ion is or what important role it plays so for this bit I definitely recommend you pause turn this into flashcards and then this will be the best way to get your head around all of this content so then let's take a look at water as a biological molecule it's a polar molecule due to the uneven distribution of charge and we can see here we've got Delta negative on the oxygen and the Delta positive on the hydrogen atoms which means a slight negative and a slight positive charge now because of that uneven distribution that enables the formation of hydrogen bonds between the oxygen and a hydrogen atom between two different water molecules and that's what we're seeing here a hydrogen bond forming between the hydrogen and the oxygen of different water molecules and a hydrogen bond is actually pretty weak in terms of bonds but collectively they do provide quite a lot of strength and it's that structure and those hydrogen bonds which form all the different properties of water that we're going to have a look at so these are the four that you need to know as an important solvent in reactions a transport medium a coolant and for providing habitats so let's take a look at the details for each one starting with water as a solvent because water is a polar molecule that means that it can also interact with other polar molecules and the reason for this is the slight positive charge on the hydrogen atoms will attract any negative solutes that have dissolved and the slight negative charge on the oxygen atoms of water will attract any positive ions in the solutes so if we think about for example sodium chloride the chloride would be negative the sodium would be positive and that is why it dissolves so readily in water nonpolar or Hydro phobic molecules cannot dissolve in water and instead are actually repelled and that's things like lipids theid salt in eukaryotic and procaryotic cells is mainly water so this ensures many solutes can dissolve within the cell and then be easily transported which is why this is such an important property this leads us into the importance of water as a transport medium once those solutes have dissolved they can then be readily transported around plants or animals and if it's in animals it'd be within the Bloods and if it's in Plants it could be in the xylem or the flum now for this bit of the topic it would mainly be the xylm that it's referring to that would be all of those ions that we saw earlier on but glucose sucrose those sugars do also dissolve and they're transported in the flow now it is possible to transport these dissolved solutes in the zylin due to the cohesion that we saw in the water molecules so we said that hydrogen bonds form between the hydrogen and oxygen atoms in different water molecules and due to that the water molecules stick together and they form a continuous column of water this is an advantage because as water evaporates out of the stomata in the leaves that leaves a negative space so negative pressure and that negative pressure pulls on the continuous column of water and it's easily transported up the stem because it is all stuck or cohes together the next one is water as a coolant and this is due to two different properties of water first of all water has a high specific heat capacity and this means it takes a lot of energy to increase the temperature of water you do learn that in more detail in chemistry but that's sufficient for biology the reason it requires so much energy is because energy is needed to break the hydrogen bonds between the water molecules to increase the temperature now that's an advantage because it means internal temperatures of plants and animals remain relatively constant so even if there is a fluctuation in the air temperature that should mean that the temperature inside of an organism and in the cells remains relatively constant and that's good because then enzymes are not going to denat or if it gets really cold they're not going to reduce in activity too far so essentially water buffers temperature changes now the other property is the fact that water has a large latent heat of vaporization and this means a lot of energy is required to convert water in its liquid state to a gaseous state water vapor and again that's due to the hydrogen bonds energy is required to break the hydrogen bonds between water molecules to turn it into a gas and that provides a cooling effect when animals sweat for example or even when plants trans transpire water also provides a habitat and we said previously that it acts as a buffer for temperature changes and that is useful for any aquatic organism as well because living in a body of water if the temperature is buffered then it should mean that your enzymes aren't going to denat if there are any significant fluctuations in temperature the other property links back to the cohesion provided by the hydrogen bonds those hydrogen bonds not only create a continuous column of water in aylin but they also create a surface tension to the top layer of water molecules and that enables small invertebrates to be able to move and even live on the surface and that provides them with away from the Predators within the water finally ice is actually less dense than liquid water due to the hydrogen bonds and as a result ice floats on top of body's water and that can provide a surface Habitat For Animals such as polar bears and it also insulates the water below keeping it a liquid for aquatic organisms so now we're moving on to the next bit in this topic which is looking at monomers and polymers and mono means one poly means so our literal definition is monomers are smaller units which can bind together to create larger molecules or in fact polymers and a polymer is made up of lots of monomers bonded together here are our examples of monomers and polymers that you need to know in this topic glucose is a monomer which forms the polymer starch cellulose and glycogen amino acids is the monomer that forms the polymer protein and nucleotides form the DNA and RNA polymers 2025 edit just to make you aware before you see me go through this whole um flow diagram you actually only need to know glucose and ribos on your spec so although I'm going to talk about others glucose and ribos are the two monomers or monosaccharides that you need to know for OCR 2025 so if we have a look at the carbohydrates first this is showing you an overview of all the carbohydrates that you need to know about we already said that carbohydrates contain carbon hydrogen and oxygen and we can split them into monosaccharides disaccharides and polysaccharides mono meaning one saccharide is sugar so it's just one sugar unit and that would be your glucose fructose and galactose and glucose is the main one that you learn about disaccharides D meaning two is Two Sugars bonded together and you'll be learning about sucros molos and lactose finally polysaccharides means many sugars and what you actually have is at least three sugars bonded together in reality it's going to be far more than three sugar units and you'll be learning about starch cellulose and glycogen so here's alpha glucose one of the isomer and it's C6 h126 so it contains six carbon atoms 12 hydrogen atoms and six oxygens and here is your structure and this is the level of detail that you need to be able to draw it in so the way that I always remember it is start off by having your hexagon and you have an oxygen in the top right every other Bend or angle in that he skin is a carbon coming off carbon one you have hydrogen on top hydroxy same for Carbon 2 same for carbon 4 but it's carbon 3 which is the opposite way around so the hydroxy group's on top hydrogen is on the bottom then we get to carbon 5 and six so you only have a hydrogen coming off carbon five and then carbon 6 is Branched off the top C6 you then would have a hydrogen here hydrogen there and a hydroxide there or in other words ch2 so you do need to know how to draw alpha glucose in this level of detail if we then have a look at our beta glucose which is our other isomer we can see that for beta glucose which is over on this side is exactly the same with the exception of this the hydroxy and the hydrogen on carbon one which is this first carbon in the ring are the other way round the hydroxy on top this time now that slight difference has a big impact on the position that bonds can form and therefore the overall shape structure and function of the polysaccharides then we have the structure of ribos one of the other monosaccharides you need to know and monosaccharides can be categorized according to how many carbon atoms they contain now ribos is classed as a Pento sugar because it contains five carbons and we can see where we've got these numbers that's indicating where the carbons are in the structure so we've got carbon 1 2 3 4 and five glucose has six carbon atoms that be known as a hexos sugar so where you see osc on the end that means it's a sugar and then the prefix in front is to indicate how many carbons it contains and here is our structure of ribos the Pento sugar which is a monosaccharide that you need to know the details of so next we move on to the disaccharides D meaning two and we said it's made off of two sugar units or two monosaccharides they're joined together by a glycosidic bond which is formed during a condensation reaction and a condensation reaction is when a water molecule is removed a chemical bond is formed to create a larger molecule and that's what we can see here glucose plus glucose forms a larger molecule the disaccharide molto and water is produced the other two disaccharides you need to know about are lactose and sucrose all three of the disaccharides are made up of one monomer of glucose and then it's the second one which is different for all three moltos is made up of an extra glucose lactose is made up of galactose easier to remember because lactose is in the name and then sucrose the second monosaccharide it's made up of is fructose now the extra detail that you do need to know for OCR is also which isomer of glucose is involved so for moltos it's alpha glucose and it's two lots of alpha glucose for lactose it's alpha glucose and galactose and then for sucrose it's beta glucose and fructose so those are the three word equations for the disaccharides that you need to be aware of so we said that disaccharides are made in a condensation reaction that is a reaction we're going to see over and over in the biological molecules topic when making polymers and also we're making other molecules so it's a key definition to learn definitely one to put on a flash card so condensation reaction is joining two molecules together by removing water and a chemical bond is formed hydrolysis reaction is the splitting a part of water molecules through the addition of water and a chemical bond is broken just an extra detail to make this really marked scheme specific of 2025 is you need say that it is a water molecule for the condensation reaction and a water molecule for hydrolysis not just the addition of water or the removal of water it is one water molecule per reaction let's have a look at a condensation reaction in action we've got a generic monosaccharide and another generic one over here we aren't really showing any of the extra details only where the bond is going to form because that the part of Interest so we can see here the hydroxy group that is where the water is going to be eliminated from and in removing that water molecule a bond forms between the carbon oxygen and carbon and that in this case is a glycosidic bond and we name the glycosidic bond by the position it is found so a 1 to four glycosidic Bond means it's a bond found between carbon 1 carbon 4 and the way we number them is always starting from the first carbon after the oxygen in the ring so this would be carbon 1 2 3 4 5 and six and same on this one 1 2 3 4 5 and six so this is a 1 four glycosidic Bond the opposite of that hydroling would be breaking that Bond through the addition of water and in doing that the water is added back in to those hydroxy groups and now we go back to having those two monosaccharides next time we move on to our polysaccharide and this is created by many condensation reactions between many glucose monomers so just as a Basics to start starch is found in plants and it's a store of glucose cellulose is also found in plants but the function is different it's for structural strength glycogen is found in animals and this one is a store of glucose also so this summary table goes through the structure and function of all three of those carbohydrates again this would be a great slide to pause and turn into multiple flash cards each of these individual boxes could be a flash card so let's have a look at starch first the monomer is alpha glucose that is the isomer of glucose that this molecule is made up of and because it's got alpha glucose it's able to form both 1 to four and 1 to six glycosidic bonds amalo is one of the polymers in starch and that only has 1 to four glycosidic bonds and due to that amalo forms these long straight chains that then coil up to make a helix so overall it's got a helix shape whereas amelotin is made up of 1 to four and 1 six glycidic bonds and as soon as there's a one six glycidic bond that results in a branch coming off so amalo pectin is a branch molecule these two we'd already said on the slide before so I'm going to skip on now to how the structure links to the function so we said it's a store of glucose the fact that the amalo forms a helix means you can compact the molecule to fit a large amount of glucose in a small space the fact that amalin is Branched increases the surface area for enzymes to attach onto the end glucose molecules hydrolize them off Breaking the Bond and that glucose can then be used in respiration the final one is actually the same for all three because it is so large it's insoluble in water and that means it can be stored within a cell and not affect osmosis so it's not going to cause the cell to swell and burst cellulose is the next one this is also found in plants but the difference here is it is for structural strength it has a very different structure and that is all down to the fact that the monomer is beta glucose because it's beta glucose we get one to four glycidic bonds only and that results in long straight chains of this beta glucose molecule those long straight chains are held in parallel to each other and many hydrogen bonds form between all of those chains one hydrogen bond is weak but because there are so many it provides this Collective Strength and those then form macrofibrils which combine to form a cellulose fiber so the function then linking to that structure is the fact that there are so many hydrogen bonds provides that Collective Strength and that is why cellulose within the cell wall helps to give structure and prevent the cell from bursting lastly our glycogen is also made of alpha glucose and it's very similar in structure to amop pectin in starch it's composed of one to four and 1 to six glycosidic bonds but it actually has far more 1 to six glycosidic bonds than amalo pectin so that means it's even more highly branched now this is important because the fact that there's even more branches means there's an even greater surface area for the rapid hydrolysis back into glucose so the glucose can be used in respiration and because this is the store of glucose in animals mainly in muscle and liver cells if that glucose can be rapidly released if an animal does need to run to either protect itself or to hunt then it will have that glucose our next biological molecule are the lipids so these are macro molecules but they're not polymers they're non-polar molecules so they don't have a charge for that reason they're insoluble in water but they do dissolve in organic solvents such as ethanol and they are hydr phobic meaning they are repelled by water lipids are made up of two molecules fatty IDs and glycerol and they do not form polymers the two key lipids that you need to know about are the triglycerides shown here on the left and phospholipid shown on the right they are very similar in structure they both have a glycerol molecule here which is sometimes described as a glycero backbone and they then have fatty acids attached to them a triglyceride has three fatty acids whereas a phospholipid has two fatty acids and instead of the third it has a phosphate group attached to it so the way that those molecules are made is very similar but this one is just focusing on the triglycerides that glycerol molecule binds to the Three fatty acid chains through a condensation reaction so water is eliminated a bond is formed and we've made a larger molecule bond that forms is an EST Bond so let's have a look at how that occurs here's the glycerol molecule and then we have three fatty acid condensation reaction is the removal of water so we need to have a look at where that water comes from so it's coming from the hydroxy group from the glycerol and from the fatty acid when that is removed we then have a triglyceride plus three water molecules that were removed and here is the esta Bond and we have three EST bonds we have one for each fatty acid that's been bonded on fatty acids can be either saturated or unsaturated a saturated fatty acid is when the hydrocarbon chain has only single bonds between the carbon atoms unsaturated fatty acid is when the hydrocarbon chain has at least one double bond between the carbon atoms the properties of triglycerides do link to the structure so first of all the function is that they can transfer energy and this is due to the large ratio of energy storing carbon to hydrogen bonds compared to the number of carbon atoms so a lot of energy can be transferred if that was to be broken down due to that high ratio of hydrogen to oxygen atoms they can also act as a metabolic water source and this is because triglycerides can release water if they are oxidized and this is essential in animals such as camels that live in the desert where there's very little water as lipids are large hydrophobic molecules they are also insoluble in water and that means they're not going to affect osmosis they're also relatively low in Mass so a lot can be stored in an animal without increasing the mass as much as muscle would and therefore making them so heavy it could impact their movement the phospholipids are made up of one glycerol molecule two fatty acids and a phosphate group the way they're formed is very similar it'll just be two condensation reactions instead of three but we still get es bonds forming but it'll be two instead of three that we saw in the triglycerides now because of this phosphate group it results in very different properties that phosphate group has a charge it's a negative charge and that means that the head which is what we call this structure at the top is hydrophilic and if it's hydrophilic and it's got a charge it can interact and attract water the fatty acid tails are non-polar so they don't have a charge and for that reason they're described as hydrophobic and they repel water but mix with fats now because of these two different charged regions they are able to form the phospholipid bilayer when you add phospholipids to water because the heads are attracted to water they will spin to be exposed on the outside the tails are repelled by water so they'll spin to be on the inside where they can interact with the other fatty acids but they not exposed to the water and that's how we get the phospholipid bilayer that makes up cell surface membranes but also some organ's membranes cholesterol is our next biological molecule and it's very different in structure because it's a sterile steril have four carbon rings in a hydroxy group at one end and they have both hydrophobic and hydrophilic regions now these are embedded in the cell membranes to impact the fluidity they help reduce the fluidity of membranes at high temperatures and they increase fluidity at low temperatures and in that way they help to control the movement across a cell membrane proteins are our next biological molecule and they are large polymers and they are described as macro molecules they're made up of the amino acid monomers and here is our general structure of an amino acid we have a central carbon with an amine group a carboxy group a hydrogen and then the R Group is the variable group and that means it is the part that changes in all 20 different amino acids proteins are organized into four different levels they are first made by the ribosome and creates this polypeptide chain and then we're going to look at how that gets folded processed with different bonds hold the structures together at each of these levels of organization so the primary structure is the order or the sequence of amino acids in a polypeptide chain and you do have to emphasize sequence or order to get that Mark the secondary structure is the further folding of the primary structure and you can either get it folding into an alpha helix or beta pleed sheets and these shapes are held in placed by hydrogen bonds we can see those just here the hydrogen bonds form between the oxygen in a carboxy group and the hydrogen on an aing group and that is what we can see down here so it's between different amino acids between those two atoms and that holds that beta pled sheet and Alpha Helix in place the next level of organization is the tertiary structure and this structure is the further folding to form a unique 3D shape held in place by four different types of bonds there are the hydrophobic and hydrophilic interactions and these are very weak inter reactions the hydrogen bonds which we already saw and again those are quite weak ionic bonds are stronger bonds and those form between the r groups of the different amino acids and the dulfi bonds which are only sometimes present because there has to be a sulfur in the R Group between two amino acids for this to form so the ionic and the dulfi bonds form between the r groups of different amino acids whereas the D and the dulfi bond as we said only sometimes occurs if there is an R group that contains sulfur between two amino acids the last level of organization is the quary structure and this is when a protein is made up of more than one polypeptide chain which is shown here by the different colors so we've got four polypeptide chains collected together to form one protein and the key example that you learn is hemoglobin which is made up of four polypeptide chains now hemoglobin also has a prosthetic group attached to each polypeptide chain CH and that is the heem group and a prosthetic group is one that is not made up of amino acids and for a hemoglobin molecule the prothetic group doesn't contain amino acids but instead it contains the ion A protein that has a prothetic group such as hemoglobin can be described as a conjugated protein which simply means a nonprotein group has been added to it you can also group your proteins as either fibrous or globular based on their final 3D shape in the tertiary structure a fibrous protein has polypeptide chains that form long Twisted strands that link together they're very stable structures ins soluble in water and all of those three points collectively helped to give structural properties so fibrous proteins provide structural strength for example collagen which is found in your bones and keratin which is in your hair globular proteins on the other hand are normally spherical in shape they're relatively unstable they are soluble and involved in metabolic functions so for example enzymes and antibodies and some hormones and if you think about enzymes we do say they're sensitive to certain conditions such as changes in PH and temperature and that's what we mean by relatively unstable for the 2025 specs change I've just added in some extra details here linked to the level of detail you need to know for fibrous proteins and globular prot proteins so if you are making notes or flash cards from this video use this slide for the level of detail that is required so three key examples of fibrous proteins that you need to know are collagen keratin and elastin collagen forms part of the skin the tendons cartilage ligaments bone and connective tissues in the Brony bronchos and trachea it's a quary structure protein because it contains more than one polypeptide chain and it contains three polypeptide chains and these are wound around each other like rope the chains are held by hydrogen and calent cross links between those molecules and the cross links are staggered for strength and chains like close to each other due to 35% of its amino acids being glycine which is the smallest amino acid it's a very flexible molecule but it's not stretchy keratin is used to form Hair Skin and Nails which all protect the body it's important that it's insoluble so these structures are not broken down by water in the environment elastin is our final example and it's a common fibrous protein and makes up the elastic fibers around the alvioli and blood vessels for example in the walls of the arteries arterials venal and veins it also allows these structures to stretch and recoil to their original shape and size the three globular proteins you need to know about are hemoglobin pepsin and Insulin hemoglobin has been described previously so it's a quarternary structure protein because it's got more than one polypeptide chain and in fact it has four it has two alpha chains and two beta chains and each one has a heem group attached to it which is a prothetic group which is where the oxygen binds enzymes are also globular proteins pepsin is an example of an enzyme found in the stomach it is a proteas enzyme which can digest proteins using its specific shaped active site which is complimentary in shape to its substrate lastly then insulin which is also a globular protein and the hormone produced by the beta cells in the pancreas to lower blood glucose concentration its specific 3D shape is complementary to The receptors on the cell surface membrane of the target cells which for insulin are liver and muscle cells so next up we're going to have a look at range of the biochemical tests starting with how you test for starch so you'd add iodine solution and you do have to State solution after all these reagents and a positive observation would be the solution terms from this orangey brown color to blue black to test for a reducing sugar you need to add Benedict solution and heat for 5 minutes at 80° C and you do need to know the duration and the temperature a positive test observation would be that that solution goes from this blue color to either yellow green orange or brick red and the more red the solution is is the higher the concentration you can actually also use reagent test strips and this can be used to test for the presence and concentration as well of reducing sugars for non-reducing sugars you would do this following a negative Benedict test result which basically means the Benedict solution remains blue you would add hydrochloric acid and boil and this is acid hydrolysis you'd be splitting apart or hydroling any dis aides into the monosaccharides you would then cool the solution and add an Alkali such as sodium hydroxide to neutralize you would then add Benedict solution and heat for 5 minutes at 80° C if it was a positive test observation the solution turns from blue to green yellow orange or brick red the more red the higher the concentration you usually get at least orange or brick red because if you did have a non-reducing sugar such as suit crows you originally had just one sugar sucrose but once you've hydrolized it you've split it into Two Sugars so you now have double the quantity of sugar present which is why it should go a more red color ignore the fact that it says one next to all of these it should be 1 2 3 4 5 to test for proteins you would add boret solution and make sure you are spelling that correctly by ett not buet like a piece of apparatus used in chemistry titrations and then the positive test result would be it goes from a blue solution to that purple color solution to test for lipids you would use the emultion test and to do this you would dissolve your sample in ethanol first of all then you'd pour the sample on top of distilled water and then finally a positive test observation would be a white Emulsion forming now you can also use colorimeters to get quantitative data instead of qualitative so if you were using a Colorimeter first of all you'd need to set the filter in the Colorimeter so set it to a particular wavelength of light then you'd calibrate to zero using distilled water to basically show that this is the amount of light that's absorbed when there is nothing in there that is providing a color so you're calibrating it to show what zero is then You' insert your samples from your biochemical test so for example different concentrations of glucose with Benedict solution and filter to then remove the precipitates and what is left is what you would put in you'd measure the percentage transmission of light and then finally draw calibration curve using the results from known concentrations of glucose you can also use bio sensors and this is when you'd have a single strand of DNA or protein which is complementary to the test sample and that is immobilized when the sample is added it will bind to the immobilized DNA or protein this binding causes a change in a trans transducer and as a result an electrical current is released and this current is processed to determine the concentration of sample present chromatography can also be used and these practical investigations are looking at the separation of proteins carbohydrates vitamins or nucleic acids conducted using thin layer chromatography or TLC or paper chromatography in chromatography there's a stationary phase so for example the silica cover plate or paper that does not move and there's a mobile phase and this is the solvent which does move a concentrated sample of the biological molecule is placed 1 cm from the end of the stationary phase the stationary phase is then placed in a beaker with less than 1 cm depth of the mobile phase which is the solvent as the solvent moves up the stationary phase it has an affinity for the biological molecules and dissolves them and this carries them up the stationary phase molecules that are the most soluble in that solvent will be carried the furthest and the molecules that are the least soluble in that solvent won't be carried as far once the solvent is carrying no more of the molecule the plate or the paper is removed from the solvent and the distance traveled by the molecules is measured so to identify which biom molecules you have present on your chromatography paper you can work this out by calculating the retention factor or RF value and here's the formula for this which you need to know it's the distance moved by the solute divided by the distance moved by the solvent and by comparing the calculated RF values with RF values of known molecules in that same particular solvent the biological molecules that you have present can be identified so this is a technique that can also be used to test for biological molecules but also for drugs and contaminants in food next move on to nucleotides and nucleic acids so first of all nucleotides are the monomers from Which nucleic acids such as DNA and RNA are formed and those nucleic acids contain nitrogenous bases which can be categorized according to their structure how many rings they have so purine has two carbon rings and that would be adenine and guanine as we can see here in the diagram we've got the first ring and then the second ring whereas peridin those are nitren bases which only contain one ring within their structure and that' be cyto and thyine and DNA and uracil for RNA the rest of the nucleotide is made of of Pento sugar which is ribos for RNA and deoxy ribos for DNA and then finally both would have a phosphate group so the thyine or uyin RNA is complimentary to the base adenine whereas guanine is complementary to the base cytosine and what that means is you'll always have a purine and a perimidine opposite each other in the double strand for DNA and that ensures that the two strands are always equal width apart both DNA and RNA nucleotides undergo condensation reactions to go from having the nucleotide to the polymer chain and it's a phosphodiester bond that forms between the adjacent nucleotides to create that polymer the polymer of these nucleotides is called a poly nucleotide and that phosphodiester bond is a really strong calent bond and that forms between the pentos sugar which would be deoxy ribos in DNA or ribos in RNA and phosphate of a different nucleotide so it' form between the phosphate group and the pentos sugar next we have a look at ATP and this is very similar in structure to a nucleotide it contains a Pento sugar which is always right ribos and it contains a nitrogenous base which is always adenine adenine and ribos together make adenosine and that's why ATP stands for adenosine triphosphates because we also have three phosphate groups attached and those three phosphate ions or groups play a significant role in energy transfer and that's why ATP is essential for metabolism it's an imediate energy source providing energy for a whole range of different reactions now ATP is made during respiration both aerobic and anerobic but most of it is made in aerobic respiration and this is through a condensation reaction using the enzyme ATP synthes so here we see ADP plus an inorganic phosphate that's what pi stands for and that forms ATP plus a water molecules released because it's a condensation reaction this is a reversible reaction ATP can be hydrolized using the enzyme ATP hydrase and in that case the enzyme plus the addition of water would split one of the bonds between the phosphate groups that releases a small amount of energy and therefore we get ADP plus pi now as well as releasing a small amount of energy the inorganic phosphate group that's been released can then be bonded onto a different compound and in doing that it makes the compound it's bonded to more reactive and we call that phosphorilation and this is actually an example of phosphorilation ADP is phosphorated to form ATP and that makes ATP more reactive it has more energy so going back to DNA deoxy ribonucleic acid codes for the sequence of amino acids in the primary structure of a protein and it's the primary structure of a protein which determines the final 3D shape and structure of a protein the polymer the DNA polymer forms a double helix made of two anti parallel strands and those two strands are joined together by hydrogen bonds that form between the complementary bases so if we have a look at how the DNA structure relates to its function it's a very stable structure and that is because of the phosphodiester bonds that form between the adjacent nucleotides creating what we call the sugar phosphate backbone and those calent bonds mean that the whole structure is very stable the fact that it's double stranded is advantageous when it comes to DNA replication means that both of those strands can be used as a template the fact that there are weak hydrogen bonds between the compliment bases is an advantage for DNA replication as well because it means that very little energy is required to break those bonds separate the two strands and therefore have those two strands acting as a template it's also a large molecule and that means it can carry a lot of information finally the fact that there is those complimentary base pairing between adenine and thymine and guanine and cytosine means that identical copies can be created when DNA is replicated now DNA can be precipitated out of cells to be examined and that's one of the methods that you need to be aware of so you can extract it from plant material using this method first of all you'd have to homogenize the cell so you'd have to break it open with a blender and also a detergent that will break open the cells and cell membranes will also be broken open by the detergent and that releases the contents of the cells you would then filter to remove any large debris add salt to break hydrogen bonds between the DNA and water molecules add proteas to digest the proteins those histone proteins associated with the DNA and then add ice cold ethanol to precipitate out the DNA from the solution and the DNA appears as white strands like we can see just here in the image so next we move on to more details on RNA and the polymers of RNA there are three types M T and R and if we start with r the r stands for ribosomal and that ribosomal RNA is what ribosomes are made up of it's the main bulk of a ribosome the ribosomes are also made up of protein so those are the two components R RNA and proteins mRNA is a copy of a gene from DNA it's created in the nucleus and then it leaves via the nuclear pore to carry a copy of the genetic code of one gene to a ribosome in the cytoplasm now it's much shorter than DNA and the reason for that is it's only a copy of one gene human DNA for example consists of approximately 23 3,000 genes whereas mRNA is only a copy of one of those genes so it's going to be much shorter and therefore it's small enough to come out of the pores in the nuclear envelope it is shortlived though and that's because it is leaving the nucleus and entering the cytoplasm and in the cytoplasm there are enzymes that can hydroly the polymer and that is why we do not want the DNA leaving the nucleus because if it did your hard copy of a genetic code is at risk of being hydrolized and broken down whereas mRNA it's short Liv it just needs to survive long enough to be involved in protein synthesis then it's digested by the enzyme and those nucleotides can be recycled to make another mRNA strand so the MRNA is a copy of one gene of DNA but it's a single Strand and every three bases in the sequence codes for one specific amino acid and these three bases are known as a codon so a codon is three bases on mRNA that codes for a specific amino acid TRNA is found in the cytoplasm it's also a single stranded molecule but it gets folded to create what we call a Cloverleaf shape and it's held in this Clover Leaf shape by hydrogen bonds its job is to transfer or bring specific amino acids to the ribosome and that's what we have here an amino acid attached at the top to this binding site now it's specific ific because it is determined by the three bases on the bottom of the TRNA called an anticodon and these three bases are complementary to a particular codon on the MRNA sequence next we move on to semiconservative DNA replication DNA replication is described as semiconservative because in replication one entire strand of DNA is conserved and one entire New Strand is Created from new nucle Tides copying errors in DNA replication can occur but they occur randomly spontaneously and they result in a change to the DNA base sequence and that's what a mutation is that would be an example of a gene mutation DNA replication occurs in S phase within interphase of the cell cycle and when describing the DNA double helix the top and the bottom of each strand have a particular term we call it the three prime and this symbol here means Prime so three prime end or the five Prime end and this is determined by which carbon within the deoxy ribos sugar of the nucleotide is closest to the top or the bottom so this side we're told it is the three prime end if we zoom in to see that in more detail what we mean by that is the number carbon that's most exposed we've got carbon 1 Carbon 2 carbon 3 carbon 4 and carbon 5 up here so the bottom of this chain carbon three would be described as being the most exposed so this would be the three prime end of this chain whereas this chain it's this carbon most exposed at the end which is our carbon five so that's what this three prime 5 Prime refers to and it's a way to describe the top and the bottom but taking into account the chains are anti parallel so they do look slightly different the enzyme that catalyzes replication is complementary in shape to the three prime end and that is the relevance of this to semiconservative DNA replication that enzyme can only bind at the three prime end of a chain and then it will move along towards the five Prime end so the key stages in DNA replication are first of all the enzyme DNA he case breaks the hydrogen bonds between the complimentary bases of the two DNA polymer chains and that causes the two chains to separate apart both of those strands then act as a template for the DNA replication and fre floating DNA nucleotides will align opposite their complimentary bases on both of those template strands and within the nucleus there are fre floating DNA nucleotides that's where they come from hydrogen bonds will then form between the complementary bases of this New Strand and the old strand and then DNA polymerase is the enzyme that will attach to join together adjacent DNA nucleotides and that means is forming the phosphodiester bond between the nucleotides to create the new polymer chain so properties of the genetic code then there are three special features it's degenerate it's Universal and it's nonoverlapping degenerate means that amino acids are coded for by more than one triplet of bases on DNA Universal means the same triplet of bases codes for the same amino acid in all organisms and non-overlapping means each base in a gene is only part of one triplet of bases that codes for one amino acid so each codon or triplet of bases is red as a discrete unit now the reason these different properties are advantageous are first of all the fact that the genetic code is degenerate means even if a g mutation occurs changing one of the bases in a triplet it might mean it still cod with the same amino acid and therefore the mutation would have no impact on the final sequence of amino acids in the polypeptide chain and therefore the protein shape and function Universal is advantageous in genetic engineering so it means that we are able to remove a human gene for example the human gene for insulin and insert it into the plasmid of the bacterium and therefore the bacterium will make human insulin nonoverlapping is also advantageous linking to the concept of mutations the fact that each base is only part of one codon means that if there was a mutation in that codon which meant it now coded for a different amino acid the mutation will only affect one codon so in your whole sequence of amino acids that get coded for only one one would be incorrect and that should reduce the overall impact that the mutation has and that leads us into this concept of protein synthesis proteins are created on the ribosomes of the rough endoplasm reticulum in two stages transcription happens first and this is when mRNA is Created from a copy of one gene on DNA and then translation is the second stage and that's where the MRNA has left the nucleus it attaches to a ribosome and it is used then to create create a polypeptide chain and that's what we're going to have a look at these two processes in detail there are a couple of key terms though that you need to be familiar with to fully understand this topic and the first is introns and exons introns are the sequences of bases in a gene that do not code for amino acids and therefore they don't get coded for to create anything in the polypeptide chain and in fact they get removed out of the MRNA after it's been transcribed and we call that splicing the introns get spliced out of the MRNA exons are sequences of bases in a gene that do code for sequences of amino acids so those are the coding sections on your mRNA then we have start and stop codons and at the start of every Gene there is a start codon meaning three bases and those bases enable the ribosome to attach to the MRNA sequence and that initiates translation at the end of every Gene there are three bases that do not code for an amino acid and that is the stop codon and when the ribosome reaches those three bases because it doesn't code for an amino acid there's no corresponding TRNA molecule and it causes the ribosome to detach from the MRNA and therefore it ends translation so the first stage is transcription and this is the process in which a complimentary mRNA copy of one gene of the DNA is created in the nucleus and the process is very similar to DNA replication it starts off the same DNA helicase breaks the hydrogen bonds between the bases in the two strands of DNA this causes the DNA Helix to unwind and one strand only acts as a template and that's what we can see here the DNA double helix is Unwound separated and only one strand is acting as a template for the MRNA three Mr nucleotides within the nucleus will align opposite their complimentary bases on that template Strand and then the enzyme RNA polymerase will join together the adjacent RNA nucleotides forming phospher bonds and creating that new mRNA polymer chain once one gen is copied the MRNA is then Modified by having those intron spliced out it then leaves the nucleus through the nuclear envelope pores and moves to the cytoplasm and that takes us on to the second stage of protein synthesis which is translation so that modified mRNA has left the nucleus through the nuclear pore and then it attaches to the small subunit of the ribosome at the Starcon the TRNA molecule with the complimentary anti codon to the star codon aligns opposite the MRNA and that is held in place by the ribosome and as we can see here the ribosome can hold two tRNA molecules at a time and once the peptide bond is formed the previous TR molecule is detached and the ribosome then moves along so that's what we can see in that image and forming that peptide bond requires an enzyme and also ATP so the ribosome continues to move along the TRNA enabling the next compliment TRNA anticodon to align to the next complimentary codon on mRNA and it continues until the ribosome reaches a stop codon which causes the ribosome to detach and it ends translation that polypeptide chain that is now created then enters the GOI body for folding and modifications the next part of this topic is enzymes enzy s are biological catalysts made up of globular proteins the active site which we can see here is a specific and unique shape due to the folding and bonding in the tertiary structure of a protein due to that specific shape active site enzymes can only attach to substrates of complimentary in shape so we describe them as being specific enzymes cataliz both intracellular and extracellular examples and intracellular means inside of a cell extracellular means outside of a cell so for example catalase is an intracellular enzyme inside liver cells that breaks down hydrogen peroxide into oxygen and water Trin is an extracellular enzyme in the small intestines that hydes proteins and the way that enzymes are catalyzing reactions is they are lowering the activation energy so so all reactions require a certain amount of energy before they occur and that's what the activation energy is taking us into chemistry now when the enzymes attached to the substrate they lower that activation that is needed and that is why the reaction speeds up so what you need to be able to do is explain how enzymes lower the activation energy and there's two different hypotheses that went about explaining this the key is the older model and this model suggests that the enzyme is like a lock and that the substrate is like a key and that key is perfectly complimentary in shape so it fits into the lock in this analogy due to the enzyme specific tertiary structure it's completely complementary so it can slot that substrate into the active site and the theory here is stating that when we then get these enzyme substrate comp lexes the charged groups within the active site were thought to distort the substrate and therefore it lowered the amount of energy required to break the bonds in the substrate now since we've started to learn more about the molecular structure of proteins and understanding that they are actually slightly flexible and can move that hypothesis was updated so the induced fit hypothesis is the current accepted model and and this one suggests that an enzyme is like a glove and the substrate is like your hand and by that we mean the glove and the hand are not perfectly complimentary in shape until you put your hand inside the glove so the induced fit model is when the enzyme active site is induced meaning it's caused to change shape around the substrate so initially the substrate and the active site aren't perfectly complimentary in shape but when the substrate collides into it it induces that active site to mold around the substrate and then it does become perfectly complementary now when that happens that enzyme substrate complex occurring puts strains on the bonds in the substrate and therefore it lowers the activation energy required to catalyze that reaction now because enzymes are globular proteins they are very sensitive to certain conditions and the following conditions can affect the rate of enzyme controlled reactions temperature pH enzyme concentration and substrate concentration one really important edit just to be aware of as I go through all of these variables now such as temperature that you're about to see here but also to do with substrate enzyme concentration you need to say the frequency of successful collisions increases and frequency is key for the mark scheme it's not going to say that all of the slides I've edited this in right now for the 2025 video but just be aware that you have to say frequency of successful collisions increases to get the marking points so if we start with temperature we can see this particular shape curve there is a increase in rate with temperature we reach our Optimum and then there is a sudden decrease in rate at higher temperatures and the explanation for this is at lower temperatures there is less kinetic energy and therefore you're less likely to have a successful collision between the enzyme and the substrate however at higher temperatures there is now so much kinetic energy it can start to cause lots of additional movement and those high temperatures will start to break the bonds in the tertiary structure so for example the hydrogen bonds are going to be breaking that causes 3D shape to unfold and you lose that unique shape active sight now the Q10 temperature coefficent is a measure of the rate of change of an enzyme controlled reaction as a result of increasing the temperature by 10° C and the formula to work this out is R2 / R1 R1 is the rate of reaction at a temperature of and your X temperature is whatever your first temperature is R2 is the rate of reaction at a temperature 10° higher than the one you're comparing it to next time we have a look at the ph and too high or too low of pH will interfere with the charges in the amino acids in the active SES that will cause the ionic and the hydrogen bonds to break and therefore that unique 3D shape of the tertiary structure unfolds that changes the shape of the active site and the enzyme the natures now as indicated in this graph here enzymes do have different optimal phes though depending on where they work so for example any of the proteases digesting protein that are found in the stomach they actually have an Optimum of around one or two so pH one or two because they are working in acidic conditions whereas some enzymes actually work better in slightly alkaline conditions for example Trin and amalay because in the small intestines it is slightly alkaline we then move on to looking at the impact of enzyme and substrate concentration now these do not cause the enzymes to denat or cause any change in shape to the enzyme these have an effect based on the idea of saturation so if there is a low concentration of substrates the reaction will be lower as there will be fewer collisions possible between the enzyme and the substrate because there are just fewer molecules there to potentially Collide if you were to increase the substrate concentration because there are now more molecules present you're more likely to have a collision therefore more likely for en substrate complexes to occur and the rate would increase however the rate would eventually Plateau so it level off at a maximum rate of reaction and that's because it had reached a point when all the enzyme active sites are in use or in other words the enzymes are saturated and you would now have to add more enzymes as well as more substrate to increase the rate moving on to the enzyme concentration effect at a low enzyme concentration there will be a low rate of reaction and that's because if there's fewer enzymes there's fewer active sites for the substrate to bind to and therefore there'd be fewer enzyme substrate complexes increasing the enzyme concentration will increase the rate of reaction because there'll now be more enzyme substrate complexes but at high enzyme concentrations unless unlimited substrate is added the rate of reaction will Plateau because there will be insufficient substrate to bind the large number of enzymes and you'd end up with lots of empty enzymes not being used competitive Inhibitors also affect the rate of enzyme controlled reactions and there's two types of Inhibitors we're going to look at competitive are the first type 2025 edit that I'm adding in here to do with Mark scheme specificity for OCR you do have to say that the competitive Inhibitors are similar in shape not the same so they are similar in shape to the substrate so make sure you are using the word similar in your answer a competitive inhibitor is the same shape or very similar in shape to the substrate and that means it's complementary in shape to the active site and it can actually bind to the active site and that's what we're seeing here this is the competitive inhibitor it's binding to the active site that forms an enzyme inhibitor complex instead of an enzyme substrate complex it prevents the substrate from binding and therefore it lowers the rate of reaction now most competitive Inhibitors are reversible and reversible means that they can be removed from the enzyme whereas if it was non-reversible that means is permanently bound to that enzyme now the importance or the relevance of that is if you were to add in a much much higher concentration of substrates they would actually start colliding and banging into the inhibitor knocking the inhibitor out and therefore the substrate would then be able to bind so with competitive Inhibitors at high concentration of substrates they actually don't have um any impact anymore and that's what we can see here in this graph at low substrate concentrations the competitive inhibitor has lowered the rate of reaction compared to the enzyme reaction with no inhibitor but at a high concentration they both Plateau at the same maximum rate the non-competitive Inhibitors though these bind onto the enzyme at a position other than the active site and we call that the aleric site because the inhibitor is bound to the enzyme it causes the protein to change shape and therefore it changes the shape of the active site and the substrate can no longer bind regardless of how much is added and that's why we see there is a lower rate and even platter at a lower rate and it doesn't matter if you continue to add more and more substrate just interrupting here to add in another 2025 edit to make sure your answers are really Mark scheme specific for this bit here you need to say that enzyme substrate complexes form less frequently so that is the phrase that they'd be looking for they're forming less frequently and therefore the rate of reaction is much lower because the active site is now a different shape we get fewer enzyme sub complexes now some Inhibitors are what we call end product Inhibitors and this is when the product of the reaction is a reversible inhibitor for the enzymes involved in controlling that reaction and this is really useful because it enables reactions to be controlled so essentially it can turn reactions on and off so if there is a lot of the product already present from this reaction that product binds to the enzyme and inhibits it and it prevents any more of that reaction happening but when the product starts to run low the inhibitor is no longer going to be able to inhibit the enzyme and the reaction starts up again so that prevents resources from being wasted that brings us on to the idea of co-enzymes co-actors and protic groups some enzyme controlled reactions require an additional nonprotein molecule such as a co-enzyme cofactor or a prosthetic group to catalyze the reaction so if we have a look at co-enzymes and co-actors first some reactions require atoms to be carried from one reaction to the next in a multi-step pathway of reactions and that is actually the case in both respiration and photosynthesis some enzymes also require a nonprotein molecule to bind to the active site to make it complimentary to the substrate and that is what a co-actor and a co-enzyme is the difference between the two is that co-enzymes are organic molecules and co-actors are inorganic molecules meaning they don't contain carbon a prosthetic group on an enzyme is a type of co-actor but they differ in that they are permanently attached to the enzyme by a calent or a non-covalent force precursor activation is when enzymes often occur in an inactive form and they require to be activated by a co-actor so that they can actually work and this prevents enzymes from causing damage within cells and ensures they are only used when they are needed an enzyme is activated by The Binding of a co-actor as this causes a change in the shape for the tertiary structure so that the active site now becomes complementary enough in shape to its substrate for it to bind we then move on to biological membranes it's a biological membrane M braines all cells and all organel membranes are composed of a phospholipid bilayer and that's what we mean by a biological membrane plasma membranes provide this partially permeable membrane and they're the site of chemical reactions and they have a role in cell communication as well and the plasma membrane has this model to represent the different components and properties known as the fluid mosaic model so the plasma membrane is described as a fluid mosaic model due to the movement of the phospholipids proteins glycoproteins and glycolipids but also the arrangement or the pattern of the proteins within the phospholipids the phospholipids Align as a by layer which we can see here we've got two layers of that phospholipid and that's due to the hydrophilic heads being attracted to water which are therefore on the outside of the membrane and the hydrophobic Tails being repelled by water which is why they face inwards to each each other proteins within the cell surface membrane can be extrinsic which means on the outside or intrinsic which means going all the way through the extrinsic or peripheral proteins provide mechanical support or they can make glycoproteins and glycolipids and the functions of those are in cell recognition as receptors the intrinsic or integral proteins are the carriers or channel proteins which are involved in the transport of molecules AC across the membrane protein channels like we can see here Form Tubes that fill with water to enable water soluble ions to diffuse whereas the carrier proteins will bind with ions and larger molecules such as glucose and amino acids they then change shape to transport the molecule to the other side of the membrane finally there's cholesterol which we can see just here that's present in some membranes and this restricts the lateral movement of other molecules in the membrane and this is useful is it makes the membranes less fluid at high temperatures and this will prevent water and dissolved ions from leaking out of the cell or out of an organel so these membranes are affected by certain factors temperature does have an effect on the structure and the permeability of that phospholipid B layer and there's two reasons why firstly at high temperatures it increases the kinetic energy of those phospholipids so they're going to have even more movement and that increase in the fluidity of the membrane means that there's going to be larger gaps periodically between the phospholipids and therefore the permeability increases and it makes it easier for particles to cross the membrane the second reason is high temperatures could denature the carrier and the channel proteins in the membrane and if that happens and the protein channels and carriers become wider then even more molecules are going to be able to move across that cell membrane that weren't initially able to so therefore it becomes more permeable solvents can also damage the cell membrane structure organic solvents like alcohol for example ethanol dissolve lipids so they will dissolve the phospholipid bilay in the membranes and that damage causes the fluidity of the membrane to increase and become more permeable next we move on to movement across the memane braines and there are six key modes of Transport in and out of cells that we're going to have a look at and it's this six just here so starting with simple diffusion this is the net movement of molecules from an area of higher concentration to an area of lower concentration until equilibrium is reached this process does not require ATP for molecules to diffuse across the membrane they must be lipid soluble and small and that's what we can see here we've got a high concentration of one side of the membrane compared to the other and these lipid soluble molecules then dissolve in that phospholipid Bayer and move down their concentration gradient and this will continue until there is no longer a concentration gradient present facilitated diffusion is still a passive process with the movement going down the concentration gradients however it's for molecules that are either too large to diffuse through the phospholipid Bayer or for molecules that are not soluble in lipids and so instead they have to move through the proteins that are embedded within the phospholipid Bayer so that movement of ions and those polar molecules would be through either protein channels or the protein carriers osmosis is the movement of water from an area of a higher water potential to an area of lower water potential or more negative and it happens across a partially permeable membrane and the more negative a water potential that means the more concentrated the solution you have less water but more solutes dissolved in it and there's different types of solutions that occur that have an impact on osmosis an isotonic solution is when the water potential of the solution is the same in the solution and the cell and because there is no water potential gradients there'd be no net movement of water in or out of the cell and in an animal cell we can see here is a red blood cell as an example that has no impact on the overall size or shape of the cell a hypotonic solution is when the water potential of the solution is more positive so it's closer to zero which basically means there is more water compared to the solute so as a result water will move from the solution into the cell causing it to swell and it could even eventually cause it to burst if enough water is moved moved in in a hyperonic solution that means the solution is more negative than the water potential in the cell so as a result water within the cell will move out bi osmosis into the solution and that causes the cell to shrivel up but the term we use for that in animal cells is crenation and we say in plant cells they are plasm in plant cells as well they will not burst as readily because they have that cellulose cell wall so instead they become really swollen and we describe it as turgid the next type of transport is active transports and this is the movement of molecules and ions from an area of lower concentration to an area of higher concentration which means it's going against the concentration gradient and for this reason it requires energy in the form of ATP from respiration and it involves carrier protein it is a selective process as only certain molecules are able to bind to a receptor site on the carrier proteins when they do that ATP will bind to the protein on the inside of the membrane it then gets hydrolized into ADP and Pi that causes the carrier protein to change shape and open towards the inside of the membrane and as a result the molecule that was attached is released to the other side of the membrane the phosphate group or that Pi molecule is then released from the protein and the protein reverts to its original shape and the process can continue to happen as long as ATP is present the next one is endocytosis and this is a type of active transports but it is the bulk transport of molecules into a cell the cell surface membrane bends inwards around the molecule surrounding it to form a vesicle and that's what we can start to see happening here it's bending inwards and eventually it folds all the way around to form a vle the vle pinches off and moves within that cytoplasm and endocytosis can be classed as either phagocytosis as we've got on the left or pinocytosis that we have on the right and when it's a solid particle being taken in it's called phagocytosis when it's a liquid being taken in that is when it's py Tois this requires energy from ATP because to change the shape of the membrane around that material does require energy exocytosis is another type of bulk transport but this time it's the movement of molecules out of a cell the molecules are contained with a vesicle vesicles move towards the cell surface membrane fused with the membrane and the content of that vesicle is then released to the outside of the cell this process requires energy because ATP is needed to move the vacle along the cytoskeleton towards the cell surface membrane cell division cell diversity and cellular organization so cell division first of all in eukariotic cells they enter the cell cycle and then divide by mitosis or meiosis prootic cells replicate by binary fision and then viruses do not undergo cell division as they are non-living the cell cycle comprises three key stages we have interface split into G1 S phase and G2 then there's the nuclear division which is either mitosis or meiosis and then finally cyesis so let's begin with interface and this is the longest stage of the cell cycle G1 which is the first part of interphase is when protein synthesis occurs to make proteins involved in synthesizing organel the organel then rep replicate the cell is checked that it is the correct size has the correct nutrients growth factors and that there is no damaged DNA if a cell doesn't pass these checks then replication does not continue then we have S phase and this is when DNA is replicated G2 is when the cell continues to grow energy stores increase and the newly replicated DNA is checked for any potential copying errors I've edited this slide for 2025 to make sure that the descriptions of what's happening in G1 and G2 are really Mark scheme specific so make sure you have a look at the level of detail on this slide when you're making your notes or flash cards because this is the level of detail required for the mark scheme so then move on to the first option for nuclear division which is mitosis one quick edit I've made here is to make sure it's really Mark scheme specific for mitosis you have to say it creates two genetically identical diploid cells so you would have to say genetically identical to get the mark and it's used for growth tissue repair and asexual reproduction in plants animals and fungi there are four key stages prase metaphase anaphase and tase or Pat as a way to try and remember it prophase is when the chromosomes condense and become visible and in animal cells the centrios which are shown here in yellow separate and move towards the opposite poles of the cell the cental create spindle fibers which are released from both poles to create a spindle apparatus and these will attach to the centromere and the chromatids on the chromosomes in late prophase early metaphase plants have spindle apparatus but they don't actually have the centrioles metaphase is the next stage and this is when those spindle fibers have attached to the Centere and it causes the chromosomes to align along the Equator of the cell the spindal assembly checkpoint also occurs in this stage and this is where there is a check to make sure that every chromosome has a spindle fiber attached to its Centere before mitosis Carries On To The Next Stage which is anaphase so in anaphase this is when the spindle fibers start to shorten and move towards the cental and pull the Cent chromatids they are bound to towards those opposite poles as well this causes the Centere to divide into two and the individual chromatids are then pulled to the opposite pole this stage requires energy in the form of ATP which is provided by respiration in the mitochondria next we have tase or telophase and the chromosomes are now at each pole of the cell and become longer and thinner again so therefore they start to no longer be visible the spindle fibers will disintegrate and the nuclear membrane starts to reform around those chromosomes cyesis is then the final stage of the cell cycle and this is when the cytoplasm splits so we get two genetically identical cells and in animals the way this happens is a cleavage f forms in the middle of the cell and the cytoskeleton causes the cell membrane to draw inwards until the cell eventually splits into two plant cells the cell membrane splits into two new cells due to the fusing of vesicles from the goia apparatus the cell will forms new sections around the membrane to complete the division into two cells just interrupting here to point out a change to this slide to make sure your answer is really marked scheme specific you have to say that it causes the cell surface membrane to draw inwards and the cell surface membrane splits not cell membrane it's specifically the cell surface membrane so you have to say that word surface now you can actually observe mitosis and this is one of the required practicals and the stages of mitosis can be viewed using a light microscope in onion or garlic root tips so You' need to take a thin slice of the root tip from either an onion or a garlic and place it on top of a microscope slide you then break it down a little bit with a mounted needle a stain is then added and the purpose of this is to make the chromosomes visible when you put your slide under the microscope you would then sometimes add acid to help to break down the cellulose connections between the cell walls then you would place a cover slip on top and push down the reason we push down is to squash the tip to achieve a single layer of cells to ensure light can pass through and therefore you can see the individual cells and the chromosomes inside of them and that's what we can see here that single layer of cells lights passing through them most of the cells here are in interphase and we can tell that because chromosomes are not visible but we do have two where the chromosomes are visible so we could use this to calculate the mitotic index so this is calculated by counting how many cells are visible in the field of view meaning the section that you're looking at and by counting the number of cells that currently in mitosis and it's essentially a percentage this so the number of cells in mitosis divided by the total number of cells and then you'd multiply it by 100 to give that answer as a percentage now when they have questions like this they usually tell you the total number of cells so that you don't end up spending lots of time in an exam just counting lots of cells and instead you just have to work out the number of cells in mitosis and like I said in this example we've got two that are in metaphase so the other type of nuclear division is meiosis and this is when we have two nuclear divisions and that results in four genetically different hloy daughter cells the two rounds of division are referred to meiosis 1 for the first round and meiosis 2 for the second both stages include prophase metaphase anaphase and tase and cyesis at the end but interface only happens at the very beginning before meiosis 1 now we said it makes a haploid cell and what we mean by hloy and diploid is a hloy cell represented by single letter N is when you have one copy of each chromosome a diploid cell or 2N is when you have two copies of each chromosome the genetic differences are introduced in meiosis by two key processes independent assortment of homologous chromosomes and crossing over so let's have a look at crossing over first during prase 1 the homologous chromosomes pair to Form B ve valence and by balent we mean two homologous chromosomes next to each other and that's what we can see here we've got our homologous chromosomes represented as one in red one in green and they look like this x structure because the DNA is replicated so we have two cister chromatids attached by a centr to make a chromosome and here is the homologous chromosome crossing over genetic material can occur so these nonsister chromatids meaning a chromatid from the different chromosomes crossing over and form what we call a kayma and that is where the crossing over happens now the tension that that creates can result in breaks occurring and we then get this Exchange in material of those chromatids and as a result the AL that were on this chromatid are now going to be part of this chromosome so we have this new combination of Al in the resulting gametes independent assortment also increases the genetic diversity and this happens during metaphase 1 where the homologous pairs of chromosomes line up opposite each other on either side of the Equator but it is random for each homologous pair which side the maternal and the interal chromosomes align and that's what we can see here we only been shown an example with three homologous pairs but it shows you all the possible combinations of how they could align at the equator and for humans we have 23 homologous pairs so that means there would be 2 to the power of 23 possible combinations of how those homologous pairs could align and that works out to over 8 million different combinations and that's what we can see here and you can use that Formula 2 to the^ of n where n is the number of homologous pairs to work out the number of possible combinations for any different organism now in metaphase 2 the sister chromatids within one chromosome also are lining up at the equator and their orientation on each side of the Equator introduces another chance for increased genetic variation and as a result each gam receives different combinations of the maternal and paternal chromosomes we then move on to this idea of organization looking at specialized cells as well now multicellular organisms are organized in the following way cells are the smallest structure then we get tissues organ organ systems and those will work together to create the entire organism now you do need to be aware of a selection of specialized cells and we've got here the summary of all of the ones that you need to know about so I recommend that you take a screenshot of this make your own table make your own notes or even turn this into a flash card so you've got the five specialized cells and for each one you've got your description here of the structure of the cell and how that links to the function now I've added this into the 2025 video you do actually also need to know about root hair cells so these are added in here so these are cell on the surface of the roots and they have long projections to increase the surface area for osmosis of water and also the active transport of mineral ions from the soil they have a thin cell wall reduc the diffusion distance we then move on to the different tissues same thing again screenshot it and print have it in your notes or copy it out or even better turn it into flashcards just to point out a key edit here these are tissues so I've edited the slides you see coming up which said epithelial cells and ciliated epithelial cells however these are the tissues so at this point you would just say aamus epithelia tissue and ciliated epithelia tissue but those are made up of ciliated epithelial cells but it's really important that when you're describing the tissue you don't put cell at the end these are the different tissues that you need to be aware of the structure of each and the function of them then move on to stem cells and these are undifferentiated cells that can self-renew meaning continually divide and become specialized different types of stem cells have different differentiation abilities and the types that you need to know about are toti poent Pur poent multi potent and uni poent toti poent cells can divide and produce any type of body cell during development toy potent cells translate only part of their DNA resulting in cell specialization PTI potent cells occur only for a limited time in early mamalian embryos they then develop into Pur potent stem cells and these are found in embryos and can become almost any type of cell the only cell that they can't form is the penta so for this reason they are used in research with the prospect of using them to treat human disorders there are issues with this though as sometimes this treatment doesn't work or the stem cells can continually divide and that results in tumors on top of those practical issues there are ethical issues as well because there's a debate as to whether it's right to make a therapeutic clone of a patient in order to create an embryo genetically identical to them to get the stem cells to cure a disease and then after that destroying the embryo as well so the other two types of stem cells are multi poent and uni poent and these occur in mature mammals and they can only divide into a limited number of types of cells multi poent cells such as the ones found in bone marrow can differentiate into a limited number of cells and in bone marrow that is into the different types of blood cell uni poent cells can only differentiate into one other type of cell so the potential uses of stem cells are in both research and Medicine and these include potentially being used to repair damaged tissues or in the treatment of neurological conditions such as Alzheimer's and Parkinson's or it could be Research into developmental biology so that takes us to the end of all of topic 2 I hope you found it helpful and if you made it to the end congratulations [Music] a