Transcript for:
Biology Module 6 Overview

hi everyone and welcome to miss estri biology in this video we're going through all of OCA module 6 now I know your time is precious because you're revising for your exam so if you do want to skip ahead then I put the time codes at the bottom so you can pick and choose which parts of this chapter you most need help with and speaking of help if you do want that extra push and support in creating notes and knowing the key marking points then definitely check out my OCA notes or my OCA flash cards which cover all the key marking points to help you to remember what to say in an exam question and I'll link them both below but for now let's get into it so in topic six these are the different parts that we're going to be going through starting with cellular control and we're looking at G mutations a g mutation is a change in the base sequence of DNA and they occur randomly during DNA replication which is within S phase of interphase these random mutations are more likely to occur if you're exposed to mutagenic agents and these are different things that incre increase the likelihood or the rate of mutations happening and that includes high energy radiation such as UV lights ionizing radiation such as gamma rays and x-rays and then chemicals which would be known as carcinogens such as mustard gas and a whole range that are in cigarette smoke the two types of G mutation you need to know are deletion and substitution so if we have a look at an example here is our original DNA based sequence and a substitution is when one of those nucleotides and therefore based is swapped for a different base and that now means we've got a different triplet of bases and it might code for a different amino acid sometimes though it will still code for the same amino acid because the genetic code is degenerates meaning multiple codons can code for the same amino acid so that would be known as a silent mutation because the overall polypeptides chain would have the same amino acid sequence a deletion mutation is when one of the nucleotides and therefore bases in the sequence is removed and we can see that one of these three cytosine bases has been removed and as a result we get what's called a frame shift and that is when all of the bases will move one position and in this case they will move one to the left because a base was deleted and that then means all of the subsequent codons will code for a different amino acid they've all been changed and that will have a huge impact on the all protein for this OCR 2025 version I've also inserted which is relevant for what I'm inserting inserting in the information about a insertion mutation so you do also have to know about the effects of insertion mutations which is when one extra base is added and that also causes a frame shift it shifts all of the bases one position to the right so let's take a look then at the effects of these gene mutations because mutations alter the gene they can result in a different amino acid sequence or the primary structure in the encoded polypeptide if the amino acid sequence changes then this has an impact on the folding and the coiling of the secondary structure and therefore it will be different when the protein is modified into the tertiary structure it will form the hydrogen and ionic bonds in different places and that causes it to fold differently and therefore it results in a different 3D shape and therefore it has a different function which is why it could become a nonfunctioning protein a base substitution could be silent though which means that even though the base was swapped it was substituted it might still code for the same amino acid as in the codon might still code for the same amino acid and this is because the genetic code is degenerate which means multiple codons code for the same amino acid base deletions and insertions collectively known as indel mutation result in frame shifts the removal or insertion of one base changes all of the subsequent codons after the point of the mutation it says as can be seen Above This was actually on the previous slide this is more harmful as multiple amino acids may be incorrectly coded for and therefore it will have a bigger impact on the change of shape of the final protein not all mutations are harmful though sometimes a new protein that is made might be beneficial such as the mutation that resulted in antibiotic resistance in bacteria and some effects are neutral so if they do not code for a protein that alters the survival of um survival chances of that organism now protein synthesis can be controlled and one way it can be controlled is through transcription factors and transcription factors are molecules that combind to the DNA and either initiate or inhibit transcription these molecules will move from the cytoplasm into the nucleus and they bind to the DNA transcriptional factors are proteins so the reason they canbin is they'll have a unique 3D shape which will be complementary in shape to bind to one particular sequence of bases and therefore one particular Gene when they bind it enables RNA poase to bind and in that way it will initiate transcription so that mRNA can be created and then that can go to be used in Translation if you don't have The Binding of a transcriptional factor the gene is inactive because transcription cannot occur but as I said sometimes the transcriptional factors are ones that actually inhibit RNA polymerase from binding and therefore it will prevent transcription but in both of these ways transcriptional factors are controlling this DNA being copied into mRNA and therefore they're controlling gene expression so here's a quick summary of what we just went through there the fact that transcriptional factors go from the cytoplasm to the nucleus they bind to the DNA to either turn on or off a gene but the mark scheme tends to want you to not use that phrase and instead say that it can either initiate or inhibit transcription and in that way it's controlling protein synthesis in Pro carots operons are involved in controlling transcription and an operon is a group of similar multaneously controlled genes that are either all expressed or not and this is more common in procaryotes than in ukar and we're going to focus on the Lac operon which is found in eoli and it's a sequence of three genes which we can see here Lac Zed Y and a and this set of genes are collectively involved in lactose digestion bacteria require less energy to break down glucose than lactose so glucose is the favorable spiratory substrate however if glucose isn't present then lactose will be digested and used so therefore proteins produced by the Lac operon are only needed if glucose is absent and lactose is present and therefore needs to be digested so this regulates the transcription of these genes to meet the demand so the three genes that we saw in the previous image like Zed Y and a are in this operon and the Lac L is a regulatory Gene found near the start of the operon so I'm just going to go back to show you that here's our Lac L and that is at the start um near the operon and that Gene codes for a repressor protein that inhibits transcription when there is no lactose present so when the lactose is absent that repressor protein is constantly produced and it binds to the operator which is a region close to the operon which prevents RNA polymerase from binding to DNA at the promoter region and in this way transcription is inhibited if lactose is present the lactose binds to the repressor protein and this causes it to change shape this change in shape prevents the repressor protein from binding to the operator and therefore RNA polymerase can bind to the promoter and transcription of the Lac operons occurs cyclic also has a role because it increases the rate of transcription of the Lac operon in order for sufficient enzymes to be produced by lack Zed lack Y and lack a cyclic receptor protein CRP must bind and the CRP can only bind and increase the rate of transcription once it has bound to cyclic next turn let's have a look at the posttranscriptional changes so mRNA gets modified once it has been transcribed so this newly synthesized strand of mRNA is called pre-mrna or primary mRNA and then once it's modified it's known as mRNA the key modifications are the removal of the introns and the rearrangement and reordering of the exons and that's what we can see here the introns are removed and those exons will be rearranged and reordered all of the introns need to be removed as these do not code for amino acids in the primary structure of the polypeptide being made these are removed by a protein called a spone and therefore the removal of them is known as spicing the exons can be reordered and some are removed to allow a single Gene to actually result in the creation of multiple proteins and this process is called alternative splicing there are also changes that happened after translation so post transational changes in addition to the activation of proteins by CM as discussed linked to the Lac operon proteins are modified further after translation nonprotein groups can be added to the protein so for example lipids and carbohy hydrates that could make a glycoprotein this happens in the GGI apparatus the proteins are then folded into their unique 3D shape and bonds are formed to hold that 3D shape in place some proteins are made inactive forms and they need to be activated by phosphorilation we then move on to the genetic control of body development and this is where we then look at the homeobox gene sequence and Hawk genes so plants and animal cells and fungi all have homeobox Gene sequences to control the development of their body homeobox genes are sequences of genes which create proteins that regulate the expression of other genes that are involved in the formation of the body in the early stages of an embryo these homeobox Gene sequences are highly conserved which means they're very similar in plants animals and fungi and that's what we can see here in this pretty complicated diagram all of these different gen and the sequences of them we can see the color and that links to the image the part of the body development it's involved in and we can see that it's pretty similar between all of these very different organisms so a bit more about Hawk genes these are a type of homeo box genes found in animals and they're responsible for the correct body development and body positioning of the different body parts the order of these genes in the DNA is the order in which their effects are expressed on the organisms and many animal bodies are segmented so for example an insect has three segments and there are segments on a worm that's what all the Rings are and invertebrates such as humans all of the vertebrae in our backbone are segments the body development of most organisms also shows symmetry some have radial symmetry like a jellyfish meaning the top and the bottom are the same others have bilateral symmetry like humans meaning the left and the right hand side has symmetry we then look at mitosis and apoptosis because these both also play an important role in the development of body forms and that's because mitosis results in an increase in the number of cells which results in body growth and apoptosis which is programmed cell death will remove unwanted cells the cell cycle is controlled by genes to ensure new cells are only made when you need growth repair to occur and that's to preserve energy but also to prevent tumors from forming and there are two genes that help this the tumor supressor Gene which is responsible for making proteins that stop the cell cycle from occurring if you don't need any more cells and Proto Ona genes which are responsible for producing A protein that initiates a cell cycle when you do need new cells if an error is detected in a cell or if it's too old to function that's when apoptosis occurs and the cell is destroyed and the useful resources get recycled so the control of mitosis and apoptosis are both in response to internal and external stimuli such as stress hog genes also regulate mitosis and apoptosis the genes that regulate the cell cycle on apoptosis are impacted by external and internal stimuli so for example temperature on the outside and hormones and psychological stress in terms of internal stimuli and the effect of this is highest during growth development the next part of this topic is inheritance and we start by looking at this whole range of key terms and their definitions so I suggest you pause at this point and turn this into a set of flashcards and you can use this to constantly test yourself to check you know these definitions that could come up as one or two Mark questions this is an edited in extra point for the 2025 version I want to draw your attention to the fact that I have changed the definition for code dominant here to match exactly what is wanted on the mark scheme both Al are expressed in the heterozygote resulting in a different phenotype so make sure that is the definition that you are using you also need to be able to do genetic diagrams to be able to determine potential phenotypes in Offspring so these are the different coding systems that you need and we'll see how these are applied in a range of examples as a brief overview monohybrid is when there is just one Gene and you either have dominant or recessive Ive shown by a capital or a lowercase letter for that particular letter of the alphabet co- dominance is when you have two genes that are both dominant and both expressed so we can't use that coding they both need a capital letter so instead you use two different letters which would both be capitals to show their dominance and the base letter represents the gene multiple Ali we do the same coding because multiple Al is when you have more than two Ali for a gene so we can't just use one letter capital and lowercase because we need more than two codes so again you choose a base letter to represent the Gene and superscript to represent the AL for sex linkage the base letter that is used is to show whether it's an X or a y chromosome and then in superscript you would show the AL autosomal linkage and epistasis are both involved in dihybrid inheritance so that's why we have two different genes shown and they're represented by different letters but in both cases it's just the capital letter is the dominant the lowercase is the recessive so let's have a look at this in action starting with monoh hybrid and for all of these examples I suggest pause it have it Go yourself and then Mark it as I go through so we're told that cystic fibrosis is caused by a recessive Al and the question is if two carriers reproduce what's the probability they'll have a child with cystic fibrosis and what's the probability they will have a girl with cystic fibrosis so step one is always working out the parental genotypes and if they're both carriers that means they don't have the condition so they must have the dominant Al but they carry the recessive Al then when we dra our planet Square we need to show the gametes so the AL that are in those gametes for both parents then we can show if those gametes fuse what are all the possible genot ypes and then it's good practice to put in the phenotype into each box to show what that genotype would result in so these three which aren't labeled would be someone that doesn't have cystic fibrosis but we can see here there's 25% probability that they'll have a child with cystic fibrosis so the probability they'll have a girl with cystic fibrosis is half of that because there's always 50% probability you'd have a girl or a boy so that's why the second part would be 12.5% then if we move on to a codominant example we're told that cows can be red white or ran in color and red and white are both dominant if two ran cows reproduce what is the probability they'll produce red cows so this is what ran looks like where you have both Ali are expressed the red and the white even though the red is kind of more brown in color we still call it red so if both parents are ran that means they have the red and the white alio so this is the genotype for both parents therefore these are the AL in the gametes of both parents and when we look at those fusing together we can see the four possible genotypes and I've matched that up to the phenotypes and from that we can see there's 25% probability that they would have a red Offspring the next example is multiple Al and this often goes hand in hand with codominance so we're going to have a look at at the example of blood group there are four possible blood groups and these are all the genotypes that would code for those blood groups so blood group a means they've got an a-shaped protein B they've got b-shaped protein on the outside of the red blood cells AB means they've both and blood group O doesn't have any protein on the outside of their R blood cell A and B are both dominant o is recessive so the information that we're told then is you've got parents with blood group ab and the other parent is blood group O and they reproduce I a and IB are co-dominant and IO is recessive and we need to say what is the probability they'll have Offspring with blood group O So step one we need to look at the parental genotypes and that is for ab they'd have one of both of the dominant Ali blood group O is recessive so they'd have two copies of blood group O then we do our pet Square to show what the gametes would contain then we can fuse all of those Gams together to show the genotypes and then I've added in the phenotypes and we can see that the genotypes along the bottom both have an A and then the recessive o so we have 50% probability of blood group a so for both of those it be blood group a and therefore 50% probability of blood group a next in a sex linkage example and we're told that color blindness is caused by a recessive Al found only in the X chromosome and we've got a parent who is a non-color blind male who reproduces with a female carrier of the Al and we've got to say what is the probability that their children will be color blind so step one we need to work out the genotypes of the parents so the mother would be XX cuz that codes for biologically female and because they are a carrier they have the dominant anal meaning they don't have the condition and they carry the recessive the male would be XY so biologically that's XY and the X capital r is because they do not have color blindness and there is no Al on the Y chromosome in sex linked examples it's too small to carry as many of the genes as the X does so then we see the potential gametes the genotypes in The Offspring with those gamet fuse and then I've written in the phenotypes and we can see that the probability they'll have a color blind child is 25% now usually you should actually add in these sex as well so this would be a female with normal vision a female with normal vision a male with normal vision and a male who is color blind we then move on to epistasis and this is when one gene influences the expression of another so that means one gene can either affect or mask the expression and three common examples are coat color and mice Coke color in dogs such as Labradors and fruit color or vegetables so we're going to go through through an example with the cat color in Labradors and the two genes are Gene e which is controlling whether pigment is expressed or not and the dominant e will code for pigment being produced the recessive Al if an individual has two copies of that that means they won't make any pigment and the dog therefore will always be this yellow color the second Gene codes for what color pigment would be expressed if they have the dominant e so capital B would code for black fur lowercase b would code for brown fur but you would only get black or brown if for Gene one they have a capital E so as soon as they have two recessive E's that means it doesn't matter what Al you have for the second gene they will always be yellow in that way it's epistasis so here's an example that we've got this time we're giving the parents genotypes and you have to work out the phenotypes so we can see that both parents have a capital E which means pigment will be expressed they both have a capital B which means they're both black now because this is di Hybrid inheritance we now need to work out all the possible gametes that these two parents could produce and that would be capital e capital b capital E lowercase b lowercase e capital B lowercase e lowercase b so for both of those dogs those are the four possible gamt so we put that into our pet Square then we can see all the possible genotypes from those gamt fusing and then I've written in the phenotypes for all of those and we have a ratio of nine black four yellow and three Brown so this leads us into the idea of di hybrid crosses and these are crosses when you're looking at two genes being inherited at the same time and a common example is mendal and his peas and the two genes are one that codes for the shape of the PE and one that codes for the color so here we've got a round and yellow PE and a wrinkled and green PE so whenever you do these genetic crosses just as we've seen in the ones we've done so far you always need to make sure you're showing the parental phenotype parental genotype possible gametes The Offspring genotype The Offspring phenotype and the portion those are typically your marking points so for this example round yellow in this case they would have to tell you that it's homozygous dominant because otherwise that could be heterozygous for both so they'd have to let you know that but for wrinkled green wrinkled is recessive green is recessive so it would be homozygous recessive but you aren't expected to know that the round is dominant and the ring cold is recessive they would have to give you that information so then if we look at the possible gametes this one can only produce capital r capital Y and this one can only produce lowercase R lowercase y so when you work out the gametes in a DI hybrid cross each gamet should have one of each letter so then because this one has only dominant and this one has only recessive that would mean all of the gametes would have to have one of each they'd be heterozygous for both genes and in this case that would mean all of them would be round and yellow so that's quite a simple di hybrid example if we then cross that F1 which means the first generation which was heterozygous for both genes it now gets more complex because it's not so straightforward in terms of the gametes we have to work out all of the possible combinations of the r and Y we could get in the gametes and these are your four possible combinations for both parents then when we get to our pet Square it's going to be 4x4 CU there were four gametes that each parent could produce then if we fuse all of those together we get the genotypes then we fill in what all of the possible phenotypes are and we can see we've got this 9: 3 to 3: 1 ratio and in a dihybrid cross if both parents are heterozygous for both genes you will always always get this ratio 9331 unless there is autosomal linkage or crossing over or epistasis so that's not written down there but also epistasis would affect that ratio this takes us into then what autosomal linkage and crossing over are and how they affect that ratio so recap on crossing over that is when in meiosis you have the noncy chromatids of homologous pair overlapping chromatids break and you swap sections of the chromatids and as a result we've now got a new combination of Al in the gametes and that then is going to change the gametes that you write in your planet square and therefore your overall prediction autosomal linkage is when the two genes that you're considering in this dihybrid cross are both on the same chromosome so if we were thinking about Gene one for shape and Gene 2 for color we're saying they're both on the same chromosome so if we stick to the example we were just doing with two heterozygous parents which meant they had a dominant R and a recessive r a dominant Y and a recessive y we're shown here that they are linked on the same chromosome and in this particular example the two dominant Ali are on one chromosome and the two recessive Ali are on the other chromosome of the homologous pair so that means it's not possible to get the four gametes that we' written it's only possible to get a gamet which would contain this chromosome which would mean capital r capital y or a gam which would contain this chromosome which would be lowercase R lowercase y so because of this autosomal linkage we've reduced the number of different types of gamt we could get and there's now actually only two so instead of there being the four possible options that we said when there was no linkage we now only have two options for both of the parents so now if we do our pet Square again and look at all the possible genotypes of The Offspring The phenotypes this time we have three yellow to one wrinkled and we haven't got that 9331 ratio because those genes were linked onto one chromosome and therefore it reduced the number of possible gametes that could be made so this is just summarizing in this example in di hybrid we would have got a 9331 ratio but with the autosomal linkage we got a 3:1 so the way that this often comes up in exam questions is they would say so the way this links to crossing over is from that autosomal linkage we say we expected a 3: one ratio in an exam question they might say though however this is what the scientists observed they actually saw four phenotypes not just yellow and round and green and wrinkled they saw all four and these were the numbers they observed and this would only be possible if crossing over happened to create new combinations of Al in those gametes so let's just have a look at what we mean by that in crossing over we've got our homologous pairs the noncy chromatids in a homologous pair can tangle up break and swap those Ali so now instead of just having the lowercase R lowercase y capital r capital Y because those two parts are swapped we now have new combinations of Ali in the gametes we have the original lowercase R lowercase y capital r capital Y but we now have these recombinants examples as well where we've got the capital r and the lowercase y the lowercase R and the capital Y so in terms of how we'd explain that in our answer the yellow and round and the green and wrinkled are most common because they're resulting from two gamt fusing together that weren't as a result of crossing over it was the original two possible gametes that's why they're the most common because crossing over is actually quite rare it doesn't happen all the time then the reason we have fewer green and wrinkled compared to yellow and round is green and wrinkled are both the recessive Ali so then explain why we got hardly any of the yellow wrinkled and the Green Round that is because crossing over is rare so we won't get very many of the capital r lowercase y or the lowercase r capital Y gametes and those are needed to create the genotypes that would code for those phenotypes so that is why we don't have very many of those two phenotypes now we can actually link inheritance to a statistic and that is Kai squar and that's because we're counting how many individuals fit into a category which would be a particular phenotype so let's look at how you could use Kai squar in inheritance so in this example we're going back to the cystic fibrosis example um that we did earlier on where we said there was 12.5% probability of having a girl with cystic fibrosis we can actually use the statistic Kai squ to investigate whether what we expect 12.5% is significantly different from what you actually observe in reality so do we actually have a significant difference or not and we'd be hoping that we'd find there is no significant difference between what you expect and You observe because that would tell you that your prediction in terms of your pent squares are accurate they are showing what happens in inheritance so we're going to do an example with corn corn can actually be purple or yellow in color or smooth and wrinkled in texture so if we use this example where we've got dominant purple and recessive yellow here are our possible gametes our possible genotypes and phenotypes and we're showing that we are expecting a ratio of three purple to one yellow if if we were to breed those two parents plants of corn and we're then told a student counted the actual number that those two parents produced and there were 21 purple kernels and 13 yellow kernels and you then need to say does what we observed match what we expected from our planet square and this is where we use Kai squ so our null hypothesis would be there is no significant difference between the expected ratios from our ponic square and The observed frequency of what we actually saw in those corn kernels so here is our table to work out the kai squar we said that we observed 21 purple 13 yellow so that means in total there are 34 corn kernels now we expected a ratio of 3: 1 so we then need to put that as an actual frequency so what is three parts of 34 and one part of 34 it's 25.5 and 8.5 we then do observed minus expected we then square that divide that by the expected to give us our overall Ki squ value of 3176 in this example we have one degree of freedom because we have two categories and it's always number of categories minus one the next step is comparing your calculated value to the critical value for 0.05 so for us we said we had one degree of Freedom so that critical value is 3.84 and our calculated value of 3176 is lower than that critical value at P 0.05 so what that means is there is more than 5% probability that the difference between our expected and observed is due to chance so we have to accept our null hypothesis which was there's no significant difference between what we observed and expected and that is what we want that means the corn kernels did follow the expected ratio of 3:1 and therefore followed the mandelian genetics that we were expecting now something else that you can use is the Hardy Weinberg principle and this is a mathematical model that's used to predict Ali frequencies within a population so just a couple of key terms to help with your understanding of this which again pors turn into a set of flashcards gene pool population an Al frequency here's what it means and we need this idea for in particular the AL frequency to know this formula so the Hardy Weinberg equation there's actually two formula to use here P ^2 + 2 PQ + q^2 = 1 p + Q = 1 now what this actually means is the p + Q = 1 p is telling you the frequency of the dominant Ali Q is telling you the frequency of the recessive Al for one gene in a population and that always has to equal one because if this is just for one gene where we just have two possible Al if you add up both of those Al that will be the total that would be all of them in the population the top equation is the same idea but for the genotypes so p^2 is homozy is dominant two copies of the dominant Ali q^2 is two copies of the essive Al and 2pq is when you are heterozygous you have one of each Al so I'm going to keep that at the top and go through an example with you cystic fibrosis is caused by a recessive Ali and we're told that 0.02% of the UK population suffer from cystic fibrosis and you have to say What proportion of the UK are carriers so the first step is always working out which bit of the formula have they given you you and what are you trying to work out so if 0.02% of the population suffer from cystic fibrosis and that is caused by a recessive alal that means cystic fibrosis is homozygous recessive and that was q^2 so Q ^2 = 0.02% but we always have to convert this back into the decimal so divide that by 100 now they have said What proportion are carriers the carriers are heterozygous we want to work out 2 PQ so to work out 2pq we need to know what p is and what Q is so if we know Q ^2 is .2 if we square root that we now have what Q is we can then use this formula p + Q = 1 to work out P so we'll rearrange that and it' be 1 - Q and that tells us that P is .986 now we just said that we're working out 2pq cu that is the carriers and 2 p q then we just do 2 * P * q and that gives us .3 now if they don't tell whether they want it as a percentage or not in the mark scheme they'd accept either of those but obviously if they say give us a percentage you'll have to times that by 100 then we get to the idea of continuous and discontinuous variation and this means that the variation within species can either be classed as continuous or discontinuous continuous is when it's a type of variation where there is a whole range of values for example height or mass whereas discontinuous is categorical for example blood group you fit into a particular group so data representing continuous variation would be presented with a histogram where discon continuous would be presented with a bar chart and this here is just showing you a summary of the differences between these two types of variation so again this would be another great example to turn this table into a flash card where you have continuous variation on one side the different properties on the other and then another flash card for your discontinuous variation then we move on to types of selection and this links to the idea of natural selection so when natural selection occurs there are three possib outcomes we could have stabilizing directional or directional selection is when only one of the extreme traits has the selective advantage and that's usually when there's a change in the environment or a new Predator a new disease so those individuals with the extreme trait are more likely to survive and the other individuals are less likely to survive and therefore they'll die out so we see over many generations a change in what the mode is and an example of that is antibiotic resistance in bacteria stay stabilizing selection is when the modal trait remains to have the selective Advantage so there's no change in what is the modal value but more individuals will have that modal trait the individuals with the extremes will start to die out so we'll lose those extreme traits so the range in alals becomes narrower and the mean even more individuals will have that mean so that means the standard deviation would decrease and an example of this is human birth weights now linking back to this idea of speciation that we talked about with the disruptive selection speciation is the creation of a new species and this happens when one original population becomes separated so that they are reproductively isolated which means those two isolated populations can no longer breed together this can result in the accumulation of differences in these separated populations in their Gene pools to the extent that those two populations become so genetically different over many many years of accumulating different mutations that if they were to then reproduce they wouldn't be able to make fertile offspring because they're now too genetically different and that's why they get class as two different species now what causes a population to become reproductively isolated could be some sort of geographical barrier and that's known as allopatric speciation or they might be in the same location but there's something that changes about their reproduction mechanism so they don't reproduce together even though they physically could reach each other and that is sympatric speciation so let's just go through those two allopatric is when they are separated geographically so it could be maybe there's a new mountain range following an earthquake and that population becomes geographically isolated that separates the original population into two and now they are unable to reproduce both separate populations will accumulate different beneficial mutations over time through natural selection and due to this accumulation of those different DNA sequences they'll become so genetically different that they aren't able to reproduce and make fertile offspring and that's why we class them now as two new species sympatric speciation is when they are not geographically isolated so they are in the same location but something changes in the way they reproduce or their behaviors around reproduction so they just won't reproduce together so this could be because of a random mutation in the gene that codes for their courtship ritual and therefore maybe individuals don't recognize their Cate ritual and they don't reproduce with them or it could be a mutation that results in them producing eggs or whatever the gam is at a different time of year in terms of plants it might be that they start flowering at different times of year so they can't reproduce with the other plants that flower at a different time so due to this again you have this reproductive isolation they accumulate different mutations there's no gene flow because they're not reproducing together and over time they become so genetically different they can't produce fertile offspring and they're classed as two different species genetic drift is the idea that in every generation there is a change in the AL frequency because you are not a clone of your parents there will always be genetic drift from one generation to the next and it's only when there is a large change in the AL frequency so substantial genetic drift that we class it as Evolution but genetic drift has a bigger impact on smaller po populations because it's all to do with frequencies so if you've got a smaller population even a small number changing would be a bigger percentage compared to if it was a large population so that's why genetic drift has bigger impact on smaller populations genetic botonics and the founder effect are the next ideas here and we're going to look at genetic bottlenecks first these are caused by events that kill almost all of the population leaving only a few individuals left behind and this has happened in the past because of over hunting of some animals so here is the original population size there might have been over hunting so now the population size has decreased but maybe the ones that were left behind didn't actually have all of the Ali that were represented in the original population so we've decreased the gene pool so many Ali for those genes are lost and the remaining breeding populations will keep passing on those same limited alals so it results in a lack of genetic diversity and therefore genetic diseases that exist in the population are far more likely to be passed on the founder effect is very similar but the reason it happens is different the founder effect is when a few individuals from an existing population relocate themselves to a new isolated area so we can see here we've got an original population a small number of them migrate to this isolated area and we can see that this genan pool is not the same as this one in the original there were more purples and reds now we've got more Reds than purple but over time this is then going to reduce the gene pool because those individuals will keep reproducing together and passing on the same Al and we can see here in this example we've got now what was a mixed set of Al we've only got one particular Al so this idea of genetic variation can occur through natural selection but also artificial selection has an effect this again would be yet another good set of flash cards so natural selection is when individuals within a population show a range of phenotypes because there is genetic variation through mutations now environmental factors or it could be biotic factors like predators and disease will determine which individuals are more likely to survive the ones that survive will pass on their Al to the Next Generation and then that Al will become more common in the population and in that way that alil is naturally selected for over many generations artificial selection is when humans deliberately select which plants or animals reproduce together based on the characteristics they want to see in The Offspring so humans here are artificially manipulating the gene pool so that the favorable Ali become common and the less favorable Al become less common this was particularly prevalent in creating dog breeds with popular features for example pugs pugs were deliberately bred by humans because it was deemed cute to have this flat squashed up little squishy face however there's lots of ethical issues around this because it didn't allow natural selection to occur which selects for the AL that increased the survival of the species and because humans selected characteristics based on what they thought looked cute it's actually had a negative impact on their survival pugs because they have this squashed face they don't have as much space in their nose for breathing and they often have difficulties breathing and it can result in lots of medical issues we then get to genan Banks and an example of this is seed banks so seed banks are where seeds are stored for lots of different plant species so that you've got a bank of that DNA in the seed in case they went extinct these are also a way of maintaining genetic material for use in selective breeding so as we just said Gene Banks there stores of biological samples for example plant seeds or it could be animal seen or eggs if we're thinking about animals selective breeding often involves in breeding so we use Gene Banks to help increase genetic diversity by deliberately breeding together the seeds or the gametes of animals from individuals that we know are not closely related so this is important as it reduces the frequency of homozygous recessive diseases in Offspring next we get on to manipulating genomes we start by looking at DNA sequencing techniques and in particular sequencing projects so we need to know the fact that the Genome of an organism is all the genetic material that it contains and sequencing projects have read the genomes of a wide range of organisms like humans and this provides opportunities to screen DNA to identify potential medical problems the human genome consists of three billion base pairs and approximately 20 to 23,000 genes the proteome is all the proteins that a cell is able to produce with simpler organisms if the genome sequence is known then the proteon can be derived from the genetic code this may have many applications including the identification of potential antigens for use in vaccine production but in more complex organisms like humans the presence of non-coding DNA and of regulatory genes means that the knowledge of the genome can't be easily translated into the proteome the last thing you need to be aware of is that sequency methods are continuously being improved updated and automated this has increased the speed of sequencing and allowed the whole genome to be sequenced through methods such as high 3ut sequencing so the principles behind DNA sequencing first of all these techniques have become faster and automated compared to the original sang method which was originally used but many of the principles remain the same the process involves Terminator bases which stop DNA synthesis which is shown here in these colored letters Terminator bases a c g and T are used if an a Terminator base is used this will bind where a normal adenine base would have and instead it terminates any further synthesis of DNA so the basic principle is firstly DNA polymerase a primer an excess of nucleotides and Terminator bases and the DNA to be sequenc are all mixed together the mixture is in a thermocycle which is used in PCR which we come into soon to synthesize DNA the DNA polymerase will add bases complementary to the DNA creating a new strand of DNA the Terminator bases are added at random and will terminate the sequence of DNA at a different point in each replicating Strand and that's what we can see here is at different points in each replicating strand this process continues until all of the possible DNA chains will be produced and the Terminator bases at every single possible position have been made so this is just a small sample here each Terminator base a D C and G are labeled with a different fluorescent color that's why these all shown in different colors and that is then used to identify those bases the DNA fragments are then separated using gel electroforesis and they separate according to their length and now each fragment is arranged by length and the Terminator base is fluorescent indicates which base it is we can use that to work out the exact sequence of bases so high throughput sequencing is where many fragments are processed and sequenced simultaneously and this has made the process far more efficient so once we had these genome sequences we could make comparisons and genome sequencing has made it possible for scientists to compare the entire Genome of individuals of the same species and also of different species so this can be used for analyzing pathogens genomes and that has resulted in many advances including identifying the source of an infection for example MRSA identifying antibiotic resistant bacteria tracking the spread of pathogens to monitor potential epidemics and pandemics identifying regions in the genome for new drugs to Target and comparing genomes has improved the accuracy of classification of species because we're used to classify according to visible character istics but now we can classify based on how similar DNA base sequences are for particular genes it's also help to understand our evolutionary relationships because more similar the sequence of DNA bases in one organism to another will give an indication of how recently they've evolved from a common ancestor knowing the Genome of an organism should mean that you can predict all the proteins that the organism can produce but the human genome as we've said a few times it it contains 20 to 25,000 genes but the predictions for how many proteins humans can make vary from 17,000 to 1 million and a lot more work is needed to be done on this to get an accurate estimate but what this has taught us is that the relationship between the genotype and the phenotype is far more complex than we originally thought so next time we look at synthetic biology and sequencing genomes has enabled the development of synthetic biology which means the creation of artificial Pathways organisms devices or the redesign of natural systems examples of this include genetic engineering where we were able to isolate the gene for human insulin and insert into a plasmid in bacteria so they can produce insulin the use of biological systems in Industry such as immobilized enzymes and the synthesis of new genes to replace faulty versions of genes it's also used in the synthesis of new or organisms so for example new bacterial genomes have been created by scientists so we then look at bioinformatics and computational biology computers are used throughout synthetic biology including using biomatics and that is the use of software to analyze organize and store biological data and this includes databases storing All the known Al Amo acid sequences of proteins and structures of proteins you also have computational biology ology and that's the use of computers to study biology so for example simulations and models and algorithms and the protein structure can be modeled including the effects of new mutations in the base sequence and therefore the altered protein structure can be observed and compared to the functioning protein now just to point out I have added this in because an OCR is often known as a short tand and repeat STS it's AQA that Ed the term V NTR so if OCR you're more likely to see St if we have a look at vntrs next 95% of human DNA is made up of introns and these are the sections within genes DNA sequences that don't code for amino acids and they consist of variable number tandem repeats so we have a variable number of bases that are repeating over and over and the probability of two individuals having the same vntrs is very very low however the more close related you are the more similar your vntrs are so we've been able to analyze vntrs through genetic fingerprinting to determine how closely related different individuals are so the process of the genetic fingerprinting is first of all you have to collect your sample and you can collect your sample from any cell that will contain a nucleus with DNA in so this could be a blood cell not a red blood cell though it have to be a white blood cell um different body cells hair follicules and if the sample of DNA is quite small you would then put your DNA into a PCR machine to get lots of copies so you've got a bank of that DNA so you can repeat this multiple times once you've collected and extracted your DNA we then have to cut it up and that's what the digestion stage is and to cut it into smaller pieces we use restriction endonucleases and they cut the DNA at specific recognition sites which will be close to the Target vntrs we then separate out all of those cut up pieces of DNA using gel electroforesis so you load your different DNA samples from different individuals into small wells in agar gel the gel is placed in a buffer liquid with an electrical voltage applied and because the DNA has a negative charge and at the other end of the gel there'll be a positive charge the D will move through the gel towards the positive and because some of those vntrs will be shorter than others the shorter ones can move faster the longer ones move slower that is what is going on in this separation stage here once we've separated those vntrs an alkaline is then added so the DNA sections are split into single strands it will break the hydrogen bonds and we now have single strands the reason we need to have that is so we can hybridize your single strands with DNA probes which are short single stranded pieces of DNA complementary to the different vntrs so the DNA probes will align opposite and hybridize meaning forming hydrogen bonds with those sequences and this is needed so that we can see where those bands are because the DNA itself isn't actually visible so the DNA probes either have a radioactive label or fluorescent label on them once you've allowed time for the probes to bind you then rinse your gel and we could then transfer all of that from the gel onto a nylon sheet because when the gel dries it cracks and therefore you wouldn't be able to visualize your results properly and the nylon sheet can then be exposed to x-rays to be able to visualize radioactive labels on a gene probe or if you use the fluorescent probe you would choose UV light to visualize the positions and what you get is something a bit like this and this takes me back a long time ago now back in 2015 where I did this Imperial College on a school trip with some of my students and we had different samples of bacterial DNA we had five species and an unknown and we can see all of the different positions that the VNS moved to we had a radioactive label and then we put it under an x-ray machine and we can see here that the bands of the unknown are in the same position of the bands for species 3 and therefore we knew that our unknown bacterial species was bacterial species electroforesis can also be used on proteins and this is known as protein electroforesis this is used in the diagnosis of medical conditions where an abnormal protein caused by a mutation in the DNA is responsible for the disease so for example in sickle cell anemia the method is very similar to that for DNA with two differences as proteins have a complex 3D shape they need to be denatured first they can pass through the gel and this is done by heating the proteins as proteins can have positive negative or no charge all proteins need to be made to have a negative charge so that they move through the gel and this is done by using a chemical Co sodium Dell sulfate or SDS 3 next we move on to PCR and this is going to be used at the start of basically all Gene Technologies because it creates a large sample of DNA so you can do multiple repeats and lots of experiments and your equipment list for PCR would be this thermocycler machine you need the DNA fragment you want to amplify you need an enzyme DNA polymerase primers which are short sequences of single stranded DNA which are needed to initiate DNA replication and then DNA nucleotides now the reason I've WR intact polymerase here is because it's a special type of DNA polymerase which is taken from bacteria that naturally grow in Hot Springs so they have adapted to survive at very high temperatures and therefore their DNA polymerase doesn't denature until very high temperatures so that means we can do this reaction at very high heat without the enzyme denaturing so here is our method of PCR step one we've added all of those ingredients and the temperature is increased to 95 C that will break the hydrogen bonds so we now have our DNA sample as two separate strands the primer will then align opposite complimentary bases to that Strand and the primer has to bind to enable the DNA polymerase to be able to attach and therefore add all of the nucleotides so to for this to happen we have to drop the temperature to 55° C so those hydrogen bonds will form between the primer then the enzyme DNA polymerase will attach all of the complimentary DNA nucleotides and make the New Strand so that is our synthesis stage and at that point the temperatures increased to 72 to speed up the process and it's also the optimum for the enzyme DNA polymerase so the advantages of PCR is it's automated you put all of those ingredients into your thermocycler and the reaction automatically happens it's also very rapid you can get hundreds of billions of copies of DNA within a matter of hours and it doesn't require living cells like invivo cloning does and that leads us into what invivo cloning is and this is just showing you an overall summary of recombinant DNA Technologies so we've gone through genetic fingerprinting and gel electropheresis and how that can be used to look at how closely related different organisms are we've just gone through how PCR is a type of cloning DNA in vitro so now we're going to have a look at how you can create DNA fragments and use those in invivo cloning so we're going to start by looking at once you've got your DNA fragment that you want to clone we're going to see how you can insert into the vector into the host which is the organism that will transcribe that DNA then we look at restriction and nucleases and these cut at recognition sites leaving sticky restriction endonucleases are enzymes that cut up DNA and they're also known as restriction enzymes they actually naturally occur in bacteria as a defense mechanism and there are many different restriction enzymes which have a unique shape active site to be able to bind to a particular complimentary DNA base sequence and therefore you have lots of different restriction endonucleases that can bind to lots of different DNA based sequences and those particular DNA based sequences that they combined to with the active site is called a recognition sequence each enzyme Cuts up the DNA at a particular location some enzymes cut at the same location in the double strand and that would mean it would cut directly down and create a blunt end and by that we mean there's no overhang whilst others cut to create this stagged end on both sides and that is these exposed bases the exposed staggered ends are palindromic which means it's the same forwards as it is backwards and because of that they're able to easily bind two complimentary base pairs and stick back together and that's why we call these sticky ends once we've done that we then need to insert this DNA fragment into our Vector which as we said is something to carry the isolated DNA fragment into our host which is the bacteria so plasma are the most common vectors used and plasmids are just circular Loops of DNA which are found in some bacteria they're separate from the bacterial genome which contains all of the genes and plasmas typically only contain a few genes and usually genes for antibiotic resistance some extra information added for the 2025 version and that is some extra vectors just here so the way we get our Gene fragment into a plasmid is we cut it open using the same restriction and nuclease that was used to cut your DNA fragment that creates sticky ends in the plasmid that will be complementary to the sticky ends on your Gene fragment therefore we can mix your Gene fragment and the open plasmid together and we'd add the enzyme DNA liase to then join together your plasmid and your fragment at those sticky ends that is then going to enable the condensation reaction to form the phosphodiester bonds between the nucleotides to create this recombinant plasmid meaning it's recombined it contains DNA from two different organisms now we've got our Vector that contains the gene of Interest we need to get that Vector into the host cell and that's what transformation means so to do this to get our plasmid into a bacterium we need to make make the cell membrane more permeable so it's more likely for the plasmid to enter so to increase the permeability of the cell membrane the host cells are mixed with calcium ions and they undergo heat shock which is a sudden increase in temperature another method that you need to know about is electroporation which is when an electrical current is applied to the membrane to make it more porous and that all of those then enable the vector to enter the host cell cytoplasm or at least make it more likely that it is able to so we should then get the recombinant plasmids entering that won't always happen though so we can see here we've got some bacteria that don't get transformed and some bacteria do get transformed but they take up plasmids that didn't contain the gene of interest and that takes us on to this last idea of how you can identify which cells are transformed and we use Gene markers for this so the three issues that might occur are number one the recombinant plasmid doesn't get inside of your bacterium so it isn't transformed number two maybe it does take up the plasmid but the plasmid rejoined before it took in the gene of Interest or number three sometimes your DNA fragment actually just loops around and makes its own mini plasmid so we need to check that the bacteria are bacteria that contain the transformed plasma before you then spend time and money growing that bacterium so Mar genes are used for this and plasmids contain marker genes they normally have antibiotic resistant genes within them there are different examples of what you could use but you don't need to know the details of all of these so we're just going to go through one example so in this example I'm going to talk you through antibiotic resistant marker genes where we have a plasmid from a bacterium that contains a gene for resistance to ambelin and a gene for resistance of tetracycline and this is the DNA fragment that we want to insert into our plasmid now that will be deliberately inserted in the middle of one of these antibiotic resistant genes to disrupt it and stop that Gene from working so that means our recombinant plasmid will be able to produce the proteins that make it resistant to ambelin but it won't be able to make the proteins that make it resistant to tetracycline so any bacter that take up this plasmid will be resistant to ambelin but not tetracycline so the way that we can identify them is following this method here we'd grow all of the bacteria on an AAR plates we would then use a sterile block to take an imprint of these colonies and print them onto a new petri dish which has AAR with illin dissolved within it and we can see which of these colonies were able to grow and we can see a d e g and I grew what that tells you is c h b and F they didn't grow so that means they must not have taken up a plasmid at all because they died when they were grown in ambelin so they didn't have this ambelin resistant gene on the plasmid we would then take an imprint of these colonies and print it onto a plate which now just contains tetracycline and this time a d and I grow so so what that tells us is colonies e and G they were resistant ambelin but they weren't resistant to tetracyclin so e and G must contain that recombinant plasmid so we could then take e and G and grow those on mass and that would then clone our Gene of Interest inside of the bacterium so that's an example of genetic engineering and if we now have a look at genetic engineering in Plants the DNA of crops have had genes added to the to make them pest resistant disease resistant and herbicide resistant and all of those result in higher yields soy plants for example are a major crop across the world and at least half are genetically engineered strains one modification was the addition of a gene so they produce BT toxin which is toxic to pests and that means that farmers don't have to add pesticides to kill the pests because they naturally have something within them which would do the killing and that results in much higher yields of soy plants crops have also had DNA manipulated to have a longer shelf life to reduce food waste and also to increase nutritional value or even to produce medicines so that all sounds great but there are some perceive negatives and that is that the genes for resistance to pests disease and herbicides could spread to other plants in the environment there are also concerns that people may be allergic to the different proteins that some of the crops might make and one big concern is that the technology is often patented and therefore buying genetically engineered seeds is very expensive and unaffordable for some Farmers genetic engineering in animals is not as widely used and it's not as easy modified viruses and gold covered DNA have been injected into animals to carry new genes into their DNA this has been used to create swine flu resistant pigs and faster grown salmon for the 2025 Edition just to make you aware that I've added in some extra details here on farming including these examples so combining genetic engineering with pharmacology so you might want to just double check you've got that written into your notes as well in genetic engineering in microorganisms farming is one of the biggest uses and this is when a human gene is inserted into bacteria so that they produce a human protein and a really common example is insulin producing bacteria my organisms have also been genetically modified for research purposes and to act as vectors so for example making nonvirulent viruses for gene therapy concerns include increasing antibiotic resistance in bacteria increased risk of cancer in patients receiving the viral vectors due to the fact that DNA is being inserted which could cause mutations and possible disruption to the expression or regulation of genes by that inserted DNA gene therapy thy is when human DNA is altered to treat disorders so for example cystic fibrosis which is caused by recessive alal and results in increased mucus production in the lungs amongst a whole range of other serious symptoms the symptoms of excess mucus in the lungs can result in lung infection and shortness of breath but it could be reduced with gene therapy so the cells lying in the lungs could have the defective recessive Al replaced or supplemented with a healthy dominant version of that Al dominant version of that Gene in order for this to work cells from the patients would have to be isolated then a viral Al which has the desired Al inserted into the viral DNA would be used to insert the Ali of choice into the DNA of the patient from the isolated human cells these genetically engineered cells would be injected or inhaled into the patient these genetically engineered cells will then produce a decide protein and this treatment is not a cure as it doesn't replace all the cells in the body with the fto gene it just supplements them and this is an example of sematic gene therapy as it's replacing body cells germline gene therapy is when you alter the DNA in a gamt so that the offspring would not inherit the faulty anal so if we compare somatic cell versus germ cell gene therapy next main differences are are somatic cell therapy is often temporary and it needs repeating whereas germ cell therapy is permanent sematic Cell Therapy only affects certain cells whereas germ cell therapy would affect every cell somatic cell therapy only affects the individual whereas germ cell therapy would affect The Offspring of the individual as well and that's because if you're editing the original germ cells that were used to create the new human or whichever organism it is all of their cells will therefore contain the edited DNA because once you have that sperm and egg fuse the zygote then divides by mitosis so they're all clone cells and have exactly the same DNA in them it also means that any sperm or egg cells that they produce will contain that edited DNA as well which is why it's passed on to The Offspring we then move on to cloning and biotechnology starting with natural clones in Plants now many plants reproduce sexually and a actually and due to their natural asexual reproduction there are parts of plants that replicate bosis from stem cells and that's known as a merry stem strawberries form Runners which are horizontal stems that Branch away from the plant and then form roots to reproduce asexually to form a clone in some plants the horizontal stems grow underground and this is called aizome this has been made use of in horiculture as it means new plants can be be created for by free and quickly as you're not waiting for a germinating seed and farmers can also clone plants that have desirable characteristics another simple method is taking plant cting and that's what we can see here plant cuttings involve cutting off a non-flowering stem from the Bunning plant dipping it imp plant hormones and also fungicide to prevent infection and then you'd grow them in a soil micropropagation is a similar method that involves taking only a tissue culture sterilizing the sample for example with ethanol and growing with hormones such as oxin and cyto kindes on agar first until the roots are developed a callus forms and this is split into cells and transferred to a new AAR plate and eventually those small platinet that form are potted in soil and that's what we can see here so we've got a summary here of the advantages and disadvantages of this micro propagation so pause at this point and turn those into flash cards next we look at natural clones in animals and some invertebrates naturally clone themselves for example starfish an entire new starfish can regenerate from fragments of the original starfish in humans and other animals identical twins are also natural clones meaning monozygotic and that is when one sperm and egg fused to make a zygote but that cell then splits into two to make two new embryos originating from that first zygote so so they're genetically identical you can also have artificial Clon in animals and the knowledge of how identical twins naturally occur has been used to produce identical animals in farming to maintain desirable characteristics and this is known as embryo splitting or essentially artificially making identical twins so two parents with desired characteristics will be bred together the female will be given hormones to make or produce many many eggs samples of their eggs and sperm are used in IVF in the lab or sometimes the eggs are naturally fertilized with the sperm when an egg is fertilized and the embryos forms which is just a small ball of cells the embryo is then split apart into many single identical cells and those identical cells are then inserted into the uterus of different host mothers and all of the offsprings would be clones of each other they wouldn't be identical to the female that they were grown in they'd be identical to each other but not their parents because the parents had an egg and a sperm fuse so they're not identical to the parents they're just identical to each other the second method used is sematic cell nuclear transfer or scnt a somatic cell which is a body cell is taken from the animal that you wish to clone an egg cell is taken from a female and the nucleus is removed so here we have that body cell the nucleus is removed that you want to clone and you take an egg cell from a female and you take out the nucleus then what you would do is fuse together the nucleus of the animal you want to clone and you fuse it into the egg cell and to make it start to divide a small electrical current is applied and it will then start to divide to form an embryo once the embryo is a bundle of cells the cells separated and inserted into the uterus of different host mothers each of these inserted cells is genetically identical to the parents that that nucleus was taken from but also to each other and this is how Dolly the sheep was made Dolly the sheep was the first animal to be cloned using scnt she was healthy but had a much shorter life it's not known why animals produced by scnt have a shorter lifespan but it's thought to be linked to the fact that they are created from older adult DNA which is already aged so here we have the pros and cons of this animal cloning which again you can turn into a flash card or two flash cards here for the pros and one for the cons now this is an important 2025 edit that I want to make you aware of you no longer need to know examples of microorganisms and biotechnology but it is still helpful to be aware of them so over the next few slides you don't need to know this information however it's useful to have an understanding of it and no examples then we move on to microorganisms in biotechnology and as a human population continues to increase the demand for food increases at a rate that cannot be matched by the space and time for farming animals therefore microorganisms have been used to try to solve this so for example bacteria and funky have been used and that's because of economical advantages so microbes are tiny so you can grow a lot of them in a small space compared to animals then nutrient requirement is also cheaper than animals and the temperatures that they grow at are low which makes harvesting them cheaper they also have a short life cycle so the food production is much much faster than it would be for growing animals their growth requirements are very basic so they're easier to grow and microorganisms have been used in food production to create the following so in breads yeast is a fungus used in baking and when the yeast respire they produce carbon dioxide which helps to make the bread rice in Brewing when yeast respire anerobic they produce ethanol and carbon dioxide and the ethanol is used to make alcoholic drinks cheese use bacteria and bacteria will use lactose and milk as a respiratory substrate and this causes the milk to start to separate into the solid curds and the liquid way and those solid curds are then used to make cheese yogurt also involves bacteria so speci ities such as lactobacillus bulgaricus and streptococus thermophilus and that's because they produce ethanol or lactic acid which results in the milk forming these polymers that give yogurt a thicker and smoother texture compared to milk microprotein or the brand named corn is produced from the Fungus fusarium Venum and it's grown and used to make proteins that make up corn other examples involve the use of microorganisms in medicine so penicillin and Insulin are both medicines produced by microorganisms penicillin is the antibiotic produced by a particular fungus and insulin is produced by genetically modified bacteria as we just went through bior remediation is when microorganisms are used to digest pollutants and contaminants so naturally occurring microbes can break down pollutants like sewage and crude oil and microbial growth can be encouraged by giving them the nutrients they need to grow this technique is common on contamination sites such as as we can see here if there has been an oil spill so then we come to our evaluation of the use of microorganisms in biotechnology so pause and have a go at turning that into a set of flash cards then we have a look at how we can culture microorganisms so when they're cultured you have to have a large enough quantity to see without a microscope and microbes must be growing with a growth medium which could be a liquid broth or solid nutrient AAR and that would contain water and nutrients such as glucose and amino acids they also require oxygen and in schools they're incubated at 25° C cuz that's warm enough for growth but not so warm that you would potentially have large quantities being produced which might then be pathogenic and cause harm when you're growing microbes you also have to work aseptically which means in complete sterile conditions to make sure that you don't have contaminations of the bacteria you're growing and so you don't infect others so this includes sterilizing all equipment so you could use an autoclave or for metal equipment you might put it into a roaring flame on the bunts and burn it until it glows red you have to sterilize all the work surfaces with disinfectant wash your hands with soap and you always work near bunson burner because there'll be a convection current that continually sterilizes the air near the bunson burner so you get this sterile Dome of air that you could work you should only open the Petri lid you should only open the lid of the petri dish slightly to again reduce the chance of microbes within the air landing on your dish and contaminating your sample and lastly as we said sterilize all the equipment which could be flaming it in a buns and burner so if we have a look then at batch fermentation in this type of fermentation all of the necessary nutrients are added at the beginning of the fermentation process and the culture is allowed to grow until the desired product is obtained or until growth is limited due to the depletion of nutrients or the accumulation of toxic inhibitory products manipulating growing conditions such as temperature pH oxygen availability agitation rate and nutrient concentrations can significantly impact crobial growth metabolism and product formation for example controlling the pH within an optimal range can en maximum enzyme activity or product yield similarly maintaining the optimum temperature and oxygen levels can promote cell growth and enhance product formation sampling analyzing the culture during different stages of fermentation allows for realtime monitoring of that microbial growth and product formation and it enables you to adjust any of those conditions if you need to to make sure you are achieving maximum yield now the other type of fermentation continuous fermentation and this involves a continuous flow of fresh sterile medium into the bioreactor while simultaneously removing an equal volume of the spent medium containing the product and cells manipulating growing conditions in continuous fermentation is essential for achieving steady state conditions and maximizing productivity so these conditions include the dilution rate the nutrient concentration residence time and bi reactor configuration and those are all needed to be looked at and controlled to determine first of all the product yield and quality in the continuous fermentation you do also need to Monitor and control other factors such as pH temperature dissolved oxygen levels because those are all going to have an impact on enzyme activity and also respiration and therefore the microbial activity and metabolic efficiency so then we look at the standard growth curve of microorganisms bacteria reproduce rapidly approximately dividing every 20 minutes therefore you can get large quantities very very quickly and when looking at the population size when culturing bacteria log scales are often used for that reason because you have such a large range in the number of values to work out the number of individual organisms you can use the following formula n = n0 * 2 n where n0 is the initial number of bacteria and N is the number of divisions or Generations when the log of the numbers of bacteria grown over times plotted on a graph just like this is called a growth curve and we have these four key stages the lag phase exponential phase stationary phase and the death phase so in that lag phase the number of bacteria is lower while the bacteria are adjusting to the new environment once they producing at their maximum rate the increase in the number is exponential and that's how we get this exponential phase there will reach a point where the number of bacteria from growth is equal to the number that dies and that is where we get this stationary phase the death phase is when the number of bacteria decreases because the number dying now exceeds the number being reproduced and the reason they start dying could be they run out of resources such as glucose or it could be toxins are being built up and that starts to cause the death of them the death phase could theoretically be prevented and you go through this stage if you remove the limiting factors so making sure they have plenty of nutrients there's plenty of oxygen maintaining the temperature and removing the toxins and also buffering the pH an alternative to using microorganisms is to isolate the enzymes they contain and then immobilize those enzymes and this is an advantage as it's even more efficient more specific and you don't even need growth mediums because it's just the enzymes so immobilized enzymes are when the enzyme required is fixed to an inert substance and the substrate is then passed over it this is beneficial as you do not need to purify the enzymes from the product at the end as the enzyme remains attached to that inner object that means you can easily reuse them and save money and having the end enzyme fixed also decreases their sensitivity to temperature so you can use higher temperatures without the enzyme denaturing this method does have upfront costs and it is more technical so here we have our pros and cons which you can summarize on flash cards the examples of the use of immobilized enzymes include glucose isomerase for the conversion of glucose to fructose penisin and aalas for the formation of semisynthetic penicillins lactase for the hydris of lactose to glucose and galactose Amino cyclas for the production of pure samples of L amino acids and glyco amas for the conversion of dein to glucose an important little 2025 notification here is you are not required to recall the examples above but you will be expected to apply your knowledge and understanding of a mobilized enzymes in the context of biotechnology so you could come across these in the exam but you don't have to remember those examples next we move on to ecosystems and we start with lots of key terms that you need to know the definitions of so pause at this point and turn these into flashcards and learn these key terms so ecosystems and biomass ecosystems are Dynamic meaning they are constantly changing and they vary in size which is determined by the biotic living factors and the abiotic non-living factors within the ecosystem so for example a rock pool a plane field and a large tree tree are all very different sized ecosystems biomass gets transferred through ecosystems and in any ecosystem plants are the producers of a food web and they are able to produce their own carbohydrates using carbon dioxide in the atmosphere or from carbon dioxide dissolved in water between each trophic level in a food web the majority of energy is lost due to respiration and excretion and the remaining energy is used to form biomass and biomass is the dry mass of the carbon containing compounds so the given amount of biomass remaining in an organism can be measured in terms of the mass of carbon or dry mass of tissue per given area how productive an ecosystem is depends on the abiotic and biotic factors so if there's plenty of water light warmth and green plants that will maximize the rate of photosynthesis and therefore a more productive ecosystem system because more carbohydrates will be produced the efficiency of biomass transfers between trophic levels can be calculated using this formula so the biomass transferred divided by the biomass taken in time 100 and humans can manipulate the transfer of biomass through ecosystems by reducing energy loss and traic levels and this is done often in farming so you could restrict the movement of your animals you could provide the animals with higher energy food you could keep them Indo to reduce heat loss and by removing competition and predators they'll also be expending less energy running to compete or running to evade Predators we then move on to the nitrogen cycle and the air is 78% nitrogen however plants and animals can't obtain nitrogen through gas exchange and that is because nitrogen has this triple bond between nitrogen atoms so microorganisms are needed to convert nitrogen gas into nitrogen containing substances that plants and animals can absorb so the reason nitrogen is so important is it's found in proteins ATP and nucleic acids which are all essential for survival the nitrogen cycle is split into four different key stages and you also need to know the importance of sa probiotic nutrition and organisms and also microbes in general in this process so here is our nitrogen cycle which we'll talk walk through let's start with nitrogen gas that nitrogen gas can be converted into nitrogen containing compounds such as ammonium through bacteria which can break the triple bond and that is nitrogen fixing bacteria which is naturally found in the soil or nitrogen fixing bacteria that naturally occurs in the root nodules of leguminous plants so if we carry on with the nitrogen fixing bacteria in the soil they're able to convert the nitrogen gas within the air in the soil into ammonium that ammonium is then oxidized by nitrifying bacteria into nitrites and we call that stage nitrification the nitrites are oxidized further into nitrates Again by nitrify bacteria and those nitrates can then be absorbed into the plants by active transport and then the plant will use those nitrates to make proteins DNA and ATP those plants will then be eaten by animals and the protein in the food that they're eating will be digested to release those nitrogen containing compounds which can be assimilated into the proteins and DNA RNA and ATP for the animals now animals will produce waste and both animals and plants die and when waste is made or when organisms die this is where we have mic mobes involved yet again and this is our Sac probiotic nutrition or the sap probiotic microbes because they are able to release enzymes that will digest the proteins in the dead plant matter or dead animal matter or to digest and break down the Ura in excretion into ammonium and in that way we then loop back around to the cycle now there's one branch here that we haven't talked about and that is when nitrates could be converted back into nitrogen gas by Den nitr find bacteria but this only happens in anerobic conditions so if the soil becomes water logged or too Compact and therefore there's not enough oxygen in the soil the den nitr find bacteria thrive in anerobic conditions and therefore they will be able to convert that nitrate into nitrogen gas and that is why in agriculture they'll often plow and toss the soil around to make sure it remains air rated so this just shows you lots of different bacteria are involved and they're important in the nitrogen cycle so that was the cycle but let's just go through the exact names of those bacteria as you do need to know those nitrogen fixing bacteria you need to know about riia aot toaa and these are the ones that can break the triple bond between those two nitrogen atoms when it as nitrogen gas in the atmosphere the bacteria are either Free Living which is the aot toaa or it could be the biotic mutualistic ones that live in the root nodules of leguminous plants such as or that is the rium in nitrification we said that we have nitr fine bacteria we have the nitrosomonas which convert ammonium to nitrite and then the nitria convert nitrite to nitrates then we have denitrification and this stage is not useful as we said and it Returns the nitrogen in compounds back to nitrogen gas in the atmosphere so it cannot be absorbed by the plants that is by anerobic denitrify bacteria and then lastly ammonification stage that's when proteins Ura and DNA are decomposed in dead matter and waste by sapo Bion and those will be organisms such as bacteria and fungi which digest waste extra cellularly and then return ammonium IRS to the soil we then move on to the carbon cycle and the carbon cycle is also dependent on or organisms we start with plants which can photosynthesize to fix carbon from the atmosphere in the form of carbon dioxide into carbohydrates those carbohydrates will then be eaten by animals that are ingesting and digesting the plant material all organisms respire and this will convert the carbon in the carbohydrates back into carbon dioxide in the atmosphere or the oceans when organisms die or through excretion the carbon is broken down to carbon diox oide by decomposers that respire using the carbohydrates within the dead or waste matter an imbalance in this cycle is leading to the oceans becoming more acidic and also global warming and this imbalance is caused by deforestation which can result in the trees being burnt releasing more carbon dioxide but also if you are cutting down trees less carbon dioxide has been taken in by photosynthesis we then move on to succession and this is a change in an ecological community over time a primary succession always starts with a pioneer species which is the first species to colonize an area which could be bare rock or sand the pioner species is often something like lyen which is adapted to survive in harsh abiotic factors and through their death and decomposition that changes the abiotic factors to make them be less harsh you often get this thin layer of humus forming this soil layer and that now means other species are able to colonize and they will actually out compete the pioneer species so that is when we get our mosses and smaller plants that are now able to survive as they die and decompose that will add to the soil further and increase the nutrients so the abiotic factors again become more and more favorable and this pattern continues to occur and the atic factors become less less harsh and larger plants are able to survive each new species changes the environment in such a way that it becomes less suitable for the previous species therefore each existing species is out competed by a new species colonizing overall during the succession we increase the biodiversity the abiotic factors become less harsh and therefore we have a more stable environment and we get to the final stage which is known as the climax community which is often dominated by large trees so in summary the species richness and the number of organisms increases so in other words your biodiversity increases and as succession occurs larger plant species and animals will be able to colonize the area a deflected succession is when human activities can prevent the progress of succession a climax community won't be reach if there are animals grazing or if there are humans that are trampling an area or you could have controlled burning and the removal of vegetation both of which prevents a climax community forming and this is your deflection succession now the reason this might be done is to maintain the earlier stages in succession so that you get a greater variety of habitats being conserved and therefore a greater range of food sources and species being able to survive this can lead to a conflict between human needs and conservation in order to maintain the sustainability of Natural Resources so to try and manage this conflict compromises are needed for example forests can be coped to provide timber for fuel and Furniture while still allowing a tree to survive now we can estimate population sizes through sampling and the reason we do sampling is it' be too timec consuming and inaccurate to say you going to count every individual within a population in an area so that's why we use sampling and population sizes can be estimated using various techniques but a few aspects are commonly used for sampling to provide an accurate estimate that is representative of the population size many samples and that means 30 plus ideally should be taken and it should be random sampling to avoid bias lastly we move on to populations and sustainability so we start by looking at factors that affect population size and we come to abiotic factors which we have touched on briefly already so these are the non-living factors or the environments and that could be temperature oxygen carbon dioxide and all the others listed there plants and animals are adapted to the abiotic factors within their ecosystem and these adaptations develop through the process of natural selection over time the less harsh to abiotic factors such as plenty of Water and Light the larger the range of species and the larger the population sizes biotic factors are the living factors in an ecosystem and this can include interspecific and intraspecific competition and predation and both of those will affect the population size inter specific competition is where members of different species are competing for the same resources whereas inra specific competition is where members of the same species are in competition for the same resources and also a mate and competition for a mate links to courtship rituals because individuals that are fitter will have more energy to perform a more impressive courtship ritual or they may have more fur or feathers in a better condition to attract a mate the idea of predation links to these Predator prey graphs and regardless of the species the graph always follows the same pattern the size of the predator and prey population will both fluctuate there is typically more prey than there are predators because they are the food source for the Predators so there has to be more of them to sustain the Predator population and lastly the size of the prey population will typically change before the Predator population and that's what we can see here the prey starts to decrease because they have been eaten by the Predators but because they are now decreasing we then get a decrease in the Predators because the Predators have decreased the prey can then start to survive and we get an increase but then that results in more food for the Predators so they increase and that pattern continues over and over 2025 edit here to make it really Mark scheme specific is just to be aware that conservation in human actions and management is to help increase biodiversity and you would have to say increase to get the mark not maintain then move on to conservation and preservation conservation is human actions and management to help maintain biodiversity and it involves sustainable development whereby management of ecosystems is in place so that natural resources can be used by humans without them running out preservation involves protecting an area by Banning visitors and this is a very effective method of protecting ecosystems but it does prevent anyone from enjoying the area conservation is really important for three reasons the ethical reasons so all organisms have the right to live and conservation helps to ensure humans are not preventing this it also helps ensure future generations of humans are able to experience and enjoy those natural ecosystems there are the social reasons which include enjoying the outdoors and providing many physical and mental health benefits to people then there's economic benefits many medicines and foods and clothes and even Timber are sourced from different ecosystems and also it can be involved in tourism as a human population continues to increase sustainable management is required to ensure that humans have food shelter and infrastructure for survival but without causing excess loss of biodiversity and the depletion of resources and that is what sustainable management is for example sustainable Timber production involves cooping and pading and these techniques are when the trees are cut close to the ground to be able to provide Timber but the plant will still regrow on a larger scale when larger forests are failed only the largest trees are removed and new trees are then replanted to replace them sustainable fishing is essential to protect future fish populations while still providing a valuable protein rich food source there are policies in place which include limiting the quantity of fish that can be caught the size of the fish as well the size of the holes and the Nets that are used and having certain areas that aren't allowed to be fished in particularly during mating season so just to make you aware on this next slide coming up this is a 2025 change to the spec you no longer need to know these examples but it does State you need to have an awareness of the impact so it's still useful to have this awareness but you wouldn't have to know these literal exact examples in the exam we then move on to the control of human activity and there are certain examples that you need to know for example the M Mara region in Kenya the masam mara National Reserve is an ecosystem under management to ensure the conservation are not negatively impacting the need of humans for example the texi fly is a carrier of African trypanosomiasis and to reduce the spread Acacia bushes have been removed as this is the habitat of the tsy fly as local tribes are not allowed in the park they now have to graze their Livestock on the outskirts of the park instead of within it and this has enabled vegetation within the park to recover Eco Ecco tourism is popular here which provides economic benefits but tourism must not exploit the natural environments or local communities the Nature Reserve also plays an important role in protecting endangered species such as the black rhino so to help strike a balance legal hunting involves the culling of overpopulated animal species only another example is the terai region in Nepal and along the southern border of nepo is the terai region which has very fertile land and wellwater flood Plains and for that region it attracts many people because you'll be able to grow lots of crops and food there so management is needed to ensure that overp population doesn't harm the environment this includes a sustainable Forest Management in this region to provide a livelihood for the locals whilst protecting the forest to ensure agriculture can sustainably occur farmers are encourage to grow crops further up the hills improve irrigation grow more than one crop variety to increase biodiversity and to grow leguminous plants because they fix nitrogen the next example is Peete bogs and Pete bogs are carbon sinks that are wet and contain decomposing plant matter as it is so carbon Rich if it was to be dried out you would get a good fuel source however in burning that you would now release lots of carbon dioxide in the atmosphere that previously was contained within the Pete bog as a carbon sink Pete has also been used in compost to improve the source structure and acidity so to help protect these Peete bogs and therefore prevent this excess release of carbon dioxide into the atmosphere so that takes us to the end of module 6 I hope you found it helpful if you have don't forget to click like And subscribe so you don't miss out on any of the latest videos [Music]