today is Monday September 30th this is lecture N9 we're going to do chapter 8 microbial genetics for attendance the access code is 444 word of the day is jeans I'm going to give you one minute and then we're going to keep going you'll notice today that the attendance ends at 5:05 so please make sure you do the attendance right now I'll give you one minute to do so if you're arriving now you're late please make sure that you are on time when we have zoom class all right I'm going to give 15 more seconds so write it down please if you don't have it remember attendance will close at :5 so make sure you do this all right let's get going so just reminder exam one you need to complete that by October 3rd which is this Thursday by 5:00 pm several of you have taken it already and done very well there's many of you that did very well we have one perfect score so far I'll announce that on Wednesday if you have not taken the practice exam online there's a few of you that have not done the practice exam and you have not taken the actual exam so please make sure that you do that practice exam the information on how to access it is in your previous lectures attendance is in um unit 2 attendance so just scroll down guys all right if you have not submitted um assignment 4 please make sure that you do so immediately if you submit any homework assignment late please let me know um by sending a message on canvas so that I can manually update your grade I'm going to go through and put you know zeros on late assignments and U missed attendance so that you can see accurately where you are um especially after exam one is submitted you'll have a good reference of where you stand remember that regardless of what you do on exam one the lowest of the four exams is dropped so if you did really well congratulations if you did not do so well you know understand that it can be dropped and make sure that you are going to office hours and getting the help that you need in order to do well in class and then again this Friday is when assignment 5 is due that's why we're going to make sure we get through chapter eight today all right we're going to move on um on Wednesday to do survey of the microbial World a lot of that is procaryotic cells then we have ukara microbes followed by um microbial ecology and then food microbiology chapter 28 on food microbiology is very small um the harder chapter in this unit oftentimes it depends you know chapter 8 is the most you know material heavy as far as the questions are concerned chapter 27 can be difficult for many people because there's a lot of plant and environmental biology that you haven't learned previous to this class all right let's roll into chapter eight so some of this you may have learned you know AP Bio or any of your previous um biology courses but we're going to go into a little bit more detail for your learning objectives honestly all of these are important I tried to bold you know um any of the concepts that can be more difficult uh to learn but just make sure that you're able to talk through these Concepts that's a good way to understand um whether or not you know the information well enough to do well on these questions all right so here's some key terms for you genes we've all heard of that before the definition of that is segments of DNA that encode functional products usually proteins genetics is the study of genes and how they carry information how information is expressed and how those genes are replicated so the study of genes is genetics we have chromosomes that's the main DNA containing structures in a Cell The genome is all the genetic information in a cell or virus and genomics is the study of genomes thanks to improved sequencing Technologies we can use a lot of Technology on the computer to really study the genes and compare them to known genes to understand just more information about the overall genome all right so this is quite important the genetic code it's a set of rules that determines how a nucleotide sequence is converted to an amino acid sequence of a protein okay so the central dogma states that DNA gets transcribed into RNA which gets translated into proteins all right so this is kind of the flow of biology we're going to learn that there's some viruses that break the central Dogma but this is the overall um you know format that you want to remember DNA RNA to protein all right so there's some of you guys that came in late if you missed attendance because you came in late sorry about that but you know make sure that you're there on time especially resume class I waited a couple minutes before we started so if you missed it sorry about that okay so your DNA that's double stranded stands for deoxy ribos backbone it's composed of a t g and C as far as your nucleotides and then your RNA that's a single stranded ribos backbone and the nucleotides are the same except for our thyine is replaced by urel so anytime you see U or urel you know that you're looking at RNA these are your amino acids charts you don't have to memorize it for this class you do have to understand how to read the chart all right so for example all of our amino acids are coded by three nucleotides so the the way to read this chart is looking at you know if the first position is one of these letters u g well excuse me u c a or G and then the second position you're going to go up to the top and find whether it's u c a or G and then on the right hand side you can take a look and figure out whether it's u c a or G for the third position position so for example if I was looking at you know the first position was um let's say C cytosine and then the second position was also C cytosine so I'm looking in this box right here and then I would know for this particular amino acid it doesn't matter what the third position is it's all going to code for Proline but there could be some differences for example you know if you have C as the first letter then a is the second letter then after that whether you have U or C it's going to be histadine or then whether it's a or G it would be this gln nucleotide or amino acid all right the third position is called the wobble position all right because there's many amino acids that are simply coated by these first two letters and the third one is not necessarily relevant to code for that amino acid so remember the third position is the wobble position all right then the difference between genotype and phenotype make sure you understand that so the genotype that's the genetic makeup of an organism we're talking about the genes and the phenotype is the expression of those genes just because you have a particular Gene does not mean that you're going to express it so the genotype is what's coded the phenotype is what's expressed or actually seen all right so what we have if you're looking at a typical chain of events by the central dogma DNA gets transcribed into RNA this is messenger RNA messenger RNA there's different types of RNA but messenger RNA has the actual message meaning the actual nucleotides that are going to code for a particular protein we're going to talk about how that happens in the next few slides and then after the protein would be a particular function all right so let's think about how mutations alter a genome if you have mutated DNA then that could have altered RNA results which could have an altered protein and therefore an altered function all right so mutations can have devastating consequences potentially and there's different types of mutations all right so make sure you understand DNA replication you have a few questions on this I'm going to go through it in as much detail as I can when you're looking at your key over to the right so this is our nucleotides for DNA adamine guanine thyine and cytosine remember all um of our DNA it has this deoxy ribos sugar and it's all linked um they have phosphates on the end all right so remember when you're looking at pairing a and t adenine and thine always pair together G and C guanine and cytosine always pair together between the two G and C has a stronger Bond because we have three Hy nen bonds here versus only two between a and t so G and C is the stronger Bond all right these hydrogen bonds they cause specific pairing again between a and t g and C that's called complimentary bases the DNA um double helix is anti- parallel so it's very important that you're able to read The genome in the right direction for example in English language we read left to right in other languages in other C cultures some read right to left some read up to down bottom to top it just depends upon the particular language that you're looking at so again in DNA we read from five Prime to three prime always always again I'm going to say that again five Prime to three prime is the direction that we read and then the reverse side it's kind of flipped so you see where there's five Prime on one end you have three Prime on the other strand all right so this is why it's compliment and anti-parallel so new nucleotides they're always added at the three prime end again we read from five Prime to three prime so if you're going to add new nucleotides it's always at the three prime end is where you add new nucleotides all right so let's see DNA again double stranded it's complimentary not identical strands so again five Prime to 3 Prime matches with this three prime to five Prime end the bases they bind a t g and C G and C is the stronger Bond because it has three hydrogen bonds and we have this anti parallel orientation okay and that also refers to just these two strands that are not exactly the same but they're complimentary they run in opposite directions all right so when we're looking at replication make sure that you understand this let's go through the numbers together this is figure 8.3 in your textbook so when we're dealing with DNA there's two parent strands right so the double helix of the parental DNA separates as weak hydrogen bonds between the nucleotides on opposite strands break in response to the action of replication enzymes so basically replication enzymes come along and they break those hydrogen bonds to separate the two parent strands that area where the two strands have been separated is called the replication fork make sure you remember that number two the hydrogen bonds form between new complimentary nucleotides and each strand of the parental template to form new base pairs all right so number two we're looking at these hydrogen bonds that are coming along and then we bring along new nucleotides right here to form the New Strand it's happening on both strands number three enzymes catalyze the formation of sugar phosphate bonds between sequential nucleotides on each resulting daughter strand all right so the daughter strand is the New Strand that's created all right so when these nucleotides come along remember there's hydrogen bonds between the nucleotides but to join the actual nucleotides that exist on one strand together those are sugar phosphate bonds all right so you see with step two we have these nucleotides that come along and hydrogen bonds step three is when we have these enzymes that catalyze the actual sugar phosphate bonds to join these nucleotides together on the same daughter strand okay and then over here so this is the replication fork in part A and then Part B is just showing us the two strands of DNA that are anti-parallel again five Prime three Prime from top to bottom and then on this right strand we have five Prime three Prime from bottom to top the sugar phosphate backbone of one strand is upside down relative to the backbone of the other strand all right so you can kind of look at it as one is right side up one is upside down you can look at it as one is running you know to the left one is running to the right all right this is a very important slide make sure you understand the steps of events all of the enzymes make sure you understand the difference between the leading versus the lagging strand all right so here's what's happening in the replication fork what is five Prime and three prime mean so let me get my pointer all right so five Prime is referring to one end of the Strand so five Prime is always the beginning of the Strand three prime is the end of the Strand the other parental strand is running in the opposite direction so of one of them is the five Prime end the other strand is the three prime end all right so we're talking about the orientation and the direction that we're reading the DNA and the direction that we replicate all right that's a good question because it's very important to remember which side is which so that you read the genes in the right order if you read in the wrong order it's going to be nonsense language or you're going to create something um that's just a mutation you won't create the right protein and genes all right so let's go through this step one the enzymes like DNA gyas and helicase unwind the parental double helix so that's what these little teal boxes are these are the enzymes DNA gyas and DNA helicase you don't have to understand this part but one of them um stabilizes the strands kind of holds it while the other one unzips it that's the function of these two um enzymes gyas is going to stabilize it helicase is going to unwind it all right so I just answered the question about five Prime and three prime I'm going to State it again make sure you're paying attention to this five Prime is talking about the orientation of the genes it's very important that you remember the orientation because they're anti-parallel meaning one of them is running to the left one of them is running to the right you have to understand the order so that you can replicate properly as we go through these steps it'll make a little more sense so remember these strands they're going to unzip and then they're going to add different nucleotides all right so maybe as we get into this the direction will make more sense so we have the enzymes right here for step one gyas and helicase step two is we have proteins that stabilize the Unwound parental DNA these proteins are basically just going to hold it in place so that we can start adding the other daughter strand all right because we always read five Prime to three prime all right one of these is going to be the leading strand one of these is going to be the lagging strand all right so number three right here the leading strand is synthesized continuously by DNA polymerase all right what does that mean so this strand because we're unzipping right here and we only add five Prime to 3 Prime and we read five Prime to 3 Prime that means that we're going to start over here on the right hand side where it says five Prime and we're going to continuously add nucleotides going to the left so we're adding as the zipper is unzipping the DNA that's the leading strand meaning as it unwinds we can just continuously add nucleotides all right DNA polymerase is what adds those nucleotides all right so what's the difference between this top Strand and the bottom strand orientation the bottom strand is called the lagging strand why is it called the lagging strand again because we have to add nucleotides in the five Prime to three prime orientation so at the top we're able to add continuously going to the left as the zipper unzips on the bottom on the other hand we have to start at the opening of the zipper and go to the right as we add nucleotides while is that because we can only add five Prime to three prime always only that's the convention all right so how do we do that so the lagging strand is synthesized discontinuously meaning in pieces primase an RNA polymerase synthesizes a short RNA primer which is then extended by DNA polymerase all right so right here we have an RNA primer that comes along and then it DNA polymerase adds nucleotides in the 5 Prime to 3 Direction which on the lagging stand is going away from the opening of the zipper all right so because we do that right here DNA polymerase it then has to digest the RNA primer and replaces it with DNA all right so the RNA primer it serves as kind of like a tag for DNA polymerase to come along but again because this is DNA we can only have DNA not RNA so that primer then gets digested or kind of degraded and destroyed and replaced with DNA by DNA prase these fragments that we synthesized are called okazaki fragments named after the um scientists who discovered this then we have DNA ligase that comes along and it joins the discontinuous fragments of the lagging strand all right so because of these many different steps and the synthesizing has to go in the opposite direction as the zipper is opening it's slower so the leading strand gets synthesized continuously because we don't have any breakes and we can just continue to add nucleotides in the direction the zipper's opening it's faster than the lagging strand because we have to synthesize in these different fragments and then join it together again just to repeat the reason for that is you have to read and add nucleotides in the five Prime to three prime Direction all right so the replication of bacterial DNA so DNA replication is semiconservative meaning the new cell gets hybrid DNA with one original strand from the parent DNA plus a newly synthesized strand another way of saying that with semiconservative meaning that each new um double helix has one parental Strand and one daughter strand all right so let's go over these terminologies so the origin of replic remember because bacteria they have these um circular chromosomes so the origin and replication is where kind of the two um DNA strands are going to pull apart right you can see right here the daughter strands are forming the replication fork right here is the area where you have um kind of the the DNA has separated and you're adding the new strands the termination of replication is the last point where the two strands are connected and pulling apart and then the very last step you can see you have two um new double helix semiconservative meaning one of them is the parental one of them is the daughter strand you can't see it too well on the zoom but in your textbook you can see the difference it's trying to show you just like on the previous slides the parental um strand is dark purple versus the daughter strand is light purple it's indicated here but um it's just not as clear on the picture but in your textbook you can see it a little bit better all right make sure you understand these terminologies with RNA synthesis so the process of going from DNA to RNA is called transcription we have ribosomal RNA R RNA that's the integral part of ribosomes ribosomes are the machines that make proteins we have Transfer RNA TRNA which transports amino acids during protein synthesis and then we have messenger RNA mRNA which carries the coded information from DNA to ribos Elms all right so transcription in procaryotes so the synthesis of a complimentary mRNA strand from a DNA template is transcription transcription begins when RNA polymerase binds to the promoter sequence on DNA then transcription proceeds in the five Prime to three prime Direction only one of the two DNA strands is transcribed why is this remember that when transcription goes in the five Prime to three prime direction that is the correct order of reading the genes only one of the strands is going to be in the five Prime to three prime Direction That's The Strand that's called the sent strand meaning that it has the information to actually make the proteins the opposite opposite strand that we created from three prime to five Prime that's called The antient Strand The anti-sense Strand is also known as the template strand because it serves as the template for transcription and it contains the complimentary nucleotide sequence to the transcribed mRNA so another way of saying that the anti-sense Strand is the same as the DNA strand except for osil is replaced by um excuse me a separate th yeah thyine is replaced by uracil because ell has RNA okay and then again just the scent strand that contains the exact nucle sequence to the MRNA which encodes for the functional protein all right so the five Prime to three prime the sent strand has information to make the protein The anti-sense Strand is the template strand all right meaning that that's the template that we can use to make more RNA in the right direction right transcription stops when it reaches the Terminator sequence on DNA which is different from stop codons the Terminator sequence is based on a hair pin or another secondary structure all right so let's go over this process of transcription all right it's very similar to DNA replication all right so we'll start on the very left with the promoter so the RNA polymerase it binds to the promoter and DNA unwinds at the beginning of the gene so so this time we have RNA polymerase that binds to the promoter then step two RNA is synthesized by complimentary base pairing of free nucleotides with the nucleotide basis on the template strand of DNA okay so again the RNA is synthesized by the complimentary base pairings with the nucleotide basis on the template strand of DNA right so looking at our picture right here this would be the template strand of DNA and the purple and then the RNA that's being um transcribed is this teal or green line all right number three is the site this is the site of synthesis which moves along the DNA the DNA that has been transcribed rewinds so the reason for that we want to keep our DNA as protected as much as possible so once we've transcribed what we need it winds back then step four transcription reaches the Terminator right here and then that's the end of the gene which causes the strand of RNA to be released and then the RNA and RNA poates are released and the DNA Helix reforms yes in the chat so someone said looking at this previous The anti-sense Strand is the one that is backwards so the S strand reads five Prime to 3 Prime The anti- Strand will be three prime to five Prime it's backwards it's the template all right so hopefully this makes sense for RNA transcription let's go over translation which is how we make our proteins so translation of mRNA it begins at the start codon which is U Au ug which codes from a sometimes methine is the start amino acid um sometimes it gets later removed but Aug is the start codon always the codons of mRNA they're red sequentially meaning in order your TRNA are Transfer RNA those are molecules that transport the required amino acids to the ribosome carrying the specific anti-codon sequence for that amino acid with the base pairs with the codon so again just looking right here this is our TRNA and it has the anti-codon meaning like the template of what is going to be on this mRNA it carries the um you know coded amino acids so for example Aug as the star codon the anti-codon has UAC again those are the complimentary Pairs and it has methionine attached to it so there's a lot of different anti-codons with the specific amino acid attached to it all right then the amino acids they're joined by peptide bonds and then translation ends at the stop codon or nonsense codon which would be UAA u a or ug all right there's something in the chat real quick so the leading and the lagging strand someone asked about the leading and the lagging strand versus the sense and the anti-sense Strand so it's similar but different the same thing you know that I see what you all are comparing is that one of them is five Prime to three prime which would be the you know leading strand within um DNA and then the scent strand within AR and then the lagging strand is what you know is going to code in the opposite direction so it's not the same thing let me go back to that slide show you real quick so this is the leading and the lagging strand so if we're looking at this top parential strand right here five Prime to three prime the leading strand is going to be continuously synthesized from this five Prime to three prime as the zipper unwinds the lagging strand on the other hand is going to be synthesized in different pieces so with the leading and the lagging strand it's just a matter of the order and how we synthesize the Strand but you know both of them as far as what's being synthesized it is complimentary when we're looking at RNA the sense versus The anti-sense Strand the sent strand is the only strand that you can read in order to get the proper protein that you need if you were to read The anti-sense Strand you would not get the Protein that's coded for it would backwards so we can go over that a little bit more in office hours but don't confuse the two they're similar but different all right so back to translation so this is figure 8.9 the process of translation so what happens is we have these ribosomal subunits the large subunit and the smaller subunit so these components are needed to begin translation they come together a lot of times images compare this to like a hamburger I could see why all right step number two is the assembled ribosome you have a TRNA carrying the first amino acid and it's paired with a start codon on the MRNA the place where the first TRNA sits is called the P site right here in the middle a TRNA carrying the second amino acid then approaches so the P site is what's in the middle all right step three the second codon of the MRNA pairs with a TRNA carrying the second amino acid at the asite so again the pite is in the middle the aite is far to the right where newly amino acids are being added all right so the first amino acid it joins to the second by a peptide bond and this attaches the polypeptide to the TRNA in the P site all right step number four so the ribosome it moves along the MRNA until the second TRNA is in the P site the next codon to be translated is brought into the a site then the first TRNA now occupies the eite all right so here's our first um start code on the AUG this is the E site the P site the a site all right so again it's the ribosome that's moving along the MRNA and the amino acids that are added they slide you know from these different sites until they exit which leads us to step five the second amino acid it's joined to the third by another peptide bond and then the first TRNA is released from the e side all right so we no longer need this TRNA now that we've joined these amino acids together so that we can create a peptide bond so amino acid chain polypeptide chain um protein it's all kind of synonymous all right this TRNA it gets released and then recycled um to get another methionine and waiting for the next um mRNA to be used and then step six right here the ribosome it continues to move along the MRNA and new amino acids are added to the polypeptide so again we just keep moving along and keep growing this polypeptide chain until we get to a stop codon all right then number seven when the ribosome reaches a stop C on the polypeptide is released this AG right here followed by this ug right here in yellow that's the stop codon so once we reach this that tells the MRNA the ribosome to release and stop then finally the last TRNA is released and then the ribosome comes apart the released polypeptide forms a new protein so immediately as this chain is being formed you'll notice there be you know tertiary structures meaning it starts to fold upon other and make its shape based upon different you know side reactions and bonds of the side chains all right the protein it can be modified through post transational modification meaning after we've made this protein we can modify it including the removal of the initial methionine it's going to be formal methionine in bacteria so again sometimes that methionine is part of the protein sometimes it gets removed just depend depends on the particular protein that was made all right so in bacteria transcription and translation they can occur at the same time but in eukariotic cells they cannot so you all have access to the slide so you can see the right answer but think about the location of where these things take place remember that pratic cells or bacteria do not have organel so therefore transcription and translation happen at the same time because it's happening at the same location whereas when you're considering UK carotic cells transcription is going to take place in the nucleus then translation is going to take place at the side of ribosomes all right so you have to allow time you know for that transcript to move from the nucleus into the cytoplasm to find those ribosomes to actually undergo trans transtion to make that protein all right so make sure you remember that that will be asked you know in some way shape or form on your exam this kind of um it's showing us the simultaneous transcription and translation in bacteria some compare this this is like a Christmas tree Arrangement as if these were like ornaments hanging from a string but again why not in UK carots because transcription takes place in nucleus then the MRNA must must be completely synthesized and mooved through the nuclear membrane to the cytoplasm before translation can begin at the ribosomes right make sure you remember that so this is just showing us the eukariotic nucleus right here these are the nuclear you know envelopes right here and the nuclear pores you can see the nucleolus right here where our RNA is made and then these little chunks right here that's chromatin so this is DNA with histones when it's not replicating the histones are how the chromosomes wrap around that ball in order to help keep the DNA preserved and protected we want to keep our DNA from degrading as much as possible all right so again this is just showing us right here the smooth endoplasmic reticulum does not have ribosomes versus these little kind of nodules those are the ribosomes of the rough endoplasmic reticulum where a translation takes place all right so transcription in ukar so in UK carots transcript destion occurs in the nucleus whereas translation occurs in the cytoplasm so make sure you remember these terms the exons those are regions of DNA that code for proteins the exons are what we're after when we're trying to make a protein whereas the introns are regions of DNA that do not code for proteins it doesn't mean that it's um you know junk DNA sometimes it is sometimes it's just not what's necessary to code for that particular protein that you're trying to make there's also something called small nuclear ribonuclear proteins snrps or snps think of them kind of like scissors they remove introns and splice the exons together so if you consider this purple to be your DNA with exons and introns then in the nucleus a gene composed of exons and introns it's transcribed to RNA by RNA polymerase so this is our RNA transcript notice that the entrons were also transcribed then it's through processing using these SNS which are like scissors in the nucleus to remove the entron derived RNA and splice together the Exon derived RNA into messenger RNA so from this singular RNA transcript we could have many different types of mRNA that's created it all depends on what's considered an Exxon and what's considered an entron in order to make the particular Protein that's needed in that moment the actual code of RNA that's going to be used to make a protein is called the MRNA or the messenger RNA all right there's something in the chat so someone said where does translation occur so remember the cytoplasm that's kind of like the soup of the cell and ribosomes are the actual Machinery so translation is going to occur at the side of ribosomes um you know like we showed in the previous slides but the cytoplasm is where all the organel and you know the endoplasmic reticulum with the ribosomes it's floating in the cytoplasm all right so hope that makes sense and then step three after further modification the mature um mRNA it travels to the cytoplasm where it directs protein synthesis so again right here the nucleus right here is enveloped and then outside of the nucleus is called the cytoplasm all right so how do we regulate gene expression in bacteria this is important so genes with related functions for example the same metabolic pathway are organized into operons so if you consider all of the genes in an organism we have many different functions many different operations going on so how do we keep that organized we put genes you know clustered together and operons that have similar functions that we think are going to work together so operons allows the efficient regulation of cellular activities according to environmental conditions so the promoter that's a segment of DNA where RNA polymerase initiates transcription of structural genes so the promoter is where we begin the operator is the segment of DNA that controls transcription of protein coding genes so the promoter is where we start the operator has the actual protein coding genes and right here so if we're looking at this entire you know piece is called the operon the promoter right here is where we begin the operator right here is the segment of DNA that controls the transcription you can kind of look at this as a onoff button the operator and then the structural genes is what you're actually coding for trying to create all right so just to read again step number one the structure so the operon consists of the promoter the P the operator the O and the structural genes that code for the protein the operon is regulated by the product of the regulatory Gene all right so meaning that if we're coding for a particular protein the way we turn this operon on or off is by measuring how much of that protein we've made if we have a lot of protein then we don't need to make more if we don't have a lot of protein and we need a lot of protein then we're going to make more so the amount of the Protein that's needed is what's going to regulate whether this operon is turned on or off okay then we have constitutive genes constitutive genes are always turned on all right again always turned on this is important because we're going to have inducible operons or repressible operons it just depends so with constitutive genes they're always turned on there's other genes that are expressed only as needed so for example you can have inducible genes which means that Gene is normally turned off and we can turn it on think about lactose catabolism we talked about glucose um catabolism in chapter 5 meaning the breaking down of glucose that is the most desired and efficient sugar source for many UK carotic cells but what happens if you run out of glucose you have to be able to use and break down other sugars so if you don't have sufficient um glucose then um we're going to need to be able to use lactose right here so we can turn on these lactose catabolism genes that are normally turned off they're normally turned off because glucose is the desired sugar on the flip side we can have repressible genes these repressible genes are normally turned off and they can be um sorry they're normally turned on and they can be turned off by the accumulation of an end product like tryptophan so for example we normally have genes turned on to produce tryptophan but if we have enough tryptophan then that's going to be a cue for that particular Gene to turn off so again that's repressible then there's a such thing as catabolite repression for example when we're looking at glucose versus lactose operon so glucose is the preferred carbon source for many different cells and organisms and when glucose catabolism is turned on that shuts down other PA waves so that we can keep glucose catabolism as the priority all right so let's go through an example right here so this is Step number two this is a repressor active meaning that the operon is off right here so the repressor protein it binds with the operator preventing transcription from the operon right here so here's our DNA polymerase here's our active repressor protein so when this protein is bound to the um DNA right here then that's going to repress the actual transcription from taking place meaning it's going to block it so this is a active repressor protein meaning that when it's active it's going to repress or stop transcription versus over here on step three this is a repressor inactive meaning that the operon is on so right here when you're looking at the repressor protein it's inactive meaning that it's not going to actually bind to the um piece of DNA to that operon so transcription is able to freely take place all right and how do we do this by an inducer so when the inducer Alo lactose binds to the repressor protein the inactivated repressor can no longer block transcription and the structure genes are transcribed ultimately resulting in the production of enzymes needed for lactose catabolism all right so basically when you have low amounts of glucose this allolactose protein comes along kind of like as a a signal if you will and it binds to this um repressor protein so that it's no longer in the proper shape to bond to the operon which would normally block transcription so this is an example of an inducible operon meaning that it's turned off normally and we can turn it on all right now let's look at a repressible operon like tryptophan so here this is just the structure again of the operon on step number one right here this is a repressible operon previously on the other side we were looking at an inducible operon meaning that we can turn it on it's normally off and we're going to turn it on right here we're looking at an operon that is normally on and we're going to turn it off so tryptophan is an example how do we do this so right here the repressor protein is inactive meaning that its shape does not bind to the DNA so the repressor is inactive the transcription Anda translation are able to proceed as normal to synthesize tryptophan in this particular example as we synthesize more tryptophan the tryptophan itself is a co-repressor meaning that one once you have a certain amount of tryptophan it's going to bind to this repressor protein and then when it binds that causes it to change shape such that the repressor protein now can bind to the DNA operon and prevent transcription so basically the amount of tryptophan that's produced is what's going to then um come back and then bind to the repressor protein to turn it off it's a way of self-regulating because you don't want to produce more of a protein than you actually need you want be able to conserve all of your functions and only you know produce and Direct Energy towards what's necessary all right so now we have catabolite repression so this inhibits cells from using carbon sources other than glucose this is a very important slide so glucose again is the preferred carbon Source we have cyclic anmp or camp that builds up in the cell when glucose is not available that's a starvation signal all right so we want glucose but when we don't have um a lot of glucose then we have more camp that starts to build up and it serves as a signal that we're starving for glucose so then Camp it binds to the catabolic activator protein cap that in turn binds to the Lac promoter which initiates transcription and allows the cell to use lactose so when we don't have enough glucose Camp is going to build up camp then binds to cap and then cap is what's going to um turn on the Lac promoter so that we can allow the cell to actually um use lactose right here so this is showing bacteria growing on glucose as their sole carbon Source it grows faster than lactose there's many different reasons it's just explaining that glucose is a preferred carbon Source has more energy and then right here what we're looking at is bacteria right here it's going to first consume all of the glucose this lag time right here is for the cell to switch over its um you know translation and transcription excuse me of the operon from you know glucose to lactose so we consume all the glucose first then we consume lactose it is 550 so if you need to go you can do so but just remember that um I'm going to stay and finish up the lecture so please watch this um so that you have all the information something in the chat um I'll have to check that after okay right here so just showing you um I said this in my own words but bacteria is growing in a medium containing glucose and lactose we first consume all the glucose then we consume the lactose during the lag time the intracellular Camp increases the Lac operon is transcribed and then lactose is transported into the cell and beta um galactose La lact oase is synthesized to break down lactose all right so it's basically just an enzyme that allows us to break down lactose all right so here's the positive regulation of the Lac operon it's just showing you in visual on what we described verbally on the previous slides so right here here's our DNA this is the promoter so we have the cat binding site so again when glucose becomes low then we have increase of Camp which is like a starvation signal our cap protein is normally inactive but when Camp binds to cap that activates the cat protein then it allows us to go to this binding site so now RNA poase is able to bind and transcribe the Lac operon all right versus right here when lactose is present the glucose um is scarce the camp levels are high right here here if glucose is scarce the high levels of Camp activates cap and the Lac operon it produces large amounts of mRNA for lactose digestion right here so here's the inactive Lac repressor right here we have inactive Camp right here and again when glucose is present Camp is scarce and then cap is unable to stimulate transcription all right so this is an example right here when glucose is scarce Camp is high at the top and then we would have want the Lac operon to be able to um digest lactose versus um when lactose is present and glucose is present that means the camp levels are low and we want to digest all of that glucose first something on the chat um someone asked about five Prime to 3 Prime I'll have to um if we have time for Alphas I can explain that but I don't want to go back at this point since we're already going over I want to make sure we finish up this information but you can stay for office hours if you have time and we can also go over this on Wednesday all right so let's go over epigenetic control so that's important because just because you have a certain Gene does not mean that they're going to be automatically on as we went over with operons so eukariotic and bacteria cells they can turn genes off by methylating certain nucleotides meaning adding a methyl group all right so methylated nucleotides will turn genes off meaning they're not transcribed methylated off genes can be passed to offspring cells so again something simple as a methyl group can turn a gene off and you can pass genes that are turned off to your offspring that brings a lot of different you know conversations about nature versus nurture just because you have a certain genetic background that does not necessitate that you're going to have the phenotype that that Gene codes for there's many different situations in which a gene can be turned off or a gene can be turned on all right so again it's not permanent unlike mutations genes can be turned on in a later generation so if you've ever heard the terminology of Silent genes this is one of those examples of a silent Gene meaning it's turned off but it could be turned on for example you know your mom or dad could have a certain you know gene or disorder and you could be a carrier of that particular um disorder but you don't necessarily have that disorder all right so epigenetics it may explain why bacteria um behave differently in a bofilm meaning that um whether something is methylated or unmethylated can turn a particular gene on when you have a bunch of bacterior together um you have a high propensity to turn a bunch of genes on and just just have functions that a particular you know Vector would not have isolated by itself all right then post transcriptional control so again after we make our transcript how do we regulate that the ribos switch it's part of an mRNA molecule that binds to a substrate and changes the MRNA structure so again translation is initiated or it's stopped depending on the structure so let's look at a and b so a is showing us a non- nucleolytic repression mechanism so we have the Lian right here this is the on state we have our ribosomes this is our start code on the AUG versus the off state right here when the Lian is bound it's in the off state that changes the orientation of this rival switch right here and we create this little hair so that means the ribosome is unable to bind to the start codon so again the ribo the ripo switch it's a structure that can bind to either initiate or stop translation so this is a non-nucleic repression mechanism we would repress um translation with this Lian to turn it off Part B is showing us a nucleolytic repression mechanism right here so we have the Lian which is naturally in the on state then we have these degradosomes that would come along right here and it degrades right here this part of the RNA structure and cuts it and degrades it so that particular degradation it causes this um you know Loop to form right here meaning that the ribosome is unable to bind to the MRNA to begin translation but notice the difference between part A and Part B part A you can go back and forth depending upon whether the Lian is bound or Unbound Part B this is a permanent off because the grome it actually degrades this part of the MRNA so that um ribosome is not able to attach ever all right so it's the difference between whether you want to temporarily turn something on or off or you want to permanently turn something off all right look at the arrows it'll tell you the difference all right we also have Micro rnas which are known as miras so these um base pair with mRNA to make it double stranded double stranded RNA it's enzymatically dist preventing the production of a protein so whenever we um as humans whenever our body reads double stranded RNA that's an immediate warning sign to degrade it something's wrong we do not naturally have double stranded RNA so it's a warning sign for the immune system for the body to just completely degrade it and we're able to use that to our advantage right here so similar to small interfering RNA serus it causes gen silencing think about like antiviral ing again some viruses can have double stranded RNA so again anytime you see double stranded RNA within you know humans in particular that's a warning sign to destroy it and these micro rnas they create double Bonds on purpose so that we can have you know transcriptional modification this is also similar to Crispers in bacteria it's a way of you know cutting out particular pieces of a segment so if we're looking right here at our DNA and then transcription of the Mr the yeah the Mi RNA occurs then the Mi RNA would bind to a particular part and then that part of the MRNA is going to be degraded where it was bound all right so it's just a way of controlling a particular um you know piece of what's going to be cut and what's going to be used to make the MRNA all right mutations so we want to think about the types of mutations that exist so because we have different you know um nucleotides we only have four of them but we can make many different arrangements and notice that there's some you know codons that um code for the same amino acid so there's going to be different types of mutations so make sure you remember this because you'll have this on your exam so a point mutation in DNA it could be silent meaning there's no change in amino acid amino acids and then um there could be a change in a single amino acid which which is called a missense mutation or there could be a change in amino acid to a stop codon which would be nonsense so a point mutation means that one of our points one of our nucleotides is mutated all right if it's a silent mutation that means we don't change the amino acid for example if we were looking at Serene right here if the original code stated um ucu but for whatever reason it was mutated to UCC that's going to be a silent mutation because even though we have the wrong nucleotide there it still codes for searing amance means that you have a change in a single point that causes a different amino acid to change again because of different um you know intermolecular forces and bonds changing a single amino acid could render the entire protein non-functional because it could change the shape potentially nonsense would mean that you've coded a stop cat on on accident and then frame shift would mean that we've shift Ed all of the different amino acids that would mean that we either delete or we insert a nucleotide this is a problem because we read in sets of Threes so if you take one nucleotide out or if you add a nucleotide you're going to shift the sets of three that we read different amino acids the whole sequence is going to be changed all right so let's look at examples so at the top part A this is our normal DNA molecule without mutations if we're looking at a missense mutation right here so instead of having um you know glycine right here we would code to Serene because we had a mutation right here the Missin mutation right here is going to show us again a change of a single amino acid so instead of glycine we have Serene instead of this um t and a right here the codes for for sering we were supposed to have this C and G right here to make Glycine and instead we made sering all because of this one single change the G and the C is the same but changing this first G to an a codes for Serene instead of glycine the nonsense mutation c means that we've accidentally coded a stop codon so again we should have lysine right here but instead of having the you know the A and the g as the second and the third we're supposed to have a a as the first nucleotide but it got changed to U so that changed us to a stop codon and then frame shift again would be if we add or take away a particular nucleotide so in this example we lost our a and so because of that they shifted the sets of three that we read so we start off with methionine lysine and then instead of pH alanine we have Lucine we have alanine so it's just the wrong amino acids it's a frame shift all right so how do we repair mutations so our DNA polymerase it has a proofreading function that catches errors right after they're made so DNA polymerase is very good at you know proofreading so one of the ways in which um we can repair mutations so UV it causes dimerization of adjacent thy Mees so again we want our thyes to bind to adenine not um each other but sometimes we can have a mutation which the thines bind to one another instead of the um complimentary base pair of the a so how do we fix that we have photo lias enzyme it can be used um visible light to split the dier right here we can also have nucleotide excision repair which cuts out the T diers and other mismatched bases and then the incorrect bases can be marked with methyl gr groups methylase enzymes so it's just showing us the difference right here so this is the nucleotide excision repair so the nucleas cuts the strands right here where the arrows are pointing and then that would remove that entire piece and then we have DNA polymerase and DNA ligase that comes along and then tries it again so it's basically we cut out the eror and we try again photo reactivation is when we're able to use visible light to try to break that um thyine dimer and cause the actual appropriate um hydrogen bonds to form between the T and the a so it's just showing us two different ways all right so this is another example again it's just showing us the exposure to ultraviolet light it causes adjacent thin to be cross length this is one of the reasons we wear you know sunblock and we try to protect ourselves from ultraviolet light because it can cause mutations in our DNA all right so an endonuclease it can cut the DNA and an exonuclease removes the damaged DNA then DNA polymerase comes in and it fills the gaps by synthesizing new DNA and then the DNA liay seals it so again with excision repair we basically cut out the error and then polymerase comes again to try again all right genetic diversity Beyond mutations thinking about homologous Rec combination and crossing over so if you can have two pieces of DNA with a similar region that swap strands and exchange genes this happens with reproduction for example you know eukariotic sexual reproduction between plasmas and chromosomes and bacteria so here we have hom Rec combination we have the endonuclease it produces Nicks in one strand or Cuts in one strand and then the three prime ends are used to extend the open strands ligation we can actually you know connect and seal where the excision was made and bomb them together and you can show right here just with the different colors of how we were able to basically swap different areas of genes again this happens with reproduction it's how we get genetic diversity all right so this is just showing us again another example a figure in your book of genetic Rec combination by crossing over so the DNA from one cell it aligns from the DNA of the recipient cell you can see the little NYX right here this would be the donor DNA and the recipient chromosome the DNA from the donor aligns with the complimentary base pairs in the recipients chromosome this can involve thousands of base pairs then wreck a protein at catalyzes the joining of the two strands and then the result is that the recipient's chromosome contains new DNA complimentary base pairs between the two strands will be resolved by DNA polymerase and ligase and the donor DNA will be destroyed the recipient may now have one or more new genes all right so it's just showing us a different figure of what we discussed in the previous slide right make sure you understand the difference between vertical Gene transfer and horizontal Gene transfer something in the chat yes endonuclease is the enzyme and then Rec a is the catalyzer correct right here so the rec a protein catalyzes the reaction but endonuclease is the actual enzyme that's causing this reaction all right so vertical Gene transfer that's the transfer of genes from organisms to its Offspring think about normal inheritance from parent to child that's vertical versus horizontal Gene transfer that's the transfer of genes between cells of the same generation think about um in bacterium there's mobile genetic elements there's plasmas there's transposons there's viruses so this is something you know as humans we only um exhibit vertical Gene transfer but bacterium and other organisms viruses you know um procaryotic cells they're able to exchange genes between you know other organisms of that same generation horizontal Gene transfer again we talked about that when we're looking at the theory of endosymbiosis of the origin of mitochondria and um chloroplast as our organel that occurred through horizontal Gene transfer all right so again horizontal is same generation vertical is the different generation or The Offspring we're almost done all right plasmids so plas mits are self-replicating circular pieces of DNA it's exis in bacterium it's 1 to 5% the size of the bacterial chromosome they often code for proteins that enhance the pathogenicity of a bacteria and pathogenicity is the um ability to kind of form a disease or form an issue in another organism that it infects it's like it's superpowers as a bacterium what causes it to be a pathogen against another organism what causes it to be a threat to another organism we have the um conjugative plasmid which carries genes for the sex pilli and the transfer of the plasmid we have the dissimilation plasmids which encode enzymes for the catabolism of unusual compounds and then we also have resistance factors or R factors that encode antibiotic resistance all right so if we're looking at the origin of replication right here in our chromosome these are just different resistance um factors on this plasmid right here here so it's just showing us um what an example of what could be on a particular plasma the RTF is the resistance transfer factor right here and the r determinant is the resistant genes all right so the transfer factor it's showing us these you know important parts and proteins that are necessarily for transfer of particular genes and then over here the r determinant it's showing us all the different resistance factors that are encoded on the plasmid all right when we're talking about conjugation so plasmids are transferred from one bacterium to another it requires cellto cell contact via sex P the donor cell carries the plasmid F factor and are called f plus cells all right the donor cell is the f+ cell and then HFR cells contain the F Factor on the chromosome so high frequency re combination cells that's what HFR stands for when you have the chromosome excuse me the plasmid on the actual chromosome itself of the bacterium you have a high probability of transferring that particular plasmid to offspring or to the next you know replicant next Generation versus if the plasma is not on the chromosome you have a variable chance but if if it is within the chromosome you have a high chance of it going to the next offspring of the Next Generation all right so here's what I mean about that the conjugation and eoli so again The Mating Bridge right here it's formed by the sex pil the F positive cell is the cell that has the plasma the F minus cell does not have it again the F positive cell is the donor the F minor would be the recipient right here so we're looking at the replication of transfer of the F Factor so after you replicate that particular F you know plasmid and it gets transferred or copied to the recipient now they're both F positive cells all right so if it has the plasma of interest it's a f positive cell that's the donor all right now let's look at um when the F Factor becomes integrated into the chromosome of an F positive cell it makes it a high frequency of Rec combination cell so right here we're looking at a f positive cell and due to rec combination sometimes that particular fact Factor can be integrated into the chromosome itself all right right so that's what that pink is showing us so when you have the plasma that's integrated into the chro um chromosome itself then that becomes a high frequency a combination cell a HFR cell which means there's a high chance of passing that plasma to the recipient all right so here's the replication and transfer part of the chromosome so in the recipient Rec combination between the high frequency re combination chromosome fragment and the F minus chromosome right here so it means there's a high chance but this is also showing you that it doesn't mean it's always going to happen it means there's a high probability though all right so this is conjugation right here it can be used to map the location of genes on a chromosome using mating Interruption experiments it takes 90 minutes for complete transfer right here so again it's just to map the location of genes on a chromosome the location is important because let's say we want to splice you know and cut out a particular Gene to be used in another organism or in another experiment we want to transfer a gene we have to know exactly where it's located how big is it all right so how do we transfer different genes so transposons transposons are segments of DNA that can move from one region of DNA to another they contain insertion sequences that code for transposase that cuts and resales DNA and then complex transposons can carry other genes like antibiotic resistance so transposon is a movable Gene so right here this is just showing us for an example the transpose a gene we have these inverted repeated sequences so an insertion sequence the simplest transpose on it contains a gene for transposase the enzymes that catalyzes transposition so this is just an example the transposase gene is bound at each end by inverted repeat sequences that function as recognition sites for the transposon insertion sequence one is is one example of an insertion sequence shown here with simplified IR sequences so we have these inverted repeats right here meaning they read the same forwards and backwards all right so inverted repeats they help the transposon to hop in and out of the genome through homologous recombination so these sequences serve like as a code for the transposon to know where to hop in and out of of different genomes because it has to hop into the right location right here so here's an example the transpose it cats the DNA leaving sticky ends because these are inverted repeats meaning they read the same forward and backwards so for example um right here we have this t g a a t g a c a t g a a t g a c so remember this is the same as this right here so you want to have these sticky ends meaning the more overhang you have the more nucleotides that are showing the more accurate you will have of that Gene to transfer into the right location all right it has to transfer into the right location otherwise it's not going to function properly so complex transposons they can carry other genetic material in addition to transposase genes example shown here is tn5 which carries the gene for canamy resistance and has the complete copies of the insertion sequence at each end right here then we we have transduction so transduction is when DNA is transferred from a donor cell to recipient via bacteria phage or just say Fage these are viruses that infect bacteria then there's generalized transduction which is random bacterial DNA is packaged inside of a phage and transferred to a recipient cell then we have specialized transduction which is specific bacterial genes are packaged into a phage and transferred to a recipient cell so again transduction is using Fage to infect bacteria Fage are viruses that infect bacteria so it's basically using that as a machine to transfer genes from one bacterium to another so right here looking at our diagram so step one a Fage infects the um donor bacterial cell step two the Fage DNA and proteins are made and the bacterial chromosome is broken into pieces step three occasionally during phage assembly pieces of bacterial DNA are packaged in the phage capsu then the donor cell Li and releases phage particles containing the bacterial DNA then step four a phage carrying bacterial DNA it infects a new host cell and the recipient cell and then step five Rec combination can occur when producing a recombinant cell with a genotype different from both the donor and recipient cells okay so again it's just showing us how Fage can be used to um transfer DNA from one cell to another that's called transduction all right so I know this was a long chapter thank you for those that decided to hang out with me to finish this up just as study tips because remember unit two and just for the rest of the semester we're going to really pick up the pace and the intensity so make sure that you're reading the textbook before class attend lecture so that you can notate the subjects and the concepts to study review the following day or as soon as possible form study groups and again come to office hours for questions and clarifications so thank you that is all for lecture nine and I will stay back for a few more minutes for office hours