Lecture 08. RNA.

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Lecture 08. RNA.
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Lec 08. Introduction to Chemical Biology -- RNA -- Part 1
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UCI Chem 128 Introduction to Chemical Biology (Winter 2013) Instructor: Gregory Weiss, Ph.D. Description: Introduction to the basic principles of chemical biology: structures and reactivity; chemical mechanisms of enzyme catalysis; chemistry of signaling, biosynthesis, and metabolic pathways. Index of Topics: Announcements 0:00:21- Announcements 0:01:24- Midterm 1 Results 0:03:24- Office Hours 0:04:28- Getting Strong Letters of Recommendation 0:15:10- Getting Strong Letters of Recommendation from Prof. Weiss Lecture 0:18:00 DNA Chemistry and Cancer 0:21:00 RNA: Soldier, Sailor, Tinker, Spy 0:22:40 Differences Between RNA and DNA 0:23:25 RNA Hydrolysis 0:27:27 Rnase Mechanism of Action 0:30:38 How to Shut Down a Very Effective Enzyme 0:33:25 The 5-Methyl Group of Thymine Provides a Chemical Code for DNA 0:36:35 RNA Bases can Be Modified 0:38:14 RNA Adopts Globular Structures 0:40:14 Systemizing Structure in RNA 0:46:20 RNA Polymerase 0:50:40 DNA Primase 0:52:27 Transcription in Action 1:15:32 The Yeast Two-Hybrid System Allows in Cell Testing for Binding 1:17:53 Comparing Bacterial and Eukaryotic mRNA Factors
Active site Explosion Drug prohibition law Chemistry Portable Document Format
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Transcription (genetics) RNA Translation <Genetik> Periodate Man page
part the mid-term once he has been posted to the course sites and hopefully you've had a moment to take a look at that your scores have also been posted in an on Friday OK and I was sent off to the your exams were sent off to the scanning service on Friday so I'm expecting some time today to appeal to distribute them back to you as usual will get distributed backed PDFs Schedule download in your mind Tripoli website said so everyone should get there I created exam sometime today OK I will talk more about examiner moment the journal article report due February 14 that's a week from Thursday and check these instructions OK so before you get too involved in and make sure that you've chosen article that conforms to instructions because again if you haven't others back to ask you to do it again and I would really be a bomber because you have waste a lot of time OK so a double-checked instructions before you get too involved before you go too far down the road to make sure that your article I get back to the midterms so
overall I think this is an acceptable job wasn't spectacular but it was the the worst an average of 56 here approximately it's where I put cost-free a minuses for minuses and see minuses note that I'm not looking to give very many geezer at a pace at the very bottom if you come to cling on and do an acceptable job on your your proposal and you're caught it's unlikely that I feeling you can I realize looking out today that the people who were probably at this end developer might not even be in the classroom today and that's fine but maybe will be watching nutrients in which case I a special message for you need to pick things up a little bit OK I'm not looking to fill you but I do have some standards and I down here is flow what I'm expecting for upper division class series here but now I realize that to was challenging and I my exams tend to be so roughly if I decide rates tomorrow about 29 people or so we get from any miners are higher and then an island somewhere a little bit below the was significantly below the average that averages around 56 cents over here said somewhere in here I would assign B-minus cut off and then a whole bunch of people get C viruses are about as something like that is how it assigned grades of flights due tomorrow all this is subject to change that OK I just know that from experience teaching this class there wants to know where they got an a or a B or whatever it's overly worried your score is back there were the poster Tripoli to look at this and get an idea of how you doing in the class of world terms of a letter grade connection not happy with how you did on this on this exam come see me in my office hours OK stopped by my office hours will talk about your study of strategies and will try to come up with something that works for you that hopefully takes you out of this new problem area the trend doesn't make you happy OK speaking
of which office hours I'm going to have my floating office our this week today the new into 1 In the usual spot my regular officer will be Thursday 11 to 1 in the usual spot as well as so I have 2 hours office hours BTA said 2 hours office hours usual times usual places so that no changes their combined stake below and talk to us about your exam tell us which I would Well what didn't go so well and I'd be interested to hear that all also give you an opportunity to provide some feedback I haven't worked out the details but are probably set up some sort of survey of some sort to I hear back from you about how the classes going it's Week 5 animal was curious to know how you how the students feel the class so it will be a chance for you to give me some feedback continues to make course corrections if necessary and properly set that up sometime this week and if you do it you get some very minimal amount of extra credit for talking like 1 or 2 points of head but wanted to point their nothing OK now something else that
comes up around this time of year is as several of you asked me to write a letter of recommendation I rate of about 100 to 120 letters a year of recommendation for my students it's something that I take very seriously and I here's what I've learned that 3 many years of doing this pair learned that you can actually control the quality of your letters of recommendation that you can actually almost orchestrate a good letter saying now the 1st thing you need to do is get to know all of your faculties you just never know who it is only writing that crucial letter for you it's just impossible to protect us so a good rule of thumb is simply get to know everyone OK and the reason is that many of the the programs and fellowships and other prestigious things Sitiveni applying for are going to require more than 3 letters because you're thinking I have my 3 letters all picked out but now they silly need another letter and so and you know at the last moment it's really too late to find someone to write that so let's just assume an advance that every 1 of the faculty here use your mind would potentially be so limited in turned to letter cases simply get to know all of the pain of not coming up to my office hours already start now on the other thing is once you get to know everyone choose your letter writers carefully you want to choose people who are going to do a good job paying all faculty are totally vested in us and you especially don't want letters from some you know your dentist said ,comma I chair the nation's committing in Department of Chemistry in fact had been honest admissions committee for going on 13 years and for a while I was also an undergraduate admissions committee which gets 60 thousand applications a year so I know a little bit something about reading letters of recommendation and no joke by someone from someone's dentist and at the end of a close by saying this person is wonderful oral hygiene and I really encourage you to accept them into your program but I could tell you as as you know as laudable that as Bureau of hygiene was it wasn't persuasive to me that this person deserves a spot in a Ph.D. program in case you need to choose people really carefully animosity lingers because when I look back when I was an undergraduate I wanna kick myself and my own I attack I was having you know professors of English sending letters for you Ph.D. graduate school it's a miracle I even got it and that's not the way it works right it's it's better if I got my science professors to you and to send letters for science graduate school weeks I got someone in sciences to do but the point is is that you have to choose these letters appropriately which people were going to take the time to do I care about you and I invest some of their own time it takes me about half an hour or so per letter that I write so a significant investment in my time but I'm willing to do it you need to find other faculty that along those lines appeared unwilling to invest that amount of time in I'm OK so choose carefully the next thing again involved the UCI I need your help and I cannot write a letter for you that's totally glowing insists as you know and this person is a genius and chemical biology and likes to play basketball with their friends on the weekends OK and no joke I've written letters like that but that letter didn't get the person medical school and that's not what I want I want help everyone of my students get it you know hit their career bowls and I and the only way I know to do this is to get involved that you see on the need to be doing something well beyond the ordinary you need some way of distinguishing yourself if you're have if you have 4 0 GPA you also need to do this paid for a GPA's are a hate to tell you this there really comment at the level of the people .period MD PhD programs and there's a lot of people applied a Ph.D. programs so you need some way of differentiating yourself and on 1 on top when talking about is a different unit differentiate yourself in some way that's extraordinary occasion what I mean examples would be you know flying to you know the border with Myanmar's during a refugee crisis and you know with a bunch of people setting up a tent and starting to you do something OK that's dramatic that gets people's attention OK that's what gets you into say a public health program of cases that kind of thing is what it elevates your application over all the other applications of people who have very good GPA's coming from very good universities and so now is the time for you to start and I look out I see some you just holding their heads Hong noted relax OK it doesn't have to be something worthy of a Nobel Prize it doesn't have to be something that's just you know totally shattering but it has to be something that comes from within you something you're passionate about something that shows evidence of altruism something that shows an ability to go well beyond the ordinary that's what gets you into a really top programs OK that's the sort of ammunition I need to help you get into those
programs as if you're not doing this start doing it now because I'm along those lines all help you by pointing out some things that come to my office hours and tell me what it is secure interested in and I'll see whether I can create those opportunities for you OK whatever it is all try to a hook you up with someone who will help you get that opportunity but you need to start now OK now than expertise you really need to give up long advance notice there's just nothing networks Katie stuff last minute and I don't think any of the faculty here camera all totally oversubscribed it's like a 100 hour week job to be a faculty member here use your right and so if you come to me at the last minute you know as you know as much as I might like you know as much as I want to help you it might be totally impossible because I might have 5 other demands on my time that also have done lights and so I just cannot do anything about it in circumstances like that so 68 weeks is kind of a rule of thumb if it's 4 weeks to kind of pushing it but that's OK but you know less than a week that I just have to you know shrug and say I'm really sorry I'm OK now all have some paperwork that you need to bring to the meeting it's really essential that you get everything put together in a folder and I'll tell you where to find that their information about that you can go to the Web site and then here's a PDF that you can use and use this to guide the paperwork that you put together all that stuff needs to be put together before you reading and send a gentle follow-up if the letter writer is not hitting the deadline sometimes they just forget OK so I tend to write all my letters immediately we need and then we write the letter within a day or so but other people kind of put them off on the desk gets buried and other stuff so feel free to send a gentle follow-up units carefully worded this is really essential it's very important that you write a thank you note for every letter writer that had to every letter writer who supports you doing this provides evidence that you that classy person that they would to back for that they put their good will on the line for a they're willing to tell their colleagues this is someone that I really like and they want some affirmation of that after immediately after the letter the other thing is it's very likely that this will be the last time that you go back to the well and go back to that same letter writer and asked for a letter another letter hit us maybe get into your dream pharmacology program and then you need you 1 apply 1st fellowship 2 years from now and so we know you need to go back to that letter writer it would be helpful if you had already sent them a thank you note now this thinking it should be handwritten don't use e-mail for thank you notes the e-mail is fine but in the in the bigger worlds e-mail doesn't is near our text messages is not appropriate for thank you notes thank you notes is supposed to be personal they're supposed to tell something about you and what will you do this is by showing your handwriting and showing that you're taking some little bit of extra time in care now the note itself doesn't have to be on super fancy stationery with your initials pseudo custom embossed on it a case so it doesn't have to be some engraved you know a thing of beauty all you have to do is take a nice piece of paper folded in quarters and then write something on that set OK but that near active doing that shows a lot of class again but provides evidence that the letter writer was right to take a bet on you OK glaciers along those closing lines of trying to make sure that the letter writers are still in your camp when you need them years from now is people letter writer for I will tell you that this is 1 of the great perks of my job had of a lot of things I have to do that I really hate to do I feel students and stuff like that I hate that aspect the job but what I love more than anything is hearing about the successes of my students it might be the only perk of my job in fact now I think about it and flights it's an amazingly it's amazing thing for me to find out that my students have gone on to do something really cool and armor rolling back the frontiers in their own fields I love hearing that I love sharing in their joy and offering them like graduations this is really essential OK this kind of closes the loop and it's the payback to ensure that other people will also be get that depend on letters from that person OK that's the kind of that's the payment for doing this opinion along those lines are speaking payment you don't have to provide gives you a letter writers in fact it might be better if you didn't OK and I think I have a rule on my website nothing over 25 dollars because I know I have a lot of students whose cultures tell women it's really essentially provide a gift for a letter writer that's fine I can respect that culturally but nothing greater than 25 dollars and I like chocolate OK so it's really so OK so anyway and you don't have to buy the gift but you do have to provide an update showing when you're successful because that's a form of payment that really is why why we do this that's why I write letters for 100 people year I like hearing about the successes of family life and love knowing that my students have gone out to do something really cool because I want to hear that I want to hear that he backed that really matters a lot to me OK now
speaking of letters from me I'm here specifically what I'd like you to take a look at the guidelines that posted to the link on the court's website that's over here
this gets updated periodically but this is more or less than the link the duty on
that read these carefully before you contact me again request these letters sometime in advance and again do anything notable IRA beyond and then I introduce yourself to make the don't have to get to know me in some deep way we don't need to know each other beyond this class that's perfectly acceptable and effective sword that's that that's the way it usually has but I just need to know who it is that I mean you're writing a letter for I want to know the person I want and I want a bill to recognize the name at some level again I will tell you that I also write a lot of letters from people whose names planned no idea who they are but I look at the course roster the greater roster and I know that he got an A-minus or higher in my class and therefore able to support them canal in order to do that I will interview that person for like 15 to 2 to 30 minutes before I write the letter occasionally during that time of the decide whether I really wanna write the letter a case so and at that point you know all the you shot even if I don't know you even if I don't know whether or not I should support you all do it just because you did well my class and then on it's up to you in the interview to kind of you know tell me why it is that you really are passionate about the dietary or whatever it is that you applied for whatever is replying for unwilling to get behind it and get on the wagon and supported by and you have to give me some reason for that OK and it's it's likely that you wouldn't have that reason today because you don't know what you're applying for you know you're a half or 2 years 3 years now that's that's fine and I understand that I don't panic I'll be there when you need a pet but again take a look at the guidelines at a time OK any questions in advance about that hopefully this is helpful I realize we took a lot of time lecture but the truth is that these types of things actually are as important as chemical biology to ensuring your success beyond the classroom at UC Irvine questions it's a good luck on your letters uh I will tell you that I am when I review applications for graduate school the very 1st thing I do is flipped up into the letters I decide whether or not it should read the rest applications based on whether or not the letter of a glowing came to get your mind for graduate school were a top 10 in our program letters going to be really glowing and some looking for those glowing letters even before I start looking at the grades and Yuri and all that other stuff that earned it up enough about that so let's talk about what we saw last week so last week we wrapped up the topic of DNA and 2 of the most important thing I can tell you but you know it is it's really a superb nucleophile This is it at its essence why DNA so reactive and this is why DNA is so susceptible to environmental fronts and we learned a lot about these views are different electoral files back and then damaged DNA can be selected files are ubiquitous in our lives these are things like pesticides but there also innocuous things water lecture is not an electrified but it can also damage DNA we talked a little bit about that X-rays could damage the array of radiation from UV light from the sun from them cosmic rays radiation cost-based all those things damage DNA and so we also talked about how DNA can be repaired and by excision repair OK so this damaged DNA can corrupt its message and then interfere with normal replication and transcription but we also talked about how mutations to disease genes associated with tumor suppression likely 53 who were on an especially dangerous for the cell because these mutations to these on genes that resulting cancer oftentimes turned oncogenes is required for tumor formation and that's why they're seen mutations in these genes that then encode these proteins are associated with higher at such high percentages of cancer or cancer has a high percentages of mutations these opportunities hence the name oncogene Ronco means cancer OK so we also talked about how cancer resulted from alterations to DNA of the growth factors that tumor suppressors and cell division checkpoint pathways and we had to have mutations to all 3 of those pathways in fact we found that there were mutations to literally thousands you know hundreds to thousands of genes before tumors really started to take off and we characterized the Sabri but pathways in the cell as being the accelerator that's the growth factor the break that's a tumor suppressor and the clutch which is the cell division checkpoint pathways and so I'm really cancer is a really had a genius disease involves lots lots of mutations involves mutations all 3 of these pathways which is mandatory for the for the cancer progress and so on hopefully you have a better understanding of why it is that cancer rises and even some strategies for helping to avoid damage to DNA and hopefully hopefully avoiding cancerous cells OK so any questions about any aspect of DNA cancer or anything like that anything we saw last week OK great don't
but next about our day so I'm last time I introduce you to the molten various roles of RNA RNA is really remarkable as a biopolymer in that really plays out a very wide range of of and it provides a wide range of skills for the cell and we talked for example about the RNA acting as a catalyst to cleave other RNA sequences will see some examples of this today and this is a property that we're going to call time that will refer to as coming from a class of RNA is called designs and we've already seen the idea that RNA can deliver on messages in the sense that a modern-day encodes proteins is translated and in addition we're going to see some writers Omar Lorene this far already which is not monster catalytic machines shown here and below and where the army is providing the essential catalytic function for translating foreign days into proteins for synthesizing proteins Tom finally you also going to talk a little bit about transfer or a day or 2 days which deliver amino acids to the ribosome these are shown here they're going to deliver me not you know a soul and the amino Wieseltier Tierney's are going to deliver the amino acids to the ribosome and activated state appropriate performing and hammered bond during peptide or protein synthesis OK so that's kind of the big picture let's dive in and start looking at the structure
of RNA 1st 1st and there are some important differences between RNA and DNA most important is the presence of this to crime hydroxyl group highlighted in green over here on the 2nd 1 is that in place of finding on a hazard yourself and that the only difference here is that the carbonates highlighting green fighting has a methyl groups and I hope by the end of today's lecture it will be apparent chemically why it is that DNA evolved to have the methyl group here in place of I just know that group in place of a hydrogen have a case so the consequences of this are pretty profound right the 1st consequence is
that on this to crime hydroxyl provides an intramolecular nucleophile to attack the fossil dinosaur backbone of RNA we've already discussed this mechanism I'm not going to belabored today on but this is you know this is a mechanism to take place at a fairly low rate at pH 7 IP H 7 This isn't much to worry about it when the pH comes off of 7 and we already talked a little bit about the half-life of our day it's surprisingly long pay the real problem is when the pH pubs offered 7 unification I others just say kitchen on creation will decoded this to prime hydroxyl making this an even better nucleophile as shown here and that in turn up leads to much faster degradation of the RNA they similarly low pH could start to predict the possible as the backbone answer to encourage this nucleophilic attack and by the 2 prime hydroxyl the other thing the real
reason while the other thing is that although on a has very long half-life when we work within the lavatory we really don't think of it as having a very long half-life in practice it's really kind of a pain in the neck to work with in and the reason doesn't have to do with the chemical stability of the RNA background rather it has to do with the ubiquitous nature of a class of engine enzymes called RNA sets so on leases are charged with high July icing on a mechanic and they look something like this but this is in black is Lorene that's going to digest and these are really literally everywhere on your skin the falling off your skin there your saliva coming off of your years you know they're they're really all over the place and so you're dealing in the sea of RNA says that your body naturally secretes as a form of antiviral and that's it's a defense against viruses because as you know there are many viruses that are already based and so any of those viruses and happened to find a way to skin hopefully they're going to get digested very quickly by any on Onasis that present and so in practice this really makes it tough for us to work with the RNA and I'll talk to you a little bit more about some strategies that are used in a moment it before I do let slip a little closer at the mechanism of RNA said they should understand this mechanism I need to tell you a little bit about the properties of emitters all OK cases this is structure here is called it is all this is found on his city's side chains in proteins like this 1 cannot here's what I want you to know about this the PKA of this nitrogen over here Of this protonated amid all it is about 7 so that means at pH 7 there is a one-to-one ratio a protonated to uncoordinated admit it's all present Hey this isn't this really gives this particular side chains some unique properties they pH 7 which is the the pH that life is taking place at the time were life in ourselves more or less like the cells is taking place at a time means that your your amid your and your minutes all side-chains will be 50 cent predicted and 50 per cent on protonated head so this is really useful this means that this particular functionality can the acted as a base In this case over here foreign acid over here depending on whether it has on other proton presence has so it's very easy for the protein too change around the charge state of this particular functionality and it turns out that's crucial to almost all of its functions in enzyme in it as a catalyst OK so let's look in greater detail this is now zooming in here is the I'm on where the say ornately to be digested again here's the fossil Odessa backbone and there are 2 emitters all functionalities found in this active site 1 of these is the coordinated to act as a base to deep-rooted naked to crime hydroxyl making it a better nucleophile and then 1 of these is coordinated to Prodi made the prosper thy Esteban and help make it a better leaving group case the 2 of these can work in concert meaning that there is a single step to this reaction where on 1 side a proton is extracted on the other side of Proton is delivered and this all happens in a single step OK and it looks so the transition state is going to look like this where the -dash lines are bonds that are either forming in the case this case will breaking in this case case of the stash lines all bonds that are a breaking in that single step but now I know what you're thinking you're wondering how it is that we know this is just 1 step actually to be up until a couple years ago I did have a good answer that they do there OK so we can actually now look at molecules and a single molecule level and then I'll watch how many intermediate steps there are by looking at distributions at different rates so there's actually a technical way of looking at whether something has 1 step or multiple steps in this case we find that this thing is just 1 step at a which means that all of the deep-rooted nation and all the presentation is taking place in 1 smooth single step motion and that's kind of amazing OK so we call this a concerted reactions or concerted transition state that allows us reaction to proceed smoothly we you talked about the strange intermediate which then very quickly gets Titleist and to yield the of the broken apart OK any questions about this I'm question What's up with this ammonium ion inactive site that's donated by lysine citations as a primary administered prorated anyone want positive propose a possible role for this might yet Chelsea good yet so Chelsea is reasoning that this phosphate group is negatively charged it's going to be leaving agreed it would be such a better leaving group if it was stabilized by a nearby lysine this nearby positive charge and that in fact exactly what it does here is that the buildup of negative charge around the prostate that the Delta minus your documents here to having the nearby positive charge to suck away some of the negative charge off the prostate and help stabilize that intermediate and lowers its energy and in doing so helps to catalyze this reaction so really in this insecticide aside there's 3 functionalities that are crucial to their 3 functionality said doing something to make this reaction possible and accelerated to an amazing degree OK now
I told you earlier that this is a serious pain in the neck for those of us who work with irony in our laboratory because of the on are totally ubiquitous their their costly attacking the very biopolymers or trying to study so I know I should tell you that we can find this already stuff in the water Casey opened the taps on your shower something like that of the water comes out like plenty of ironies is available to start chewing apart any orally understand searching apart any on it you haven't had your reaction tested so what we do is we treat all of our water with a region called up Dempsey which looks like this is by Apple Pyro carbonate OK so here's our names and when you treat this with Dempsey from 1 of those that both histidines are on Kirby a more elated meaning that you switch them from having a free nitrogen with the lone parents did now having a car beyond the functionality of a notice that this reaction is driven by the release of 2 carbon-dioxide molecules and I think this is actually a pretty good reaction I don't think the mechanism is in the book trade OK so maybe I can ask you guys in the critical and other Marines coverted discussion section this week OK thanks his reaction on but again this this is about driving the reaction lowered by releasing carbon dioxide is a prime chested and I very viable mechanism for a very viable strategies for accelerating reactions because remember this carbon-dioxide is going to go bubbling out of the reaction class in this case a big fan of water and the result will be a reaction that that's driven the word by the Shatt his principal paid by the fact that this carbon-dioxide bubbles away preventing the reaction from going in reverse it's so this is a very effective reagent the other thing we do is we then take this reagent and make a solution of it and start waking down all the surfaces in the laboratory and then we're really rigorous about wearing lots of gloves and um you know very carefully putting on a you know coats that haven't been Khatami of aces and a fact if in my lab if we had been doing as well actually designated one-dimensional that no 1 is allowed to even stand near OK because little story you know spit blobs and stuff like that would be enough to ruin the whole experiment so no one's allowed to even look at the bench set off in a corner and I ask everyone not even to walk near the bench a paid but that's the kind of paranoia that ensures that your experiments with Arnie go well because otherwise the stars stars degraded drives you actually bad faith are at but let's get
back to structure of foreign aid and REA as we discussed earlier has said they are fired up and lacks the 5 of finding so it has a yourself in the place of tiny now let's talk a little bit out why DNA of all to have this this extra methyl groups OK so all DNA here's the structure of DNA is subject to hydrolysis by water In final number if we mention this when we talked about the united city 1 recalled mentioned as the I don't think I did we buy did I actually think that took it out of the start of sideshow in any case water can hide utilize this cited the place over here removing replacing the United the Amin functionality with now a the carbon functionality and of this week this not should not be a huge problem of peso Indiana 1 0 by the way the result here is you're being on notice that this the result of switches the pattern of hydrogen bonding over here it goes except the accepted dogma and now it goes accepted donor accepted big difference right again it's a D and over here it's a D and that's a big difference that means that you're going to get inappropriate base pairing that means the replication of DNA is going to give you the wrong sequence transcription will give you the wrong sequence peso Indiana there are ends on there are apparent signs that are constantly circulating and looking for examples of European the security in in the DNA and when they encounter them they will replace that you're being back with the sea back to the correct base because they know that that's the 1 based at susceptible to this hydrolysis OK and this happens at a fairly fast rate I think the half-life is somewhere on the order of a year or something like that so 1 this means that on pretty much all the seized in your body had been replaced a couple of times at this point in your life and so without this mechanism the code would have been scrambled around a long time ago cases this essential really for life that's based on DNA which is all life on this planet OK so the shorter lived on a however does not need this code on a doesn't have to hang around for years upon years right and so for this reason REA has a ball with just using Yuri being in place of finding and by the DNA which has a much longer half-life really does need this mechanism for repair this makes sense questions about this concept 10 please get nervous when asked this question the notice any questions you know you feel free to stop me if anything comes up apart
and the other thing in addition to the bases that I showed you go in addition to this business about replacing by meeting with urinating on a bases are subject to heavy heavy modification and I'm sure you've just a few examples on the slide in political these highlight changes and some of these changes a relatively minor like this 1 used to have a I'm carbon-carbon double bonds and now it's a carbon-carbon single 1 but some of these modifications are you know Darius it kind of radical like this 1 over here which I has acidic gasses functionality appended to and these and these alterations to the RNA seek the RNA after it's been synthesized drastically affect its function of cases they control things by like altering the structure of Voronezh they can also affect the recognition this becomes especially important when looking at transfer are inmates were transferred on days are going to be delivering these amino acids to the ribosome during protein synthesis during translation and so it's not easy to get all of the encoding identity from this tiny little amino acid so instead the Cheonan EIS include on different modifications that make these changes to the amino acid a little bit more apparent to the ribosome during translation just allows a little bit extra testing or even a little bit extra testing during the amino acid loading step with amino-acid is loaded onto the Tr
OK so let's talk a little bit about structure 1st years the structure of the TRD that I alluded to on on the previous life and and on compare that against the structure of DNA so the big difference here is that DNA is always double-stranded it at least you know 99 . 9 per cent of the time in the cell so does not this opportunity the folded in on itself and for Watson Crick the base pairs on itself rather it has a 2nd complementary strands that conform this nice the DNA structure that we've come to know and love on the other hand on days are often single-stranded typically single-stranded and so for this reason they can readily form Watson Crick base period as exemplified by this region over here where this region over here but in addition they can also form boosting base there's little hard to see here but there's some non-canonical base pairs taking place in the center of the of the structure so in addition to the regular Watson Crick base pairs that we've discussed in the context of DNA we're going to start seeing some of the non-canonical who abstained base pairs which I believe we mentioned earlier we talked about DNA so we've delivered EC indecency base pairs for the good of come up more often again here's another example of RNA in this case Assistant strands of RNA forming a ribosome and I will topple our sorry forming a wide designed this is an enzyme catalyst that's based on on the has already as its backbone and so a wide variety of different structures of you know no holds barred all kinds of things are possible in the structure of RNA that formerly twisty structures that are continually surprising and that's 1 of the great joys of working with Lorene is that there is a large capacity forcing stuff that hasn't been observed previously OK so let's talk
of that Stratus systematized structure and and this is the same nomenclature that were going to use in the context of talking about protein structure as well so I want to get control of this idea of primary secondary and tertiary structure so starting at the top of the primaries to sequence our primary structure either RNA or proteins is simply it's sequence of cable listing on CGA cities etc. Ellen if you look carefully here you'll see some other weird stuff right like this 1 weird you know Greek symbol outside the middle of this sequence that's for 1 of those bases that I showed earlier where the base had been modified a pin that base happens to be essential for the structure of the resultant and tried to urinate in this case OK so there's a couple of weird ones in here and again there's a wider so this I think those again are modified basis a special cases that have been modified so and that's the primary structure simply the listing of its sequence and again were always want to try to in the fight crime to 3 prime direction so if the pipeline and 3 prime not depicted you can assume that the pipeline is on the left and the 3 crime is on the right OK that's the convention that will always be used for the secondary structure is on a listing of the Howard .period deformed Watson Crick base pairs and base pairs and what we take this primary structure we find that the I'm that these the yellow region informal loop and the region's nearby can actually form perfect Watson Crick base pairing complementarity to each other where if you look closely at this is actually 3 Hajime bonds the GC too for the USA 350 seats cetera going across here and then but those regions that are called loops beeps the sees loops at the ends of and then but there's 1 live in Bulawayo which is termed the in the code on the that's the loop that's going to then hybridized Watson Creek hybridized to the Ambonnay during protein translation Caracol again at Turin Iskandar liver the amino acid direct to the ribosome during translation that amino acid is attached as an ester to the 3 primed and of the Turin met again last thought about secondary structure and in this case the secondary structure looks a little bit like a cloverleaf OK that shown here and so for this reason this is often called a cloverleaf structure under the 1 problem is that what we actually look with that exactly what the structure looks like has solved by X-ray crystallography and shown in 2 views over here and it doesn't look anything like a cloverleaf anymore because it gets so bad idea in itself they so twisted around that it no longer looks cloverleaf like but the cloverleaf nomenclature has stuck with us and so we're going to refer to this as a cloverleaf structure OK I'm again down here in this loser so this is the intercut on loop that's going to bind to the Ambonnay tried form perfect what a great period complementarity if that happens that tells the writers that this is the correct amino acid way here at the 3 prime hydroxyl take away and that the 3 prime and of the T OK let's take a closer look at
secondary structures I've shown you some examples helices are secondary structures that are forming Watson Crick base pairing Jesus sees facing news on a new source Europeans are regions that are unpaired and allowed turns to take place let's take
a closer look so in blue and red and yellow these are examples of loops there's no base pairing this taking place but these form you know 108 of this form of tolerance in the secondary in the structure of the protein shake
it also had internal loops and where their servants across from each other and injunction lives where the 2 strands that might actually be connected join each other and need to sort of you know 3 arms leading away so there's really a wide wide variety of secondary structure good news in this day and age is actually totally predictable their programs called and fold in other programs that will actually predict the secondary structure of on the day and doing that the giving some insight into what the tertiary structure might look like and so you can actually just simply take the sequence in and they get a pretty reasonable approximation of what the I'm with the SEC with the structure of the on with the secondary structure of irony is going to look like vendors actually work pretty well they work by trying to maximize the number of the stability of the resultant Khamenei a by maximizing these Watson Crick base pairs OK any questions about our a structure In have of the tertiary
structure is very hard to predict it's
amazingly hard to get the stuff to crystallize this week does not like to crystallize in the past crystallization of course forces it to get closely packed up with other RNA molecules RNA as possible after backbone is negatively charged it doesn't like getting all packed together with other already molecules so structures like this 1 are pretty far and few between we don't have nearly as many already structures as we do proteins and again that's due to the fact they just don't like to crystallize with each other OK
switching gears and let's talk about the synthesis of a modern-day and a lot of what we know is that do you really to and some phenomenal work by the court Burke's father and son Roger Kornberg and in 2006 won the Nobel Prize for 2 determining structure on a plane raised His father in 1959 here's father and won the Nobel Prize for studies of DNA polymerase I've actually met Arthur Kornberg the father they were here when I suppose stock and on a group opposed stocks that met with them he actually carried this book with them like 1 of those blank pages books and asked everyone who met with him to sign the book because he wanted to keep track of everyone he met with his entire life which I thought was a economy eccentric but attaching a hobby so I don't know exactly what he's doing that you know and all the signatures of etiquette imagining 1 going back and looking up at the end Met then went on in the youngster has really those little there he was also a fascinating person to talk to really really smart unfortunately has passed away but really phenomenal scientists and OK so let's talk a little bit about on a plane race will talk a little bit more about the structure of a moment this is kind of a crude overview of the structure and short on this is that the enzyme responsible for transcription of converting DNA into RNA and on enzyme synthesizers this new this RNA in the 5 . 2 3 prime direction this is good news right there was the same direction malady that DNA polymerase and we talked about how all life on this planet synthesizers in that direction on the other really curious thing about this enzyme or the remarkable thing about this enzyme is it doesn't rely on a primary so I talked about how DNA polymerase always requires a primer and importance to the primer was to direct the DNA polymerase to a specific spot in the DNA RNA polymerase relies on transcription factors proteins that land on a plane raced into a particular region of the DNA and get it started
OK so let's zoom in and take a closer look so this is a very large enzyme pay and it looks a little bit like a job so the enzyme itself as it moves as it makes its response has kind of a job like structure has has a different mechanism than the right hand structure I told you about all of DNA polymerase looks more job like it would help make so much more 0 much-larger Makram mechanism we think you wouldn't think again so well sorry in-joke we're thinking that this bigger wanted to do some experiments with but we'll talk about it again so back to the top of the ingredients this is the on it's the on anything synthesized in red This is the on incoming DNA thus providing a template for the other for the for the DNA that's going to be transcribed and I'm hears a zoo the EU showing how please on the day that the synthesizer getting green forms of Watson Crick base pairing with the idea now and that is kind rejected out of the of the enzyme active site in addition there is a long tunnel through which the nucleotide triphosphate switches the building blocks of RNA travels to get to this active-site appear to these guys are kind of being sucked into this final and the zoom in here and that's where they're actually built OK moral less so the mechanism is more or less exactly what we solved with DNA polymerase has some different kinetics it has yet to differences in terms of the shape of enzyme but it's more or less the same mechanism has everything I told you about the magnesium comes out with the carboxyl key to many everything we talked about last time with DNA polymerase of applies on inquiries as well except for a the major exceptions there have been daily about that game mechanism exactly the same OK let's take a closer look at the the at transcription so during DNA replication there are many is synthesized to act so I'm not talking about transcription of actually talking about replication of DNA during DNA replication of all a little short stretches of RNA are synthesized actors primers for DNA repair replication case of the enzyme DNA primaries is actually an RNA polymerase and again this is his only takes place in the pipeline to 3 find direction OK so here's the parental DNA and purple that's going to be replicated in red this is the new strand of DNA that's going to be synthesized OK and so on I'm pulling thing these 2 strands of DNA apart are on an enzyme called Killer case and there's also some single-stranded DNA binding proteins that get in there and start to stabilize this single-stranded DNA DNA primates thing comes along and synthesizers these green on a primers that then are extended by DNA polymerase during our conversation OK so questions the head of the 6
closer look at the unit primaries and in red and this is the single-stranded templated this requires a R short primer to get the summarization started Oh OK so in this case I'm sorry I'm losing track of things so transcription also depend upon DNA primaries as well to provide the that our primary OK let's
take a closer look at transcription inaction so transcription that takes place at multiple sites along the along the DNA and that also involves not just you know 1 transcription event and then back to the start rather it's sort of like parallel growth of large numbers of em on days that are all being synthesized in parallel and at the same time OK so over here this is really and this is the but this is 1 end of the DNA here's the DNA here's 1 gene here's a 2nd gene over here and I'm here are some small and marinades have already been synthesized so what we're looking at is a looking at 1 2 3 4 5 6 7 8 9 10 etc. I'm on a play worries molecules zooming along here and as they get further and further along the gene these on a center be synthesized get longer and longer cases this is net result as a gives something it looks a little bit like a Christmas tree so this is an electron microscope micrograph it's an image that was taken using electron microscopes and to me it's actually spectacular as I don't fault my friends who use its image as a present for the Christmas cards because it really does look like a Christmas tree and I think it's just actually spectacular mope image over here OK let's
zoom in a little bit in order to get transcription started the art of the DNA passed it has the PCB and it's going to be transcribed gene it's going to be transcribed has to be identified using transcription factors said Trent Barrett declined to transcription factors and there are transferred there they all involve proteins so some of them sit on the promoter regions of DNA and there were another words they promote or accelerator or a in some way encourage the transcription of the DNA and then there's others that so our regions called Terminator is to shut down the transcription of of the DNI and we're going to talk next about the stuff about how it is that these proteins that bind to DNA and get on a plane race to come along and start transcription case of many of these transcription factors then and there our some of them the DNA into some pretty dramatic shapes because this involves Nunavut bending the the on sequence 180 degrees around them and the transcription factor and the vast majority of the majority of transcription factors and have healthy helices that fit neatly into the major groups and we've talked about this before we talked about how the sizing is almost perfect for a alpha-helix secondary structure of a protein to fit into the major agree but that's not the only way the transcription factors can find that can bind to DNA in this case for example that a set these are beta-sheets there their beta-strands to beta-strands that fitting into the major group there's no alpha-helix here so you can have a beta-strands and out helices binding to major groups of DNA let's talk a little bit about this venue next to the bending it's
actually and here's an example of this is terror binding protein riding the double-helix it's described as looking like a saddle here the stirrups down here here's the saddle appear the Selby Hewlett's is the Cowboys and on it's actually grabbing onto the DNA and forcing it into this bed configuration this business about forcing the DNA into particular structure provides an additional level of sequence specificity writing is recalled earlier we talked about how DNA structure was set by by the piste stacking and the different bases different base pairs had different ability to pie stacked different stickiness with each other so now we have this transcription factor that's literally sitting astride the idea may and forcing it into a particular configuration thus testing on the strength of its of its I stacking in its base pairs so in addition to the molecular recognition of specific bases which all describing a moment this has another level of sequence specificity in terms of just bend bending nests of the DNA which again is a sequence dependent properties OK so not all sequences will tolerate this From but and this is pretty dramatic rate is 100 degree angle that here OK so Our
transcription factors that decide whether or not they're going to bind to the US to the DNA based upon binding to other molecules transcription factors and rarely operating by themselves more commonly they form these large hole low complexes of lots lots of proteins that kind of pig pile on each other and then pig pile on the DNA OK it's like the Super Bowl Sunday except with 2 good teams on the field hockey but here is an example of what I mean by that case so in this case this is a transcription factor called the trip the family requests and no surprise the name actually here is very descriptive This is the this is the transcription factor that provides feedback the biosynthesis of tryptophan case of the air the cell has too much trip being synthesized and the transcription factor then jumps onto the gene and our forces it to shut off so shut down the synthesis trip that so what happens is stripped of them which is an amino acid combined directly to the transcription factor when it does these 2 out the helices here swivel consider going go from this configuration to this configuration and I know that seems very small were just talking about a little changed but that changes enough to allow Albert helices Canal it down into the major Group were previously they couldn't do that they previously like this the tryptophan binds that pushes the mentors other configuration and allows the binding to take place OK so this stuff is very tightly regulated by multiple binding events and when we take a closer look at the interactions that highlighted with the use of Idaho to call special once over here playing with
zoom and I want to talk to you about how the transcription factors recognize specific sequences of year that it would be bad news for example if the tryptophan repressor starts grabbing onto random sections of DNA and preventing the synthesis of essential and housekeeping genes for example there would be a total disaster for the cell the cell can have transcription factors running around and shutting off random things rather transcription factors have amino acid side chains that recognize specifically particularly DNA sequences and here's the way this works OK so In this case on showing you a DNA sequence and I've tried to simplify it as much as possible on the rightmost ratings are the Pentagon's that circles are the falsehood Istres of the DNA sequence and on the transcription factor binds to the backbone of the DNA OK and that's shown by these moves -dash lines and errors a cases it move on the arrows indicate hydrogen-bonding functionalities and the -dash lines indicate other interactions so for the most part the transcription factor is lapping onto the Oslo-based a backbone of the DNA and more less riding along at a pace so I like to think that this is kind of like a gymnast with parallel bars OK for a train on railroad tracks the where the tracks on the parallel bars are the fossil best a backbone of the DNA test the transcription factor was measurement here all of our cities you'd better focus I'm up on the parallel bars focus on the transcription factor undoubtedly walking along the and the backbone of DNA but I'm making the contacts through my hands on the parallel bars which are the transcription factor interacting with the backbone of the DNA notice that there no interactions with the the bases of the DNA OK and now as the DNA starts moving along this this is our sorry a transfer factor start moving along this DNA sequence it looks for places where its side chains can form interactions with the bases of the DNA the base pairs of the DNA of OK 0 and by the way although I'm using this analogy words parallel bars and I'm kind of standing part of this thing is moving at the speed of a free trade agreement is really cranking it standing through thousands of bases of 4 minutes a is really really move along at a fast fast clip and as is moving along it dangles on its side chains into the space OK so it's forming specific contacts over here but it's got you know it's it's it's a hazard that you know it's feet running along the bases over here kind of like a finger moving along a piano cases is moving along thousands of base pairs a minute and eventually it finds bases that have particular contacts that are complementary to the side functionalities of the transcription factor and those are highlighted by these areas a and notice now we have lots of areas that are going to the bases in the middle of the year what we switch from a non-specific complex meaning it's not recognizing a particular DNA sequence to it a specific complex there's a big difference in where these interactions take place over here they were entirely on the rails apostle Esteban wheels of the DNA the backbone rails and then over here about its found very specific places to interact with furthermore it turns out that it doesn't make direct interactions a transcription factor does not make direct interactions with the DNA base pairs rather it looks forward intermediate water that's been set up in a particular configuration determined by the sequence of the DNA this is a very important point OK and I want to repeat it because it's so important on the DNA is that is has ordered water on its surface there are water molecules that are patent by appropriate hydrogen-bonding donors and acceptors and that water sets up a pattern on the surface what this means that it is that when the transcription factor binds it can actually read out the sequence of the DNA by interacting with those ordered water molecules meaning that it doesn't have to push apart all those water molecules that would be naturally found on the surface of the DNA became the words it doesn't have to refer to put in all the energy associated with that kind of effort this year allows a transcription factor to race along the DNA sequence much work fast much much faster than it would otherwise be able to so when it finally do alights on the correct sequence of DNA can then form all of these contacts highlighted by the errors and many of these contacts are indirect meaning that the through the waters that are bound to the surface of the DNA that's a little bit of romance concept any questions about that yet has a slope along the lines of what the driving force OK excellent question randomly Sean O'Casey chance question is and why shouldn't bother moving along at all why doesn't get stuck there under the deal the transcription factor is looking for a more stable situation a so it when it's in this configuration over here and you know it's like me on the parallel bars it's not all that happy up there apparently you know it's it's a little uncomfortable and what looking for is looking for a greater number of interactions that stabilizes OK and so it's really thermodynamics that striding along OK so what it's looking for is the net energy gain that it gets when it forms a perfect hydrogen bond over here when forms lots of hydrogen bonds uniforms other contacts with the DNA sequence and that's what's driving along the question of equilibrium so yeah could get stuck over here but it's not all that happy being stuck over there and so it's looking for something more stable the request ensured the questions there it's 1 that's take a look at a few
other examples of transcription factors that this is a class of transcription factors called zinc fingers are there named after the zinc iron and zinc ion which is he waited between the middle to emitters also checked out here's the functionality that we saw earlier in this lecture in this case now it's it's forming the against to rising to plus ion and in addition to 2 violates their also relating to the zinc and zinc in this case is playing a role of structuring what would otherwise be a very tough sequence to structure the relatively short protein a real relatively small protein and so really relies upon this a help and help it forced it into this particular confirmation otherwise instances very small small proteins Smalls short sequences of a protein often called peptides meaning that the unfolded that they don't have any inherent structure in this case the zinc contributes inherent structure by warming covalent bonds to specific site genes found in the protein OK on something that's notable about this Is that there is that these are actually 2 transcription factors that are joined by linking sequence over here and so on the advantage of the zinc finger scissors you can string them together like beads on a string and in doing so you get greater sequence specificity where this guy over here would be reading out State for 5 base pairs and in this guy appeared be reading an additional 4 5 star putting together a bunch of us for applies and pretty soon you get something at specific for the 18 base pairs necessary to call out the particular ZIP code of the again 18 is the magic number where he has something can specify 18 bases that can then be a unique address within the human genome the figures are emerging as a really exciting powerful technology for directly manipulating DNA and were actually at the point where we can sort of program and specific sequences of the of zinc fingers that we know will then bind to specific sequences of DNA and doing this we can design their own transcription factors and even do things like bring along nucleus is to chop apart specific sequences of DNA and I do waiting for this my entire scientific career but I don't think I that much longer it looks likely that this is the sort of technology Bellamy gene therapy possible will be allowed to go in and fix .period incorrect sequences of DNA using artificial transcription factors like seeing fake like designed to rising figures like these
OK here's another example of a transcription factor this season Graille Tommy and I mean this is a transcription factor from we originally named for a particular phenotype in fruit flies and software again this has this nice alpha-helix fitting into the major groups in this case this alpha-helix acts as kind of like a bar-code reader because everything I told you previously about riding the rails that's applicable here OK but the thing that's scanner tickling the piano keys it's checking out the sequence is this major alpha-helix that's fitting neatly into the major groups K and like a bar-code reader you know you're at Albertsons over here and I you decide to get the option that doesn't have a line we have to do the scanning yourself you know what a pain in the neck at right yes you can in there you can of swiveling that the barcode back and forth on this relies upon a similar swiveling kind of action in a case where the alpha-helix is kind of twisted backwards forwards twisted like that and doing that then checks the sequence of the DNA and we know that because of the May changes to over here that affects how it swivels and effects of specificity in the major grew for the DNA from 1 last thought this useful trailing part over here that's the 1 of the terminal I this protein and it's interacting just a little with the minor groove up here and there it's a little bit unusual in terms of arms In terms of transcription factors but we found that actually that little tailing peace is not essential for the function transcription factor you can cut away and transcription factor remains the same case and by the way those kinds of experiments on describing chopping apart transcription factors to check how they function does make for great proposal topics OK this is 1 of my
favorites of a huge fan of just collecting protein structures I love this chopsticks and this is a leasing zipper and it's name for the hydrophobic functionality is found in the very center of these site to help helices that form a coiled-coil with each other and their held together by this season for Beasley site sightings from leasing functionality simply a hydrophobic functionality and on this grips the DNA like chopsticks and with 2 of the Ulysses 1 interrogating this major grew up here and the other 1 interrogating this major Group down here and I am it is truly beautiful structure OK let's put everything
together as it turns out that would have been showing you with the isolated you know
chopstick said accident this
guy that's not the real picture of how transcription works transcription works again
by having large numbers of proteins pink piling on top of a specific DNA sequences and that in turn can recruit RNA polymerase and other factors that are necessary for on a polymerase to start cranking out on during transcription and arms there's a lot say here I think I'm going to keep a relatively short me show you some specific examples but they're actually useful
laboratory of RNA a transcription OK so a
classic and 1 that's used the routinely that applying small-molecule control over Cheney's transcription is the lack repressive so the lack repressor binds to DNA and then in the presence of unit of lactose and changes its sequel changes its conformation and then is released from the DNA and then that in turn turns on expression OK so that turns on transcription which in turn Trans turns on translation and that combination of transcription :colon by translations were going to call expression because it means the expression of a protein from a DNA sequence now here's the this works case here's the structure over here and then ingredient the use of the Galacticos molecules so here's what lactose looks like recalled that lacked lactose is a dies after I consisting of a Galacticos and a glucose and held together by a bit like a sites at once but it turns out that yes you can even go so this is used very routinely in biochemistry and chemical biology laboratories as a technology for turning on expressionist specific gene OK said for example if you want you know I'm just making this up if you want to meet us there were red or something like that you might want a gene that can be turned on in the presence of lactose no exactly like the 1 that but that's century your goal OK in my laboratory turn on the expression of a particular protein that you in a study and in greater detail and I would actually be better example so that if they have the DNA in black and the call I you then add lactose appear the problem there's a lactose has a very short half-life in In cells it can be hired to relies for example by bitter Gladys ideas into the tumor on sack rides on and so on oftentimes instead of adding will added a synthetic analog collectors called by PTT and this has the bio like acidic born in place of a regular quite acidic born so it's no longer recognized by data collector societies and has a much no longer half-life its half-life is still not break its Tiger lies by water but very slowly over the course of a few hours so this you know how it works but it's not the world's greatest so the way we did this is we grow the call ourselves we then dose and IPT GE that in turn frees up the DNA sequence and the DNA sequence gets turned on and the protein of interest gets us emphasize forests can we do this all the time and were not alone in this balance if not hundreds of thousands of laboratories across the country are doing this as we speak in cases very common technology it's something everyone needs to know about but a major goal of Chemical Biology of course would be the exhibit this level of control over specific genes it would be very cool if you can add drugs small molecules given to patients that would turn on specific genes or shut off other genes and if we can do that we basically cure many many many diseases that would be very powerful and we're not there yet but that's 1 of the a major goal of a number of chemical biology laboratories and also pharmaceutical companies OK so
here's the other thing you can do With this this particular transcription factor it turns out that you can become separated out the DNA binding domains shown over here separate from the transcription activation domain OK and on you can then use the DNA binding domain to some sort of the protein and use the transcription activation domain to say a protein and when these 2 interact with each other then you get the functional complex of the 1 of the transfer of the transcription the transcription factor allowing transcription down here OK so these 2 this interaction is protein-protein interactions on is enough to bring together the missing pieces and the restored the transcription factor in then initiate transcription turns out that this is a very powerful test for whether or not proteins will interact with each other whether B and pray will interact with each other and this is something is called a yeast to hybrid systems so the hybrid of these 2 proteins over here and used again very routinely hears the way this
works Casey do this experiment where if the protein that is if the proteins can interact with each other it turns on transcription of the gene that encodes beaded what decide it's bitter Gladys side is in turn can hide realized this and oxtail Anderson Doc salt and then spontaneously .period dying deformed in deep indigo blue I see people go their genes today blue jeans are dyed using this guy right here take that step precipitates out a solution and forms an intense intense blue and you can actually see that here OK so clear colonies like these no buying blue colonies that equals a protein-protein interactions have because that means that in prior interacting with each other and that in turn means that that we're getting a transcription to result in Over expression of the data Gladys student don't think now
so far I've been showing you some pretty simple examples turns out that things get a lot more complex when we start looking at you carry out morally processing and I think will do .period here when we come back next time we'll be looking at all the ways commodities modified during the periodic transcription and translation


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