Lecture 05. Non-Covalent Interactions, DNA.

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Lecture 05. Non-Covalent Interactions, DNA.
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Lec 05. Introduction to Chemical Biology -- Non-Covalent Interactions, DNA.
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Weiss, Gregory Alan
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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: 0:10:56 DNA 0:11:11 The Lennard-Jones Potential 0:14:28 Rouges Gallery of Non-Covalent Interactions 0:21:44 Comparing Energetics 0:25:06 All Biology Involves Water 0:28:36 Receptor-Ligand Interactions 0:33:01 Biooligomers on Earth: Modularity 0:34:35 Form Follows Function to Biology 0:39:51 Non-Covalent Bonding Summary 0:43:31 Structure of DNA: Double Helix 0:49:02 The DNA Bases 0:52:40 The Missing 2-OH of DNA Confers Stability 0:59:25 The DNA Bases are Subject to Modification 1:01:39 Watson-Crick Base Pairs form U-Shape 1:02:35 Molecular Recognition 1:14:13 DNA Intercalation: Untwisting of DNA
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my name is John there was suddenly Cisco's Russell Crowe OK so we're ready to get started 1st of a quick "quotation mark chemistry is the biology would notation is to music To be this really grabs at the essence of chemical biology in the sense that the notations on musical scale allow creativity they allow other reformers to interpret the works in new ways and I give the work context chemistry does that a biology chemistry gives us an opportunity for us to be creative about biology and invent new ways of thinking about biology it's sort of the underlying basis at the level that is a bonsai keeps saying or biology and to me in some way this really captures what kind of you in this class OK I think so I had this week we're at 30 week 3 which is amazing the OK so it's with
3 so we're the Chapter 3 and we're talking about DNA and all our knowledge of DNA was really I said in place by the people of front of you these are the Giants really field structural biology determine structures a DNA and in the 1950's this includes the great Rosalind Franklin whose very accurate X-ray diffraction structures the pictures of the X-rays deflected off of fibers of DNA has set in motion the determination of the structure she was working with Maurice Wilkins and 2 physicists Francis Crick and Jim Watson went on to solve the structure of DNA as will see in a moment really 1 of the key insights well as at the level of Adams of bonds in the sense that they discovered interesting to Tom realization of the DNA bases that made it possible to have what we now call Watson Crick base period between the strands of DNA getting a little ahead of myself but so that's where we're going in the next week or so and so we're going to be finishing up non-covalent interactions than talking about the structure of DNA property and finally DNA reactivity of small molecules is a large chapter we have a lot to talk about so but there are 3 things are going to go up and not the fastest in the same speed but we're going to gloss through a few topics that are less important and what we do this means then that you can focus your reading in your study just on the level of detail that recovery in the class
and some announcements in the textbook read Chapter 3 against skin concepts not presented a lecture don't get too worked up about them and Chapter 3 problems do all the odd numbered and all the asterisk problems and in addition I want to encourage you to get involved here is hereby this is a super recorded many of you I know I aspire to become physicians or scientists or pharmacists or whatever it is that you aspire to do all those big plans require preparation they require some evidence that you've gone beyond the ordinary and I might encourage you to do this offense and 1 way to get involved is to look around for other opportunities to volunteer this is 1 that's run by my friend who was but with 1 of the founders called the social assistance program for Vietnam if you go to this website there are opportunities to volunteer to spend 2 weeks in Vietnam in a rural part of Vietnam and administering medicine you know you'll probably not be of course you know drilling people's teeth and you unit doing open-heart surgery but you will get a unique opportunity to actually see those types of things happening and I and that's really important if you aspire to that kind of career it provides evidence that you're qualified picture committed and unambiguous someone who's altruistic all of those things professional and I graduate schools look for a new application you need to be doing those things now OK and I'm on your side on this book and I will help you get in the finals opportunities will bring them to your attention like this 1 and if there's something in particular that I can do to connect you with a let me know and I'll do my very best on your behalf OK I knew along those lines are laboratory always has openings for talented undergraduates and it's competitive but you have a chance to participate at the poor level of graduate students undergraduates in our laboratory at doing actual science the publishing papers with us there are making discoveries and the participating as full members of the team on OK here's how you apply US-India paragraph describing your career bowls and how research in our laboratory would advance those career and educational calls and in addition sending a copy of your college-level transcripts this includes any transcripts at community colleges if you're transferring many my best students who transfer students stimulus transcripts as well and also sent me 3 names and e-mail addresses of TVA's know you well in labs sections OK and I'm going to e-mail them and a master what would what was this person like that in the laboratory where a you know the first one out of the room where the last 1 out of the room under their new fall you around the laboratory you this is looking to the slipping core with a pretty independent OK so or find out about that sort of thing and that's how I make that a decision on who acceptance the laboratory OK and and then of course the residents of this is pretty standard if you're interested in doing research here your mind which I highly highly encouraging today so this is a pretty good way to go about it OK this is an effective way to get noticed and to get that job that you did any questions about these opportunities why think important things like that OK see me in office hours if there's something in particular that you want from me and I'll try to help you out OK office
hours this week speaking of which I am tomorrow I'll have my usual office our 245 to 345 usual location Thursday all have my office 11 to 1 usual location and in addition Miriam will have Oropesa Friday's 132 230 and critical could you are written so critical .period ETA should be joining the team an unprecedented this time were viewed Tuesday's 233 said that and should be having her office hours Tuesday so that is that we spread out of office hours so that there's 1 every day the week except Monday and because I knew you very busy on Monday doing all kinds of things I hope you're having fun yesterday but I'm not yet so every other week there's an office our the Staggers there at different times so you can have your questions answered and again I'm critical is a graduate student in my laboratory she knows this material as well as I do she's really smart and you can go to the office and couldn't answer that's as good as an answer that I will give you a pay and for that matter you can also e-mail the tears with your abandon questions OK I'm looking at you we find that person again was like 1 person the classes Buscemi 10 e-mails a day but you know I will do my best but you can also e-mail the tears as well we had all along those lines I send you an e-mail saying I don't send the Book of potential journal articles and the reason is I must I open my box and I had like 15 of those and I got to the point where I was bouncing messages because inbox was so full so if you send me those I can't do very much with them obtain my client my box so I propose we do use instead of you e-mailing me them instead bring them to my office hours bringing cricketers office hours are Miriam's office hours and answered questions that a and now the standard question I get asked is is this article appropriate and my answer to that is if you follow the guidelines it will be appropriate now in addition when you're writing your summary your new report on the Journal article focus on aspects of the article that fit the definition chemical biology Caso paper and sell for example is going to be a very needy paper going to cover about 10 pages it's going to have you know it online figures and of some of those figures some of those experiments on exactly what we'll call Chemical biology don't focus on those focus on the ones that chemical biology related otherwise I don't know that you know the definition chemical biology OK any questions that I guess what we're heading into midterm season this is Week 3 so we force next week but we will have to add a midterm next Thursday a week from this Thursday and there will be a review session in advance by the TAC time to be announced in critical will arrange for this and the seeding for the midterm will be assigned Miriam noted assignment and it's really essential that you bring a UCI student ID will check the idea is to make sure you're seated in the right see if you're not seen in the rights ito be treated as an academic honesty infection and no notes no calculators and electronic devices you don't need them the smart phone had many questions about the OK now I know you want to know what will be on the mid-term OK so let me tell you it will cover 3 Tuesday's lecture 1 week from today and so we will be about halfway through Chapter 4 on on Tuesday OK so plan to read to you about halfway through Chapter 4 and that's the chapter on and that's where I expect to be for Tuesday's lecture it's possible I might get behind but I'm really trying hard not to do that the paper I will also post a practice turned to the Web site and you can use that along with the discussion worksheets the assigned problems as a guide for what will be on the mid-term apace the will look very much like a compilation of discussion worksheets of assigned problems and and the practice mid-term OK and I'll be about as long as the practice mid-term as well so in the practice mid-term comes out of those 2 versions 1 version will be blank 1 version will be the key the blind Virginia should print out and then give yourself an hour and 20 minutes and make sure that you can handle it OK and I at the end of that and check your answers against the key but give yourself a real practice OK that's pretty important I think OK so anyway and that's the plan any questions about the midterm I know you will have a of questions I look forward to hearing about the my office hours erect I want to go back to
finish up a discussion of non-covalent interactions hands out where we left off last time with charge charge
interactions and now ready to talk to you about about interactions between atoms that are charged OK neutral atoms that are interacting with each other and these are described by a Leonard films potential which is an equation that describes how he's neutral atoms would interact with each other another way of describing these neutral atoms another term that's used in probably 1 you can is higher London dispersion force prepared so you have to say neon atoms that cozy up next to each other then on they will interact through London dispersion potential of force and that's what I'm describing here OK so it's just a couple of different ways of saying the same thing this happens a lot of biology not necessarily between Leon Adams but certainly between the aliphatic side chains hydrophobic side chains in proteins and in interactions with each other interactions with lipids at the a plasma membrane of the cell phone and a whole host of other non-covalent hydrophobic hydrophobic type interactions this turns out to be a very potent and and very strong force in biology professor we need to understand it better and so the energy the potential energy of a vendor walls interaction yet another word to describe it is equal to but that is proportional to 1 over the 12 minus 1 of our part of the 6 these terms the segment term deals with the diamond earnest but that's what I did not so important so let's ignore that lets focusing on the 1 over on the 12 term and 1 over artist 6 1st notice that it's is 1 of Nevada 6 and my and potential terms means more stable energy lower on this Y axis of potential energy over here OK so that's going to be attractive terms hydrophobic if things attract each other pay not just due to whip repulsion from water will talk about that next but hydrophobic things want to stick to each other and they're going to do this with an attraction that's proportional to 1 over on the 6 the fact that it's 1 over to the 6 as opposed to our this 2nd in the charge charge interactions means that this is a much shorter range attraction this attraction takes place on a very tight the distance scale a now eventually the the the 2 Adams in this case as described here 2 molecules 2 molecules and banging into each other and go past the point where attracted to each other again at that point the electrons are trying to overlap with each other that's really bad news right window by the Polly exclusion principle that that's not allowed and so in the same way that my fingers are never going to fuse with each other just gonna bang off of each other on the Adams push away from each other and they push away from each other with the repulsion for hours or repulsion potential that's proportional to 1 over or to the 12th OK and so this means that this is extremely short range and extremely short right to the 12th power a large number so this means that this really dramatically up pushes apart the Adams if they happen to get too close to each other turns out that arm there are a whole series of other non-covalent interactions that we find in biology that actually contribute quite a bit of non covalent binding energy here for example are the dispersion interactions that we discussed before and the previous slide and cities include things like aliphatic aliphatic interactions but also aliphatic interacting with the Hydro filler ahead of Philex molecules so here's water interacting with methane they're going to interact with each other and have some attraction on this number here minus . 5 deminers .period 70 calls from old is pretty low but this is not a tremendously strong interaction work its strong is when you have a molecule that has become a hot large number of functional groups each 1 with . 5 K calls from all here . 5 years .period five-year winning some up across all of those you're starting to talk about big energy OK now just to give you an idea you need to know 1 fact that I think is really important and the fact is important enough that I'm going to try to ride on the board over here in the corner but the fact is that about a factor 1 .
4 K calls from all over will be a factor of 10 in In fact equilibrium constants OK so 124 were take calls from all it is a magic number in chemical biology OK so look for 1 . 4 K cost more because that tells you that that's fevered tenfold over non-binding in other words the interaction is going to be 10 times more likely to form the not form a case of factor 10 in terms of equilibrium constants OK so if we're talking about something over here that's only . 5 . 7 3 calls from all you have to start summing up a whole bunch of these to get anywhere in terms of enforcing the interaction on the other hand some of these other interactions can be quite strong and let's take a closer look at those nets OK case so
for example we talked a little bit about hydrogen bonding hydrogen-bonding of course has a donor and accept the and here's a range of strength hydrogen bonds vary enormously in estranged from about 1 takeout from all all the weight of 70 calls from the strength of the interaction depends enormously on the identity of the donor and accepted when the donor at work and or acceptors are charged if either 1 is a charge of functionality the strength of this hydrogen hydrogen-bond goes up enormously and this kind of makes sense right because remember earlier I described a hydrogen bond as a kind of a special case of a charge charge interaction in which a hydrogen is being shared between 2 adults OK so if 1 of these happens to be charged as we do much stronger charge charge interaction speaking of charge charge interaction salt bridges are the crew of the potential that we saw on Thursday the use of the charge charge interactions on these very also enormously depending upon the environment that the US bridge has defined itself where a R A where water can shield discharged water or pick counter lions can shield discharge decreasing at considerably and making the interaction much much weaker so assaulted or assault bridging interactions a charter which is a way of saying charge charge interaction found in a hydrophobic environment say the interior of a plasma membrane is going to be a much stronger interaction than 1 that's found out in water where there's plenty of water and and counter ions to shield the a charge of Hayward does provide accounted for and against the charge recall at those in environmental terms are embodied by the 1 over for pie excellent term and in the economic potential that I showed you on Thursday OK in addition there's also dipole dipole interactions which are all alignments of densities of charge where we have a little bit more had negative charge on oxygen over here the dipole is pointing in this way on 1 the road to the right on upper of acetone and to the left on the lower acetone the to the the stifles want to cancel each other out by canceling each other out that will come give you a more optimal interaction and that's where some potential energy finally there's also a whole series of aromatic eerie interactions and aunt in general all these include both face-to-face interactions where you have achieved faces of AI benzene ring that are interacting with each other notice in this picture over here that the top benzene ring is offset from the bottom 1 and this makes sense we're going to be looking at regions of electron density interacting with Redrock regions of electron poverty OK that that's actually the basis for the interaction and so for that reason we also see very commonly edged face interactions they said this is the 1 that will see in a moment when we start looking at high stacking Indiana but in addition you could have a hedge of an aromatic system interacting with the face of another aromatic system down here and that's I'm as strong credits as equivalent strength even know you expect no tasted the ideal that's actually not what we see when we start looking at large numbers of popular Matic your manic interactions we see these age edge face interactions all the time OK and then finally there's some other ones that are really bizarre and they include charged interacting with the electron rich aromatic rings in this kind of makes sense right you have something that's that's of positively charged have something it's very electron rich in terms of the ring system so these had iron pipe interactions which is what this 1 is called found pretty ubiquitously in biology oftentimes playing a commanding role playing a really key role in our chemical biology OK so these are ones that I'd like you to memorize and like you to know something about the strains which 1 strong which ones we don't want you memorize the numbers per say but I want to know something and be conversant on the relative strength of a relative strengths matters if anyone think 1 last thing to keep in mind if you're going for this 1 .period K help promote again but you can have a summation of a large number of interactions to achieve that 1 . 4 4 key Kallstrom all or even more energy example that very shortly now it turns out that it's actually a little bit tricky to start comparing energetics when design and say the perfect had high interaction and what ends up
happening is that you get all the the complications due to water a so let's imagine that you are designed in the perfect can pie interaction and in doing so he put this possibly charge saying that forces all of the water around it to rearrange itself rearrange itself turns out that such a complicated thing out of to mutation of water but it cannot be neglected a peso what we do it is but we make a very important simplifying assumptions and I'll talk more about water on the next flight but before I do want waters since we we just happen knowledge in advance of water can complicate everything right it's president 55 Moeller and concentration in yourselves and we can't neglect of peyote has its own energetics it's does not as a should of the
slide over here if examples interacting of hydrophobic things aren't so it's own
interjects a really complicated upon actually very hard for us to understand that pinned down and so on it's really difficult to estimate the entropy lost or gained in interaction due to that rearrangement of water when you start making changes so what we'd like to do this compares things that are similar to each other as possible said this is the simplifying assumption that I alluded to earlier here for example is an example of that OK so here's to possible transition states and in intransigence to our 2 possible mechanisms mechanism number 1 involves it into reaction mechanism number 2 involves the same molecule undergoing in elimination reactions and the key here is that the molecules are identical OK that I that extreme similarity makes the comparison between these 2 much easier to make a pay and so for example if you're looking at 2 proteins we can look at Andy protein was like the bound protein but on the other hand we're not trying to sneak all kinds of changes to the protein structure over here problem is proteins are rarely you know like looking like this 1 that when the wagons on balance so the simplifying assumptions will start to cause all kinds of problems here is 1 that works and you can make a single change to the surface of a protein and then compare the altered protein the prepare interaction with the it with a lie again so for example we could change the size of pro program to a methyl group and then compare them what's happened what's different in that I receptor like in directions a case all you've done is moved to methyl groups that's about as simple as it gets right answer so that type of that type of experiment is an easy 1 to make comparisons to again by doing that we're trying to minimize how much of the water has to rearrange itself at that interface a competitors out actually this assumption works most of the time and so In short of being good scientists not changing lots of variables at the same time pays off biology because underlying everything we do is as complicated solvent that we operate in cold water but stick closer look
at the structure of water from the face of heroes water in ice and notice how neatly regular it how much the auditors had any here's water in a solution as liquid water on initial screens the complicated 1st on notice that they're always starts at the bottom lines of the hide your mind these high bonds are pretty much maximized waters not passing up any opportunities want to itself OK but the hydrogen bonds in the liquid solution are non optimal care water in solution each water molecule is on jam-packed with other water molecules and oftentimes the hydrogen bonds are slightly distorted or they don't have the the right distances of those little distortions and that lack a perfect distances makes the hydrogen bonds in liquid water weaker than they are in our solid water furthermore I have molecule of water in its own you but a lot of other molecules of water is it behaving kind of like it's on a crowded dance floor the paper said on its bouncing around wildly against its other you know molecules at a nearby and on interacting with lots of lots of different molecules hereby constantly breaking interactions and forming new once in head so on water is actually very complex week and distorted hydrogen bonds pay
and in addition when water cozies up to hydrophobic services it tends to perform a very ordered structure that starts to look a lot like the structure down the ice and on this this works by water for satisfies its propensity for 100 bonds by forming up clathrate like structure so for example here's a molecule of methane encapsulated in 1 of these clathrates of water were clathrate is just simply a structure of water that satisfies its desire to form hydrogen bonds with itself appear with other molecules of like kind and this really dramatically changes the strains of nearby non-covalent interactions of this does things to you on strengthen those non-covalent interactions because every time 1 of those matches a hydrophobic hydrophobic interactions breaks than water hazardous smog in between now broken interaction and 1 of these clathrates OK that the formation of the clathrate the formation of an ordered structure costs energy it's it's a loss of entropy this is a more ordered structure than the structure of disorganized water that I showed you earlier in solution OK so for this reason hydrophobic the hydrophobic molecules are women against each other they also want to find each other in water and and this is sometimes referred to as they are it is this is this is actually a water rebound effect forgetting that the technical at 1st OK anyway so "quotation mark it's it's it's sometimes referred to as a hydrophobic effect of in water OK now let's take a
closer look at a receptor like interaction of zooming in and at the level of atoms and bonds this is a molecule called human growth hormone and yes that Lance Armstrong admitted to open that he took human growth hormone to win either help him recover basically from different stages of the Tour de France during all 7 of his victories in really annoys me actually I think it's a lot more about that but I'm of myself back OK Gowen human growth hormone binds to which receptor on the surface of cells it's it's stimulating the growth and recovery of those cells of stimulating protein production etc. and when filings to the surface of the cell that to the group to the binding partner on the surface of the cell receptor then all of the region that's in on this surface is very OK so in other words if you common binding protein binds over here and then makes contact with each of these colored by and Adams Gay everything that's in white here is still out in water out in the solvent it's not interacting with the receptor at all now when I was a opposed stock I would repeat a classic experiment that was done by Jim Wells and Jim Wells and his co-workers found that even know there are 19 residues that are buried on the surface there 19 amino acids that are buried only the ones in red are actually contributing binding energy OK so notice that all of this other stuff is and that is in bloom that is buried is not at all contributing binding actions although there's there's interactions between the side chains of this these 2 proteins there is no binding energy that's being exchanged ordained by that interaction has said just because 2 molecules .period each other to functional groups find each other in space does not ensure that there's actually going to be a net gain in binding energy because again that NEC gaining binding energy includes both the the strength of interaction but must also include the water ordering and disorder in terms which we've been calling entropy earlier OK so in order for this election to take place you're going to be pushing out ordered water and giving some entropy in some places and other places losing symmetrical they know we look even more closely let's just zoom in on this red patch over here this red patches and turned the hot spot a binding energy that's where the by the energy allowing these 2 molecules interact with each other is found it this is the essence of the non-covalent interactions between human growth hormone and finding part of human growth hormone binding protein and reading these are the functional groups that are found in this red patch a case of red patches over here and I'll show you that the functional groups where ingredients these are on carbon atoms in blue that's a nitrogen and red that's enough oxygen paying noticed that the and hide durability functionalities the guanine of enlarging over here a bunch of nitrogen and nature over here and oxygen oxygen over here notice those are around the periphery of this red region the around the outside of this hot spot a binding energy at the center of the hot spot is largely hydrophobic attack notice that it has lots lots of carbon source of benzene ring smack in the center there's this aliphatic chain that's capped by any means functionality but nevertheless this is an aliphatic chain out of the aliphatic functionalities over here and over here and over here etc. case so in other words the outside Hydeville like the inside hydrophobic and so when I come molecules functional molecules find each other this is a very common way for them to interact with each other through a small set of residues that warm this hot spot a binding energy which again kind looks like a core sample through protein outside is high due filet inside hydrophobic I think the question so far OK let's talk 1 last about 1 last section of Chapter 12 . 2 4 about Chapter 3 there's this concept that modify Gomez on Earth ,comma highly modular we've discussed this before this also extends the Polly key times and the terpenes which would oppose place of grains and the polypeptides which are cause which are composed of your Maloney or acid your subunits that strung together with the red bonds indicate the where the connection between these modules such is the amino acids as individual modules in a protein K and furthermore this is also found in the sack rights where you have this bunker-like acidic bond that connects the guy can fragments together but there is
also a numerical amplification and biosynthesis so if there is only 1 or 2 copies of DNA Purcell depending upon whether it's a opera carrots celery you cannot excel on some prepared cells and William or the 1 that was to simplify the and then on a beach DNA is transcribed 10 to 50 times and then each RNA was translated say 10 to 20 times so in the end you end up this massive amplification of the signal going through the seller with 1 copy of DNA you can end up with millions of products from some enzyme reaction down here last thoughts on
the form follows function in biology please the bonds that joined together at the A-League generics subunits and are also have a strain that follows the function of the functional requirements of and simple example and when we look at the half-life of lipids we find that actually the Astor bonds in Olympic have a half-life on the order of yourself a peso Esther is not so stable compare that against you a down here which has a half-life on the order of 220 million years and that's its half-life for DNA and on In retrospect this kind of makes sense right because on DNA has to be a on you know has to be a buyer would remove the wife of the organisms OK and so on more down the point where were routinely taking advantage of this tremendous stability of DNA to the amplified DNA France even extinct organisms like wooly mammoths and a species of all of us a prototypical humans that happenings haven't lived on the planet for tens of thousands of years and that sort of thing is going on right now in laboratories taking advantage of the tremendous stability of DNA now that you're here which is approaching and has a lifetime and order a new 300 years or so and then we you can see that way we can find no motive not anyway so His depends on the humanoid happy about my here obviously doesn't exist that long but and didn't so I certainly the lifetimes here on the island Our following the function they proteins don't have the last as long question how does 1 get a PhD that's going to take a 5 or 6 years studying them in trying to measure these have wives of 220 million years they would have any ideas how to do that experiment I can guarantee to you it's not like you know you set up this tested and then you check it every 20 years to see how much gets exclusive How would you yes yes thank you at that a small amount of on him now he use a large amount because very little skirmishes degraded how would you do that yes it is OK but then you and I know if the decomposing environment is different than in the cell that we about half lies in the itself and yet model organism you mean now I wanna know what it's going to be like the last 7 years out in the cellar this other 1 of your question over here OK deftly India's radioactivity because you need something that super-sensitive how would you do this more on the Net al-qaeda getting close Kurdistan and Ryan compliance binds getting closer the suggestion was radioactivity suggestion is to look for a tiny little quality radioactivity gives you that sensitivity but I am a unit is for 220 thousand euros a 220 million years a case a Harry and his experiment we have a sensitivity winner look for tiny quantities and extrapolate How you into model 220 thousand years yet Carl OK but look the fusses yeah we do that more yet you have to do so you you don't have a pacy 14 a pair of yes you do that the yield on the 10 year period more and more of what you have OK so but the problem is you know all the conditions it's experienced over the Yellow Sea 100 thousand years or something right so I mean how you want to do this in a controlled circumstances you wanna have everything decimal testing or you know exactly what's been festive right but you know areas wait around for 220 thousand years at 20 20 million years when he entered OK I'd like you know what this 1 up through the 1 that you should be able to design look it up and Andaman come back on Thursday will talk about this but I'd like everyone to have a look at some of her support I'm OK let's
talk let's summarize what we've been talking about in terms of non-covalent interactions these are completely ubiquitous in biology good news we only have to learn to equations which govern all interactions in the chemical biology those were the cool onslaught for the charge charge interactions and the Lennard-Jones potential for the uncharged interactions of pay and so we know those 2 equations set what's really important what's important to us is not the word wouldn't the plug-in and you no charges amendment a radius that's what's important to us are the relationships the distance dependents the 1 over our squared versus 1 of our 6 that type of distance dependence makes a big difference in knowing that sort of thing and having surrendered to the grass but that time is going to be very important so and I'll just give you quick example on for example and we now know but if DNA is negatively charged it's going to attract other charged ions to it from great distances right because this independence was only 1 of the artist's 2nd power which is 1 of the hardest 6 and in addition we learned that these non-covalent interactions are very sensitive to the environment the distance and the geometry of water is a really slippery molecule to understand to disable leased as malleable structure and on they can dramatically alter the strength of non-covalent interactions this makes it really tough for for us to draw any generalities because water is and a intermediate lubricant between all of these interactions and it plays a complicated and sometimes hard to us at hard for us to define role and they're still big arguments that are going on and in water chemistry to the state for example but there's an argument going on about how many answer found on the surface of the water rats the pH at the surface of the water and there's been a set of dueling papers that have appeared that contradict each other the 1st paper had a title like the pH of of the surface of water is more acidic the next article the next article by the competitors said the pH of water at the surface is more basic and the 2 and these groups have been arguing backward and forward and both making very reasonable arguments for years OK the truth is what we found is actually and it's somewhere in between those 2 and you can actually see evidence for either 1 and it turns out to be a very minor effect that's not so important biology but the point is is that water itself is such a complicated fluid that were still using the latest techniques to try to understand it better it's not fully understood the pension bonds have donors and acceptors and there are also very susceptible to competition with water for those hydrogen bonds but I would like you to know that the approximate strength the relative strengths not approximate with the relative strength and this is dependent of non-covalent interactions that's important in a case that's a summary of Chapter 2 any questions about Chapter 2 yes Chelsea in yeah I really want to know that appeared at Super reported that said Henderson Hossa Bach equations and that hopefully will become 1 dutifully need to know that questions OK
let's move on I want to talk to you about the structure of DNA and this is the classic structure of DNA 1st proposed by Watson and Crick in the 1950 to yeah 852 somewhere on the part of the structure of DNA has 2 strands running in opposite directions to each other so empty parallel to each other the strands are held together by fossil investor bonds which will look at more closely so here's a schematic diagram of what the structure of DNA looks like and the use of space-filling Vero where each 1 of these spheres is Abendroth Creole to approximate where the Adams are where the outermost electrons of the Adams but 1 thing to notice is that DNA has on 2 groups of carrot has had the distance here between these 2 strands is very close versus the distance here between the 2 strands being much further away these are going to be called the minor and major groups respectively and this is the origin of the fact that the is a double helix I think it's commonly thought that DNA is a double helix because it's true but relatively watching molecules that a twisted with each other but that's actually not the case as a double helix because it has a minor groove and a major creative and I believe the next
slide will show us that more closely cases in blue this is the major group of DNA and ingredient this is the minor groove in the red this is the possible disaster backbone of DNA that we've seen before Faso again notice that there are 2 once there are 2 helices better running parallel to each other on major groove and a minor role of the structure of the bases is going to set up this major and minor groove relationship as we will see shortly DNA bases base pairs and that U-shaped ensures that you're going to get a Major and the Minor grew for the inside of the you know it's going to be this minor groove and outside will be the major grief but I'm getting a little bit ahead of myself the reason why this is important is as see in a moment proteins like to interact with the media group of DNA whereas they can fit in to the much closer in the cities of the minor groove of DNA rather small molecules will fit into this minor groove and try to meet largely avoid the less cozy major groove of DNA tests almost immediately we can start to make some predictions about where stuffed lions just knowing that DNA is a double helix double by virtue of the fact that has 2 parallel helices minor and major growth so this DNA
structure immediately sets up replication this is the original 1953 paper by Watson and Crick and this is the very last sentence the paper in which they had this incandescent understatement it has not escaped our attention has not escaped our notice that the specific pairing we're postulated immediatly suggests a possible copying mechanism for the genetic material in case of you have 2 strands of DNA running into parallel to each other and then simply separated out the 2 strands and then get it perfect copy of 1 strand over here and a perfect copy of a 2nd strand over here OK so here's the that the parent stranded DNA and again here the 2 new strands in orange and blue note to that DNA forms a right-handed helix and see that you can trace out along the right with your right hand over here on the structure of DNA because we're trying not where's your left hand kind of slips off a dozen trace out effectively someone see the Cervantes DNA is always a right-handed helix
I just as beautiful structure Indiana but this is 1 that was solved by X-ray crystal structure before then the remark number of wrong incorrect predictions about DNA structure including by people who I know I think the world of a you know absolute heroes and science for example the great Linus Pauling who proposed a triple helix of DNA with the fast-food Astor backgrounds would be in the center of the molecule and the bases would be out on the outside this kind of this is a somewhat into this is intellectually attractive if you don't think about the package of to parents and but for the most attractive because of leased the base appears to be out here in space where they can interact with transcription factors we now know of course and that's not correct instead of mission will take a look at a moment when the transcription factors interact but before we do let's zoom out a little bit tired so DNA in the cell this concentrated in To into regions and nuclear zone in the probiotics also it's kind of concentrated in the very center of any call myself in EU carousel low-cost units found exclusively but is found in the nucleus and also the minor contrary ability focus on DNA that's on in the nucleus which and the bases
themselves but part connected together to form a ligand nucleotides through these are the phosphate but these fossil digester functionalities OK so this is and this is called a fast-food I Esther functionality on the DNA also has a direction associated with it Tyson and if we look closely at this deoxyribonucleic please there is a fight crime and there's a five-time drop to over here and 3 prime hydroxy over here and so the convention is always right DNA in the direction of from 5 prime to 3 crime in the same way that we read English going left to right DNA is always read out by 5 . to 3 .period this is a really important inventions everyone on the planet follows this convention and I'm going to hold you to it as well OK because if you read the DNA in the opposite direction you get a different of over a different word coming out of it spells something else that might not be this it will almost certainly not be the same thing and it might actually be no might actually cause a lot of trouble so we're always going to be reduced by Prime to 3 prime direction Ali answer this sequence here would be read out as they CGE entry they were the structures of ACG and as shown here don't bother memorizing the stress sorry don't bother memorizing the structures of these all simply given to you on the mid-term effect so that a graduate level you should know the these of Miriam only need to know these for their roles exam but that the rest you're in luck but because I'm not going to test you on the least for this class and then again this is the direction matters a lot and if there is a lifeline phosphate despite Prime phosphate is indicated by lower case and finally last Saturday nomenclature Oleg nucleotides that are connected together from often referred to as all those and that's how all described them can I realize all those is not the the most and descriptive nomenclature because simply means in a ligament or something but that's the dimension that we've been operating under 50 years has so all of those will virtually be nucleotides that typically DNA nucleotides composed of dioxin nucleic acid OK now on even the DNA is 1 of the bases of DNA are called bases it turns out they're not that basic and fewer coordinated at physiological pH it's missus kind 1 of those historical anomalies and here's a bunch of PK is unforeseeable starting with a trifle mean here's the peak care of the Parliament of the protonated triathlon being the conjugate acid travel mean peaking at 10 . 8 1 hears the PKK of cytosine finally adenine and guanine and you can see none of these will be remotely considered basis whereas this 1 over here and trifle mean definitely a base pay as evidenced by the fact that its conjugate acid is on there is no time OK questions over right now the DNA of course
is missing 8 2 prime hydroxyl OK so here's on a it has 8 2 prime hydroxyl over here this to prime hydroxyl makes on a considerably less stable than DNA I don't I didn't point this out when we go back to it when we talked earlier about half lives and religious zoom zoom back to that really fast the half-life of RNA is considerably lower than the half-life of
DNA OK so here's the half-life of RNA 220 thousand years whereas the half-life of DNA at 220 million years is much much greater thousandfold difference in the entire stability would be possible died as the backbone of the DNA was a farce Odessa background of on this makes sense the 2 prime hydroxyl of RNA sets you up the wall the hydrolysis using a on intramolecular attack so
here's the again the structure of behind a to Prime hydroxyl this to prime hydroxyl can act as a nucleophile to attack the fostered Esther backbone of the RNA setting up cleavage 31 C the mechanism of the I'm ready just take a quick look the
case in this mechanism we just drop the structures and all like the board 1 I'm sure OK so in in this mechanism heroes are structure of the bank so here's our backbone structure of on on it and understand each other's as faced over here OK OK so if there is any
basis that's present was just saying hydroxide this contain protein the 2 prime hydroxyl giving us said alcohol 6 sure adjacent to the phosphor best about founder of the DNA this neighbouring Alcott's now attack the shh shh back well in the fossil Odessa backbone giving you a five-member ring intermediate care which ushered down here 2 To end and five-member ring intermediates and on this intermediate collapsed leading to cleavage both the warrant OK so here is that collapsed and so on we're going to be making 2 strands of that separated from each other OK so here's 1 strand over here and then it here is the 2nd strand down here at the time but I'm just differentiate these base 1 in these 2 cases notice that the still strand has actually cleaved apart you can then high relies this bus Odessa backbone this this also onstage Back to a foster home on a minor Western using another equivalent of hydroxide well this year and then finally collapse of this stature he joined immediate gives us speed up product that which it was the intent questions about perspectives right now notice again and if DNA lacks his to prime hydroxyl over here and I just wanna make this totally exposed prime hydroxyl 3 5 .period so DNA laxity prime hydroxyl and therefore does not have an opportunity for this intramolecular nucleophilic attack on the faster as the backbone so for this reason DNA is a thousand times more stable than on the right lacking this intramolecular nucleophile makes sense questions about this OK it's go back down Turns
out there when you look at the life of ability of on the bases we see actually a different trends have
and actually think a mistake that
will be gone said like you learn what I just told you don't worry so much about the based of stability and DNA bases are subject to important modifications these modifications have dramatic roles on the phenotype of organisms OK so for example of methyl groups are often transferred to DNA I showed you structures of the basis again the subject to massive modification by methyl transfer races and other modifications said so for example here's by metal cytosine over here and warm apple cider seeing on and then and 6 methyl added 18 of these modifications can dramatically alter transcription levels they can set up the organism to transcribe some genes but more often because so that for example on lacking pigmentation of the genes that encode pigmentation or in my skin cells might at themselves yet they're not transcribed very often in so and it's likely that my DNA has not been methylated in those regions however when I go out and spend a lot of time in the sun and I'm getting additional spots called freckles and which are resulting from methylation of those DNA sequences which in turn then turns on transcription of the US pigmentation of and resultant freckles upon so the environment environment that you're exposed to can alter this is these transcription factors 1 of the ways that organisms like ourselves respond to changes in the environment very important when in fact and on oftentimes goes through the methylation of DNA testing a methylation is really as important as as sequence or genomics and this is an area called at the genetics that's really an area of great active from research that's taking place a chemical biology OK so it looked structures of the bases themselves with look the structure the past Modesta backbone stop putting things together to start to understand the structure of
DNA on the bases themselves are slightly U-shaped OK so here's a base between 82 AT and T Anthony in finding notice that this place is composed of 200 demand here a base of G & C which has 3 hydrogen bonds but notice more importantly that the bases are you U-shaped or equally importantly K U-shaped here the inside of this year with is going to be the Towards that the right the deoxyribonucleic the inside of this year is going to form the minor groove which I showed you on an earlier slide the outside of that could be part of this year is going to form the major grew as you have these users stacked on top of each other and each 1 is slightly offset with each other this is outside is going to result in a much bigger he elects then the inside over here OK and here's an here's
what this looks like a case of USA traces of the fossil Lester backbone and then I've highlighted just 1 Watson Crick based their case and out again notice that it's U-shaped but there's more to section traced out over on this side that will be the major group and the inside will be the minor groove furthermore the green Ferraro's those defined hydrogen-bond donation and acceptance by the I'm base pair I notice that there is a pattern suggests that there is a 1 and it's except the accept the donor of peso this is a donor accepted blown up over here so there's actually a little bit of a pattern to I'm a mother of this is a G undecided as seen side or CNG on opposite sides so in other words they are not the same as the because they're going to presented a different pattern of 1 of the hydrogen bonds for molecular recognition were again the proteins are going to be the transcription factors are going to be interacting every here in the major groups and small molecules be interacting in this minor groove down here and I should mention there's also some protein per DNA interaction minor groove it tends to be more money minor however OK let's take a closer look at 1 example of a transcription factor and how it works this is the transcription factor costume it consists of the day of the scene zipper which is a 2 helices that interact with the DNA like chopsticks capacities of fitting neatly in the major prove turns up in Major Group has exactly the right size to accommodate an alpha-helix old protein present this posthumous absolutely perfectly fits neatly in the major groups now these the hydrogen-bond donating functionalities are going to then read out the sequence of the DNA and and look for a specific sequence of DNA to interact with trying to form complementary hydrogen bonds trying to form complementary vendor walls interactions but in this sequence let's take a closer
look now at the forces holding together the on DNA double helix earlier I alluded to the fact that 18 base pairs formed to hydrogen bonds and GC base pairs 3 which 1 strong just stare from a crude approximation yeah the stronger than to go OK so in addition to this be on the 1 DNA structure is held together by stacking between the bases again this is a face-to-face interaction typically not perfectly face-to-face rather it's typically offset and that offset means the basis to stack not directly on each other but slightly twisted from each other setting up this helical structure that were not familiar with In order for
this space-faring to take place the base pairing that I
showed on the previous slide you need a particular taught America and these aromatic rings and the first one that should strike you as funny is this 1 over here these you can imagine another resident structure that would make this I see of aromatic right notice that this city as and it's not matter in this polymer shown here that it only has to apply electrons rather than the requisite 6 that it would need to be here Matt OK that's almost that's bizarre
to begin with the case what's going on here is that there is a preference for on this 1st as this 1 this one's actually Thurman economically more stable and the reason for this is that the carbon-oxygen double bond over here is quite strong I will tell you that I think any chemists looking at this could not have predicted this in advance and in fact action is tremendously slowed us which structure a determination of the original structure of DNA back in the 1950's Watson and Crick World more physicists and work as familiar with the whole notion notion of talked harmonization and as the chemical counterparts were racing to solve the structure of DNA and for them this did not look funny whereas to us I think it does look funny right because it lacks impetus at U.S. structure on the left is aromatic again and this happens to be just a little bit more stable because the strength of the carbon-oxygen double bond that I don't think anyone would have predicted that I think now we know the 20 century guys we can predict but I'm going back in time I don't think we could have predicted it so readily but similarly over here these Aberdeen's I'm actually going to be more stable and aromatic structure then in Emogene structure and in this case that's due to the much more overlap between a carbon nitrogen double bonds than a carbon oxygen double bond OK so all of this leads to the base
pairs with the hydrogen
bonding preferences that are shown here OK where's for example this is an honor Mattock wearing that could be about activity Tom rise that it doesn't prefer to be tough to Tonga as well as this 1 over here and seems to prefer to have an Aberdeen in this structure because of the strength of a carbon nitrogen double bonds paying out here is another example of that over this 1 prefers aromatic and because carbon nitrogen double bonds are relatively weak a pretty interesting unnatural basis
however could dramatically shift these on preferences for 2 harmonization and a good example of this year's on 5 Romo yourself case of this compound here is unfair to organisms that happens it is an unusual to conversation present preference where b on the eve of the E in all forms realm of you is actually more preferred that it would be if there was no running over here OK so most of the time it forms the regular based here however time they can actually form the incorrect based here because they can actually more readily access this time you know all forms of the base OK so that's due electron withdrawing functionality of bromine over here and that's support that's changing this to conversation preference the consequences of this are really dramatic because there incorrectly sparing is not followed as closely and what ends up happening is on the DNA comes out with all kinds of his or her breaks and lesions OK so here's on chromosomes from a normal organisms I think it's a hamster in this case and and then hears chromosomes from hamsters that were exposed to promote yourself and you could see they have all kinds of bizarre shapes to them things are incorrect cases that around this causes cancer and and I break is using DNA which then eventually will lead to cancer or cancer cells in tumors in the organism so furthermore it turns out that we can test this the importance of the strangest of these hydrogen bonds by on synthesizing unnatural bases so this is 1 of the great things about chemical biology if you up this hypothesis that something's important then you could test that hypothesis by synthesizing compounds which are saying missing and that the functionality so From Watson and Crick we expect the fine that hydrogen bonds are holding together the structure of DNA and Chemists went out and synthesized variants of DNA bases that were lacking that ability to hydrogen bonds pay structures of these are shown here cases for example and this compound here is simply a piracy in place of of the base and it actually prefers on the base pair with a missing base over here OK so these guys over here now -dash money no idea bonding over here and get these actually prefer a pair with each other a pasty can actually have completely unnatural bases missing bonds that inspire yet able to form on base pairs with each other preferentially what this tells us is that there's more to to going on in DNA structure principally hydrogen-bonding hydrogen bonding is a nice simplifying assumption of war biochemical France molecular biology friends but in actuality the Depuy stacking of DNA is a driving interaction the on edge to edge interactions of aromatic functionalities are also providing this interaction of between strands of DNA and so well we can do quite a bit with Huygens bonding and there's quite a bit more that's left to be explored yes OK
last thought showing you and it's not last fall but had been showing you but before I get to that 1
hears here for example Is that this illustration here on emphasizes the importance of pies stacking in here and so 1 look at 1 thing is that bigger bases tend to Piseco better for example the guanine based upon pies that better than saysIDC but in
addition show you Watson Crick sparing where it's a canonical based Jesus CDs have 300 reminds isn't have only to other kinds of hydrogen bonding possibilities are not only possible but have been observed these were proposed by calling steam and we observed these a lot in on a structure we don't necessarily see these Indiana but we definitely season on day and they're going to come out later so I'll just show you the structures here but this is an alternative to the usual 18 based there and this is an alternative to the usual CG based here this 1 being driven by a coordination of that predation of this nitrogen over here OK so this is actually the services edge to edge interactions rather than the sort of need more typical Watson Crick based here OK any questions about the structure of DNA anything whatsoever I want to see change gears and start talking about how small molecules interact with DNA and the 1st mode that small molecules can interact with
DNA it's actually slipped into this pie stack of DNA so aromatic compounds can slide into the pie stack of DNA and we're going to see the consequences of this can be quite destructive and let's
take a look at some examples is the class of molecules called in Tucker leaders and meaning that the interpolated into the pot pie stack of the DNA they are get the integrated into the DNA structure and so in order to fit into this pie stacked these molecules must be also hydrophobic and also it's a matter right they will form competing pipeline stacking interactions with the DNA and so they must also be aromatic note too that in order to force their way into the pie fact these molecules of Force India laced a double helix despite the unwind to accommodate the DNA interpolated here are some
examples of this but these are examples of interpolated notice that they're all on the amount of compounds that any amount to slide into supplies that many of these molecules also have positive charge is positive charges useful right because the DNA With the possible addressed the backbone of the DNA is negatively charged this gives us the molecule away to be attracted to the DNA To a long-range charge charge interaction rates of these molecules in a seek out DNA like a homing missile and once they slide into the pie stacked the consequences can be I'm pretty bad or actually fairly useful kind militia you an example of a useful interpolation over here on the right this is actually an agarose gel which is an important way that chemical biology Laboratory separated out DNA structures the different DNA sequences can be separated out on the basis of their size using these agarose gels after you what that looks like of the couple flights are now on to visualize the DNA however this molecule over here at City in bromide is incorporated the jail and it gets concentrated into the DNA by interpolation interaction so it slips into the piste the DNA and it's a fluorescent molecule many aromatic compounds of fluorescent we talked about fluorescence before and so you can actually showing you the light on the gel and wary Sunnis from these pinkish Beyond's that's where the DNA is present and seek actually take a razor blade for example and cut out the DNA of a particular sites and here's a couple more denatured
leaders but here's 1 that's designed to interpolate and then have a linker Terkel laid down below the compound and here's 1 of the
sites truculent structure late so there's interpolated intercollegiate up here for example I think that this is a great over here these are also
compounds that are used but to treat cancer said Donna Meissen Jemison are used as beating cancer compounds some of the 1st rounds of anti-cancer compounds are used as chemotherapeutic and OMB will talk more about the mechanism of action a leader in the class were not quite there yet OK let's stop here we come back next time will be talking more about structure of DNA


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