AV-Portal 3.23.2 (82e6d442014116effb30fa56eb6dcabdede8ee7f)

Lecture 04. Combinatorial Chemistry and Biology.

Video in TIB AV-Portal: Lecture 04. Combinatorial Chemistry and Biology.

Formal Metadata

Lecture 04. Combinatorial Chemistry and Biology.
Alternative Title
Lec 04. Introduction to Chemical Biology -- Combinatorial Chemistry and Biology
Title of Series
Part Number
Number of Parts
CC Attribution - ShareAlike 3.0 Unported:
You are free to use, adapt and copy, distribute and transmit the work or content in adapted or unchanged form for any legal and non-commercial purpose as long as the work is attributed to the author in the manner specified by the author or licensor and the work or content is shared also in adapted form only under the conditions of this license.
Release Date

Content Metadata

Subject Area
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: 0:28:06 MO Theory 0:32:32 Do Not Use Curved Arrows for Hydrogen Bonds 0:34:00 The Molecules of Life on Earth 0:37:40 Chemistry of CN 0:50:27 Formation of DAMN 0:53:32 Prebiotic Synthesis 1:06:29 Oligomers of Nucleotide Subunits 1:08:00 The RNA World 1:09:19 Synthesis of Amino Acids 1:12:35 Non-Covalent Interactions Dominate Biology 1:16:35 Charge-Charge Interactions
Nuclear pore Sense District Ionenbindung Biosynthesis Mashing Chemical property Hydrogen bond Topicity Bock Wursthülle Chemistry Block (periodic table) Electronic cigarette Chemistry Wine tasting descriptors Reactivity (chemistry) Molecule Chemische Synthese Lactitol Covalent bond Salt Modul <Membranverfahren>
Insulin shock therapy Activity (UML) Bohrium Ethanolamine Maskierung <Chemie> Wursthülle DNS-Synthese Chemistry Man page Zeitverschiebung Ageing Magnetometer Meeting/Interview Cell (biology) Altbier Protein Insulin Explosion Medroxyprogesterone Setzen <Verfahrenstechnik> Malt Grading (tumors) Mashing DNS-Synthese Hydrogen bond Ethylene-vinyl acetate Manganese Multiprotein complex River source Polycyclische Aromaten Anomalie <Medizin> Electronic cigarette Chemische Biologie Vancomycin Functional group Azo coupling Hydroxybuttersäure <gamma-> Chemical structure Cigar Screening (medicine) ISO-Komplex-Heilweise Biomolecular structure Stuffing
Ionenbindung Sodium hydride Ion transporter Chemistry Man page Necking (engineering) Magnetometer Controller (control theory) Film grain Faserplatte Explosion Ausgangsgestein International Nonproprietary Name Sea level Pain Area Setzen <Verfahrenstechnik> Atom probe Potenz <Homöopathie> Vulcanization Grading (tumors) Oceanic trench Walking Physiology Topicity Manganese River source Electronic cigarette Joint (geology) Chemische Biologie DNS-Schädigung Vancomycin Materials science Azo coupling Breed standard ISO-Komplex-Heilweise Thermoforming Stuffing
Setzen <Verfahrenstechnik> Area Potenz <Homöopathie> Secretion Bock Wursthülle Man page Multiprotein complex Wine tasting descriptors Man page Lava Chemische Biologie Enol Coordination number Explosion Chemical structure Stuffing
Glucose Homocysteine Kohlenhydratchemie Ionenbindung Chocolate Electron donor Atomic orbital Economic sector Wursthülle Vakuumverpackung Atomic orbital Hydrogen Deterrence (legal) Molecule Enzyme Electron Ageing Essenz <Lebensmittel> Ausgangsgestein Pain Setzen <Verfahrenstechnik> Molecularity Homocysteine Stickstoffatom Hydrogen bond Puff pastry Chemical reaction Erdrutsch CHARGE syndrome Electronic cigarette Hydrogen Atomic orbital Azo coupling Proton-pump inhibitor Covalent bond Elektronentransfer Base (chemistry) Cobaltoxide Stuffing
RNA General chemistry Wursthülle Adenosine DNS-Synthese Block (periodic table) Chemistry Man page Molecule Titanium Dreifachbindung Exon Active site Chromatography Area Stickstoffatom Concentrate DNS-Synthese Carbon (fiber) River source Cancer Electronic cigarette Agriculture Proton-pump inhibitor Ultraviolettspektrum Elektronentransfer Chemical structure Multiple organ dysfunction syndrome
Cyanide Gum arabic Sunscreen Bohrium Wursthülle Acid Adenosine Organ donation Block (periodic table) Chemistry Origin of replication Block (periodic table) Meeting/Interview Process (computing) Chemical property Formaldehyde Asset Protonation Chemical reaction Blausäure Acid Yield (engineering) Ultraviolettspektrum Pharmaceutical drug Dehydration reaction Base (chemistry)
Cyanide Ionenbindung Bohrium Diethylstilbestrol Growth medium Atomic orbital Adenine Wursthülle DNS-Synthese Man page Atomic orbital Reactivity (chemistry) Klinisches Experiment Molecule Meat analogue Electron Lecture/Conference Lactitol Insulin Orange juice Elektronentransfer Mixture Sea level Medroxyprogesterone Periodate Area Stickstoffatom Walking Carbon (fiber) Ethylene-vinyl acetate Chromosomenaberration Protonation Antibodies (film) Chemical reaction River source CHARGE syndrome Blausäure Water Lone pair Vancomycin Amine Coordination number Mixing (process engineering) Soap Nitrosamine Stuffing
Cyanide Sense District Ionenbindung Reaction mechanism Bohrium Growth medium Wursthülle Block (periodic table) Man page Optische Aktivität Ammonium Klinisches Experiment Meat analogue Ocean Elektronentransfer Conjugated system Stickstoffatom Walking Carbon (fiber) Protonation Chemical reaction Blausäure Neoteny Drop (liquid) Chemical structure Base (chemistry) Condensation Biomolecular structure
Adenine Wursthülle DNS-Synthese Block (periodic table) Man page Klinisches Experiment Molecule Lone pair Electron Meeting/Interview Dipol <1,3-> Base (chemistry) Setzen <Verfahrenstechnik> DNS-Synthese Walking Chromosomenaberration Man page Erdrutsch Blausäure Electronic cigarette Gesundheitsstörung Azo coupling Ultraviolettspektrum Penning trap Cigar Base (chemistry)
Nucleobase Setzen <Verfahrenstechnik> Biosynthesis Octane rating Cytosin Wursthülle Cytosin Pyrimidine Block (periodic table) Man page Perm (hairstyle) Molecule Oppression Meeting/Interview Cycloalkane Biomolecular structure
Biosynthesis Aldol DNS-Synthese Benzoin Aldosterone Ribose Bock Benzoin Chemical reaction Wursthülle Cytosin Knot Pyrimidine Blausäure Man page Magnetometer Meeting/Interview RNA Periodate Uracil
Cyanide Separation process Kohlenhydratchemie Ionenbindung Bohrium Cider Atomic orbital Benzoin Wursthülle Bis (band) Block (periodic table) Man page Elf Molecule Ageing Electron Meeting/Interview Lactitol Nucleic acid Chemical formula Calcium Nucleobase Fatty acid methyl ester Organische Chemie Stickstoffatom Arginine Chemical property Nitrogen fixation Formaldehyde Walking Sodium cyanide Carbon (fiber) Benzoin Protonation Chemical reaction River source Electronegativity Water Optische Analyse Coca Chemical structure Cobaltoxide Forkhead-Gen
Aldehyde Semiotics Kohlenhydratchemie Biosynthesis Walking Benzoin Ribose Chemical reaction Knot Man page Reactivity (chemistry) Ring strain Vancomycin Acid Chemical structure Base (chemistry) Thermoforming
Chain (unit) Bohrium Diethylstilbestrol RNA Wursthülle Acid Quartz DNS-Synthese Block (periodic table) Man page Reactivity (chemistry) Molecule Sample (material) Amino acid Chemische Synthese Meeting/Interview Protein Translation <Genetik> Biopolymer Nucleobase Polyphosphate Abiogenesis Biosynthesis Oligosaccharide Proline Precursor (chemistry) DNS-Synthese Walking Ethylene-vinyl acetate Kohlenhydratchemie Chemical reaction Solution Sodium Vancomycin Acid Gesundheitsstörung Phosphate Amine Calcium phosphate RNA Triterpene Polymer Base (chemistry) Thermoforming Pharmacy Biopolymer
Cyanide Aldehyde Biosynthesis Reaction mechanism Peptide Strecker degradation Wursthülle Chemical reaction Acid Man page Molecule Chemische Synthese Amino acid Amine Protein Protein Peptide synthesis Ammonia
River delta Ionenbindung Ionenbindung Topicity Chemical reaction Man page Alpha-1-Rezeptor Ring strain Clenbuterol Lead Protein Meeting/Interview Cell (biology) Covalent bond Transformation <Genetik> Storage tank
Ionenbindung Homocysteine Potenz <Homöopathie> Ionenbindung CHARGE syndrome Chemical reaction Electronegativity Wursthülle CHARGE syndrome Knot Wine tasting descriptors Food additive Man page Molecule Emission spectrum Vancomycin Electron Meeting/Interview Van-der-Waals-Kraft Covalent bond Library (computing)
Cell fusion CHARGE syndrome Wursthülle Lewisite Man page Formaldehyde Atomic orbital Ammonium Molecule Magnetometer Cell (biology) Discharge (hydrology) Molecularity Stickstoffatom Concentrate Formaldehyde Action potential CHARGE syndrome Electronic cigarette Water Hydrogen Drop (liquid) Salt Acetone Chemical structure Atom
OK welcome back back and so on hopefully everyone got to see the lecture on on the YouTube channel said you it's been posted there that was Tuesday's lecture I'm a little concerned if you haven't seen it you might fall behind so make sure that you get up on it right away and I'm going to try to set today's lecture so it's not totally dependent upon Tuesday because I haven't had checked out how many views were on the last lecture and I know they can't possibly be everyone in this classroom so I'm setting it up today's lecture so that it's not totally dependent upon the material presented on Tuesday but I do think the material on Tuesday's foundational and so future lectures will refer back to that material and OK now what is going on here OK so last time I was talking about what causes reactivity and 2 of this is the property by which molecules that impinge upon each other decide the war bonds or break bonds due to that of a tight interaction with each other and we're going to look at some examples of that and examples in the beginning of the class are going to focus on and on pretty bad except the sense so this is synthesis of biologically relevant molecules the building blocks of life really but the chemicals that might have been down before any life on the planet existed and I'll talk some more about that in a moment on and then we're going to switch gears to a very important topic and non-covalent interactions non-covalent interactions dominate all biology and while huge fan of Europe pushing a covalent bonding and the truth is we will get a complete and accurate picture of of how biology works if we don't also consider the possibility that molecules can brush up against each other and then stay interacting with each other close close proximity bye non-covalent interactions not by forming any bonds but actually buy on forming hydrogen bonds by forming salt bridges by forming vendor walls interactions stifled Dybul attractions etc. so we need to talk so about that because I really the next 8 weeks or so we are going to invoke a lot of non-covalent interactions a case of both these concepts early foundational for the rest the class Tuesday next week will then on beyond 2 Chapter 3 RNA and armed uh will be doing to lectures on and on chapter 3 so if you have time this weekend you might wanna skim through Chapter 3 take a look at what's coming up next OK on 0 and then finally at the very end lecture all talk a little bit about modular design in biology and because it turns out that 1 of these concepts that's very important in the Middle East started to see a little bit of that but we can look at it in greater detail effect on unsure exactly what this working knowing that OK go OK so on some announcements of told you to read chapter 2 about Chapter 2 on changing this to every odd and asterisk problem so this the answers to all asterisk problems are available on the Web site for the textbook the answers to the on problems you can get from critical who will be here on Monday and I Miriam on who will also be here as well 78 have the answers to all the problems that have been assigned and seeking credit check the work of that but I would like you to do all of the assigned problems please OK let's see there is a 1 0 and and Chapter 2 worksheet of course posted to the Web and there is 1 hand out this week and I'd like to take a moment to go through that if we could so bear with me I have to up
my browser and so on yes so that the problem this at work she focuses on a on that this is not the Journal article assignment at 1 moment OK so here I am on what's considered too quickly OK so this is from was my cursor for always manage try to find where the cursor is on 2 screens that's what's on the screen here OK so
here's the obviously the can 128 website and down here down journal article Report 2013 that's what I'd like
you to focus on OK so there there are 2 sides to this hand the 1st side is an example of what I'm looking for and if a journal article report that will receive an a grade a case so this assignment asks you to write one-page obtain no more than 1 page of more the 1 page not following directions OK so just 1 page and the way this assignment will work is you will pick an article from the current literature the Curragh chemical biology literature and provide a one-page summary about that article the format of the summaries as follows at the very top I'd like you to have a complete reference the army journal article OK the article that you've chosen and on note that this this note the format up here that's the format that I'd like you to use there many different formats I'd like to use this 1 OK and just be consistent throughout the class and then in the next paragraph you're going to have a very short interest so that describes the broader implications of the paper the last sentence of any the abstract a in show should be the home run what it is that's important about this paper and why it is that people should care so here it says the results provide important insights into the nature of protein DNA interactions taking place in the cell that sounds so I'm pretty important OK there has to be some reason that this paper it would be useful for other people to read OK and that's that last sentence is a key sentence any paper it's the last sentence of the abstract at the beginning of the paper OK and then I'd like you to provide 1 paragraph of background and then a couple of paragraphs down here which he experiments and discussion of pay and some other I always notice there's lots of figures in here it's OK to borrow these figures in other words rip them off the Web on that's fine perfectly acceptable but credit the sources for your figures obtained by an offer you were to put the credits in a moment OK and in addition of you have put your name appear etc I'd like you to write using an active voice and us not be engaging writing this is crucially important in fact it's so important to you and to me that I'm going to reserve about arms somewhere between us and that's a 33 per cent of the points just based on the writing a love of pay and here's why I think this is so important when you graduated from UC Irvine you're going to be expected to communicate effectively and that's part of having a college degree and a fact people are going to make snap judgments based upon on the effectiveness of your ideas based on how you communicate those ideas you might have the most brilliant ideas on the planet but if he can communicate them effectively people will be unwilling to listen to those ideas it is crucially important for you to be able to communicate ineffective English and to grab people's attention and to armed convinced them that your ideas worth listening to and the 1st thing that rankles reviewers are readers is simple and basic mistakes a things like spelling errors and things like grammatical errors OK if I see those as I will take a substantial points regardless of the brilliance of the rest the paper a candidate will drop you a letter grade on this assignment if you have a single uh you know Major Garrett major grammatical error and it's that important so another way of saying is in this day and age and where your computer or your computer tells you if have spelling errors use that spell-checker grammar checker and make sure that everything is totally perfect furthermore on before you turn in your assignment to me you should have revised it many times is OK so don't turn in something and it's the 1st time that it's been a downturn in the 1st draft really it should be about the 4th or 5th draft before it hits my desk OK that's how important visits a peso even small errors are going to really hurt on this assignment and that sort of the way life works when she graduated from UC Irvine you don't get a chance to revise and your you know proposal to the NIH or something like that it's it get 1 shot at this OK so make sure that what hits my desk has been revised many times and I guarantee to if you're revising it will be a much better quality than if you want and I'll tell you I this is the way I write OK so when I'm writing something I am revise it many many times before goes out the door I've noticed that my papers the papers that my laboratory publishers go through 25 revisions before they're ready to go out 25 is on average some papers go through 30 to 40 revisions before I send them out a case that's like 30 or 40 drafts of the same 15 pages 115 pages and will distinct doing it back and forth between me and the co-author until we decided that it's perfect because even tiny tiny little errors on bias the reviewers against you it projected force it makes people prejudge the quality of the work even if that's not an accurate assessment so this really does matter a lot for the rest your career and it matters a lot to me so again we're going to be using active voice and US snappy engaging writing OK on now let me talk to you a little bit about the figures and experiments the papers you're going to be reviewing her from the primary literature meeting there from the cutting edge of chemical biology reports and I'm in general in this field that papers tend to be rather meet OK it's not unusual to have papers have 7 or 8 figures each 1 with a ton of data we know that this is basically the fire hose school father how to impress somebody the case was not unusual for 1 of these papers to have you know and you know terabytes worth the data in 7 figures so the challenge for you is you only have you know like half pages so to summarize that stuff so what I would like you to do His only include the important experiments a pay don't try to include every experiment in Europe in your a one-page right pesos just 1 page in this it's just happened pages so that should be dedicated to the key experiments in the discussion in this key experiments a discussion you quickly summarize the most important experiments and then you discuss what the implications are what was learned from these studies a pair that what was learned is crucially important to right this is really on when you read a paper this is the kind and nugget that you get back out the reward for reading the paper and kind it tells you you know what it is that they learn of pay and then at the very end of the last sentence here is going to summarize the key findings and again this last sentence that is sort of highlighted and so in that way it's as it gets more attention than the rest of the work that so and it becomes crucially important that last sentence reads in this case does this work demonstrates how proteins traverse along the negatively charged back when DNA until finally a correct sequence causing a remarkable change in the structure the complex through a series of hydrogen bonds and vandals interactions to major groups of cases some sentence like that just summarizes everything because I guarantee to when people read papers and they look at just a few fixed a pair of studied how people read papers because that in turn will make you more effective communicator what they look for if they look at the last sentences of the paper itself they look at the last sentences of paragraphs like this 1 up here and then they look at the figures gave you don't have a lot of time to read something that switching to a pay and on this matter is a great deal so my chair admissions in chemistry the chair of the mission's committee and we get like 500 applications a year for of applicants trying to get a PhD in chemistry and I have to read all those applications kind so what I do it's Ise here and when I skim I start looking at these last sentence is much more closely than the inside here I look at the 1st sentence 1st sentence interesting or read the rest of Europe persons looks ordinary and then maybe I'll go on to take a look at the last sentence Justice you missed in the rest of us but that's the way people really fast and the truth is found in science where there's like this fire hose knowledge that's pouring out at you and you can't possibly drink at all and we all read very quickly so it's important that we cater to that style of reading OK so again I'm just focus on this last sentence here and this last sentence here I'll be looking at those really in great detail OK now on the 2nd day in any questions so far and don't hesitate to interrupt a few questions OK no 1 the
2nd stage I have found some directions down here and then I have the references to your references can appear on the 2nd page otherwise you simply would have room of inorganic like you use the same format the same style for the references but this is required you must have references and figure credits and these are the the figure credits are where you got the figures were you those figures from and the references are what you're referring to 1 in terms of your background knowledge OK so what it is that you used to tell you to help you understand the paper OK they appear here under references OK couple thoughts here is number 1 on I'd like you to use references that are from the peer-reviewed literature so the Wikipedia does not count as a reference because it's not peer-reviewed OK and furthermore 99 . 9 per cent of websites also don't count your references must come from peer-reviewed sources the 1 exception that all our textbooks so if you want to have a textbook as a reference I guess all except that if it's not too order textbooks but on the most part you your references should be coming from led us scholars would consider good sources and that means period and if you have any questions about whether or not something's peer-reviewed scenery and in general the rule is if it's found in Pub its peer review effect on OK so this these are required and I you can use Wikipedia websites for background knowledge you give you quick heads up but don't use them as references and if you're wondering where it is you can find good references to take a look at the articles intro and look at what the authors are a power of reference thinks that's a good start OK assignment requirements and I'm going to walk through these additional questions later on the 1st thing I'd like you to do is choose a research article not a review article OK so review articles don't report any new experiments Review article summarized a bunch of other experiments oftentimes done by another scientist peso irate review articles when I wanna learn something new about the field when I move into a new area of science 1st thing I do is write a review article is a great way to learn the field pay but you know since I'm new to the fields and my sought a 10 thousand foot you is different than the view from the trenches a case of for this reason and also because I want you to get comfortable the primary literature I'd like you to choose an article that supporting new experimental results the way you'll know that you have an article that supporting new experimental results and if that's not a review article is if there's an experimental section somewhere in the article there has to be something about how the experiments were done and if you have that thing you know that you're not really reading a review article again if you have any questions about whether it's a review article not a review article see Miriam or critical but and I have some directions about the type of thought that I'd like you to use you must pay attention to this and this is important number 3 is choose an article a paper relevent to some aspect chemical biology which again is using chemical techniques to advance in understanding of biology at the level of Adams and bonds that's all kinds of great articles out there there is a lot of science that's taking place in astronomy in human physiology and all kinds of cool areas of science and I love reading this stuff OK at the end of the day I go home and I read science and nature for fun and there's nothing I like to do more than to read about that stuff but I'm teaching a class chemical biology today and so Our this court and so for you I'd like you to be reading the chemical biology literature the peso it has to be a chemical biology paper and your choice of article will tell me whether or not you understand the definition of chemical biology if you have any questions about whether or not it fits this definition seat Miriam are critical for myself the article must have been published in these journals Science Nature PNAS chemistry biology Nature Chemical Biology ACS chemical about yourself during the year 2012 to 2013 this is essential if you turn an assignment that doesn't conform to the standards I will hinder back to you and tell you to redo it minus a substantial . 4 penalty another reason why I'm doing this is to form a number 1 by restricting you to just these articles on ensuring that shouldn't be finding something that's really important in the field that other people in the field of thought was noteworthy and exciting it's really hard to get a paper published in Science to do so it has to be something really extraordinary peso can buy a paper that appears in science chances are it was something that was sort of earth-shattering to the scientists in that field OK so you must use it from these journal articles and then it must be published in the year 2012 to 2038 ideas 2012 to 2013 business to ensure that no 1 out there is trying to use last year's assignments in time so I'm 1 step ahead here and again if it doesn't conform to these comments all the skin back to you and tell you redo the effect on now this next 1 is is it is 1 of these just tips die if you think it's a good idea for your journal article reported to relate to your proposals in other words if you're interested in doing a probe proposal on DNA repair and how to control DNA repair or maybe it amplify and accelerate DNA repair maybe as your proposal topic then she a journal article that relates directly to journal article here OK that's so that's always a good idea right because now the new you're reading the current literature in that area OK it again the book The Journal article Portuguese single-page were figures references on the 2nd page do not include any other materials for example do not attach the paper to the journal article again conform to the directions here and this is the reminder that the February 14th at 11 league policy strictly enforced OK now the 2nd part is to receive credit for this assignment you also must turn and in addition to the hard copy at 11 you must turn an electronic copy determined dot-com and here's the course ID and a password that you need for that tournament up it's essential that you do that this will tell me whether or not you were you should receive points for turning an assignment on time OK and I think you know why I'm doing this we talked about plagiarism before it is a substantial problem and you cannot have succeeded in life if you do not have your own ideas and your own thoughts so I care about your own thoughts not someone else's thoughts I want to hear your own thoughts and so for that reason I will use turning . com and it turns out actually turned outcome works pretty well and every year someone tries to plagiarize this assignment in again and if this is a year where I don't have that I will increase the grades for everyone in the class of like we like I think I said something about right at the joints so we will be moving up the grades of that total grain distribution for the entire class if I don't have a single plagiarism thing to deal a day for me this is a total would when a pay because it's a real pain in the neck for me to have to write a letter to the dean and then you know perhaps even got testified before and board tester was thrown out of school for doing it in academic honesty infractions place he doing that drives me nuts but I will because I think these academic integrity rules fire where the forces of terror so if I don't have to waste time on that we all benefit I'm OK In addition on the 2nd page down here I have an academic honesty form which shows I think how serious I am about this OK so the next stage as on something that I'm
asking you to sign reason why have you sign this is it turns out that 1 year someone's of parents brought a high-powered lawyer to argue with me about this so it turns out you can't do that because ominous is that you sign this in time Europe the report created Our now
creating I know this is a credible blighted teaching for 12 years I found every possible crazy us scenario and so this why it seems so pedantic that I'm going through all this I'm OK and tell you how many great that's for maximum points use correct English grammar spelling and diction case choose the correct words spelled correctly and if you have any trouble of this if you know that your English isn't so great don't have it we have resources on campus there's a campus writing coordinator who can help you there's an office across campus where people can read your your work and they give you feedback and correct things about that work you need to tap into that resource right away because I'm talking to you about this a month in advance and so you plenty of time to get to tap into that resources really important that you do so if you're writing is not your thing don't panic government to get the Simon Dunn is only 1 page but you're going to make it a perfect page OK the next part of the strive for simple clear sentence structure and I'm really a strong believer that you should write like a journalist you know like writing for a newspaper and actual newspaper like New York Times not like this summer other stuff but if you have simple sentences people can better understand you I know I know I have the Warhurst uh I routinely make this mistake all the time so I have to eat consciously when I'm writing I forced myself to simplify my sentences and I realize at that last sentence that I read you earlier today was kind of a mess there was way too long and so a sentence like that I might divide up into 2 sentences now and so a good rule of thumb is if your sentence goes for more than 2 lines it's to walk start cutting it up into a shorter sentence at shorter sentences it is easier to understand and the goal here is for you to communicate clearly and to impress people with the power of God your ideas not snow them with just complex of concepts a pay your your idea the goal here is to be simple direct and clear and powerful in ideas less powerful and just you know Over intellectual most of you know complexity OK next thing on summarize article careful correctly I read those journals I will probably of red featured article that you're proposing is report before as will Miriam a critical so if you're wrong you're wrong and call you wanted on include useful figures Idaho doesn't seem like that should never happen right but it actually does happen and if you have questions about the Journal article secret scenery and see myself we can try to help you interpret what's going on our carefully follow directions regarding the format that's right here and then again do not plagiarize even short phrases became now hopefully haven't scared you too much about the plagiarism every year people complain and scaring them too much about plagiarism but I wouldn't have to do this if I didn't have this problem every year OK so let's make this the wonderful year right don't have this problem but many questions the yes side of hopefully covered every possible outcome O'Grady custard over here with us today actually OK so yes you can use quotes 1 but put the quotes and then put a reference to show where you got the "quotation mark a pepper gas of course that's perfectly acceptable but I think that's actually a good way to do things other questions yes and what Israel says absolutely OK thanks for asking services question she told us not to use a review article as the as the thing that you're going to be doing a report on but you can certainly review article used review articles as background material and references but in fact it's an excellent use of review articles serve review articles a great way they're like textbooks basically out of the current studies you know the most recent stuff OK very good luck on this aside and I can't wait to read them it turns out it's a really fun assignment for me to read it's like a manual report of what's happening Chemical Biology of the last year and I might add that make the very best these available on the court's website and I found that some years of and stresses the really good ones are like the top say 20 per cent or something a really great they're actually terrific summaries of cool papers of chemical biology area look forward to that OK I that sit on announcements I know we spent a long time announcements but it was worth it because we covered a lot of jury
arms OK let me
summarize where we were on Tuesday at the end of Tuesday's lecture and that will jump right in 2 today's lecture on Tuesday I taught you a really powerful equation that pretty much governs every interaction between molecules OK this is the simple stuff like your fingers touching your desk this is a complicated stuff like on digesting the glucose that you had with your Cocoa Puffs this morning OK so this 1 equation governs all of those types of interactions and between molecules which showed us is that the energy required for that energy involved in the interaction is is proportional to this summer Of the field field overlap a case of this is where the molecules decide that they're not going to form a bond with each other and instead they're going to repel each other a case that this is your finger touching the desk right the electrons on the tip to your fingers are interacting with the electrons on the tip of the wood desk of pain is preventing your fingers from going plunging right through that would justice spike the fact that there's a lot of there is a lot of vacuum in there as well as well a space that's not covered by this electron despite that there so the Pelly exclusion principle teaches us that electrons cannot overlap with other electrons and so for this reason this field build overlap dominates repulsion in addition visitor work who want the court charge charge interactions and then there's a term for field unfilled overlap and last time I spent a lot of time talking about this field of overlap this is a minister in the above equation it turns out this is a minus a number basically that's the term if the molecules decide they're going to react with each other that glucose sugar that you hate the on this morning for breakfast decides to interact with them you know an enzyme in your stomach and starts getting digested and served in that case what's happening is theirs for battles that have fields that have electrons and their findings a lower unoccupied molecular bill to interact with OK and we also discussed how Aeros depict this overlap of the lowest limo and the highest homo OK so in this case these errors are showing us how the electrons are flowing between a high occupied molecular orbital electrons and a high of high molecular orbital down to a lower energy lower Lois is unoccupied molecular orbital and then that's the essence of forming a covalent bond when that happens that's when you get bonding depend on we also talked about some very specific rules for air pushing errors began electron spin and on empty orbitals that's it the United begins base that on a gun charge and they're going to be ending directly awareness that molecular orbital that unfilled molecular orbital should be so it supplies star orbital you should draw arrow that's going to end approximately where the pie it'll actually exists because this is a language that we use to communicate with each other to tell each other how this bonding actually happens a K without this language and some rules to this language some diction some grammar and you know we will be as communicating as effectively OK any questions about Tuesday's lecture care what we saw on Tuesday I'm going to be showing a specific examples yes question over here yeah and what it should the surgery and if you will OK fair enough when I start there OK other questions on Tuesday Price on Tuesday steamy 1 sector pulls and I showed you the slide that had described to from hydrogen bonding money to see if I defined as saying yeah and so in this case
and this is a depiction of hydrogen bonds notice that there is a donor lists and age and there is an accepted this oxygen the load perilous oxygen and on the problem is that this depiction of pension bonds which and that we were going to use massively complicates our attempts to draw errors OK so while it is true but the hydrogen in this on hydrogen bond is hanging out with oxygen and also hanging off the nitrogen but it makes it very complicated for us to draw heroes involving use hydrogen bonds so instead of drawing hydrogen bonds like this in an armed reaction diagrams were doing arrow pushing instead what I'd like us to do is actually show the hydrogen fully donated over to the oxygen over here OK so fully donated to the parliament accepted pay so here's a load parent oxygen picking up this croutons and then electrons dancing to the the odd nitrogen surgeon some of that great I write I would pick up where we left off last time and again will be looking at a couple were examples of this yet OK here's on the
molecules of life under the honor Our planet and are actually pretty simple molecules OK and we've actually seen them structurally because so this is the chemical structure of the DNA and leaving out stereo centers but it definitely provides head of a quick overview and the question I wanna start with today OK so here's what they're made out here is to question started that 1st one and composers these molecules OK where this DNA staff originate from what is it made out of and then where did these pieces these building blocks here the pieces over here and where those pieces come from cancer that's this the questions there dinner challenge us today and we're going to be talking about this in the context of the
prebiotic chemistry so this is chemistry that we hypothesized might have taken place before life on the planet arose again and we have some ideas about what the planet's chemistry looked like by looking at the records geological record and also by studying other celestial bodies OK other moons and planets so for example when we look up at the end of the mood of site Saturday called Titan which looks like this we can see building block molecules chemicals that are present in high concentrations and we could see the seizing spectroscopy the peso this same UV absorbency techniques that you learned about back in general chemistry the applicable here we see you know characteristics stretching of a carbon nitrogen triple bond that tells us definitively that HCM must be present on this mood of tied Caso based upon that example 1 known example and also looking out on the geological record our planet we hypothesize are planted in the area early days must have had those chemicals available and if those chemicals were available they can compose on the building blocks that are shown here on the last occasion these pieces over here from these pieces we can then build much more complicated things like this adenosine building block of farm in this case are a day but also DNA as well OK so the key that is that there has to be some energy source and 1 very effective energy sources ultraviolet light which will be invoking today said the OK so
here's the picture in the book of the same as what I showed you earlier so again here's adenosine down here adenosine is composed of a ride those and an admin and you can actually derive this ad directly from just a bunch of hydrogen cyanide so that our react with each other cases they react with each other in the presence of UV light you basically put these things in UV light shine a light on it and then you know wait a little while you will get out of a low but on significant yield the base and you can also get out right those if you have a bunch of formaldehyde so that a bubbling around OK so for Malahide sobering this reaction at Indians in this reaction if you do it dehydration reaction you will then get adenosine which is 1 of the building blocks for RNA pay and so on today as as an example of Arab pushing we're going to show exactly what's going on there come OK but before I do I need to talk to you a little bit
about 100 cyanide also called press accounts said and this is a very weak acid on and it has some rather unique process properties low it's called acid it's PKK of 9 hardly qualifies it to be an asset right to give 9 is not what we call a really great asset affair but nonetheless it has the ability to donate protons and arms I want to remind you of a rule which is the PKK is equal to the pH where half is protonated in other words this nite of 9 tells us that a pH of 9 50 per cent of the Huygens cyanide will be each CNN and then 50 per cent will be cyanide because this is 1 of those things that I'm hoping everyone knows that if you don't know go back and review of original chemistry but and here it is pH 9 you have a one-to-one ratio of hydrogen cyanide to cyanide pay and then each pH unit is a factor of 10 on this ratio so as the pH drops you get more each year and down to pH of 7 of neutral we have 100 fold more hydrogen cyanide than actual cyanide case turns out that Huygens cyanide is actually very very reactive and so on the 1st
thing I'm going to be showing you is and how hydrogen cyanide can be used to form a molecule we affectionately called down for Diomede overlay a I trial a price so that's the 1st challenge is at a pH of 9 we have a 50 50 ratio of cyanide to hydrogen cyanide and we can actually Mix sees things together did the pH tried and then extract out of it this diary anomaly a trial be and let's start their OK before I do any questions but what we've seen so far always makes me nervous when there's
no questions OK I'm
OK the at pH of 9 we have a 50 50 ratio of hydrogen cyanide to hydrogen cyanide these 2 I have and I would say opposite reactivity to each other where the cyanide is a terrific nucleophile the hydrogen cyanide is a terrific electric pile so ,comma tracing same molecule behaving in 2 different ways depending on its coordination state OK so on the very 1st step here this will give us what soap soaps 1 moment something overlooked so this is the incoming cyanide having attacked C on and on we could do a bunch of proton exchange reactions which I'm going to show you at 1st and eventually I will leave out that I will expect you to know them and here is the first one of these this is the nitrogen picking up a proton from HA that's nearby what is the identity of a it's probably cyanide and its exact identity not so important to us OK all the reactions I'm talking to you about that over the next actually for the entire quarter are going to take place in water there's plenty of other sources of protons available and there these are complex mixture so I encourage you to use this speech 8 nomenclature which I will accept on exams and quizzes OK OK so we pick up a proton in this 1st step a case of a word about these equilibrium errors for steps that for many of the steps I'm going to be using these backwards forwards areas indicating that in equal abrasion is taking place honestly I'm a your .period I'm not so concerned about that appear in other words I'm just put some areas there but it's nice to show that you can have predation and indeed nations could go backwards if the words but that's not my primary concern for a class at this level OK so don't get worked up about the arrows as 1 of trying to tell you the zeros here get worked up about the orange areas that are showing the reaction OK another 1 proton transfer OK I noticed that I'm adding again the formal charge and the formal charges useful because it helps us keep track of electrons furthermore noticed that each of my heroes is starting on a lone pair and ending directly on and we're approximately the antibody little should be there'll be a Sigma star and all that is and in line with the bond between H a over here and so this era ends directly where that Sigma star orbital should be heroes again show overlap of orbitals and it's important that our heroes depict that overlap of 1 of the bill's accurately OK so and that brings us to our next step we now have a protonated nitrogen it's actually a medium on a and is on an exceptionally good electrify you could think of it as equivalent of a pro to curb until that is a nitrogen analog to this carbon he'll pay so this is a very effective electrify all year to pick up the bill this cyanide and for this but this stuff to happen and about that neatly sets us up to have this guy here sorry case so this guy here and H from there is the lone pair from the 2nd Aero OK so that sets us
up nicely and then we can do exactly the same step yet again OK so exact same steps this time on the cyanide over here and that play by the way this time the sequence of errors is of course covered in the book from show you because we can discuss it a little bit and I will show you all of the reactions depicted in the book has kind of early days for us for starting off slow down but later also tell you about reactions that are and where the mechanism is depicted in the book and I'll ask you to go and learn that mechanism but for now on understand starting off things and a nice comfortable pace OK so this sets us up with the following products so here is 1 triple 1 to an 2 it here this guy over here and on this is starting to look very much like a dire need no millionaire trial we have to sign by the way admitted that the structure of this just by the way this is what we're trying to make it's always good to keep in mind what the structure of the target of your mechanisms a cases this is our target attempted to put it there after that exhalation .period little myself back In any case hadn't yet another proton transfer steps he's become very routine after a while they should be almost 2nd nature and I'm also going to do and of a bond rotation steps as well OK so rotating around this carbon-carbon single bond should be very facile at this point but the OK so we're here and the next step is a crucial 1 case remember earlier I told you that am "quotation mark slips by the way if you guys spot please correct them there's please drop of it's very easy for me care them standing up for those and have a lot of young people looking itself and often times I make errors please do not hesitate to interrupt the aircraft that I don't mind at all that gets us to another medium ion again this ammonium ion you could think of as being equivalent of a protonated carbon Hill at sea as the odd nitrogen analog to a Carbondale terrifically reactive that sets us up to have the mine and this is the conjugate base of the HA that I've evoking all this time to do to do this last supranational Kenny said that sets us up for forming this guy and I'll just rejoined over here so it looks just like it does think so Damiano Milan I tried that makes sense pretty straightforward reaction right what's extraordinary about this week as we've seen a condensation of 3 cyanide 300 cyanide have come together to give us a building block 0 sorry make that hydrogen cyanide and 2 cyanide to hydrogen cyanide in any case we built up before carbon building block using nothing but 1 carbon fragments OK so in a very straightforward sequence I'm pretty amazing bomb of what we take a look next at the next step here to form adenine and then I will move on and from there come from any more questions about this again on this is very since this is identical to the book this is basically
figure to 20 and so on on the go on from here OK now the next step but that involves that will carry OK
so we've seen formation of this time the anomaly and my trial on skipping a couple of slides here that seem redundant what's going on OK
there is a R U B catalyzed step over here where this dire need only at nite trial is then on converted using another I'm just now I I tried using the molecule that's depicted here there's a UV catalyze stepped from which you can convert this . man to AIC had and actually that's step is a little bit more involved I had students over the years figured out for themselves and you could certainly do that it's not that crazy involved but on it's evolved enough that I believe it out OK and so this step here don't worry about it involves UV light on but this gives us a key building blocks from which you can make either adding if you add added HC and another hour hydrogen cyanide or you can make 1 even if you add in Nuria K 2 molecules again that we suspect were available and provide conditions of peso in 1 step you can go either here or here in question over there yeah and that was that and you know this OK that's a good question and there is the To ensure that the answer is no In likely both come from both the ends the idea molecules where sounds funny are being formed OK and the ratios however probably not perfectly fifty-fifty due likely to dipole effects OK so when molecules formed tried and minimize and having a dipole entitles a higher energy state and you can imagine these nite trials pulling electrons in 1 direction in this case both titles will be pointing off to the left OK interesting question but don't get too worked up about 10 other questions arrange on so this gives us 2 key building blocks to bases of DNA quite straightforwardly and I'm going to not show you these 2 steps here prepared but I suspect that all of you can do them and we have a work she problem like that OK get a pen so we don't have to necessarily get through to them but in addition so on
these types of molecules that have 2 ratings are called Floridians and will talk more about that when we get to be on DNA bases well you not realizing next week is not warranted oppressor next week will be talking about today and we'll talk about more about what this definition of Providian needs now it turns out a primitive the college for
these are purines had purines the prove Indians have 1 ring
like these 2 guys a case of cytosine and yourself are examples of permanence and undue could form the provisions in a quite straightforward manner using these simple building blocks over here and this is I have this is a bigger to 23 in the taxes that actually gives you exactly the mechanism and because it said the text and I'd like you just go and I'll learn it for yourself OK that I'm not going to spend time actually doing errors today said but it's a very straightforward sequence the paper To me In
addition and so OK so from this week inform
all the period so we can form all the provisions using these reactions that evolved hydrogen cyanide and a on occasion this time sigh analysts steadily in this is I and was settling over here and but from their weakened basically derive all kinds of things In addition In order to
make DNA or RNA we also need some way of making OK when the case of foreign aid or deoxyribonucleic case of unit turns out that you can actually make the right rings quite readily the Thurman intimately very stable using a series of foremost reactions that form this right both during a structure OK and this uses something called the foremost reaction foremost reaction consists of that held all and then to benzoin reactions OK so we need to know to reactions to understand this foremost reaction and B the Aldo which hopefully you know and then also the benzoin reaction which will be unfamiliar to you and I'll go through it OK everyone so think so far let's take a look 1st at this benzoin
reaction the benzoin reaction is on the 1 that stitches together to tell the hides using sodium cyanide as a as a I to the reactive intermediate case going to the cyanide is going to form a key intermediate and make possible this is because otherwise kind of unusual although reaction OK several with the OK good while we take a look 1st at the on benzoin reaction and then we'll took to take a look at the foremost reaction for long OK so To recap what I've shown as you can make the DNA bases using the reactions that are
depicted here you can line them up and out in different ways and now I'm going to be showing you how to make the right those readings that are also an integral part of both DNA and RNA focus so let's get
started 1st with the benzoin reaction the name isn't so useful but I actually got as so important but I actually find the names of reactions useful to kind of organized around in my head you know a large amount of material pay so I'm in this reaction we're going to start with formaldehyde hides and in the presence of cyanide news To make this guy here who's sure during straight yes OK so cyanide act as a nucleophile before age 10 formaldehyde terrific electrify all you can't go wrong if you start lining up the Electra files together with the nuclear files so here we go so here's cyanide princess cyanide can attack here giving us a but I can't so cyanide attacks there and that gives us an Alcock cider and a cyanide now amongst its many properties that make cyanide such a terrific intermediate traffic reagent is is extremely electron withdrawing so that makes a proton center all but to the cyanide very susceptible to deeper nation OK so here is that deeper nation another resultant electrons can be in residence that will actually be stabilized by virtue of being adjacent to this cyanide so I'm sure you go know this as a on as you this intermediate reverberated looser credit occurred Florida case showing you this as Kirby in Ireland but I'm really what's going on here in a more appropriate way to describe as would be as a resident structure with the electrons bouncing to the a lecture negative nitrogen I'm also a little uncomfortable fly you have to negative charges of same molecule and from the pedantic party would actually insist that we rejoice but I don't have time today so I trainer that was working at a quarter get some crazy thing on a mid-term and be forced to accept that but so be it OK 2nd molecule formaldehyde can then and the attacked by this Caribbean and note that I'm drawing this era in this rather convoluted s configuration on doing that on purpose because I want to have the euro attacking the piste star the bonding orbital of the carbon if I don't draw the their going zooming down here than zoomed up here it's not going to land on that star in the bonding orbital and I think that's important because again and that's how I communicate effectively that I know what's going on OK last step here kicking back out the cyanide and so that gives us the product it's 1 1 step from the product product then picks up another protons change and then this is to the product OK now here's the thing if we can form L the hides in like this 1 there and were in good shape to actually be able to start doing Allred all reactions to build up to I'm carbohydrates like rivals a case of this menswear reaction immediately sets us up to actually start building diagnoses a upon Indiana ride busses are these building blocks of life but notice how close we are right we have 2 carbons we have to oxygen so this is starting to look very much like a carbohydrate right where carbohydrates these hydrated a carbon that have an equal number water molecules are from I'm an empirical formula has water in addition to each carbon OK so let's do the elder all part of the reaction so in this reaction what we're going to have is the same starting material up there and the same product up there now is starting material for and Algol reaction then this is the 2nd part of the former US 1st part was up there that's the benzoin reaction 2nd part has about I'm doing it the protonation this the protonation is likely stabilized by and calcium but I'm not going to show the coronation calcium suffice it to say tradition a calcium massively accelerates this reaction but I'm going to skip through that today this gives us a on very popular intermediate called it in and on this in 8 is highly reactive so if we have this you know in a way we can then line up another 1 of these products from the benzoin reaction appear and now do the famous Balboa reaction this is easily my favorite reaction because 90 per cent or so of all the carbon bonds that are found in biology use this algal reaction OK so here is the products and then in the last step we can readily pick up a proton from age it so this starts to give us something that really does start to look carbohydrate like press questions OK pretty straightforward series of steps on music reactions that we've seen before at least that you saw back when he took 51 state if this Aldo reaction is unfamiliar to go back and read about the elbow reaction in your reference organic chemistry text it is essential that you get comfortable elbow reaction is 1 are going to be using repeatedly this quarter compared this reaction here is going to be an essential reaction for you OK ,comma let's now see how we can take this these building blocks and build it into I'm not into something more complicated can no questions
OK so there is however a I'm step here OK so you can
build this using the for most reaction that I just showed you and then you go From the AL the Hive formed to this handy acid help for review carbohydrates in your old handbook if this reaction here is unfamiliar to you but I'm hoping that everyone is comfortable this idea that all the heights have you there a key tone are sorry carbohydrates heavy there at all the high heat form or hand acid help for and this acid help form is the ring form of aldehydes again we read the chapter of carbohydrates if you're not ready for that and by late chapter of 7 I think will be into and go icons and carbohydrates in a really big way a case of long before they get familiar with this concept with their structures and reactivity a carbohydrates and OK so we can now build the rival strains we can fill the bases let's put things
together OK so in the 1st that you can do a guy consolation reaction whereby you go from this right Bowstring to actually having a base attached to this right bolstering the key step this reaction is shown here In this but in this case that there's an not sodium ion case these on hand acid tells conforming sodium ions this Sox sodium ion is like a positively charged it is a fantastic electoral file to which a nucleophile can attack if the nuclear file happens to be big say this added 18 then the result will be adenosine as shown here furthermore these on things can be stitched together into a the chains that have a possible thereafter backbone akin to what seeing an RNA and DNA actually nite identical to what scene in RNA and DNA using on reactions that can be that can evolve on long polymers of phosphate there found for example in calcium phosphate crystals OK fast it is a fascinating little molecule it forms of all kinds of interesting polymers and crystals of but in any case you can make the triphosphate version the triphosphate version can be then stitched together into this and of only it turns out using what I
told you you can synthesize all of the be I'm pretty much all of the biopolymers there found in biology OK that we can now you're now ready to synthesize all of the RNA bases although Lauren is attached a rider as it turns out the delays are a little bit more complicated getting rid of Antioch CA is kind of a challenge and I am to ask chemists that racism quandary and at the same time the poses a solution OK so our thoughts is that since we can readily answered the size or Our thoughts are that the very 1st polymer to emerge on the spot might have been on day and it turns out that on the day it has sufficient reactivity to really handle that role OK so for example the proteins that are being synthesized by yourselves right now are being synthesized using RNA as the catalytic biopolymer on a portion of your right as is what's responsible for translation of RNA into proteins OK so Amadeus amazingly capable molecule and that's not a totally crazy experiment we haven't talked about the prebiotic synthesis of proteins and it turns out that you can also use very basic building blocks and build amino acids and there's a now-classic experiment that was done in the 1950's ,comma Yuri Miller experiment that I think everyone has learned about at some point in their lives and that basically consists of having very simple precursors an electrical spark meant to mimic lightning and from this you get out you can extract out amino acids in fact I have to know this was done at ease your mind as an the this was 1 of experiments son 1 of the 2 the teaching lapse right as and when the room this experiment done this start running that's OK that's too bad but it's a really fun experiment to do I recommended but maybe not in your garage but it's a work that actually works you can extract out pretty readily amino acids I'm in great quantities recently the original samples of the 1950's were found and then are tested using more modern analytical techniques and indeed in addition to amino acids that are shown here you can actually find lots of other amino acids as well OK
so this involves a Strecker synthesis of
of amino acids and I'm going
to refer you to the figure in the book that actually depicts the and this mechanism the figure is 231 in the book a case of the mechanism is in the book it's actually pretty straightforward and is on the worksheet as well OK a case will have a chance to To do error pushing involving amino acid synthesis I want you to do it I think it's really important I'd like you to be ready to do a tax but it's familiar players although hides Huygens cyanide ammonia is new but everything else is familiar the reactions are very similar to what I've shown you today and then I finally you
can stitch together on amino acids using it to them peptides and proteins using this reactive molecules as a peptide coupling agents and is actually found in volcanic vents
OK I need to switch gears that I want to talk to you about non-covalent interactions in talking about covalent interactions it's now time for us to talk about but that other super-duper reported topic of non-covalent bonding on pretty much everything in biology involves non-binding non-binding or what are called non-covalent interactions so the user crucially important they also tend to be very very weak so what we find is that small differences in energy the 2 very big effects OK so this is for example it enzymes and it's going to In a non-covalent way blocked by to a US starting material and catalyze the transformation of that starting material at a product it's never going to form a covalent bond to the starting material on the substrate starting material the reactants of this reaction no covalent bonds yet this transformation this catalysis and has really important implications for the cell so we definitely need to understand how
non-covalent interactions work because they really dominate the biology and I want to give you an idea of the strains of these these are on the order of 10 to 100 times less strong then accountability direction Caso a simple covalent bonds might be 90 K Khalsa so of of bonding energy but I non-covalent interactions between receptor my and over here or set our own receptor might get over here another was several again and is going to have a delta G for that not action on the order of maybe tank a Cal's role so it's going to be considerably weaker pay and this makes a transient this means it's not going to last forever now this kind of a
spectrum of bonding that we use to describe the interactions between 2 molecules so here's 2 molecules cozying up next to each other and they have a choice of what they can do on the 1 hand they could decide to form covalent bonds if they decide to share electrons and that's what we've been talking about that requires a homo and a limo there are kind of appropriately positioned and about national energy to allow that reaction to take place that doesn't always happen right not all molecules decide to react with each other and on so at the other extreme are much weaker actions involving charges if these 2 molecules have charges on and then you'll get charged charge interactions or ionic interactions and then somewhere in between the spectrum of really strong interactions the very weak are the walls interaction OK where the molecules interact with each other through London dispersion forces I'm going to talk to you about equations that govern all of those interactions the necessary questions so far right on here
is the room here is an equation that I'd like you to memorize because it describes on the terms for non-covalent interactions OK so non-covalent the energy involved in a non-covalent interactions is proportional to the 1st first-term cool on small OK so cool onslaught is the energy between 2 . charges case of how much energy is that work how much to those guys want interact with each other how much potential energy is available OK so if Q 1 and Q 2 are the same sign the boat negative charges and 41 times due to it's going to get us on a positive turn here if however the opposite charges will get in negative terms and note that negative terms means a more stable interaction a so energy over here is starting up here and we want to go down lower or to be more stable can the big goal in life for molecules like this is stability OK that's what these molecules creative that's what makes them run to work OK they're looking for a more stable situation said there like Steve announced the slopes and they're looking to get to the bottom as readily as possible where the bottom is lower in energy in addition there is a on the 2 other terms which embody the vandals interaction so this 1 is the charge charge interactions this 1 includes repulsive interactions which are proportional to are the inverse are at distance between the 2 molecules recent 12 power or attractive interactions which raised to the 6 power and these numbers here start to tell us quite a bit about the distance dependents of these different terms where this one's raised to the inverse 1 inverse 12 inverse 6 that makes a really big difference OK let's dissect each of these interactions and turn let's start with the
charge charge interruptions 1st charge charge interactions again are governed by this Colombia's potential where and we have the charges up here and then we have a on epsilon turned over here this is the dielectric constant K this dielectric constant is very environment and context-dependent so in different portions of the cell you might have different salt concentrations which dramatically affects the straight the discharge charge interaction OK so for example if the 2 charges happened to be present where there's no water and there's no ions from this term over here is going to be and a lot lower and in turn that's going to make the charge charger interaction much stronger OK so this is going to be very dependent upon the surrounding environment OK now as we said earlier Adams with the opposite charge are going to attract each other and so in turn this means that the potential energy is going to go down as the distance between the 2 decreases on the other hand with the same charge are going to repel each other and that's going to force them apart as they get closer and closer to each other notice that this does not go go all the way down you know to run until like some ridiculously low number eventually you get you know fusion between Adams and that doesn't happen there requires some unseen amount of potential energy so it's going to drop down here and then all the centers can last up to the mood over here in the drop back down again OK so that's why we're leaving off what happens over here OK last
part of the day formal charges are not the same as the partial charges that actually dominate when we look at molecules because I've been drawing formal charges all day it's useful shorthand but it doesn't tell you exactly where the charges and the right location of the charge is critically important to determining what really what the calamity interaction tells you a case so for example on furor some Lewis structures over here here's an ammonium ion you would be quite proper to put the positive charge under nitrogen and have the Huygens just hanging out here is a resident structure for for a and Tito acetone and on what we actually look at where the charges are distributed we find something as kind of mind-blowing newly we a pay so rather than having neatly a single positive charge just at the nitrogen instead what ends up happening is the hydrogen end up picking up on a little bit of positive charge and the nitrogen ends up with the negative charge similarly With the key talent over here the situation is more complicated as well and what's going on here is a redistribution of charge based upon the reorientation of the molecular orbitals that govern this complicated molecule over here so when we come back next time will be looking at houses molecular orbitals interact with each other in other non-covalent interactions and then will be talking about the United that weaken