Lecture 01. Introduction/What is Chemical Biology?

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Lecture 01. Introduction/What is Chemical Biology?
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Lec 01. Introduction to Chemical Biology -- Introduction/What is Chemical Biology?
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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: 0:30:30 What is Chemical Biology? 0:42:01 The Central Dogma of Modern Biology 0:46:54 What is in a Gene? 0:53:31 What is a Genome? 1:00:33 Inside a Human Cell 1:09:58 Combinatorial Assembly Generates Diversity
Chemische Biologie Sea level Stuffing Chemistry Electronic cigarette River source
Ionenbindung Ice sheet Set (abstract data type) Korngrenze Erdrutsch Wursthülle Chemistry River source Molecule Stuffing Stress (mechanics) Tidal race Protein Library (computing) Active site Cycloalkane Signal transduction Sea level Chemistry Erdrutsch Wine tasting descriptors Biochemistry Chemische Biologie Collecting Transcription (genetics) Horse meat Zunderbeständigkeit Filtration Stuffing
Cosmetics Kohlenhydratstoffwechsel Setzen <Verfahrenstechnik> March (territory) Steel Korngrenze Grading (tumors) Chemistry Alpha particle Hardness Ballistic trauma Chemical structure Stratotyp Library (computing) Cosmetics Notch signaling pathway Explosion Topicity Multiprotein complex River source Erdrutsch Electronic cigarette Chemische Biologie Vancomycin Soft matter Yield (engineering) Azo coupling Dietary supplement Zellkontakt Ice shelf Ionenbindung Reaction mechanism Peptide Organische Verbindungen Wursthülle Oppression Cell (biology) Orange juice Faserplatte Explosion Sea level Stream bed Drug prohibition law Process (computing) Setzen <Verfahrenstechnik> Dietary supplement Grading (tumors) March (territory) DNS-Synthese Singulettzustand Carbon (fiber) Chemistry Flood Agriculture Organic food Base (chemistry) Chemist
Thermalquelle March (territory) Fatty acid methyl ester Poppers Chemistry Grading (tumors) Californium Columbia Records Man page Inflammation Vancomycin Functional group Magnetometer PICT Magma Explosion International Nonproprietary Name Lymphangioleiomyomatosis Medroxyprogesterone Tin National Rifle Association Chewing gum
Angular mil Katalase Grading (tumors) Metal Anomalie <Medizin> Wine tasting descriptors Altbier Data conversion Marl Medroxyprogesterone Periodate Alum Pitting corrosion Mashing Dihydrofolate reductase Brauwissenschaft Ampicillin Chemische Biologie Locus (genetics) Auxin Lymphangioleiomyomatosis Chewing gum Condensation Kreide <Gestein> Phase (waves) 11 (number) Talc Coiled coil Mill (grinding) Organische Verbindungen Wursthülle Columbia Records Man page Lamination (geology) Adversary Puff pastry Thylakoid Ham Zeitverschiebung Magnetometer International Nonproprietary Name Sea level Mixture Grading (tumors) Agar Corpus mensurabilis musicae Darmstadtium Glycosaminoglycan Maid Vakuumverpackung Psychological trauma Water Dichloromethane Organic food Drop (liquid) Diatomics-in-molecules-Methode Anaerobic digestion Coca Pan (magazine) Methylphenidate Flux (metallurgy) Tin Nitrosamine
Ionenbindung Gas Ocean current Wursthülle Chemistry Molecule Cupcake Cell (biology) Lactitol Respiration (physiology) Library (computing) Cobaltoxide Organic food Sea level Chemist Periodate Silver Molecularity Gas Pedosphäre Topicity Chemistry Biochemistry Molecular biology Chemische Biologie Gesundheitsstörung Radical (chemistry) Azo coupling Elektrolyse Molecule Cobaltoxide Chemist
I'm going to run the classes follows all have the most important announcements at the very beginning of the class so I'll be talking about stuff like what's covered on the mid-term and what's expected from your proposal Simon etc. at the very beginning so beautifully wanna show up on time job-related a seat on be prepared because most supporters stuff is going in the 1st 5 minutes OK Oh and by the way I feel free to interrupt if you have any questions OK so don't hesitate to the becomes OK so some announcements today and again announcements will come out at the very beginning of each class Obeidi assignments this week I'd like you to obtain the textbook it's available on the bookstore the big stack them when I visited last week they ran out of bullets good Irish the if they ran out of the Amazon . com has on sale in and out and you can get them delivered very quickly effect on I know for a while Amazon was selling them at some ridiculous discount so I know because as 1 of the co-authors of interest some very interested in how the selling them along those lines up as 1 of the co-authors of planning to donate the profits from the book to anyone in this classroom back to UCI for but to support research in chemistry said so I'm requiring a book that I wrote on I'm obviously aware that I'm going to profit from that profits will go back to use your OK so if you have a copy of the course reader from previous years please throw away OK it's not going to be any get immediate skillet but I've changed the material quite a bit and the textbook is significantly improves the problems a slightly different but I think it's so the figures are much better etc. editor of course was edited soak Austria for previous years is not going to carry you need to buy a copy of textbook so Natalie had as the sounds of and and and and I think that the end of the court it thank you Natalie yes so that yes they will be posted online for you so you can enjoy them and study from them etc. other the goal here is that I use your mind is 1 of the very 1st called universities to have both the lecture classes and a laboratory classic chemical biology we started these back in 2000 when I was an assistant professor and since that time we've obviously built up quite a bit in terms of our sophistication of presenting the subject and so my goal is to really bring that level too other universities around the world and around the country so anyway that's why we're doing this but it also has a benefits you as well OK and I'm so greedy assignment for 2 for the 1st week of the Chapter 1 I'm going to be covering all the material a Chapter 1 so there's nothing for you to skim through or anything like that on future chapters there will be stuff that I will be covering and I'll tell you when that happens OK and you'll you'll notice when it happens OK if you want to get ahead start reading chapter to chapter 1 is pretty basic Chapter 2 then starts getting more advanced some homework due to problems in Chapter 1 all the odd problems and also all of the asterisk problems and let me add that that to so
all the problems that have an asterisk are built the answers to all the problems of an asterisk are available online so I'd like you to do
this as well OK and then in addition I will be posting a work sheet number 1 on the site it's not there yet but be posted notices will be posted after it's OK said I will be posting that that will form the basis for the discussion sections please work the worksheet as well OK so before I get started out before I go through very much more on tell you are what you should be paying attention to words and the 1st thing are these announcements and giving on what's discussed in lecture the discussions so they give you a lecture are your guide to what I think is important OK so right before the midterm you're going to want to know what do I need to know on the mid-term to get an a in this class and my answer is always the same which is what I talk about elections when I talk about a lecture is what I think is important have a limited amount of time for these lectures and I'll be doing to lectures per chapter of an hour and 20 minutes each and so on if I talk about it in lecture I'm telling you I think is important this is something you need to know for the mid-term OK and so what's discussed the lecture is reported this includes those slides and anything else that's posted to the Website on discussion worksheets and then the discussion in discussion as well if you're sitting on the left side of the classroom class students who listened to if you have an empty chair in your right said just to create more extra chairs because we have people arriving late service future replaced thank you I'm OK the next most important thing a sign reading light filter the sign reading through the filter through the lens of what I talk about in class if I talk about in class that's telling you it's important if I don't talk about it the less important and then finally the problems in the textbook as we support the good news is there's a few things that you don't have to worry about and the 1st Eleazar references on the slides I find it almost impossible to do stuff that without having some referral back to the literature and that's part of the nature of scholarship and it's totally impossible to get me to stop doing this and when we went even I wrote the textbook for example we had a list of references it's like 10 times longer than the 1 that's posted to the Web site and I we found it totally possible publisher told us to stop doing it to leave out those references and so and references are basically that currency that underpins and 1 I'm telling you but on the other hand this is an introductory class so don't get worried about those OK if you take a graduate class may have references on slides you want to look up those references but in an undergraduate level don't get worked up about the case said don't stress about those in addition don't stress about stuff that's covered in the textbook that we don't discuss in class specified United exodus before a final discussing class and it's in the textbooks don't worry about it a case of the text is written as sort of an advanced undergraduate early graduate level and there's material there that's frankly graduate level but I want you to get stressed out about it a case of I don't talk about and class that's my signal that I don't think it's so important for you to learn that the questions about what I'm telling you the thing I answered a question Commissioner David Marin could you look into the affidavit in OK so go be eventually will appear there but not yet thanks for asking the question was now so we will not be collecting the problem sets but plenty of other chances to learned about intelligent creatures from another question slides will be posted perhaps that's a good question all tried by unusually frantically getting ready the daylights out onto my that's certainly the Thursday lecture will be but maybe not the Tuesday of the library that's other questions OK more background of course instructors on Professor Weiss I've be teaching his class for about 12 years and I absolutely love chemical biology is what makes me want to work it's is my sole passion in life was that's a little bit of exaggeration but close and OK so what else would you like to know about me here's your chance for the next 5 minutes you can ask me anything you want personal not personal go ahead in the back I so my laboratories at the interface a chemistry biology and were trying to develop new ways of looking at individual molecules and under undying setting how membrane proteins work thanks for asking him a question over here it was a kind of a competitive guy I like driving fast I liked the horse racing and so yeah question over here chemical biology emphasize that this is a great question so the question was What is the difference between biochemistry Chemical Biology Chemical Biology emphasizes what's happening at the level of Adams and bonds and biochemistry emphasizes what's happening at a larger scale so in biochemistry and my colleague circuit tend to look at proteins sort large molecules without getting too worked up about hygiene volunteered Hajime bond there sometimes they get worked up about the things that most the time on the diagram signal transduction diagrams and things like that are just large blobs and in this class will be zooming in and looking at the actual Adams and bonds a the question I'm anything else personal this is your last chance as being personal that's not my pets my hands so go ahead now I wish I did I only get to go out once a year it's kind of the limitations who's not thanks for asking OK well I should also let you know I have 2 cats and unmarried and that's it for the personal information had been OK let's question go ahead of you have 0 kids for a two-seater cars without OK guys and that's it on the personal stuff enough about me and I'm very pleased that this quarter we have really the very best years in the chemistry department I've gone through an IFA hand-picked by
ITA is Miriam if the car is up and there is a great example is Miriam and I talked this class last year and I she knows everything there is to know about this topic and her research is a chemical biology and she's actually superb and if she tells you something about the class you could take that as good as coming from a local farm in addition our 2nd TA could Millheim isn't here today she's been tied up in India but should be back in the next week or so and she is also a great source of information she also a graduate student in my laboratory tests were really lucky to have him California's finest natural resource cheering for us a critical and Miriam OK so terms of office hours I will be having to office hours a week my Thursday office hours set by Wednesday office our however will float a case I will always have office hours Thursday at 11 today there was this other office tower the 2nd office our will float meaning that my schedule's costly changing it's all have to change the surround a case so every week I will announce when an officer will take place if for example my office hours don't think your schedule tell me at the beginning of the week when you like my office hour to be an altered my best to accommodate as many people as possible each with effect so 1st office our fixed 2nd office our floating I will always have office hours set up in a way that's at the interfaces between classes so you don't have to attend the whole office hours if you can attend as the 1st 15 minutes or so or 10 minutes and then fly after class that's perfectly OK short for 5 minutes get your question answered and then disappear I don't care I don't mind but always set them up so their time at the junction between classes that then you know it's less likely that you'll be able to tell me that you have a scheduling conflict with every 1 of my office hours I've heard that before and I usually ask those people to show me their schedule classes and I've never seen it actually that way especially since I had the 2nd office flooding so as to me plenty of time for you to meet me this quarter and in fact I really want to get to know you have I will get to know the names of 95 per cent of you in this room I will know something about what you're career aspirations are and I will know something about your creativity in terms of your ability to come up with novel ideas you're writing ability and a lot of other characteristics as well so at the end of this I will deal to write a very good letter of recommendation for you OK and this is not a proposed last topic but I would like you to shut off your cell plays cut and that also includes text messaging as well thank you I'm OK so anyway come out my office hours especially in the 1st couple of weeks introduce yourself tell me why it is you're taking this class what it is you hope to learn what it is that you're hoping to do what you graduated from UC Irvine and if there's anything I can do to help you in that course I will do it OK that's 1 of my jobs and furthermore even after you graduate from this class you can still keep in contact with the can still get letters of recommendation from me and you can still have my support in your career aspirations that's my promising commitment to you OK and on the TAS also have office hours each week here office hours will always be on different days and times in my office hours and their office hours are much more fixed that my office hours so any questions about anything I've ever said any of announcements so far OK I very textbook parody of mention this again it's available on on Amazon understand it sold out but you can get it again from Amazon supplemental text I'd like you to have available in organic chemistry supplemental text when I talk about peptides for example when I talk about in bonds I'm going to see that you've read the chapter on Emad bonds and peptides in this supplemental text even if wasn't covered 51 state a pale just ask you to go back and read that chapter of pay and say you need some sort of supplemental text available in organic chemistry .period as basically as reference it's nice because this will provide a kind of a lower key our treatment of a more complex topic server example if you wanna learn the sort of the ferry fundamentals of DNA of carbohydrate chemistry the best place to start is whatever textbook used to 51 C now I realize many a few soldier textbook right after the class was over there was a huge mistake but it's not too late to change things number 1 but I can give you are alone you a supplemental tax if necessary come to my office hours 1st by people a shot will get 1 of those and 2nd that the the library the Science Library has about 3 shelves there like this wide the field of organic chemistry texts the exact text does not matter a paid basically if you look at some organic chemistry but textbooks they're all more or less the same pay what really matters so as have 1 available to you that you can refer to as reference you need that for this class of Haiti's I'm going to assume that you know the material in there now along those lines spiked on a couple of e-mails from some of you are concerned that you had trouble in 51 C a troubled organic chemistry and now you're taking the sort of advanced organic chemistry class in your worried OK here's what I want to be there 1st don't panic pay I will do my best to get you up to speed on Aguero pushing and some other fundamental common fundamental principles in the next 2 weeks they later don't panic yet at the end that 2 weeks if 1 I'm doing on the board and your ability to keep up a discussion section and homework are just you know apples and oranges you know feels a part of the uniting on the same racetrack then you can start panicking but for now no panic a play and if you were really really weak in a soft organic chemistry I'd like you to open the chapters on carbon he'll chemistry whatever book it read the chat reread the chapters and Carbondale chemistry and get up to speed on those if you understand how Karniol chemist heels react called Alpha carbon is acidic and a few other things he'll be fine in this class turns out that's like 60 years 70 per cent of the organic chemistry that underlies biology involves carbon yields cases start their 1st AFC the advantage of the carbon deals come see me again and I'll get you don't give you the next topic which will probably be a means or something like
that appeared some Texas hopefully have allayed some of your fears .period don't panic yet but I get ready to panic in the next week or so and also to get ready to take your game up a notch OK so that you know even if had a bad time 51 see you can do pretty well miss classic you're ready to work pretty hard need lots of problems and come up with creative ideas center OK found discussion sections these are mandatory this especially important a few weak in organic chemistry discussion sections are going to be run in a problem-solving format and this is your chance to show that you could do era pushing with the best of them so a lot of the problem from this class involved mechanisms and set in discussion sections you'll have a chance to demonstrate your ability to do mechanisms you'll you'll get up to speed on doing these correctly etc. OK so again the 1st work she will be posted shortly the 1st discussion section will start this Wednesday and Marion will be teaching that 1 and then after that it will continue but could have your honor Monday if you were scheduled for Monday discussion section of don't panic what the material that will be covered on Wednesday will then be covered on the next Monday OK so we'll have them slightly staggered throughout the class OK and it turns out that actually works out fine because the midterms are on a Thursday at a Tuesday case there'll be 2 midterms in this class and on there are no makeup exams available and they they will consist of the full hour and 20 minutes but there's going to be an emphasis on pushing and constant problems will be things like short answer there'll be no multiple choice and there's going to be like short essay type problems will be problems we have to design experiments things like that but lots lots of Europe which said get ready for air oppression is on in addition the other way that I'm going to assign your grade is I'll be looking at 2 written reports that you're going to submit in the class the 1st of these is the Journal article report due unfortunately on Valentine's Day Happy Valentine's Day from your chemical biology friends on and in this 1 and this report you're basically going to be doing the equivalent of a book report but using an article from the primary literature to provide a report I've already posted to the Web site an example of this and in addition instead of a final exam this class will have a mandatory proposal that's due on the last day of class March 14 OK that's and mandatory proposal you cannot pass this class without turning in of the proposal but there's no final exam day and the proposal will consist of an original idea a chemical biology now I know this is daunting I thought this classy foreign notices really intimidating don't panic and I will have a series of exercises for you this quarter that will get you up to the point where you're ready to come up with creative novel ideas in the cutting edge of chemical biology so you will be ready for this you'll be ready to contribute and the good news is a chemical biology there's so much that we don't know but there's lots of room for smart people like yourself to come up with a really great new ideas can I see this every year every year I would take the very top proposals from art from this class and I could resentment in the National Institutes of Health and they would get funded had the best ideas I can put up for faculty ideas anywhere OK so I've seen that before and the other thing is I'm looking for a small idea and not looking for a you know the next Manhattan Project or something like that I'm just looking forward to a base said you know something that will work that will teach us something new about chemical biology and you're going to I'm quizzes I will have a series of quizzes in this class bomb that will number between 1 and 5 became more likely to be 1 to 2 there will definitely be a acquitted 1 sometime in that last week and the reason is our 2nd midterms in February and the classics going till March accessibility and easy quiz the quizzes in general are designed to be easy they're basically you recapitulates something that you just saw on the board of peso will run the easy there at the beginning of the class of the the class cannot be something along the lines of the Solis mechanism show me again how it works OK something like that just basically tells me whether or not you're paying attention and he's showing up for class and by the way I'm delighted to see all of you happy people up this morning but welcome but I know as the class wears on you guys get very uh the busy and I Of course lectures will be posted online there has to be some incentive here to get you rolled out of bed at 9 30 in the morning OK so and we will have some quizzes it will be too many and they will be hard to that I promise you in terms of per cent of your grade those quizzes only account for 5 per cent the same level of participation participation counts about lecture and discussion and on for that matter even office hours peso being and Marianne mn critical getting-to-know-you that's how we determine the the the quiz courts are the participation sport 0 and by the way I am I will post all these slides online a possible be all opposite the website on steel have copies of them not personnel but the because the shortly OK each major will count for 30 22 per cent of your total grade but the Journal article report will account for 16 per cent and the proposal which is in place of the final exam accounts for 30 per cent of your great pesos a pretty even distribution there's lots of opportunities to get for you to get feedback etc In questions so far yes in that was honor it is I haven't talked about that yet takes readers that agog at that in just a moment of Thanks for and I me Steve now question Carl OK Carl he had no problem Carl's question is whether a and assigned to some discussion section doesn't fit my schedule to another 1 No problem and you can even go to 1 1 week in a different actually the problem the and posted online will are it's posted on the syllabus exactly when the discussion sections will take place and let me
show you that "quotation mark so this is the course website pay on notice over here that there are instructions for the book report all changes very slightly after 2013 instructions for the proposal all changes very slightly there are 3 examples of proposals that are today and then the syllabus In the
syllabus of 5 listed the discussion sections and where they need etc. feel free to go to any of these Hi I'm let me zoom through this this is online I'd like you to read this carefully I'm going to hold you to all the provisions that are in here a peso anything that's written in near it's equivalent to me saying I'm not sure exactly why this is because of the rain I In a lot of this recapitulates what I just said OK let's get to this on this question Over here and there will be C 1 moment
OK on February 20 1st 2013 you will turn an abstract for your proposal OK so abstract is the short condensate of what your proposals going to consist of this tells me whether or not you are on track and I'm going to use this as a way to give you early feedback about your idea and tell you whether or not I think your idea fits the definition a chemical biology whether or not I think your idea here is a creative 1 or not so creative OK so this gives me a chance to give you feedback before you turn in your proposal the and on this abstract is worth 10 per cent of the points for the proposal assignment a case in other words 3 per cent of your course created will be determined by that abstracts of papers note that all assignments are due by 11 AM on the due date there is a league policy but I hope that doesn't apply to you questions of rights yeah never distracted by this information here about ads and drops on news that frequently have asked questions section 22 10 discussion sections yes discussing paper turn in the final assignment at all if you have not taken all three-quarters of 1051 2 semesters of organic chemistry you should drop the class OK you're going to get blown out of the water in case so you must drop the class now it's a prerequisite and that every year someone slips through don't take this class if you haven't taken the .period Organic Chemistry Series have I'm OK there's a whole thing on incomplete over here
but no economic policy unfortunately we're going to talk about this later in the class I do not want to apply to you there that the major portion of greatest .period to be writing assignments and so academic integrity issues loom large unfortunately in this class every year I have to give someone of of F grade on assignment which and that's turning into like a C minus D plus kind of deal because they try to plagiarize assignment don't let that be a let's make this the year don't have this problem and along those lines if this is the year I don't have any plagiarism problems I will give an additional 3 per cent higher grades solve assigned the grades and then I'll go through and all pumped up 3 per cent of the course grades to the next higher grade OK so if everyone in the class avoids having any plagiarism or academic honesty issues said no cheating on exams no plagiarism no academic honesty I will bump up the grades by 3 % became means for 5 of you at each level are going to get a higher grade OK so that means like 4 people 3 or 4 people who were going to get a B-plus ,comma variety minus I'll take the top of the 3 or 4 top the minuses in movement today OK that's the deal will talk some more about this because it's a slippery slope and it's best that we don't have that this ,comma conversation later OK so anyway on that's information on the best-seller
syllabus ,comma holding due entirely to the US contents of that sold some expecting you to go home and read the Silvers carefully I don't have time to talk about every aspect of it now I'd like you go home go and read it carefully please current questions questions OK that you that OK let's
get started so we are adhered heard the question what is chemical biology Hauser differ from biochemistry I gave me kind of a quick answer I want to delve into this topic a little bit further OK so here's the working definition of chemical biology that will be using this quarter and it's important that you understand that this is the definition is using chemistry to advance and understand molecular understanding of biology at the level of Adams and bonds so the way I know that we're talking at the level of of of molecular at the molecular level is if we're talking about Adams and bonds OK and that's what I'm looking for in terms of definition of chemical biology there is a on a 2nd corollary to this definition which is using techniques from biology to advance chemistry and some examples of this are for example using molecular biology techniques to develop ,comma tutorial libraries of chemicals which is something that will is 1 of the projects of my own laboratory does affect so there are 2 parts this using techniques from chemistry to study biology or using techniques from biology to solve problems a chemistry in both cases these involve looking at molecules at the level of Adams of bonds and that's where it's distinct from biochemistry biochemistry also uses techniques to chemistry but oftentimes there with looking at molecules search amorphous blobs that are represented as you know spheres or something like that in textbooks in this class will be down at the level of abounds in bonds and that's how you know we'll be talking about chemical biology cell leader in the class when I asked you to come up with an idea in chemical biology a proposal idea that you should be thinking at the level abounds in bonds and then unit tells you whether or not your idea would be acceptable OK so Chemical Biology advances both chemistry and biology and I want to give you a couple of historical examples of this and for my money the very 1st chemical biologist was Joseph Priestley does this guy over here he was a remarkable and character so the isolated oxygen and other gasses cases he was isolating these using electrolysis and other techniques and on he would isolate these and bell jars and then he'd use these chemicals to study biology so 1 of the experiments he did for example was subjecting poor mice my said he would travel from fields and to these different but chemicals that he was isolating any found the mouse for example can live in oxygen but could not live in many of the other gasses that he was isolated OK so that's really interesting example because using the very latest techniques from chemistry to understand better how respiration works how organisms taken oxygen and at the same time it's using a technique from biology as a way of solving a problem in chemistry and the technique of biology is does the mouse lives or dies does the organism can organisms survive under these conditions to tell me something about those chemicals right Joseph Priestley didn't have any spectroscopy available to him so he's using a technique from biology Avery qualitative technique to be sure but I'm the nonetheless to and to tell me something about what's happening at the chemical level cake now and suggested .period Joseph Priestley had radical ideas about colonists in America and a theological dissents that were going on in England at the time and I like to say that the very 1st chemical biologists had his house burned by an angry


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