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5th_lecture - MCB 102 Professor Fyodor Urnov Lecture 5 ASUC...

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MCB 102 Professor Fyodor Urnov 06/28/10 Lecture 5 ASUC Lecture Notes Online is the only authorized note-taking service at UC Berkeley. Do not share, copy, or illegally distribute (electronically or otherwise) these notes. Our student-run program depends on your individual subscription for its continued existence. These notes are copyrighted by the University of California and are for your personal use only. D O N O T C O P Y Sharing or copying these notes is illegal and could end note taking for this course. ANNOUNCEMENTS Your sections will begin today and continue for the rest of the semester. Remember that attendance is mandatory and will count toward your final grade. LECTURE I decided to start today a highly important and extremely boring list: what proteins do. As enzymes, they catalyze reactions in order to convert A to B. They do this to either produce more A or get rid of A. They catalyze a chemical reaction degradation for the purpose of releasing energy (such as with ATP or GTP). They form a structure that can be used for various purposes such as DNA binding with histones. They create channels which allow for communication between different areas of the body (such as the nuclear pore complex ). They bind to other things (like sugars or other proteins) to make something else happen. Protein regulation is one example of this. Homework: I will send a YouTube version of a video that illustrates many different biochemical processes, nearly all of which use proteins for one purpose or another. Make sure you watch it because it actually gives a really good overview of nearly everything you need to learn. Now I know many of you have are worried about learning the amino acids and I’ve had many students e-mail me about what exactly they should know regarding them. For this class, you will have to learn the structure, the single-letter code, and the three-letter code for every amino acid . I will test it on the final by presenting one of the amino acid’s qualities, such as its three-letter code, which you will use to answer the question I give. Yes, the test will be open book, but you won’t have time, so you need to memorize it. And I advise starting early, because even though you won’t be tested on it until the final, it is useful to understand for everything else we go over. Over the next four lectures, we will take a considerable look at proteins, especially their roles as enzymes. To start off, let’s first look at the different levels that make up proteins. At its heart, proteins are a linear chain of amino acids (as opposed to some glucose polymers, which have branched chains). The first level is the primary structure , which is the sequence of amino acids that form the protein. After that are the secondary structures , which are made up of common formations seen in many proteins. These structures, like α helices, β turns, and β pleated sheets, are folds in the DNA structure. Hydrogen bonds formed from the amino acid backbone, rather than the side
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