Syllabus chem 153B Summer 2020 Last modified 20-08-2-20-33 PDF

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Chemistry and Biochemistry 153B DNA, RNA, and Protein Synthesis Summer 2020 SYLLABUS

Chem. and Biochem. 153B – Summer 2020

I)

Syllabus – p. 2

Course organizational details •

Instructor:

Cuiwen He [email protected]

Class time and location: •

Teaching assistant Christoffer Caro

•

MTWRF at 10-10:50am on zoom

[email protected]

Instructor’s and TAs’ Office Hours

Name Cuiwen He

M&W, 12–1pm

Zoom

Location

Christoffer Caro

Fri, 9–10am

Zoom

I strongly encourage attendance at office hours. They provide a great opportunity to ask questions about the course materials, work through the problem sets, and get to know your instructor, TAs, and fellow students. My office hours are not for discussing matters with me privately since there will usually be multiple students in attendance. If you need to speak privately with me about something, you are welcome to set up an appointment by sending me an e-mail. •

Online resources 1) Course web site: https://ccle.ucla.edu/course/view/201C-CHEM153B-1 . All course materials (including PowerPoints, problem sets, online quizzes) will be posted here. I strongly suggest you look over the powerpoint slides before lecture with special attention to the learning objective slides. Your grades will also be available through the course web site. 2) Zoom recording: All of the lectures will be recorded and the link to the recording will be posted after each lecture.

Chem. and Biochem. 153B – Summer 2020

Syllabus – p. 3

Discussion sections

II)

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Times and locations Section Time 1A T&Th 11-11:50am •

III)

IV)

Location Zoom

TA Christoffer Caro

Discussion section activities 1) Working together on problem sets 2) Working together on previous exams/sample questions

Attendance •

Lecture attendance: Attendance at all lectures is strongly encouraged. To be honest, the reason for awarding i>clicker participation points during lectures (see section VI of this syllabus) is to enforce attendance since you will get the most out of the course if you attend and actively participate.

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Discussion section attendance: Attendance at weekly discussion sections is strongly encouraged.

Course goals and learning objectives This class, which builds upon concepts of biomolecular structure, catalysis, metabolism, and bioenergetics that you learned in 153A, is organized around the Central Dogma of Molecular Biology (DNA makes RNA makes protein). Topics include nucleic acid structure and chemistry, DNA replication and repair, transcription, RNA processing, translation, and nucleotide metabolism. In this section of the syllabus, I list four broad learning goals (A-D). Underneath each learning goal there are a number of bullet pointed learning objectives (or learning outcomes), each of which starts with the phrase “You should be able to….” The powerpoint presentations will contain frequent slides with more detailed learning objectives. If you master all the learning objectives given here as well as those in the powerpoint slides, you should do very well in this course.

By the end of the course, you are expected to understand following: •

The basis of molecular recognition. By learning about the details of nucleic acid structure, you will gain an appreciation for the macromolecular interactions that allow sequence-specific interactions among nucleic acids as well as sequence-specific interactions between proteins and nucleic acids.

Chem. and Biochem. 153B – Summer 2020

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Syllabus – p. 4

You should be able to draw the covalent structures of nucleic acids (including the basepairs) and show how environmental mutagens can change this covalent structure leading to mutations. You should be able to recognize and describe the differences between the various types of nucleic acid duplexes and explain what influences the equilibria between them. You should be able to look at protein:nucleic acid complexes and identify the non-covalent interactions responsible for DNA binding stability and specificity.

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The thermodynamics of structural transitions in DNA. These transitions, which are essential for nucleic acid function, include DNA melting and DNA supercoiling. • You should be able explain what influences the equilibrium between duplex and singlestranded DNA and predict the temperatures at which duplexes will melt. • You should also be able to explain how DNA supercoiling influences DNA conformation, DNA melting, and nucleosome formation.

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The role of complex supramolecular machines in the highly coordinated events of nucleic acid metabolism. These machines, which contain both proteins and nucleic acids, include the replisome, the transcriptosome, the spliceosome, the ribosome, and others. In our study of these machines, the focus will be on: 1) The relationships between the structures and the functions of these machines. • You should be able to identify the critical structural features of these machines and explain the function of these features in DNA replication, DNA repair, transcription, splicing, and translation. • You should also be able to explain how conformational changes in these machines drive the above processes and how these conformational changes are coupled to the hydrolysis of nucleotide cofactors. 2) The catalytic mechanisms through which the machines act. These involve: a) Active site metal ions. • You should be able to explain how metal ions function in the active sites of supramolecular machines to accelerate reactions that make and/or break phosphodiester bonds. b) Catalytically active RNA molecules. • You should be able to describe the mechanisms by which the catalytic RNAs in supramolecular machines mediate catalysis, as well as the kinetic approaches used to characterize these mechanisms. • You should be able to explain why the existence of these catalytic RNAs suggests that life evolved from an ancient RNA world. 3) The mechanisms by which these machines achieve high fidelity (high accuracy) in the replication and decoding of genetic information. • You should be able to describe the strategies used by various supramolecular machines to ensure selectivity and to edit mistakes. • You should be able to explain the commonalities and differences between these strategies. 4) The mechanisms by which these machines are regulated to control gene expression.

Chem. and Biochem. 153B – Summer 2020 • •

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V)

Syllabus – p. 5

You should be able to explain how regulatory factors interact with supramolecular machines to control transcription, RNA processing, and translation. You should be able to discuss the phenomenon of epigenetic gene regulation, in which changes in the chromatin modification state influence gene activity in a manner that can be inherited from one cell generation to the next.

The pathways by which nucleotides, the building blocks of nucleic acids, are synthesized and degraded. • You should be able to explain how and why the reactions in these pathways are coupled to ATP hydrolysis. • You should be able to discuss the regulation of these pathways. • You should be able to explain how these pathways use channeling to ensure that intermediates are not wasted and to prevent the release of toxic metabolites. • You should be able to discuss ways in which these pathways are targeted in disease therapy.

Reading assignments: textbook and primary literature Textbook: You will need a copy of a biochemistry textbook. Many of the content you will see will be based on one of two books. They each have relative advantages: • _Lehninger (6th edition or later); students claim this has the clearest explanations • _Voet, Voet and Pratt (4th edition or later); This book has the great detail about fundamental topics • _Voet and Voet; this is the most in depth biochemistry book. It will go beyond the level of detail in the course, but may be beneficial to you in further Biochemistry studies. The suggested reading for Lehninger and VVP is listed in section XIV.

VI)

i>clicker The i>clicker response system allows you to respond to questions posed during class. The goal is to get you to think actively about what you are learning and to help the instructor gauge student understanding. To respond to the questions, you need to purchase a REEF polling subscription, which will allow you to respond to questions using your smart phone, tablet, or laptop (see instructions below). i>clicker participation points will be awarded starting the first day of class. If you answer one or more i>clicker questions in any class meeting you will earn one participation point for that class meeting. While there are 26 class meetings during which i>clicker participation points can be earned, the maximum number of i>clicker participation points allowed is 25. Responding to i>clicker questions in the name of any student other than yourself or allowing another student to respond to questions in your place is a violation of the student conduct code and will be h andled accordingly. Set up a REEF polling account and purchase a subscription, which allows you to answer • questions through your smart phone or other internet device. Both iOS and Android compatible apps are available (or you can respond to questions through a web browser). To download the app, visit https://www.iclicker.com/students/. To create a REEF Polling by i>clicker account, visit https://app.reefeducation.com/. Once you create your account, make sure you add your Student ID to your profile to complete the registration process. Creating an account automatically starts a free 14 -day trial subscription. Please wait until just prior to the beginning of the quarter to create your account so that you will have the entire trial period to make sure REEF Polling will work. It is not possible to receive a refund after you purchase a subscription. Subscriptions include an unlimited number of courses, and prices range from $15.99 for a 6-month subscription up to $48.99 for a 4-year subscription.

Chem. and Biochem. 153B – Summer 2020

Syllabus – p. 6

Problem sets

VII)

Seven problem sets will be handed out during the quarter. These will not be collected or graded. They are intended to help students prepare for exams and many of the questions come from old exams. The instructor and the TAs will help you with them during discussion sections and in office hours. I strongly suggest that you work on them in groups.

VIII)

Exam submission/Gradescope

All assignments other than participation will be graded and returned using Gradescope.com. Gradescope is integrated with CCLE. You can access gradescope through the course CCLE page. Exams will be posted on CCLE. You will access the file and complete the assignment in one of three ways: a. Print the file and complete it by hand b. Fill in the answers on a computer, though this may be difficult as there will be some drawing or diagrams and/or chemical structures. c. Write your answers on a blank sheet of paper with each question clearly indicated. In this case please have each full question on a separate page. You will then upload the file as a pdf to gradescope by either: a. Saving it as a pdf b. Scanning the papers and saving as a pdf c. Scanning the physical assignment with your smart phone using the “Scannable” app by Evernote on iOS, the “Genius Scan App” on Andriod. This is a how to guide for those apps: https://gradescope-static-assets.s3-us-west2.amazonaws.com/help/submitting_hw_guide.pdf Here is information from UCLA on how to convert your images into a single pdf: https://moodle2.sscnet.ucla.edu/wiki/index.php?title=Student_Assignments#How_do_I_convert_my_images_ to_a_single_PDF After you upload the pdf you will be asked to select the pages of your document where your answer to each question can be found. Please be considerate of the graders and do this accurately and it makes the grading much more efficient and less frustrating. Instructions for selecting pages: https://www.gradescope.com/get_started#student-submission The midterm exams will be posted on CCLE 1 hour 30 min and the final exam will be posted 3 hours on CCLE before they are due on gradescope. They will be open book and open notes, but you cannot discuss with your classmates and the TA. You can ask me if you have any questions about the exam and the submission. The two midterm exams will be on Friday of Week 2 and Friday of Week 4 and the final exam will be on the Friday of week 6 (September 11th). Late exams will not be accepted unless they are caused by situations that are out of your control. There will be 5 points deducted for not properly selecting pages associated with each question or not having the pages upright (you can adjust this in gradescope after uploading).

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IX)

Grade components/Grade cut-offs •

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Quizzes: There will be 6 online multiple-choice quizzes. These online quizzes will often be based on some videos and/or lectures. Unless noted otherwise, they will be due at 11:59 PM on the dates indicated in the class schedule (section XIV of this syllabus). I can’t give extensions since we will be discussing the quizzes in class soon after they are due. Midterms: There w ill be two midterms, one at the end of week 2 and the other at end of week 4. Attention to the learning objectives that you will find in the powerpoint slides, and study of the problem sets and i>clicker questions will help you to score well on the midterms. Final exam: The final exam is not cumulative and will mostly focus on materials covered after the second midterm which typically include transcription, RNA processing, Translatin and nucleotides metabolism. However, the basic conceptes of nucleic acids structures and recognition need to be

Chem. and Biochem. 153B – Summer 2020

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understood. As with the midterms, attention to the learning objectives that you will find in the powerpoint slides and careful study of the problems sets and i>clicker questions will help you to score well on the final exam. Participation: Part of your course grade is based on participation. To encourage attendance and active learning in class, iClicker questions will be used during lectures. 0.6 points are awarded for each answer to an i>clicker question. 2-3 iClicker questions will be used during each lecture. If you attend all lectures, you can maximize your participation points before the end of the class, but will not earn extra credit if you answer more iClicker questions after you reach the points maximum (25pts for lectures). In addition, 5pts are given for filling the online evaluations at the end of the class. Weighting of the grade components Midterm 1 Midterm 2 Final Exam Homework (base pairs) Online quizzes (six) iclicker questions course evaluation Total

40 pts 40 pts 75 pts 5 pts 60 pts 25 pts 5 pts 250 pts

Grade cut-offs 92-100% 88-92% 82-88% 76-82% 70-76% 65-70% 60-65% 55-60% 40-55% 0-40%

X)

Syllabus – p. 7

A/A+ AB+ B BC+ C CD F

Pymol In some of the class meetings, a molecular graphics program called Pymol will be used to explore protein and nucleic acid structure. In addition, some of the problems in the problem sets and possibly some of the online quizzes will ask you to explore molecular structures using Pymol. Pymol is available for download to your own computer. The “Educational-Use -Only” version (which is completely adequate for this course) can be downloaded for free after registering at the followin g web site: http://pymol.org/edu/?q=educational/. Som e of the basics of P ymol are explained in a Youtube video of professor Courey’s making (https://www.youtube.com/watch?v=c8RoP6eeYUg&t=1). A Pymol manual can be found here: http://pymol.sourceforge.net/newman/userman.pdf. Additional tips and tutorials can be found here (http: //ww w.pymolwiki.org/index.php/Biochemistry_student_intro) and here (http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners). Finally, a lot more information about Pymol can be found through Google searches.

XI)

Collaborative learning Learning works best if it is a collaborative process. The best way to master a difficult concept is to explain it to someone else. Therefore, I strongly encourage you to form study groups and to work together with your classmates on the problem sets and on coming to grips with all the course material.

Chem. and Biochem. 153B – Summer 2020

Syllabus – p. 8

The course is not graded on a curve. So you are not competing with your classmates for a limited pool of A’s. In principal, the whole class can get A’s if the whole class demonstrates sufficient mastery of the material. Here’s the bottom line: there is a huge amount of upside and no downside to helping your fellow 153B students learn the course material!! XII) Student conduct •

Academic integrity: Students suspected of academic dishonesty as defined in the Student Conduct Code will be reported to the Dean of Students. Possible penalties include probation, suspension, and dismissal. Academic dishonesty includes, but is not limited to the following: Cheating: Unauthorized acquiring of knowledge of an examination or part of an examination • Allowing another person to take a quiz, exam, or similar evaluation for you. This includes allowing another person to submit iClicker responses for you. • Using unauthorized material, information, or study aids in any academic exercise or examination – textbook, notes, formula list, calculator, etc. • Unauthorized collaboration in providing or requesting assistance, such as sharing information • Unauthorized use of someone else’s data in completing a computer exercise • Altering a graded exam or assignment and requesting that it be regraded •

Plagiarism: Presenting another’s words or ideas as if they were one’s own

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Submitting as your own through purchase or otherwise, part of or an entire work produced verbatim by someone else Paraphrasing ideas, data or writing without properly acknowledging the source Unauthorized transfer and use of someone else’s computer file as your own Unauthorized use of someone else’s data in completing a computer exercise

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Multiple Submissions: Submitting the same work (with exact or similar content) in more than one class without permission from the instructor to do so. This includes courses you are currently taking, as well as courses you might take in another quarter Facilitating Academic Dishonesty: Participating in any action that compromises the integrity of the academic standards of the University; assisting another to commit an act of academic dishonesty • Taking a quiz, exam, or similar evaluation in place of another person • Allowing another student to copy from you • Providing material or other information to another student with knowledge that such assistance could be used in any of the violations stated above (e.g., giving test information to students in other discussion sections of the same course) Fabrication: Falsification or invention of any information in an academic exercise • Altering data to support research • Presenting results from research that was not performed • Crediting source material that was not used for research While you are here at UCLA, you may find yourself in a situation where cheating seems like a viable choice. You may rationalize to yourself that “Everyone else does it…” Well, they don’t. And will that matter when YOU get caught? NO! If you are unsure whether what you are...