Fall 2020 Syllabus Biochemistry PDF

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Download Fall 2020 Syllabus Biochemistry PDF

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Syllabus – Fall 2020 MCB3010/MCB5001 Biochemistry (Version 8/28/2020) Excluding materials for purchase, syllabus information may be subject to change. The most up-to-date syllabi are located within the course in HuskyCT. This includes both the course and lab syllabus. The instructor reserves the right to change dates for assessments as the semester progresses. All changes will be communicated in an appropriate manner.

Instructor Information Professor: Dr. Judith Landin Email: [email protected] (please use e-mail as the preferred form of contact) Telephone: 860-486-0476 Office: TLS404 Office Hours/Availability: Please contact me by e-mail to arrange a time to meet. Lab Manager: Dr. Linda McCollum-Guilani Email: [email protected] Telephone: 860-486-4972 Office: TLS260/266 Teaching Assistants Joshua Calabrese [email protected] Boyang Li [email protected] Richard Whitehead III [email protected]

Course Description Students will learn fundamental concepts of Biochemistry including structures of proteins, carbohydrates, nucleic acids and lipids; techniques for studying these molecules and metabolic pathways including synthesis of DNA, RNA, proteins, carbohydrates, and lipids and the breakdown of carbohydrates and fatty acids for production of ATP. The lectures will be presented as asynchronous videos to minimize issues from synchronous learning. Review questions will be posted on the Discussion board on most days that class would occur. Students will be expected to provide answers. In addition, synchronous review sessions will occur once or twice a week for students to ask questions and clarify the material. These sessions will depend on the attendee’s input. There will be 3 exams during the semester and a final exam. The lab will provide additional exposure to some lecture topics, but for the most part is intended to educate you on Biochemistry laboratory techniques as well as common scientific practices such as keeping a lab notebook and writing a manuscript. The lab will be in-person as long as in-person classes are occurring. The final week of classes, which will be online only, will consist of an online lab practical. There is a separate HuskyCT site for each lab section where you will submit assignments and take quizzes and the lab practical. There is a separate lab syllabus that you will follow for the lab portion of the class.

Course Materials The textbook will be Lehninger: Principles of Biochemistry by Nelson and Cox, 7 th Edition. It is not required to purchase the textbook and most students do not. The Study Guide and Solutions Manual are packaged with the textbook from the Bookstore. Lehninger is a classic biochemistry text that was recently revised. It contains a comprehensive overview of the basics and includes coverage of several topics at an advanced level. The text can serve as a useful reference source if you continue in the field. To save money, Lehninger 6th edition or 5th edition or frankly any recent comprehensive Biochemistry textbook will still be of value as you try to learn Biochemistry. The textbook for MCB2000 does not really match this course. The textbook is available for purchase through the UConn Bookstore. Textbooks can be shipped (fees apply). You will need an appropriate computer, a webcam and a microphone to take exams online using Lockdown Browser with Monitor. For lab, you will need a notebook with a hard cover that can be disinfected with alcohol at the end of each lab period.

Course Outline

Topics

Chapters

Molecules in Water Weak interactions in aqueous systems pH: acids, bases and ionization Buffering against pH changes

2

Thermodynamics Gibbs Free Energy Applications of structures and reactions

1, 13

Amino acids, Peptides and Proteins Amino acids Peptide bond and primary structure Purification and characterization of proteins

3

The Three-Dimensional Structure of Proteins Overview of protein structure Protein secondary structure Protein tertiary and quaternary structures Protein denaturation and folding

4

Protein Function: Ligand Binding Myoglobin and hemoglobin

5

Protein Function: Enzymes Introduction to enzymes Enzyme mechanisms Enzyme kinetics and inhibition Regulation of enzymes

6

Exam I (10/2)

Carbohydrates and Glycobiology Monosaccharides and disaccharides Polysaccharides Glycoconjugates

7

Nucleotides and Nucleic Acids Structure and properties of nucleotides Structure and properties of nucleic acids

8

DNA Techniques Agarose gels PCR DNA fingerprinting DNA sequencing

8, 9

DNA Metabolism and Analysis Replication of DNA DNA repair

25

RNA Metabolism DNA-dependent RNA Synthesis RNA processing

26

Protein Metabolism The genetic code Protein synthesis Protein targeting

27

Lipids Structure and chemistry Structural lipids in membranes

10

Exam II (10/30) Biological Membranes and Transport Membrane composition Membrane proteins Transport across membranes

11

Phosphorylation and Redox Reactions ATP and other high energy molecules Energy transfer Redox reactions and reduction potential

13

Carbohydrate Metabolism Glycolysis Fermentation of glucose Gluconeogenesis Glycogen synthesis and breakdown

14/15

The Citric Acid Cycle Production of acetyl-CoA Reactions of the citric acid cycle

16

Oxidative Phosphorylation Electron Transport Chain Mitochondrial ATP synthesis

19

Triacylglycerol Catabolism and Ketone Bodies Breakdown of glycerol Oxidation of fatty acids Formation of ketone bodies

17

Exam III (12/4)

Synthesis of Fatty acids and other lipids Fatty acid and glycerol synthesis Formation of triacylglycerol Formation of glycerophospholipids

21

Light Reactions of Photosynthesis Light-driven electron flow ATP synthesis by photophosphorylation

20 (or 19 in previous editions)

Carbohydrate Synthesis in Plants Calvin Cycle Starch and Sucrose synthesis Cellulose synthesis Glyoxylate cycle

20 (glyoxylate cycle in 16 in previous editions)

Accessing Material on HuskyCT There are 2 HuskyCT sites. The main site will have everything you need to do for the Lecture portion of the course and all the lab information that you must read such as the lab syllabus, lab protocols, and TA office hours. There will also be a HuskyCT site for your lab section. You will submit your work on this site and take your lab quizzes and the lab practical. Lectures are separated by week to try and help you pace your learning. Each PowerPoint is in a separate folder with the accompanying video lectures. Each PowerPoint has blank slides to mark where a new video lecture starts. In the weekly folder containing the last material for each exam, a study guide will be posted that will have a list of topics that will be on the exam. Discussion forums are available. You may access them through the Discussion Boards content area. There is one for you to ask questions as you work through the lecture material. You may ask questions there anonymously. A second forum will have review questions posted several times a week. Hopefully different students will answer the questions. Collaborate Video Meetings will occur on Monday at 10:10am and one other day a week unless there does not seem to be a need for these meetings. You may access the meetings through the Collaborate Video Meetings content area. I will host the ones for lecture from the main meeting room. Please consider sharing your video and audio although I will ask you to mute your audio unless you are speaking. There is also a chat function which can be accessed by clicking on the pink tab at the bottom right. The T.A.s will also host their office hours through Collaborate as well. Exams will have their own content area. You will take the exams using Lockdown Browser with Monitor. See the exams section for more details. A practice exam will be posted early in the semester so you can verify

that Lockdown Browser with Monitor is working for you. You will be able to take the practice exam multiple times in case you need to work things out. It would be wise to check again on the week of the exam.

Exams Exams will be given from 6-8 p.m. on the dates below: 1. 2. 3.

Friday, 10/2 Friday, 10/30 (Note final drop day is the Monday after this exam) Friday, 12/4

The final will be given on the day and time indicated by the University. Semester exams will only be given at the scheduled time to maintain integrity in the course unless a University policy specifically negates this policy. Student athletes traveling for a game may take the exam if the exam can be given at the normally scheduled time. The final exam is given in accordance with University regulations. Because one exam grade is dropped, you are free to miss an exam for any reason, and that exam will be used as your dropped exam. Each of the semester exams will be focused on the material from that section of the course. However, you will be expected to utilize appropriate ideas learned in previous sections that are required to understanding the new material. The final exam will be roughly 40% new material and 60% percent cumulative material. The exams have open ended questions, and many of you will work for the whole 2 hours. These questions may require anywhere from a word to a short paragraph or two. There will also be math problems when quantitative topics are included in the material. Unless you have a photographic memory, please study every week (preferably every day). Studying for a couple of days before the exam will not get you an A. There are Study Tips in the Introduction to the Course folder. I especially encourage you to use the study tips from the book Make It Stick, most of which are based on scientific studies about learning. The exams will be given using Lockdown Browser and Monitor through HuskyCT. Lockdown Browser is a special browser that limits what you can access from your computer. Monitor uses your webcam and microphone to monitor you taking the exam to make sure it is you taking the exam and that you are taking the exam without assistance. Lockdown Browser must be downloaded from HuskyCT from the Institution page. Please familiarize yourself with all the information about Lockdown Browser that is available to you if you have not previously used this browser to take exams. If you encounter issues with Lockdown Browser that are not solved by restarting the Browser and accessing the exam again, please utilize help within the browser or the help listed in the Help section below. You will need a webcam, a microphone and an approved ID in order to take the exams. This is to fulfill the Federal government’s requirement to verify the identity of the students taking the course. If a calculator is required, you will have access to one through the browser. You will be expected not to use any other assistance in answering the exam questions. This includes but is not limited to notes, books, electronic devises or another person. A video will be made of you taking the exam which I will be able to view. Suspicious behavior may result in deductions from your grade or a zero on the exam. Monitor does notify you when it detects suspicious behavior. When I grade, I can only read what you wrote to determine whether you answered the question correctly. I do not assume or infer anything. Please write your answers clearly and thoroughly. If I can’t understand what you meant, I cannot give you points for your answer. I do not give full credit to answers that sort of sound like the right answer or to answers that do nothing more than restate the question. I grade each question across all exams in order to be as consistent as possible.

Course Grading

Final grades will be determined with 75% weight given to the exams and 25% weight given to the laboratory grade. The three exams and the final have equal weight. One of the three semester exam grades will be dropped. This allows you to miss an exam without penalty or an excuse. The two highest grades for the semester exams will be averaged with the final exam grade. The final examination will be partially cumulative, i.e. it will cover material from the entire course. Students need to earn a passing grade for the exam average to obtain credit for the entire course. If the average for your exams (the two highest semester exam grades and the final) is not a passing grade, the lab portion of the course will not be included in the final grade, and you will fail the course. Grades may be curved when the final letter grades are assigned. However, I do not curve to the mean or median. This ensures that grades reasonably represent a student’s knowledge of the Biochemistry material that was covered.

For additional information on undergraduate grading policies see here: https://registrar.uconn.edu/grades/ For additional information on graduate grading policies see here (note that effective Fall, 2020, the grade of A+ no longer exists) https://gradcatalog.uconn.edu/grad-school-info/academic-regulations/#Grades

Student Authentication and Verification The University of Connecticut is required to verify the identity of students who participate in online courses and to establish that students who register in an online course are the same students who participate in and complete the course activities and assessments and receive academic credit. Verification and authentication of student identity in this course will include:

1. Secure access to the learning management system using your unique UConn NetID and password. 2. Verification during exams using Lockdown Browser with Monitor showing ID card or other instances of using a webcam and ID to prove identity Exam Proctoring Exams will be given with Lockdown Browser with Monitor. You will have to download Lockdown Browser through HuskyCT. Instructions can be found on the Institution page of HuskyCT. Respondus Lockdown Browser with Monitor’s minimum system requirements are listed on this page. Monitor requires the following:      

Windows: 10, 8, 7 Mac: OS X 10.10 or higher iOS: 10.0+ (iPad only). Web camera (internal or external) A microphone A broadband internet connection

A short practice exam will be available in the first week of class to allow you to practice

How to Succeed in this Course You have signed up for a large challenge, a 5 credit Biochemistry course. You will need to study frequently to be successful unless you have a good mind for learning lots of facts. You will be taking open answer exams which are quite different than multiple choice exams. Open answer exams require that you read the question thoroughly and give an answer without the cues you get from a multiple-choice exam. I recommend that you write questions for yourself and answer them by writing or typing out the answers. Writing out the answer will make it clearer to you that you either know or don’t know the answer. It helps if you can wait a while between writing the question and then answering them. You might also want to find other students who would be willing to exchange questions so you get exposed to different ways to

approach the material. You will be expected to learn certain molecular structures and metabolic pathways. I recommend writing them out until they become second nature. You need to pace yourself to keep up with this course as well as your other courses. For instance, lab reports aren’t due every week. Use the off weeks during the 8 week Taq lab to start writing up your manuscript so you don’t have to do it all at the end. Need support? Consider contacting:

Dean of Students Office Academic Achievement Center Center for Students with Disabilities Student Health and Wellness -- Mental Health

Husky Study Groups Are you interested in forming a study group with other students in the class? There is a study group application in Nexus that can help you get started. There’s a video with students and you may go here (https://nexus.uconn.edu/secure_per/studygroups/index.php) for more information.

Software/Technical Requirements (with Accessibility and Privacy Information) The software/technical requirements for this course include: ● ● ● ● ● ● ● ●

HuskyCT/Blackboard (HuskyCT/ Blackboard Accessibility Statement, HuskyCT/ Blackboard Privacy Policy) Adobe Acrobat Reader (Adobe Reader Accessibility Statement, Adobe Reader Privacy Policy) Google Apps (Google Apps Accessibility, Google for Education Privacy Policy) Microsoft Office (free to UConn students through uconn.onthehub.com) (Microsoft Accessibility Statement, Microsoft Privacy Statement) Dedicated access to high-speed internet with a minimum speed of 1.5 Mbps (4 Mbps or higher is recommended). WebCam Microphone Camera

For information on managing your privacy at the University of Connecticut, visit the University’s Privacy page. NOTE: This course has NOT been designed for use with mobile devices.

Help Technical and Academic Help provides a guide to technical and academic assistance. This course uses the learning management platform, HuskyCT. If you have difficulty accessing HuskyCT, you have access to the in person/live person support options available during regular business hours through the Help Center. You also have 24x7 Course Support including access to live chat, phone, and support documents.

Student Technology Training Student technology training is now available in a new HuskyCT short course created by students for students. It will prepare you to use the IT systems and services that you will use throughout your time at UConn, whether learning online or on-campus. It is available at https://lms.uconn.edu/ultra/courses/_80016_1/cl/outline .

Minimum Computer Technical Skills To be successful in this course, you will need the following technical skills: ● ● ● ● ●

Use electronic mail with attachments. Save files in commonly used word processing program formats. Copy and paste text, graphics or hyperlinks. Work within two or more browser windows simultaneously. Open and access PDF files.

University students are expected to demonstrate competency in Computer Technology. Explore the Computer Technology Competencies page for more information..

Accommodations for Illness or Extended Absences Please stay home if you are feeling ill and please go home if you are in class and start to feel ill. If illness prevents you from attending class, it is your responsibility to notify your instructor as soon as possible. You do not need to disclose the nature of your illness, however, you will need to work with your instructor to determine how you will complete coursework during your absence. If you are experiencing a significant illness or life circumstances are affecting your ability to focus on courses and your UConn experience, students can email the Dean of Students at [email protected] to request support. COVID-19 Specific Information: People with COVID-19 have had a wide range of symptoms reported – ranging from mild symptoms to severe illness. These symptoms may appear 2-14 days after exposure to the virus and can include: ● ● ● ● ● ● ● ● ●

Fever, Cough, Shortness of breath or difficulty breathing Chills Repeated shaking with chills Muscle pain Headache Sore throat New loss of taste or smell

Additional information including what to do if you test positive or you are informed through contract tracing that you were in contact with someone who tested positive, and answers to other important questions can be found here: https://studenthealth.uconn.edu/updates-events/coronavirus/

Mask and Social Distancing Expectations To ensure a saf...