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MCB 102 SYLLABUS SUMMER 2020 LATEST STUDY NOTES UPDATED FOR 2025- 2026
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Molecular and Cell Biology 102 [4 units]: Summer 2020 Survey
of the Principles of Biochemistry and Molecular Biology Course
Description
A comprehensive survey of the fundamentals of biological chemistry, including the structure and function of biological macromolecules, the properties of intermediary metabolites, the logic of metabolic pathways, and the molecular basis of genetics and gene expression. This is an online course. Each lecture will be prerecorded and released at least three days prior to a live zoom Question and Answer session specific for that lecture. The Lecture Q&A sessions allow students to ask the Instructor questions about the lecture material and provide a forum for discussing administrative announcements. In addition, students participate in two one hour live zoom Discussion Sections per week and have the option of attending Instructor and GSI office hours. Online courses have a number of benefits, including the ability to review recorded material. Our goal is to use this opportunity to provide a more effective learning experience. Prerequisites: Biology 1A, 1AL, and Chemistry 3B (or equivalent courses). Recommended : a course in physical chemistry. Credit Restrictions: Students will receive no credit for MCB 102 after taking MCB 100B or C100A/Chemistry C130 or Chemistry 135. The course is not repeatable for credit. The course meets Biological Science, L&S Breadth.
Instructor’s Information
Instructor: Mark Biggin Office Location: Remote Lecture Q&A sessions: MWF 10-11 am (live via Zoom - required) Office Hours: Tuesdays: 9-10 am and 6-7 pm (live via Zoom - optional) E-mail: [email protected]
GSI's Discussion Sections and Office Hours
GSI email office hours* (live via Zoom - optional) sections Elsie Sawai [email protected] Thursday 6-8pm 101, 201 Jessica Lutz [email protected] Monday 5-7pm 105, 205 Marycon Jiro [email protected] Monday 10-11am; Thursday 9-10am 102, 202 Nina Wang [email protected] Friday 2-4pm 103, 203 Yanan Wang [email protected] Thursday 10am-noon 104, 204
- First GSI office hours Thursday June 25th Discussion Sections (live via Zoom - required). First section. Wed, June 24th. No section on exam days. Section 101 MW 12-1 pm GSI: Elsie Sawai
Section 102 MW 12-1 pm GSI: Marycon Jiro Section 103 MW 12-1 pm GSI: Nina Wang Section 104 MW 12-1 pm GSI: Yanan Wang Section 105 MW 2-3 pm GSI: Jessica Lutz Section 201 MW 9-10 am GSI: Elsie Sawai Section 202 MW 1-2 pm GSI: Marycon Jiro Section 203 MW 1-2 pm GSI: Nina Wang Section 204 MW 1-2 pm GSI: Yanan Wang
Section 205 MW 3-4 pm GSI: Jessica Lutz
Requirements Prerecorded Lectures, Lecture Q&As, and Discussion Sections: Students are responsible for all materials presented in the pre-recorded lectures, Lecture Q&A sessions, and Discussion Sections. Students are expected to attend live the lecture Q&A sessions (MWF 10:10 am – 11:00 am). Students must also attend via Zoom two one hour Discussion Sections per week, except for those few students who have made a prearrangement with Jessica Lutz, head GSI, due to a scheduling difficulty or poor internet connectivity. Discussion Sections and Lecture Q&A sessions will be recorded and the recordings made available on bCourses via the "Pages" navigation link. The required contact hours per week are thus 3 + 2 = 5 hours in addition to the time watching the pre-recorded lectures. Students should attend only the Discussion Section that they are assigned. Check on bCourses for which Section you are assigned to as some students have been reassigned to allow more students to participate live. If you wish to be assigned to a Section that meets at a different time, email the Instructor ([email protected]) ASAP. Experience shows that Lecture and Discussion Section attendance correlates with how well students perform on the exams. The move to an online format will not change this, but without the collective energy of the UC Berkeley student body nearby to encourage you, there could be more temptation to miss contact hours. Do not let this happen. Discipline yourselves to attend and participate in the live zoom meetings. Keep up with the lectures. Do the practice problems. Discussion Section & Practice problems: Practice problems and the GSI led discussion of them are an integral part of the course material. They are designed to amplify and extend the material presented in the lectures. Practice problems are not graded. Instead, the answers to these problems and the explanations for the answers will be discussed in section. Mastery of the practice problems is excellent preparation for the exams. Don’t worry if you cannot answer all of them on your own. Realizing that you have not understood something is the start of learning. Attend the Discussion Section and hear the solution to the problems explained. Answer keys to the problems will be posted on bCourses after Discussion Section. To encourage attendance of the Discussion Sections and attempting the Practice Problems, 10% of the final grade will be awarded to students who attend at least 10 out of the 13 Discussion Sections. As an exception, students with poor internet connectivity, scheduling clashes or in distant time zones can obtain 10% of their grade by submitting Practice Problems that show a serious attempt to answer most questions. Answers to Practice Problems must be submitted on the day of the Discussion Section designated for addressing a particular group of Practice Problems. The GSIs will specify in advance which Practice Problems will be associated with which day's section. Students who fall short of these requirements will receive a proportionally reduced grade. For example, students attending (or submitting Practice Problems for) only 6 Discussion Sections will receive 6% instead of 10%. Students MUST obtain prior approval to not attend Discussion Section live. Send requests by June 19th with an explanation for your reasons to Jessica Lutz, head GSI, [email protected]. Office hours: The Instructor and the GSIs will each hold two one hour live zoom office hours. Office hours are optional for students. They provide a forum for more a detailed examination of areas anyone is having trouble with, as well as picking up points not captured during the required contact hours. They can be a further chance to go over the answers to practice problems. Office hours will not be recorded. Live zoom events: Links to all live zoom events (Q&A, Discussion Sections, office hours) are on bCourses via the "Pages" navigation link. For security purposes, all live zoom events for this course will only allow entry to participants who are logged into a zoom account. You must use a zoom account linked to your correct name and your berkeley.edu email account. All UC Berkeley students have free access to a free Zoom pro account, see link for details https://studenttech.berkeley.edu/zoompro. Please ensure that you have one of these accounts. Attendance at Discussion Sections will be determined based on a usage report provided by Zoom after each meeting that records login and out times for each participant
using the zoom login data to identify participants. To obtain credit for attending Discussion Sections, you must be logged in with your correct name and berkeley.edu email. Students in the US who do not have full access to a computer or have poor internet connectivity should contact the Instructor, who is working with UCB to obtain resources to improve your situation. Piazza: We will use “Piazza” to facilitate group discussion. Group discussion threads are moderated by the Instructor and the GSIs. Please use Piazza instead of email to ask questions if you’re struggling with concepts or problem sets. Emails will not be answered in written form. Posts to Piazza can be completely anonymous to your classmates and can be answered by fellow classmates as well as by GSIs or the Instructor. (Email questions sent to the Instructor prior to the Lecture Q&A sessions will be answered during the live zoom Q&A session—send these emails to [email protected] and include the lecture number and slide number(s) to which your question refers). Exams: There will be three exams, one for each part of the course. All exams are non-cumulative and aim to test your learning and understanding. Each exam will constitute 30% of the overall grade. They will include a mixture of multiple choice and short answer questions. Make-up exams will not be considered. Missing exams without prior communication with the Instructor results in a zero grade in the exam. We will be using gradescope to grade exams. What will you be tested on? You are responsible for (1) all theoretical, conceptual and practical topics covered in the prerecorded lectures, in the lecture Q&As, and in the lecture notes placed on bcourses (slides and what the Instructor says); (2) being able to solve problems similar to the practice problems given at the end of each lecture and discussed in section; (3) being able to answer questions similar to those in the examples of prior exams provided. Exams will test the application of knowledge, as well as content. Don't just memorize each slide, work to understand and apply concepts. What will you NOT be tested on? You will NOT be tested on topics from the book that were not covered in lecture / lecture Q&A / lecture notes / practice problems / discussion sections. The exams will be released on GradeScope on the days indicated on the schedule at 9.45 am PT. Each exam will run 2 hours from 10 AM to noon PT, with additional time for students who have arranged for DSP accommodation letters, see below. Alternative times will be available for students in distant time zones or with unbreakable scheduling clashes by prearrangement with the Instructor. Requests for alternate times along with an explanation for the request should be sent to [email protected] before Monday June 29th. Completed exams should be uploaded to GradeScope within 15 minutes after the scheduled end of the exam. Later uploads will be accepted pending a suitable explanation. No one will be penalized for any technical difficulties or disruptions that they have experienced. Students should ensure that they have had 2 hours (or longer for DSP stuents) of quiet time to take the exam. Exams will be “ open book/open note ”. You are welcome to consult any notes, lecture recordings, Lehninger chapters, Piazza posts, or worksheets we have generated during this class. Do not consult the internet for content related to this exam. Do not ask for help from others to complete this exam (either MCB 102 students or anyone else). Do not give help to other students in MCB 102. Unlike a practice problem, group work is not allowed on the exams. This includes posting questions/replies on Piazza at any time on the 24 hours of the day of the exam. While you may look at old posts, please do not create new posts during the exam period. Failure to follow these rules will be considered a breach of the Student Code of Conduct (Section 102.01 Academic Misconduct) and will be grounds for discipline. More information can be found here: https://sa.berkeley.edu/code-of-conduct. Please do not break the rules. It's not the right thing to do, and it wastes everyone's time because we do take it very seriously. During MCB 102 this spring there were a few cases where students did get unfair assistance with one midterm. Anyone receiving unfair help will receive a 0 and will be referred to the center for student conduct.
III. Cheating: Cheating will not be tolerated. UC Berkeley’s cheating policy will be followed http://bulletin.berkeley.edu/academic-policies/#studentconductappealstext. Copying another's answers during an exam and other forms of cheating including plagiarism will result in the same penalties. In order to guarantee that you are not suspected of cheating, please keep your eyes on your own materials and do not converse with others during quizzes and exams. The UC Berkeley honor code is posted at http://asuc.org/honorcode/. The code of conduct is available at https://sa.berkeley.edu/student-code-of- conduct. IV. Incomplete: Students who miss an exam (see Item V below for additional info) due to an emergency that could not have been predicted in advance can request a grade of “incomplete” and complete the missing section in the following semester. Please note however that an incomplete grade can only be issued for students who have missed no more than one of the three major exams and who are doing satisfactory work (C- or better) in the exams completed. V. Missed exam: Students are required to take all of the exams. If you have a schedule conflict with an exam or are in a distant time zone, it is your responsibility to inform the Instructor, in writing, no later than end of the second week of the semester. A standardized exam such as the MCAT or GRE is an acceptable excuse only when the standardized exam occurs at the same time as the MCB 102 exam and no alternative exam date is available. In the event of an emergency that could not have been predicted in advance, the Instructor is to be notified within two days after the missed exam. Examples include incapacitating illness or death in the immediate family, with a doctor’s note; or a serious traffic accident, with a police report, etc. If you are excused, you will take a make-up exam as soon as you are able. Alternatively, you may request a grade of “incomplete” (see above). VI. Religious accommodation: In compliance with Education code, Section 92640(a), it is the official policy of the University of California at Berkeley to permit any student to undergo a test or examination, without penalty, at a time when that activity would not violate the student's religious creed, unless administering the examination at an alternative time would impose an undue hardship that could not reasonably have been avoided. Requests to accommodate a student's religious creed by scheduling tests or examinations at alternative times should be submitted directly to the faculty member responsible for administering the examination two weeks before the relevant exam, per UCB policy: https://teaching.berkeley.edu/academic-calendar-and-student-accommodations-campus-policies-and- guidelines - anchor2. VII. Letter of recommendation: The Instructor may be approached for a letter of recommendation. I am quite willing to provide a written evaluation for this purpose. So that I may prepare effective evaluations I ask that you follow the procedure outlined here. i). Be sure to attend at least 2 of the Instructor’s office hours. ii). Ask your discussion section GSI to write a brief note about your participation in section to the Instructor. iii). Sometime soon after the end of the course, request an interview with the Instructor and bring a copy of your complete transcript, your CV and Personal Statement along with any recommendation forms that need to be filled in. iv). The Berkeley Career Center runs a Letter Service that can collect reference letters and hold them for future use: https://career.berkeley.edu/Letter/Letter VIII. Grading: We will electronically scan and grade exams using Gradescope. Exams will be returned to students via Gradescope and a link sent to the email address of the student. Requests to correct clerical or procedural errors in grading midterm exams must be submitted through GradeScope no later than one week after the exams have been returned to the class. The Instructors and GSIs will not discuss such issues until you have explained your case in writing. Exams will not be re-graded when less than one point is at issue. Answers that are illegible or in any other way ambiguous will be given zero points when grading. In accord with University Policy, no change of the grade filed in the end-of-semester course report is permitted “…on the basis of reassessment of the quality of a student’s work.” Changes can only be made to correct clerical or procedural errors such as “…errors in adding scores or transcribing grades.”
Letter grades for the course are assigned on a “curve.” The Instructors review the grades of each student and make every attempt to be fair. In the past, scores in the range of the mean and the median have been assigned a grade of B-. Fraction Description 30% Midterm exam # 30% Midterm exam # 30% Final exam (not cumulative) 10% Discussion section / Practice problems 100% of final grade IX. Enrolment change deadlines: For this summer term UC Berkeley have extended the deadlines for enrolment changes. The new deadline to add, drop or withdraw with refund is July 2nd. The deadline to change grading option (grade of pass/fail) is August 7th. Please check the following link for any updated information. http://summer.berkeley.edu/registration/schedule - deadlines Schedule Lectures will be prerecorded and released at least three days before the day indicated below. On the day indicated for each lecture a live zoom Q&A session will run from 10:10 am to 11:00 am pacific standard time for the Instructor to answer your questions on that lecture. Lecture Date day topic Chapter***** 1 6/22 Mon Overview; Thermodynamics; Water 1.2-1.4; 2. 2 6/24 Wed pH, Buffers; Amino acids 2.2-2.3; 3. 3 6/26 Fri Proteins 3.2-3. 4 6/29 Mon 3D protein structure 4 5 7/1 Wed Ligand binding 5. 7/3 Fri Independence day observance 6 7/6 Mon Enzymes: mechanisms & kinetics 6.1-6. 7 7/8 Wed Enzymes: examples & regulation 6.4-6. 8 7/10 ***** Fri Lipids; Membranes; REVIEW 1- 7 10.1-10.3; 11.1-11. 7/13 Mon Exam 1. Lectures 1-7 (not 8) 9 7/15 Wed Carbohydrates; Bioenergetics 7.1-7.2; 13.3-13. 10 7/17 Fri Glucose & glycolysis 14.1, 14. 11 7/20 Mon Citric acid cycle; Gluconeogenesis 16.1-16.2; 14. 12 7/22 Wed Oxidative phosphorylation 19.1-19. 13 7/24 Fri Regulation of metabolism 15
