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5.07 Biological Chemistry Syllabus - Fall 2014

I nstructors: Professors Alexander M. Klibanov (AMK) and Alice Y. Ting (AYT)

Date Lect
. #
Lecture Topic Reading
(Voet et al., 3
rd
edn.)
Lecturer
Wed., Sept. 3 1 Organization of 5.07.
Life, cell, metabolic pathways,
regulation, building blocks
Chapter 1 AMK
Fri., Sept. 5 2 Water, hydrogen bonds, amino acids Chapters 2 and 4 AMK
Mon., Sept. 8 3 Primary and secondary structures of
proteins
(PSet 1 due)
Chapters 5 (91-114) and
6 (125-134)
AMK
Wed., Sept. 10 4 Tertiary and quaternary structures of
proteins
Chapters 6 (134-151)
and 7 (176-197)
AMK
Fri., Sept. 12 5 Enzymes and mechanisms of catalysis

Chapter 11 (322-339
and 347-359)
AMK
Mon., Sept. 15 6 Enzyme kinetics
(PSet 2 due)
Chapter 12 (363-376) AMK
Wed., Sept. 17 7 Enzyme inhibition and control Chapter 12 (377-393) AMK
Fri., Sept. 19 NO CLASS (Student Holiday)
Mon., Sept. 22 8 Introduction to metabolism Chapter 14 (448-459,
475-477)
AMK
Wed., Sept. 24 9 Phosphoryl group transfer; ATP
(PSet 3 due)
Chapter 14 (459-469) AMK
Fri., Sept. 26 10 Redox cofactors Chapters 11 (326-328)
and 14 (469-474)
AMK
Mon., Sept. 29 EXAM # 1 Lectures 1-8, PSets 1-3 AMK
Wed., Oct. 1 11 Chemistry of sugars Chapter 8 (219-234) AMK
Fri., Oct. 3 12 Glycolysis
(PSet 4 due)
Chapter 15 (485-504)

AMK
Mon., Oct. 6 13 Glycolytic endings and regulation Chapter 15 (504-515) AMK
Wed., Oct. 8 14 Pyruvate dehydrogenase reactions Chapter 17 (566-576) AMK
Fri., Oct. 10 15 TCA cycle I Chapter 17 (576-583) AMK
Mon., Oct. 13 HOLIDAY (Columbus Day Holiday)
Wed., Oct. 15 16 TCA cycle II
(PSet 5 due)
Chapter 17 (583-594) AMK
Fri., Oct. 17 17 Lipid structure, digestion, absorption,
and transport
Chapters 9 (245-259)
and 20 (677-685)
AMK
Mon., Oct. 20 18 Fatty acid oxidation Chapter 20 (685-700) AMK
Wed., Oct. 22 19 Pentose phosphate pathway
(PSet 6 due)
Chapter 15 (506-513) AYT
Fri., Oct. 24 20 Electron transport chain I Chapter 18 AYT
Mon., Oct. 27 EXAM # 2 Lectures 9-18, PSets 4-6 AMK
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Wed., Oct. 29 21 Electron transport chain II Chapter 18 AYT
Fri., Oct. 31 22 ATP synthase Chapter 18 AYT
Mon., Nov. 3 23 DNA structure Chapters 3 (40-51) and
24 (821-828)
AYT
Wed., Nov. 5 24 Overview of DNA replication Chapter 25 (867-889) AYT
Fri., Nov. 7 25 DNA replication speed, sliding clamps,
and clamp loaders I
(PSet 7 due)
Chapter 25 (867-889) AYT
Mon., Nov. 10 NO CLASS (Veterans Day Holiday) Chapter 25 (867-889)
Wed., Nov. 12 26 DNA replication speed, sliding clamps,
and clamp loaders II
Chapter 25 (867-889) AYT
Fri., Nov. 14 27 DNA replication fidelity I Chapter 25 (867-889) AYT
Mon., Nov. 17 28 DNA replication fidelity II Chapter 25 (867-889) AYT
Wed., Nov. 19 29 DNA replication coordination I Chapter 25 (867-889) AYT
Fri., Nov. 21 30 Modern DNA sequencing methods I Chapter 3 (55-58) AYT
Mon., Nov. 24 EXAM # 3 Lectures 19-30, Pset 7 AYT
Wed., Nov. 26 31 Modern DNA sequencing methods I Chapter 3 (55-58) AYT
Fri., Nov. 28 NO CLASS (Thanksgiving Holiday)
Mon., Dec. 1 32 Overview of RNA transcription Chapter 26 (919-927) AYT
Wed., Dec. 3 33 RNA transcription initiation Chapter 26 (919-927) AYT
Fri., Dec. 5 34 RNA transcription elongation Chapter 26 (919-927) AYT
Mon., Dec. 8 35 Mitochondria
(PSet 8 due)
AYT
Wed., Dec. 10 36 Mitochondria-endoplasmic reticulum
communication
AYT
Dec. 15 19 FINALS WEEK


Instructors: Professors Alexander M. Klibanov, klibanov@mit.edu
Professor Alice Y. Ting, ating@mit.edu

Teaching Assistants: Alex Genshaft (genshaft@mit.edu)
Shuo Han (shuoh@mit.edu)
Kellie Kolb (kekolb@mit.edu)
Louis Papa (papa@mit.edu)

Textbook: Voet, Voet & Pratt, Fundamentals of Biochemistry, 3rd (or 4th) edition.
Lectures: Mondays (M), Wednesdays (W), and Fridays (F), 9-10am, in Room 4-370.
Recitations will begin the 2
nd
week of the semester, i.e., on Monday, September 8. The
recitation (R) schedule is as follows:
R#1 MW 12 (4-257) Louis Papa R#5 TR 10 (36-144) Shuo Han
R#2 MW 1 (4-257) Louis Papa R#6 TR10 (38-166) Kellie Kolb
R#3 MW 1 (13-5101) Alex Genshaft R#7 TR11 (36-144) Shuo Han
R#4 MW 2 (13-5101) Alex Genshaft R#8 TR11 (38-166) Kellie Kolb
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Mid-term exams: There will be three exams during the term. The exams are closed
book, closed notes; any necessary information will be included at the end of the exam. The dates
are in your syllabus: Monday, September 29; Monday October 27; and Monday, November 24.
Please look at the dates and determine whether you have conflicts. (You must request the
conflict exam in advance and it will be administrated the afternoon before or morning after the
scheduled exam.) If so, please contact us immediately and we wish to make alternative
arrangements. Each exam will be worth 100 points.
Final Exam: There will be a three-hour final exam held during the Final Exam period.
The exam will cover the material for the entire semester and it is also closed book, closed
notes. In this course everything builds on the information from the preceding lectures, so the
final is cumulative. The final exam will be worth 300 points.
Make-up exams: There are no make-up exams. If you miss an exam because of illness or
an unexpected and urgent personal matter, please present us with a note from MIT Medical or
the appropriate Dean. Under such circumstances, the points from the missed exam will not be
considered in the calculation of your final grade (e.g., 500 total points, rather than 600 total
points, if one mid-term is missed). If you miss an exam without a note from MIT Medical or a
Deans authorization, you will receive a score of 0 points and this score will be factored into
your final grade.
Problem Sets: Every week you will be given a problem set. These problem sets are
worth 10 points each. The goal of the problem sets is to focus you on important concepts
covered in the lectures and the textbook. A second goal is to help you keep up with the material
covered. It is OK, and indeed encouraged, to collaborate on the problem sets, but you must not
copy another students work. In other words, it is important that you master the material on your
own because exams are taken individually. Problem sets are due as indicated in your syllabus
and should be turned in right before the lecture (9am) the day they are due in 4-370. Answers to
the problem sets will be posted on the web site within one day after the due date.

Relationship between 5.07 and 7.05: These courses offer two perspectives on the same
discipline: 5.07 is only offered in the Fall, 7.05 only in the Spring. You may not take both
courses for credit.
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Website: All relevant course information (syllabus, announcements, lecture notes, lecture
powerpoint presentations, PSets and answer keys, etc.) will be available on the 5.07 Stellar
website: http://stellar.mit.edu/S/course/5/fa14/5.07/