5.

07 Biological Chemistry Syllabus - Fall 2015

Instructors: Professors Alexander M. Klibanov (AMK) and Alice Y. Ting (AYT)
Date

Lect.
No.

Lecture Topic

Wed., Sept. 9

Fri., Sept. 11

Organization of 5.07.
Life, cell, metabolic pathways,
regulation, building blocks
Water, hydrogen bonds, amino acids

Mon., Sept. 14

Primary and secondary structures of

proteins
(PSet 1 due)

Wed., Sept. 16

Tertiary and quaternary structures of

proteins

Fri., Sept. 18

Enzymes and mechanisms of

catalysis

Mon., Sept. 21

Wed., Sept. 23

Enzyme kinetics
(PSet 2 due)
Enzyme inhibition and control

Fri., Sept. 25

Introduction to metabolism

Mon., Sept. 28

Wed., Sept. 30

10

Phosphoryl group transfer; ATP

(PSet 3 due)
Redox cofactors

Fri., Oct. 2

11

Chemistry of sugars

Mon., Oct. 5
Wed., Oct. 7

12

Exam # 1
Glycolysis I

Fri., Oct. 9

13

Glycolysis II
(PSet 4 due)

Reading
(Voet et al., 3rd edn.)
(Voet et al., 4th edn.)
Chapter 1
Chapter 1
Chapters 2 and 4
Chapters 2 and 4
Chapters 5 (91-114) and
6 (125-134)
Chapters 5 (93-116)
and 6 (125-136)
Chapters 6 (134-151)
and 7 (176-197)
Chapters 6 (136-152)
and 7 (176-196)
Chapter 11 (322-339
and 347-359)
Chapter 11 (315-331
and 339-350)
Chapter 12 (363-376)
Chapter 12 (355-368)
Chapter 12 (377-393)
Chapter 12 (368-385)
Chapter 14 (448-459,
475-482)
Chapter 14 (436-446
and 462-468)
Chapter 14 (459-469)
Chapter 14 (446-456)
Chapters 11 (326-328)
and 14 (469-474)
Chapters 11 (319-320)
and 14 (456-461)
Chapter 8 (219-234)
Chapter 8 (217-230)
Lectures 1-8, PSets 1-3
Chapter 15 (485-510)
Chapter 15 (472-496)
Chapters 15 (510-520)
and 16 (530-539)

Lecturer
AMK
AMK
AMK

AMK

AMK

AMK
AMK
AMK

AMK
AMK

AMK
AMK
AMK

Chapters 15 ( 496-506)
and 16 (517-525)
Mon., Oct. 12
Tue., Oct. 13

14

NO CLASS (Columbus Day

Holiday)
Pyruvate dehydrogenase complex

Wed., Oct. 14

15

TCA cycle I

Fri., Oct. 16

16

Mon., Oct. 19

17

TCA cycle II
(PSet 5 due)
Lipid structure, digestion, and
transport

Wed., Oct. 21

18

Fatty acid oxidation

Fri., Oct. 23

19

Electron transport chain I

(PSet 6 due)
Exam # 2
Electron transport chain I
Electron transport chain I
Electron transport chain II
Electron transport chain II
ATP synthase
DNA structure
(PSet 7 due)

Mon., Oct. 26
Wed., Oct. 28
Fri., Oct. 30
Mon., Nov. 2
Wed., Nov. 4
Fri., Nov. 6
Mon., Nov. 9

20
21
22
23
24
25

Wed., Nov. 11
Fri., Nov. 13

26

Mon., Nov. 16

27

Wed., Nov. 18

28

Fri., Nov. 20

29

Mon., Nov. 23
Wed., Nov. 25
Fri., Nov. 27

NO CLASS (Veterans Day

Holiday)
Overview of DNA replication
DNA replication speed, sliding
clamps, and clamp loaders I
DNA replication speed, sliding
clamps, and clamp loaders II
DNA replication fidelity I
EXAM # 3

30

DNA replication fidelity II

Chapter 17 (570-576)
Chapter 17 (555-561)
Chapter 17 (566-570
and 576-583)
Chapter 17 (551-555
and 561-568)
Chapter 17 (583-594)
Chapter 17 (568-578)
Chapters 9 (245-252)
and 20 (677-687)
Chapters 9 (241-248)
and 20 (657-666)
Chapter 20 (688-700)
Chapter 20 (667-680)
Chapter 18, Chapter 18

AMK

Lectures 9-18, PSets 4-6

Chapter 18, Chapter 18
Chapter 18, Chapter 18
Chapter 18, Chapter 18
Chapter 18, Chapter 18
Chapter 18, Chapter 18
Chapters 3 (39-50) and
24 (848-855)
Chapters 3 (40-51) and
24 (821-828)

AMK
AYT
AYT
AYT
AYT
AYT
AYT

Chapter 25 (893-914)
Chapter 25 (867-889)
Chapter 25 (893-914)
Chapter 25 (867-889)
Chapter 25 (893-914)
Chapter 25 (867-889)
Chapter 25 (893-914)
Chapter 25 (867-889)
Lectures 19-27, Pset 7

AYT

Chapter 25 (893-914)
Chapter 25 (867-889)

AYT

AMK

AMK
AMK

AMK
AYT

AYT
AYT
AYT
AYT

NO CLASS (Thanksgiving
Holiday)
2

Mon., Nov. 30

31

DNA replication coordination

Wed., Dec. 2

32

Modern DNA sequencing methods

Fri., Dec. 4

33

Overview of RNA transcription

Mon., Dec. 7

34

RNA transcription initiation

Wed., Dec. 9

35

RNA transcription elongation

(PSet 8 due)
FINAL EXAM

Dec. ?

Instructors:

Chapter 25 (893-914)
Chapter 25 (867-889)
Chapter 3 (53-57)
Chapter 3 (55-58)
Chapter 26 (942-950)
Chapter 26 (919-927)
Chapter 26 (942-950)
Chapter 26 (919-927)
Chapter 26 (942-950)
Chapter 26 (919-927)
Lectures 1-36

AYT
AYT
AYT
AYT
AYT
AMK
and AYT

Professors Alexander M. Klibanov (klibanov@mit.edu)

Professor Alice Y. Ting (ating@mit.edu)

Teaching Assistants:

Lisa S. Cunden (lcunden@mit.edu)

Nicholas A. DeLateur (delateur@mit.edu)

Textbook: Voet, Voet & Pratt, Fundamentals of Biochemistry, 3rd (or 4th) edition.
Lectures: Mondays (M), Wednesdays (W), and Fridays (F), at 9-10am, all in Room 4-370.
Recitations will begin the 2nd week of the semester, i.e., on Monday September 14. The
recitation (R) schedule is as follows:
R#1 MW 1 (36-372) Lisa Cunden

R#3 TR 10 (36-144) Nicholas DeLateur

R#2 MW 2 (36-372) Lisa Cunden

R#4 TR 11 (36-144) Nicholas DeLateur

Mid-term exams: There will be three exams during the term. They are closed book,
closed notes; any necessary information will be included at the end of the exam. The dates are in
the Syllabus above: Monday, October 5; Monday, October 26; and Monday, November 23.
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 will 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 will be none. 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 (PSets): Every week you will be given a PSet. They are worth 10 points
each. The main goal of the PSets 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 in the lectures.
It is OK, and indeed encouraged, to collaborate on the PSets, 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. PSets are due as indicated in the Syllabus above 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 12 hours after the due date.
Letter grades for the course: After the final exam, the 5.07 teaching staff will tally up
the exam and problem set scores and determine what sum constitutes "Excellent, Good,
Satisfactory, or Unsatisfactory" mastery of the course material. No letter grades, only
numerical scores, will be assigned to the midterm or final exams. Rather, only the overall letter
grades will be assigned based on the cumulative score from the entire semester.
Relationship between 5.07 and 7.05: These courses offer two perspectives on the same
discipline: 5.07 is only offered in the Fall, while 7.05 only in the Spring. You may take only one
of these courses for credit.
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/fa15/5.07/