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BCM 262, Trimmer: Spring 2002
Introduction to Biological Chemistry
Professor:
Elizabeth Trimmer
Office: Science 2007
Phone: (641)-269-4398
Email: trimmere@grinnell.edu
Office Hours:
No formal office hours. You may call or email to set up an appointment.
I am available for drop-in visits, whenever my door is open.
Blackboard:
accessed at http://blackboard.grinnell.edu
Here you will find the syllabus, handouts, problem sets, and class
announcements, updated at least weekly.
Class Web Site:
Created by Janelle Hare.
Class Meetings:
Lecture:
Laboratory:
Required Text:
Biochemistry, 5th ed.
2001, Berg, Tymoczko, and Stryer
(Web site for text: http://www.whfreeman.com/biochem5)
Mon., Wed., Fri.
Mon. or Thurs.
10-10:50 AM
1:15-4:05 PM
Science 2132
Science 2102
Additional readings will also be assigned from time to time. These will be
on reserve in the Science Library for short-term checkout. For example,
Ch. 20 on Redox Chemistry in BLB, 8th edition will be assigned.
Supplies:
Molecular Model Set
Bound Laboratory Notebook
Description of Course:
BCM 262 is an introductory course in biological chemistry. Biological chemistry is the
study of the chemical reactions of life at the molecular level. The chemistry of life is
predominantly organic chemistry.
The first part of the course will focus on the structure and function of the four classes of
biomolecules – proteins, nucleic acids, carbohydrates, and lipids. Each of these important
biomolecules are biopolymers formed from monomeric units.
The second part of the course will focus on the metabolism of carbohydrates, lipids,
proteins, and nucleic acids. We will emphasize the reaction strategies, types of chemical
conversions, enzyme mechanisms, thermodynamic and kinetic control, the conservation and
utilization of energy, regulation, and communication between metabolic pathways.
Prerequisites for Course:
Organic chemistry I (CHM 221) and Bio 150, 251 are prerequisites for this course.
Concurrent (or past) enrollment in Organic chemistry II (CHM 222) is required. It is the
responsibility of the student to make up any possible deficiencies in background through
independent review.
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Preparation for Class:
It is your responsibility to be on time to class and to be actively involved during class.
Class will include both lectures and activities which will require your active participation.
It is imperative that you come to class prepared. Each Friday, you will receive an
assignment sheet which lists the specific readings and class topics for each day of the following
week. It is important that you already be familiar with the material prior to hearing about it in
class. The minimum that you should do is read the assigned reading for that day.
Problem Sets:
Ten Problem Sets will be distributed during the semester and graded for a total of 100
points. They will generally be handed out on Fridays and due the following Friday in class (see
schedule). You may work on these together, but you are expected to turn in your own answers
written in your own words. Late homework will not be accepted.
Quizzes:
There will be several short (10-15 min.) quizzes during the semester (see schedule) for a
total of 100 pts. The quizzes will cover the material on the preceding problem set.
Exams:
With the exception of the final exam, the dates for exams are tentative, but should take
place within one class meeting of the scheduled dates. Exams will cover the material up to and
including the class period one week prior to the exam. I will hold a review session prior to each
exam (specific times will be announced). I must be informed in advance if you must miss an
exam due to serious illness or other emergency. To make up an exam, you will need a written
medical excuse or documentation justifying your absence.
Group Presentation:
This assignment will be discussed in more detail later in the semester. The format will be
small groups teaching the class topics in weeks 12-14.
Laboratory:
As chemistry is an experimental science, the lab is an important part of the course.
Successful completion of the lab is required to receive a passing grade in the course.
Course Grade:
Grades will be assessed according to the following point scheme:
Exam 1
100
Exam 2
100
Exam 3
100
Final Exam
200
Problem Sets
100
Quizzes
100
Group Presentation
50
Laboratory
250
Total
1000 pts.
Final grades will be determined using the following scale:
880-1000
A-/A
740-880
B-/B/B+
650-740
C/C+
550-650
D
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Useful Texts in Library:
Enzyme Kinetics:
Understanding Enzymes, 1981, T. Palmer
Enzyme Kinetics, 1981, P.C. Engel
Enzyme Catalysis:
Enzymatic Reaction Mechanisms, 1977, C. Walsh
Protein Structure:
Introduction to Protein Structure, 1991, Branden and Tooze
Proteins: Structures and Molecular Properties, 1984, Creighton
Biochemical Laboratory Techniques:
Protein Purification, 1982, Scopes
Modern Experimental Biochemistry, 1986, R. Boyer
General Biochemistry:
Biochemistry, 1990, Voet and Voet
Biochemistry, 1990, Matthews and van Holde
Biochemisry, 1988, 2nd ed., Zubay
Principles of Biochemistry, 1993, 2nd ed., Lehninger, Nelson, and Cox
Biochemistry, A Problems Approach, 1981, 2nd ed., Wood et al.
Biochemical Calculations, 1968, 2nd ed., Segel
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Week Date
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Jan. 21
Tentative Schedule
Topics
Reading Assignments,
Problem Sets, Quizzes
Ch. 1-2, 3-4, 7
Introduction to Biological Chemistry
Protein Structure (Ch. 3-4)
Evolution (Ch. 7)
Proteins as Catalysts: Enzymes
Enzyme Kinetics
2
Jan. 28
3
Feb. 4
Enzymes: Catalytic Strategies and Mechanisms
4
Feb. 11
5
Feb. 18
6
Feb. 25
Proteins as Regulators: Allosteric Enzymes
Covalent Modification
Proteins as Binders:
Myoglobin vs. Hemoglobin
Cooperative Binding
Nucleotides, Nucleic Acids: Structure and Function
Drug Binding to DNA
Application to Site-directed mutagenesis of proteins
7
Mar. 4
Carbohydrates (Ch. 11), Lipids (Ch. 12), Coenzymes
Basic Concepts and Thermodynamics of Metabolism
Signal Transduction (Ch. 15)
8
Mar. 11
Glycolysis and Gluconeogenesis
9
April 1
Tyrosinase Poster Presentation: Fri. Mar. 15
SPRING BREAK
Citric Acid Cycle
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April 8
11
12
13
14
Oxidative Phosphorylation continued
April 22
Pentose Phosphate Pathway (Ch. 20)
*Glycogen Metabolism (Ch. 21)
*Fatty Acid Degradation (Ch. 22)
April 29
May 6
May 17
Q#3 on Wed. Feb. 27
PS#5 due Fri. Feb. 29
Ch. 14, 15
EXAM 2 Fri. Mar. 6
Ch. 17
Q#4 on Wed. April 3
PS#7 due Fri. April 5
BLB, 8th ed. Ch. 20
Stryer Ch. 18
Q#5 on Wed. April 10
PS#8 due Fri. April 12
Ch. 18, 20
Q#6 on Wed. April 17
PS#9 due Fri. April 19
Ch. 21, 22
*Fatty Acid Biosynthesis (Ch. 22)
*Urea Cycle and Amino Acid Degradation (Ch. 23)
*Biosynthesis of Amino Acids (Ch. 24)
*Nucleotide Biosynthesis (Ch. 25)
Integration of Metabolism
FINAL EXAM 9:00 AM
PS#4 due Fri. Feb. 22
Ch. 5, 6, 11, 12
Ch. 16
PS#6 due Fri. Mar. 15
Introduction to Redox Chemistry
Electron Transport and Oxidative Phosphorylation
April 15
PS#1 due Fri. Jan. 25
Ch. 8
Q#1 on Wed. Jan. 30
PS#2 due Fri. Feb. 1
Ch. 9
Q#2 on Wed. Feb. 6
PS#3 due Fri. Feb. 8
Ch. 10
EXAM 1 Fri. Feb. 15
Ch. 10
EXAM 3 Fri. April 26
Ch. 22, 23, 24
PS#10 due Fri. May 3
Ch. 25
* = Group Presentations
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