Biology 306 / Chemistry
306: Biochemistry
Course Outline
Spring 2004
Biochemistry
is a non-laboratory course in which emphasis will be placed on topics of particular
interest to students who plan to pursue health professional degrees or graduate
degrees in biomedical sciences. It is intended to complement Chemistry 307 Mechanistic Biochemistry,
a course of particular interest to students who plan to apply to graduate
programs in chemistry or biochemistry. In lieu of laboratory work, emphasis will be placed on reading
the biological literature and using bibliographic aids for conducting library
research in biochemistry.
Text: Biochemistry by Jeremy M. Berg, John L. Tymoczko, and Lubert
Stryer, Fifth Edition 2002, New York:
W. H. Freeman and Company.
The following schedule is subject to minor changes.
| Date | Lecture Topic | Text Assignment |
| W Jan 21 | Introduction to literature and to biochemical evolution | Sections 1.2 & 1.4 & Chapter 2 |
| F Jan 23 | Complete intro; water and chemical bonds, | Section 1.3, |
| M Jan 26 | Acid/base equilibrium and amino acids Library test due | pp 73-74 |
| W Jan 28 | Protein Structure | Section 3.1 |
| F Jan 30 | Protein structure | Complete Chapt.
3 |
| M Feb 2 | Techniques | Sections 4.2-4.3 |
| W Feb 4 | Techniques Problem set I due | Complete chpt 4
|
| F Feb 6 | Nucleic acids |
Sections 5.1-5.2 |
| M Feb 9 | Replication | Sections5.3;27.2.1& 5;27.4 |
| W Feb11 | Transcription | Sections 5.4 & 5.6;
28.1 -3 |
| F Feb13 | Translation | Section 5.5 & 781-790;797-800; 815-818;823 |
| M Feb 16 | Genetic analysis and molecular evolution | Chapts. 6 & 7. |
|
Problem set II due at review session for test
|
||
| W Feb 18 |
* Hour Test
|
|
| F Feb 20 | Intro to Enzymes and Bioenergetics | Sections 8.1-8.2 |
| M Feb 23 | Enzyme Kinetics | Complete Chapt. 8 |
| W Feb 25 | Serine proteases and catalytic antibodies | Sections 9.1-9.2; 10.5 |
| F Feb 27 | Begin allosteric control | |
| M Mar 1 | Allosteric control | Sections 10.1-10.2 |
| W Mar 3 | Carbohydrates Problem set III due | Sections 10.3-10.4; 11.1 |
| F Mar 5 | Membrane Lipids | |
| M Mar 8 | Membrane Proteins | |
| W Mar 10 | Membrane Channels and Pumps |
Complete Chapt. 12 |
| F Mar 12 | Membrane function | Complete Chapt. 13 |
|
Problem set IV due at review session on Mar 10
|
||
| M Mar 15 | Metabolism and bioenergetics | Chapter 14 |
| W Mar 17 |
*Hour test
|
|
|
–Spring
Break–
|
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| M Mar 29 | Complete Metabolism Begin signal transduction | Section 15.1 |
| W Mar 31 | Signal transduction | Complete Chapt. 15 |
| F Apr 2 | Glycolysis | 16.0-16.18 |
| M Apr 5 | Control of Glycolysis; Gluconeogenesis | Sections 16.19-16.2 |
| W Apr 7 | Complete gluconeo.; Cori cycle; pyruvate to acetyl CoA |
Sections 16.3-17.12 |
| F Apr 9 | Citric Acid cycle *Term
paper outline and prelim. list of sources to be cited |
Complete Chapt. 17 |
| M Apr 12 | Complete Citric acid
cycle topics |
|
| W Apr 14 | Oxidative phosphorylation |
Chapter 18 |
| F Apr 16 | Pentose phosphate pathway | Sections 20.3-20.5 |
| M Apr 19 | Glycogen metabolism | Chapter 21 |
| W Apr 21 | Triglyceride and Fatty acid catabolism | Sections 22.1-22.3 |
|
Problem set VI due at review session
|
||
| F Apr 23 |
Hour Test
|
|
| M Apr 26 | Fatty acid and triglyceride synthesis | Complete Chapt. 22 |
| W Apr 28 | Protein catabolism | Chapter 23 |
| F Apr 30 | Complete proteins; start nucleotides *Term paper drafts due in class | Sections 24.0 – 24.2 (parts |
| M Msy 3 | Nucleotide metabolism | Chapter 25 |
| W May 5 | Integration
of metabolism
*Final Drafts of Term Papers Due at midnight |
Chapter 30 |
|
Oral Reports this week (to be assigned
|
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|
Sat May 8 |
9:00 am
Final Exam
|
| Final Grade |
|
| Three Hour Tests | 300 |
| Assignments |
125 |
| Term paper | 100 |
| Final Exam | 125 |
| Total | 650 |
In lieu of laboratory work in this course, each student is expected to spend
approximately three hours a week 1. in the library reading the biochemical
literature, 2. solving problems which will be distributed during the term,
and 3. writing a term paper. Until midterm, a cumulative log of the reading
will be kept in a three-ring binder and turned in on Friday of each week.
The log will consist of summaries of the works read and complete citation
of the sources read using the format found in the journal Biochemistry with
one exception--include the name of the article or book chapter between the
names of all authors and the title of the book/journal. As a rule of thumb
(but not graven in stone), one review article and one paper from the primary
literature each week will be the minimum acceptable amount of reading. The
reading should be concerned with some aspect of the topics currently being
covered in lecture whenever possible; your book lists excellent papers at
the end of each chapter. Grade will be based on the appropriateness and depth
of the selections and the quality of the summaries.
During the second half of the term, each student will write a term paper of approximately 8-10 pages using the guidelines below. Each student will present a seminar (time to be scheduled) of approximately 20 minutes duration on the content of the paper. Oral presentations will be scheduled one afternoon during the last week of the term.
The purposes of this exercise are to give the student an opportunity 1. to
use the scientific literature and the library tools available for conducting
a careful literature search of some topic; 2. to review the literature on
the topic critically; 3. to use appropriate style for writing review articles
for the scientific literature; and 4. to make an oral presentation on the
results of the project.
The following guidelines are to be followed in the development of the term
paper and oral presentation