Interdisciplinary Biochemistry Graduate Program | Integrated Biochemistry
B501 | 1294 | Drummond, J


Basic principles and methodologies of biochemistry; essentials of
macromolecular biosynthesis; mechanism-based examination of
biochemical aspects of cell biology; material is presented with an
integrative approach designed to illustrate the inter-relationship of
biochemical processes.

2.	Logistics

4.5 credit course to meet three times per week (1.5 h/session) in
each Fall semester.

Required for Biochemistry Program graduate students.

3.	Prerequisites

Undergraduate biochemistry (C483 or C484 or equivalent) or consent of
instructor.

4.	Objectives

1. Introduce students to the principles and methodologies in modern
biochemistry.
2. Prepare students for more advanced treatment of topics in
biochemistry.
3. Expose students to the integrated nature of biological processes
and their analyses.
4. Expose students to current topics in biomedical science that would
benefit from more biophysical and quantitative analyses.
5. Demonstrate to the students that a range of molecular,
biochemical, biophysical and quantitative approaches can be used to
solve biomedical problems.

5.	Basis for Grading

50%: Weekly problem sets will be assigned.  Successful completion of
the problem sets will require the students to design experimental
approaches and predictions of possible outcomes of the experiments.
The instructors will grade both for the quality of the answers and
for writing style.

20%: A take-home midterm exam consisting of mostly problems that can
be answered by short essays The students will have one to two days to
complete the exam.

25%: Take-home final exam consisting mostly of problems that can be
answered by short essays. The students will have one to two days to
complete the exam.

5%: class participation.

6.Textbooks (on reserve)

Bloomfield VA, Crothers DM & Tinoco I Jr. Nucleic Acids: Structures,
Properties, and Functions. University Science Books, Sausalito, CA.
2000.
Creighton TE. Proteins.  2nd edition. W.H. Freeman & Co. 1993.
Lewin B. Genes VII. Oxford Press. 2000.

7.	Course topics

	Although the course may be taught in a style chosen by the
instructors, the following topics will be covered:

1.	Macromolecular structure (15)

a.	Nucleic acids (4)
Comparison of DNA and RNA structures. (1)
Methods used to analyze DNA structure, denaturation and renaturation.
(1)
RNA structure prediction and computer visualization of RNAs. (1)
Gene structure (1)

b.	Proteins (5)
Bonds and forces that determine protein structure and function. (1)
Introduction to protein secondary structures. (1)
Critical analysis of methodologies to characterize proteins. (1)
Principles of protein-protein interaction. (1)
Computer visualization of model proteins. (1)

c.	Structures involving proteins and nucleic acids (2)
Nucleic acid binding motifs (1)
Chromatin structure (1)

d.	Oligosaccharides (1)

e.	Membranes (3)
Membrane components and properties (1.5)
Membrane proteins (1.5)

2.	Genetic information: access and replication (15)

a.	Signal transduction (7)
Heptahelical receptors (1)
Receptor tyrosine kinases (1)
Nuclear receptors (1)
Covalent protein modifications (methylation, phosphorylation,
degradation) during signaling (1)
Second messenger systems (2)
Kinase cascades (1)

b.	Replication (6)
Regulation of DNA replication (1)
Mechanism of initiation and elongation (prokaryotic and eukaryotic)
(3)
Telomerase mechanism and function (1)
Biochemical, structural, and functional analyses of topoisomerases (1)

c.	Repair and Recombination (2)

3.	Genetic information: transfer and regulation (15)

a.	Transcription (6)
Analyses of the E. coli RNA polymerase in initiation, elongation and
termination. (3)
Eukaryotic RNA polymerases (3)
RNA processing (2)

b.	Translation (4)
Structures and interactions within the ribosome during translation
initiation, elongation and termination.
c.	Post-translational modifications (1)
d.	Protein and vesicle trafficking (2)
e.	Regulation of cell growth/death (2)