Biochemistry and Molecular Biophysics Graduate Group

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BMB 509 - Structural and Mechanistic Biochemistry

Spring, every year

Course Directors:

Kathryn Ferguson, Ph.D., ferguso2@mail.med.upenn.edu and Gregory Van Duyne, Ph.D. , vanduyne@mail.med.upenn.edu


After some introductory material on macromolecules, lectures will focus on the key biochemical 'task areas' of living cells. The course progresses from primarily molecular level events such as storage & translation of genetic information, creation, control & removal of proteins etc. to higher organization levels such as metabolic pathways, signaling pathways, regulation and homeostasis. The presentation for each topic will be 'vertically integrated'. Each section will cover structure details of the relevant molecules, appropriate binding/catalysis events, regulatory aspects, and how they fit into the relevant pathway(s) and cell function.

Prerequisites:BMB 508 and BIOM 600, or permission of instructor

Recommended Textbooks: Berg, Tymoczko & Stryer, Biochemistry, 7thEdition, W.H. Freeman

Course Outline:

PROTEINS

1

Composition and structure

2

Carbohydrates and glycobiology

COMPOSITION AND PROPERTIES OF BIOLOGICAL MEMBRANES

3

Chemical heterogeneity/lipid protein complexes

4

Physical properties of lipids & consequence on membranes

5

Physical properties of membranes & consequences on protein binding

MANAGEMENT OF GENETIC INFORMATION

6

Composition, structure and chemical biology of DNA

7

DNA packaging: nucleosomes and chromatin

8

Regulation of chromatin structure

9

Chromosome movement

TRANSCRIPTION AND MODULATION OF DNA/RNA

10

RNA structure and catalysis

11

RNA binding proteins and regulation of RNA processing

12

Enzymes of DNA transcription, replication, recombination and repair

13

Translation and the ribosome

14

Motor Proteins

Midterm Exam

PROTEINS THAT MODIFY THE FUNCTION OF PROTEINS

15

Kinases & phosphatases

16

Reversible acetylation and methylation

17

GTPases

PROTEIN FOLDING AND MISFOLDING

18

Protein assisted folding

19

Protein misfolding

20

Protein Breakdown: Proteases, degradation, the proteosome

CELLULAR REGULATORY CIRCUITS

21

Bi-stability and robustness

22

Signaling networks

METABOLISM

23

Metabolism I

24

Metabolism II

25

Metabolism III

26

Metabolism in cancer

27

Topics in metabolism

28

Oxidative phosphorylation

Final Exam