BIO 401/501 Advanced Molecular Biology I

BIO 401/501 Advanced Biological Chemistry

Fall 2011

TENTATIVE TOPIC LIST & Lecture Schedule

FOR SPECIFIC PRE-REQUISITES AND GENERAL DESCRIPTION LOOK HERE

FOR REGISTRATION AND LOCATION INFORMATION, CLICK ON THE APPROPRIATE LINK

Instructors: G. Koudelka, Cooke 607, 645-4940 (koudelka@buffalo.edu); G. Snyder Cooke 513, 645-4939, (gsnyder@buffalo.edu),
M. Hollingsworth (hollings@buffalo.edu) Hochstetter 653 645-2968

Dr. Koudelka is course coordinator, please address all questions about course administration to him.

I. Lecture Schedule

Nucleic Acids (click here for information on supplemental material)
Proteins
Enzyme Kinetics
Catalytic Mechanisms

II. Policies & Pre-requisites

III. Tentative Exam Schedule

Nucleic Acids


1	Structural Properties of Nucleic Acid Building Blocks	Aug. 29 (Figures)	Koudelka
2	Forces That Stabilize Nucleic Acid Double Helices	Aug. 31 (Figures)	"
3	Double Helix Stability and Base Composition	Sept. 2 (Figures)	"
4	Assembly and Characteristics of Nucleic Acid Double Helices	Sept. 7 (Figures)	"
5	"" ""	Sept. 9	"
6	Protein-DNA Interactions	Sept. 12
7	Unusual DNA Structures/DNA bending	Sept. 14
8	Mechanical Properties of Helices	Sept. 16 (Figures)	"
9	Supercoiling and its energetics	Sept. 19 (Figures)	"
10	Nucleosomes	Sept. 21 (Figures)	"
11	RNA Structure (tRNA) & Sequence-dependent RNA Structure	Sept. 23 (Figures)	"
12	Protein-RNA Interactions	Sept. 26 (Figures)	"
13	Nucleic Acids Review- EXAM AT 7PM on 9/29	Sept. 28

Proteins


14	Amino acids : Predict helices : membrane, amphipathic	Sept. 30	Snyder
15	Struct 1o : Sequencing fibrin peptide (mass spect)	Oct. 3	"
16	Struct 2o : Alzheimer beta sheet formation (CD)	Oct. 5	"
17	Struct 2o : Helix stability : pH, temp, ions, urea, [peptide]	Oct. 7	"
18	Struct 3o : PDB data base, JMol modeling	Oct. 10	"
19	Struct 3o : Charybdotoxin (2d NMR)	Oct. 12	"
20	Struct 3o : Charybdotoxin family : 3d homologies	Oct. 14	"
21	Post-trans : SS formed : stability of engineered mutants	Oct. 17	"
22	Post-trans : BPTI folding intermed : in vitro 6-cys protein	Oct. 19	"
23	Post-trans : BPTI folding : in vivo 7-cys precursor	Oct. 21	"
24	Post-trans : Chaperonins	Oct. 24	"
25	Proteins Review EXAM 10/27/11 at 7PM	Oct. 26

Enzyme Kinetics


26	Chemical Kinetics:Role of thermal energy	Oct. 28	Koudelka
27	Chemical Kinetics: Potential energy, transition states & catalysis	Oct. 31	"
28	Reaction order & experimental determination of velocity	Nov. 2	"
29	Steady-State Concepts and Consequences	Nov. 4	"
30(.ppt file)	Deriving rate equations	Nov. 7	"
31	“ “	Nov. 9	"
32	Inhibition mechanisms	Nov. 11	"
33	Binding & Equilibrium	Nov. 14	"

Catalytic Mechanisms


34	Catalytic strategies: Covalent catalysis.	Nov. 18	Snyder
35	Catalytic Strategies: General acid-base catalysis	Nov. 21	"
36	Catalytic Strategies: Catalysis by approximation and metal ions	Nov. 28	"
37	Structural and Functional Analysis of Enzymes (Part 2)	Nov. 30	“
38	Ribozymes	Dec 2	Hollingsworth
39	Ribozymes	Dec 5	“
40	Ribozymes	Dec 7	“
41	Mechanisms Review (Exam-Finals week)	Dec 9

BIO 401/501 Advanced Biological Chemistry

Policies

Prerequisites. This purpose of this course is to give students a rigorous grounding in the fundamental structural, physical and chemical properties of the important biopolymers. These fundamentals will be described in effort to show the roles of these properties in determining the function these molecules. NOTE: this is an advanced course-a basic class in Biochemistry is a strict pre-requisite; those who choose to remain in the class without the requisite background do so at their own peril.

Grading. This course is cross-listed for both graduate and undergraduate students. The graduate and undergraduate final grades will be determined separately. The grade will be determined from a weighted average of separate evaluations in the five individual sections of the course. Performance in each section will be determined by written exams and, in certain sections, graded homework problems. The grades from each section will be weighted according to the number of lectures in the section. The final grades will generally be determined using the +/- system. The faculty of this course reserve the right to not utilize all grades in the A» F grade range.

Exams. As stated above, there will be four exams, each covering the material presented in one and only one section. The exams will be exclusively of the essay type. The exams will not test rote memory, but instead will examine a student's ability to synthesize and use their knowledge in solving problems. In the past, many exam questions tested the ability to analyze and interpret data from literature. SOME of the exams WILL BE GIVEN IN THE EVENING-NOT DURING CLASS TIME! The exams have been scheduled to be held in the evening of the following dates:

Nucleic Acids: September 29 (NOTE: NIGHT EXAM)

Proteins: October 27 (NOTE: NIGHT EXAM)

Enzyme Kinetics: Take home –DUE 4 PM Nov. 21

Catalytic Mechanisms: Finals week

Required Texts. Lecture notes for most of the lectures will generally be available on UBLearns or distributed by individual faculty. Readings from research literature or monographs to supplement lecture material will be assigned in class and available on-line. In addition, the Catalytic Mechanisms section of the course will require the purchase of ONE shrink-wrapped chapter from the Voet & Voet (Wiley Publishing) Biochemistry textbook. This will be available in the bookstore. The remainder of that text is NOT REQUIRED for other sections of the course.