Bio 5410 Biochemistry of Proteins and Nucleic Acids Fall 2000

Instructors Room No. Telephone No. e-mail Office Hours <![endif]>

Robert Marsh FO3.310 x25 l l rmarsh@utdallas TR 11:30-12:30
Jeff DeJong FO3.306 x6882 dejong@utdallas drop by or call

Required Texts: Proteins: Structures and Molecular Properties, 2 nd Ed., 1993 (C)
by T. E. Creighton

Biochemical Calculations, 2nd Ed., 1976 (S)

by I.H. Segel
Recommended Texts: Biochemistry 3 rd Ed., 2000 (M)
by Mathews, van Holde, Ahern

Genes VII, 1997 by B. Lewin (L)

PART 1: Nucleic Acid Structure and Biochemistry

Date Topic Reading/Problems

Aug 24 Nucleotide Metabolism Chap 22 (M)

Aug. 29 Nucleotide Metabolism Chap 22 (M)

Aug 31 Nucleotide Metabolism Chap 22 (M)

Sep 5 DNA structure Chap 4 (M)

Sep 7 DNA structure Chap 4 (M)

Sep 12 Topics in Genome Structure/Organization Chap 28 (M)

Chaps 1-4 (L)
Sep 14 Topics in Genome Structure/Organization Chap 28 (M)
Chaps 1-4 (L)

Sep 19 EXAM 1!!

Sep 21 DNA Replication Chap 24 (M)

Chap 12, 13 (L)
Sep 26 DNA Replication Chap 24 (M)
Chap 12, 13 (L)
Sep 28 DNA Replication Chap 24 (M)
Chap 12, 13 (L)
Oct 3 Topics in Restriction/Repair/Recomb Chap 25 (M)
Chap 14 (L)
Oct 5 Topics in Restriction/Repair/Recomb Chap 25 (M)
Chap 14 (L)
Oct 10 Topics in Restriction/Repair/Recomb Chap 25 (M)
Chap 14 (L)

Oct 12 EXAM 2!!

PART 2: Protein Structure and Biochemistry

Date Topic Reading & Suggested Problems

Oct. 17 Proteins: an overview C Chap. 4.1 - 4.3
Weak interactions See also M Chap. 2

Oct. 19 Structure of H2 O S Chap. 1, sec. C -D

M Chap. 2
Acids, bases, and buffers

Oct. 24 Entropy, enthalpy, and free energy S Chap. 3, sec. A -B

Oct. 26 Amino acids: structures, chemical properties, C Chap. 1.1 -1.3, 2.1d, 2.4
and posttranslational modifications M Chap. 5
S Chap. 1, sec. E -F & PROBLEMS 38, 40, 45,
46, 52 on p.93

Oct. 31 Protein purification, characterization, and C Chap. 1.4 -1.5, 2.2

engineering M Tools of Biochemistry 2A, 5A, 6B, & 7A
NEW NOTES not in handout: 1a, 1b, 2, 3

Nov. 2 Amino acid sequencing C Chap. 1.6 -1.8

Protein modification M Tools of Biochemistry 5B-D
Chemical synthesis of polypeptides Problems on Handout A pp. 1, 2, 3

Nov. 7 EXAM 3

Nov. 9 Protein structural organization: primary, C Chap. 5.1 -5.2.1, 5.3, 5.5, 6.2
secondary, tertiary, quaternary M Chap. 6

Nov. 14 Predicting protein structure C Chap. 6. 4-6.5, 7-7.1.1,7.1.4-7.3

General properties of proteins M Chap. 6

Nov. 16 Protein folding: mechanism and C Chap. 4.4, 7.4-7-5 with PROBLEMS 2, 6, 11
thermodynamics on p. 168; 2 on p.198; & 9 on p.260
M Chap. 6

Nov. 21 Degradation of proteins C Chap. 10

M Chap. 20, pp 722-726

Nov. 23 THANKSGIVING
Nov. 28 Active sites of enzymes C Chap. 9.2 -9.3
Catalytic mechanisms M Chap. 11
Coenzymes

Nov. 30 Enzyme kinetics& assay S Chap. 4, sec. B - H with

Reversible enzyme inhibition PROBLEMS 8, 9, 10, 13 on p. 320 and
PROBLEM 13 on p. 395
M Chap. 11

Dec. 5 Ligand binding S Chap. 4, sec,. B - H cont. & sec. I with

Irreversible inhibitors PROBLEMS 15, 16, 19, 25 on pp. 321-322
Bisubstrate reactions M Chap. 11

Dec. 7 EXAM 4