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Bio 5410

Instructors
Robert Marsh Jeff DeJong FO3.310 FO3.306

Biochemistry of Proteins and Nucleic Acids
x25 l l x6882

Fall 2000

Room No.

Telephone No. e-mail Office Hours <![endif]> rmarsh@utdallas TR 11:30-12:30 dejong@utdallas drop by or call
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Required Texts: Proteins: Structures and Molecular Properties, 2 nd Ed., 1993 by T. E. Creighton Biochemical Calculations, 2nd Ed., 1976 by I.H. Segel Recommended Texts: Biochemistry 3 rd Ed., 2000 by Mathews, van Holde, Ahern Genes VII, 1997 by B. Lewin

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PART 1: Nucleic Acid Structure and Biochemistry Date Aug 24 Aug. 29 Aug 31 Sep 5 Sep 7 Sep 12 Sep 14 Topic Nucleotide Metabolism Nucleotide Metabolism Nucleotide Metabolism DNA structure DNA structure Topics in Genome Structure/Organization Topics in Genome Structure/Organization Reading/Problems Chap 22 (M) Chap 22 (M) Chap 22 Chap 4 (M) Chap 4 (M) Chap 28 (M) Chaps 1-4 (L) Chap 28 (M) Chaps 1-4 (L) (M)

Sep 19 Sep 21 Sep 26 Sep 28 Oct 3 Oct 5 Oct 10

EXAM 1!! DNA Replication DNA Replication DNA Replication Topics in Restriction/Repair/Recomb Topics in Restriction/Repair/Recomb Topics in Restriction/Repair/Recomb Chap 24 (M) Chap 12, 13 (L) Chap 24 (M) Chap 12, 13 (L) Chap 24 (M) Chap 12, 13 (L) Chap 25 (M) Chap 14 (L) Chap 25 (M) Chap 14 (L) Chap 25 (M) Chap 14 (L)

Oct 12

EXAM 2!!

PART 2: Protein Structure and Biochemistry

Date Oct. 17

Topic Proteins: an overview Weak interactions Structure of H2 O Acids, bases, and buffers

Reading & Suggested Problems C Chap. 4.1 - 4.3 See also M Chap. 2 S Chap. 1, sec. C -D M Chap. 2 S Chap. 3, sec. A -B

Oct. 19

Oct. 24

Entropy, enthalpy, and free energy

Oct. 26

Amino acids: structures, chemical properties, and posttranslational modifications

C Chap. 1.1 -1.3, 2.1d, 2.4 M Chap. 5 S Chap. 1, sec. E -F & PROBLEMS 38, 40, 45, 46, 52 on p.93

Oct. 31

Protein purification, characterization, and engineering NEW NOTES not in handout: 1a, 1b, 2, 3

C Chap. 1.4 -1.5, 2.2 M Tools of Biochemistry 2A, 5A, 6B, & 7A

Nov. 2

Amino acid sequencing Protein modification Chemical synthesis of polypeptides

C Chap. 1.6 -1.8 M Tools of Biochemistry 5B-D Problems on Handout A pp. 1, 2, 3

Nov. 7 Nov. 9

EXAM 3 Protein structural organization: primary, secondary, tertiary, quaternary C Chap. 5.1 -5.2.1, 5.3, 5.5, 6.2 M Chap. 6

Nov. 14

Predicting protein structure General properties of proteins

C Chap. 6. 4-6.5, 7-7.1.1,7.1.4-7.3 M Chap. 6

Nov. 16

Protein folding: mechanism and thermodynamics

C Chap. 4.4, 7.4-7-5 with PROBLEMS 2, 6, 11 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 Nov. 28

THANKSGIVING Active sites of enzymes Catalytic mechanisms Coenzymes Enzyme kinetics& assay Reversible enzyme inhibition

C Chap. 9.2 -9.3 M Chap. 11

Nov. 30

S Chap. 4, sec. B - H with PROBLEMS 8, 9, 10, 13 on p. 320 and PROBLEM 13 on p. 395 M Chap. 11 S Chap. 4, sec,. B - H cont. & sec. I with PROBLEMS 15, 16, 19, 25 on pp. 321-322 M Chap. 11

Dec. 5

Ligand binding Irreversible inhibitors Bisubstrate reactions

Dec. 7

EXAM 4