Molecular Biology, Spring 2003 Exam 2, 04/09/03 Page 1

STUDENT NAME: ______

1. The picture below shows a GC base pair as it would appear if you looked from one end of the double helix down the helix axis toward the opposite end. The positions of the major groove and the minor groove are shown. a) Label the atoms of both bases that can serve as a hydrogen bond acceptor (A) or a hydrogen bond donor (D) in either groove (5 points).

b) In which of the two grooves could a protein that approached the DNA to engage in hydrogen bonds discriminate better between this GC base pair and a CG base pair? Explain (5 points)!

c) Which structural element of a protein typically acts as the binding module in a DNA-protein interaction (2 points)?

d) Which interactions other than hydrogen bonds can contribute to the binding affinity between a DNA binding protein and its DNA binding site (2 points)? Molecular Biology, Spring 2003 Exam 2, 04/09/03 Page 2

2. The picture below shows figure 6.24 of your textbook, including the relevant paragraph of the figure legend. As described in the legend, the figure demonstrates the specific interaction between region 4 of the σ-factor and the tac promoter (an engineered hybrid promoter). The experiment measured the binding of labeled DNA-σ-factor complex to nitrocellulose in the presence of different competitor DNAs.

a) Explain how part (a) shows specific binding of the σ-factor to the tac promoter (4 points).

b) Explain how part (b) shows specific binding of the σ-factor to the -35 box of the tac promoter (4 points). Molecular Biology, Spring 2002 Exam 2, 04/10/02 Page 3

5. Each of the following 30 definitions describes a term in the alphabetical list shown below (next page). Place the term that is best described by the definition to the left of each number. Terms may be used more than once, or not at all (45 points).

Definitions:

______1. Subunit of RNA polymerase that interacts with the UP element of a prokaryotic promoter..

______3. Part of a protein that adopts a distinct conformation independently of other parts of the protein.

______5. An antibiotic that blocks the initiation of transcription in prokaryotes.

______7. Phage genes that are expressed towards the end of the infectious cycle.

______9. A sequence at the end of a transcript responsible for the release of the RNA from the template without the assistance of proteins.

______11. The region of an operon that binds RNA polymerase.

______13. Molecule that acts as corepressor in the Trp operon.

______15. A protein that is expressed upon exposure to an abnormally high temperature.

______17. A repressor molecule controlling the life cycle of the λ-phage.

______19. The transcriptional start signal upstream of genes.

______21. Group of genes that contains the gene for β-galactoside permease.

______23. Small molecule that assists the catabolite activator protein in DNA binding.

______25. A protein that decreases the rate of transcription.

______27. The phenomenon in which the effect of a mutation in one gene is neutralized by a mutation in a second gene.

______29. The phase of transcription after the RNA polymerase leaves the promoter and moves along the template. Molecular Biology, Spring 2002 Exam 2, 04/10/02 Page 4

Terms:

allolactose lacIS α subunit lacI- ampicillin lac operon antitermination lactose ATP late genes attenuator lysogen β subunit lytic phase CAP operator core enzyme operon cro protein PRE cyclic-AMP PR DNA-RNA hybrid polygenic mRNA DNA-RNA copolymer promoter elongation protein domain galactose rifampicin gel retardation essay rho-dependent terminator heat shock protein S1 nuclease homologous regions σ-factor immediate early genes stem-loop initiation ternary complex intergenic suppression trypsin intrinsic terminator tryptophan

4. An increase in the rate of transcription is generally caused by facilitating binding of RNA polymerase to a promoter region. How does CAP facilitate the binding of RNA polymerase to the lac promoter (3 points)? How does CAP facilitate the binding of RNA polymerase to the malKp promoter (3 points)? The malKp promoter controls the expression of one of the mal operons that is regulated by CAP and MalT.