UNIVERSITY OF OSLO
Faculty of Mathematics and Natural Sciences
Exam in:
MBV2010 Molecular Biology
Day of exam:
June 6, 2007
Exam hours: 9:00-12:00 (3 hours)
This examination paper consists of 2 pages.
Appendices: None
Permitted materials: None
Make sure that your copy of this examination paper is complete before answering.
Numbers in brackets indicate the maximum number of points for each question. The maximum
number of points for the entire exam is 100.
1. In which molecular processes are the following proteins involved
DNA polymerase I (replication, DNA repair)
DNA polymerase V (DNA repair)
RuvC (homologous recombination)
RecBCD (homologous recombination)
RNA polymerase III (transcription)
Single strand binding protein (SSB) (replication)
DnaB (replication)
Janus kinases (signal transduction)
Telomerase (replication)
Small nuclear ribonucleoproteins (snRNPs) (RNA processing)
Guanylyl transferase (RNA processing)
GreB (transcription)
“Flap endonuclease” (FEN 1) (replication)
Cohesins (cell division, replication)
MutS (DNA repair)
2.
(15)
Are the following statements true or false?
a) Telomerase is an RNA-dependent DNA polymerase. (true)
b) DNA polymerase δ is the main replication enzyme in the nucleus of eukaryotes.
(true)
c) Activation of proteins in signal transduction occurs primarily by acetylation. (false)
d) The DnaA protein binds to the replication fork. (false)
e) Heat can lead to breaks in DNA. (false; correct if single-strand breaks mentioned)
f) Steroid hormones (e.g. estrogen) bind to receptors on the surface of cells. (false)
g) Horizontal resolution of the chi form of a Holliday junction yields crossover
products (reciprocal strand exchange). (false)
h) attP and attB sites are involved in site-specific recombination. (true)
i) Inteins occur in messenger RNA. (false)
j) Isoaccepting tRNAs can interact with more than one codon in mRNA. (true)
k) Histones are primarily acetylated at serine amino acids. (false)
l) Methylation of histones results always in silencing of a region of DNA. (false)
m) Bacterial RNA polymerases attach to promoter sequences. (true)
n) An enhancer is a protein that enhances transcription. (false)
o) DNA and proteins interact via hydrogen bonds. (true)
(15)
3.
Point out the differences between prokaryotes and eukaryotes in
a) initiation of transcription (15)
Prokaryotes: direct binding of RNA polymerase to promoter; only one RNA
polymerase; promoter sequences differ from eukaryotic sequences
Eukaryotes: indirect binding of RNA polymerase to promoter via general transcription
factors; three RNA polymerases which recognize different promoter sequences
b) initiation of translation (15)
Prokaryotes: binding of small ribosomal subunit to ribosome binding site about 3-10
nucleotides upstream of translaton initiation codon; binding of formyl-met-tRNA
binding and large ribosomal subunit.
Eukaryotes: formation of a (pre-)initiation complex consisting of small ribosomal
subunit, met-tRNA and initiation factors; binding to mRNA at the 5’ cap (to capbinding-complex); scanning of mRNA until initiation codon (within Kozak sequence);
binding of large ribosomal subunit
(initiation factors involved in both cases; identity and function not important here)
, and
c) initiation of replication. (15)
Prokaryotes: one origin of replication (≈245 bp) consisting in E. coli of five 9nucleotide sequences and three 13-nucleotide sequences; DnaA binds to 9 nucleotide
motifs; opening of DNA helix around 13-nucleotide motifs;
Eukaryotes: many origins of replication; in yeast (ARS=autonomously replicating
sequence) 200 bp containing conserved motifs (A, B1, B2, and B3); origin recognition
complex (6 proteins) binds to A and B1 (origin recognition sequence); ABF1 binds to
B3 and opening of DNA helix occurs at B2; different proteins than in prokaryotes
involved
(45)
4.
a) What is the difference between homologous recombination and site-specific
recombination? Name (don’t describe) an example for each process. (10)
Homologous recombination: usually exchange of long DNA sequences (cross-over in
meiosis, gene conversion in yeast); catalyzed by a number of specific enzymes (see for
example the RecBCD pathway below).
Site-specific recombination: no exchange of long DNA sequences but insertion of a
DNA sequence into another; short identical DNA sequences required; catalyzed by
specific recombinases (integrase) enzymes that cut on either side of the homologous
sequence (e.g. insertion of phage lambda into the E. coli genome).
b) Explain the RecBCD pathway in E. coli. (15)
(25)
double strand cut; binding of RecBCD; scanning and DNA degradation until next chi
site; creating a recessed 5’ end at chi site; binding of RecA; strand invasion and search
for homologous sequences catalyzed by RecA; D-loop formation; Holliday structure;
branch migration catalyzed by RuvA and RuvB; cleavage of Holliday junction by
RuvC.