Download Exam V2002 - English

UNIVERSITY OF OSLO
Faculty of Mathematics and Natural Sciences
Exam in:
MBV2010 Molecular Biology
Day of exam:
June 7, 2006
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 50.
1. In which molecular processes are the following proteins involved
RNA polymerase III
transcription
DNA polymerase III
replication
Catabolite activator protein (CAP)
transcription
Photolyase
DNA repair
Ku-proteins
DNA repair
Aminoacyl-tRNA synthetase
translation
MutH
mismatch repair
Ras protein
signal transduction
Telomerase
replication
Ribonuclease P
RNA processing
(10)
2. a) What is hypermutation? Describe an example in which hypermutation is important. (5)
p. 521-522.
A rate of mutation that is higher than the average mutation rate of a genome.
For instance, in the variable region of immunoglobulin genes. Mutation rates are
higher because of mismatch repair that repairs the mother strand instead of the
daughter strand and because of cytosine deamination followed by removal of the
resulting uracil and resynthesis with any nucleotide.
b) Describe the mutagenic effect of heat on DNA and how mutations caused by heat are
repaired.
p. 514-516
(5)
Heat hydrolyzes the beta-N-glycosidic bond between bases and deoxyribose leading to
an baseless or AP site. This is repaired by removal and re-synthesis of the affected
nucleotide.
c) How is bacteriophage lambda DNA integrated into the genome of E. coli? (5)
p. 550-551.
By site-specific recombination between so-called att sites on the lambda and bacterial
genomes. Insertion is catalyzed by an integrase (recombinase) and IHF (integration
host factor) that bind to sequences at the ends of the att sites.
3. a) Why must DNA replication be primed? Describe the priming process in E. coli and in
the nucleus of eukaryotes. p. 479; 481-482.
(5)
Priming is necessary because DNA polymerases need a 3’ end to attach new
nucleotides.
E. coli: primase synthesizes a short ≈ 10 nucleotides RNA primer that is elongated by
DNA polymerase III.
Eukaryotes: A primase that is in a complex with DNA polymerase alpha synthesizes a
short RNA primer that is extended by DNA polymerase alpha before DNA
polymerase delta takes over.
b) Which elements are found in the origin of replication in E. coli and in yeast? Explain
the function of these elements. p. 475-477.
(5)
E. coli: five 9-nucleotide repeats that bind DnaA proteins. Three 13-nucleotide
elements where the double helix opens up (melts).
Yeast: ARS (autonomously replicatin sequence): origin recognition sequence to which
an origin recognition complex binds. Region B3 to which binds an ARS binding factor
(ABF1). Region B2 where the double helix opens up.
c) Name all the proteins involved in DNA replication and explain briefly (1-2 sentences)
their function. p. 476-493.
(5)
Prokaryotes. DnaA, melting of DNA strands. DnaB, DNA helicase, breaks hydrogen
bonds. DnaC, function unknown. DNA topoisomerases counteract torsional stress.
Primase, priming of DNA synthesis. DNA polymerase III, main DNA synthesizing
enzyme. SSB, single strand binding protein, protection and avoiding reannealing.
DNA polymerase I, removal of primer. DNA ligase, joining of Okazaki fragments.
Tus proteins, trapping of the replication forks.
Eukaryotes: helicases,
topoisomerases, DNA polymerase alpha, DNA polymerase delta, RPA, replication
protein alpha. FEN1 flap endonuclease I. Telomerase, maintaining length of
telomers.
4. a) Describe transcription initiation in E. coli and point out the differences between
bacterial and eukaryotic initiation of transcription. p. 312-315.
(5)
Binding of RNA polymerase (with its sigma subunit) to promoter. Conversion of a
closed complex to an open complex. Promoter clearance.
Eukaryotic promoters more complex. Platform onto which RNA polymerase binds.
More initiation factors. Otherwise similar.
b) Explain ways in which transcription initiation can be regulated in bacteria and in
eukaryotes. p. 315-325.
(5)
Bacteria: promoter sequence, sigma subunit; transcription factors (mostly repressors),
Eukaryotes: Chromatin structure, nucleosome positioning, transcription factors