Biochemistry and Molecular Biology II – Tutorial club 3: Questions on
Replication & Cell Cycle (28-05-18)
BMB2 tutorial (May 2018) DNA metabolism (Lodish 7 Chapter 4)
Q1: (a) What are the known functions of human DNA polymerase and
?
- Pol a: the RNA and DNA primers are necessary, in order for the okazaki-
fragments on the lagging strand to be transcribed.
(b) Which of these polymerases have proofreading activity? DNA pol and
have 3’ → 5’ exonuclease activity.
(c) What happens if DNA pol has an impaired proofreading activity in mice?
There will be a greater risk on mutations to form. Removal of the proofreading
function of DNA pol y leads to loss of mitochondrial functioning which can/will lead to
premature ageing. The concept is that mutant mitochondrial ATP synthetase subunits
generate reactive oxygen species (ROS) that damage the proteome and the nuclear
genome, causing aging.
Q2: a,b,c) Eukaryotes have repair systems that prevent mutations due to
copying errors and exposure to mutagens. What are the three excision-repair
systems found in eukaryotes.
1. Base excision repair (BER) → caused by a deamination of cytosine. Corrects
G-U and G-T mismatches. It removes T and U. Eventually DNA ligase seals
the gap. Should happen before replication. DNA glycosylase flips out the
wrong base. Then APEI endonuclease removes the incorrect base.
2. Mismatch repair (MMR) → This is caused by faulty proofreading. MS2 MS6-
complex recognize the mismatch. DNA helicase unwinds the DNA, allowing an
exonuclease to remove the mismatch. After, DNA polymerase can correct the
mismatch. In the end, DNA ligase seals everything up again and the mismatch
is corrected.
3. Nucleotide excision repair (NER) → Sunlight can cause NERs (UV-radiation
causes thymine-thymine dimers). RNA polymerase II only recognizes NERs
within a gene and the gene has to be transcribed. XP-G and XP-F are two
endonucleases which cut into one strand, in order to remove the damaged
part.
, d) In what way will repair of a transcribed region differ from a non-transcribed
one when it comes to UV-mediated DNA damage? Cell cycle (Lodish 7:
Chapters 19 and 24)
Breaks in the existing (transcribed) region need to be corrected, but it is not known
which bases were in the position to be repaired. Because UV-mediated DNA damage
has an effect on both strands.
*Non-homologous end-joining repair mechanism can be used which repairs double
strand breaks but causes mutations at the repair junction.
The recognition mechanism now occurs by RNA polymerase II and not by XP????
The name XPC comes from xeroderma pigmentosum.
The name CS comes from Cockayne syndrome.
Q3: What is a yeast cdc mutant? Give one example
1. S.pombe (fission yeast)
Replication & Cell Cycle (28-05-18)
BMB2 tutorial (May 2018) DNA metabolism (Lodish 7 Chapter 4)
Q1: (a) What are the known functions of human DNA polymerase and
?
- Pol a: the RNA and DNA primers are necessary, in order for the okazaki-
fragments on the lagging strand to be transcribed.
(b) Which of these polymerases have proofreading activity? DNA pol and
have 3’ → 5’ exonuclease activity.
(c) What happens if DNA pol has an impaired proofreading activity in mice?
There will be a greater risk on mutations to form. Removal of the proofreading
function of DNA pol y leads to loss of mitochondrial functioning which can/will lead to
premature ageing. The concept is that mutant mitochondrial ATP synthetase subunits
generate reactive oxygen species (ROS) that damage the proteome and the nuclear
genome, causing aging.
Q2: a,b,c) Eukaryotes have repair systems that prevent mutations due to
copying errors and exposure to mutagens. What are the three excision-repair
systems found in eukaryotes.
1. Base excision repair (BER) → caused by a deamination of cytosine. Corrects
G-U and G-T mismatches. It removes T and U. Eventually DNA ligase seals
the gap. Should happen before replication. DNA glycosylase flips out the
wrong base. Then APEI endonuclease removes the incorrect base.
2. Mismatch repair (MMR) → This is caused by faulty proofreading. MS2 MS6-
complex recognize the mismatch. DNA helicase unwinds the DNA, allowing an
exonuclease to remove the mismatch. After, DNA polymerase can correct the
mismatch. In the end, DNA ligase seals everything up again and the mismatch
is corrected.
3. Nucleotide excision repair (NER) → Sunlight can cause NERs (UV-radiation
causes thymine-thymine dimers). RNA polymerase II only recognizes NERs
within a gene and the gene has to be transcribed. XP-G and XP-F are two
endonucleases which cut into one strand, in order to remove the damaged
part.
, d) In what way will repair of a transcribed region differ from a non-transcribed
one when it comes to UV-mediated DNA damage? Cell cycle (Lodish 7:
Chapters 19 and 24)
Breaks in the existing (transcribed) region need to be corrected, but it is not known
which bases were in the position to be repaired. Because UV-mediated DNA damage
has an effect on both strands.
*Non-homologous end-joining repair mechanism can be used which repairs double
strand breaks but causes mutations at the repair junction.
The recognition mechanism now occurs by RNA polymerase II and not by XP????
The name XPC comes from xeroderma pigmentosum.
The name CS comes from Cockayne syndrome.
Q3: What is a yeast cdc mutant? Give one example
1. S.pombe (fission yeast)
