BIOC0007 EXAM QUESTIONS AND ANSWERS WITH
COMPLETE SOLUTIONS VERIFIED LATEST UPDATE
Where does the glycosidic bond form between a nucleobase and the sugar?
C1 of sugar and N1 of pyrimidine or N9 of purine
Polynucleotide
A polymer consisting of many nucleotide monomers in a chain (DNA or RNA)
B DNA
No. Bases per turn = 10.5
Helix diameter = 20 A
Major groove = 13 A
Minor groove = 9 A
Solid Core
Right handed
A DNA
Dehydrated conditions
No. Bases per turn = 11
Helix diameter = 26 A
Hollow Core
Right handed
Z DNA
,High Saline / Stress / Methylation
No. Bases per turn = 12
Helix diameter = 18 A
Solid Core
Left handed
Nucleosome
Octamer of histone proteins (H3-H4 tetramer, 2 x H2A-H2B heterodimers) surrounded
by 146 bp left-coiled DNA.
H1 histone protein
"linker histone" binds to DNA in the linker region - helps compact adjacent nucleosomes
(to 30nm fiber)
Histone Tails
Strings of 19-39 amino acids protruding from nucleosome.
- H3 and H4 only have N terminus tails
Helicases
Hexameric ATPases - break hydrogen bonds in double stranded DNA
For replication:
- Prokaryotes = DnaB
- Eukaryotes = MCM Complex
Primase
RNA polymerase
Adds 10 bp primer onto 5' end of single-stranded DNA
DNA Polymerase I
,RNA primer removal and DNA repair (1 subunit)
- Removes RNA primer and replaces with dNTPs
DNA Polymerase II
Enzyme that proofreads the daughter strand of replicated DNA and corrects any base
pairing errors
DNA Polymerase III
DNA replication (holoenzyme = 9 subunits)
DNA Polymerase alpha
contains primase activity and initiates DNA synthesis by synthesizing an RNA primer,
followed by a short string of DNA nucleotides.
(4 subunits)
DNA Polymerase delta
Lagging strand synthesis
Also nucleotide and base excision repair
DNA Polymerase epsilon
Leading strand synthesis
Also nucleotide and base excision repair
Sliding Clamp
ring-shaped protein that holds the DNA polymerase on the DNA strand
- Loaded by Clamp Loader using ATP
origin recognition complex (ORC)
A protein complex that initiates DNA replication at eukaryotic origins
DNA error rate
, 1 in 10,000, but 1 in a billion go unfixed
Intrinsic cellular processes that cause DNA damage
- DNA replication
- rNTPs used instead of dNTPs
- Spontaneous hydrolysis of covalent bonds (depurination, depyrimidation, deamination
etc)
- Metabolic biproducts (e.g. O2- in H2O2 breakdown)
External factors for DNA damage
- Environmental (UV, ionisation)
- Alkylating agents (add CH3 etc groups to backbone)
- Intercalating agents (e.g. EtBr)
- Base analogues being incorporated
- Genotoxic substances (e.g. Phthalates)
Nucleotide Excision Repair (NER) - Eukaryotes
1) XPE, XPC, RAD23B recognise distortions
2) XPB, XPD open DNA around lesion (helicase activity)
3) XPG, RPA unwind and stabilise DNA
4) XPF cuts 5' upstream of lesion
5) XPG cuts 3' downstream of lesion
- Gives 24-50 bp region long
6) Gap sealed by DNA polymerase and ligase
Single Stranded DNA Repair Mechanisms
COMPLETE SOLUTIONS VERIFIED LATEST UPDATE
Where does the glycosidic bond form between a nucleobase and the sugar?
C1 of sugar and N1 of pyrimidine or N9 of purine
Polynucleotide
A polymer consisting of many nucleotide monomers in a chain (DNA or RNA)
B DNA
No. Bases per turn = 10.5
Helix diameter = 20 A
Major groove = 13 A
Minor groove = 9 A
Solid Core
Right handed
A DNA
Dehydrated conditions
No. Bases per turn = 11
Helix diameter = 26 A
Hollow Core
Right handed
Z DNA
,High Saline / Stress / Methylation
No. Bases per turn = 12
Helix diameter = 18 A
Solid Core
Left handed
Nucleosome
Octamer of histone proteins (H3-H4 tetramer, 2 x H2A-H2B heterodimers) surrounded
by 146 bp left-coiled DNA.
H1 histone protein
"linker histone" binds to DNA in the linker region - helps compact adjacent nucleosomes
(to 30nm fiber)
Histone Tails
Strings of 19-39 amino acids protruding from nucleosome.
- H3 and H4 only have N terminus tails
Helicases
Hexameric ATPases - break hydrogen bonds in double stranded DNA
For replication:
- Prokaryotes = DnaB
- Eukaryotes = MCM Complex
Primase
RNA polymerase
Adds 10 bp primer onto 5' end of single-stranded DNA
DNA Polymerase I
,RNA primer removal and DNA repair (1 subunit)
- Removes RNA primer and replaces with dNTPs
DNA Polymerase II
Enzyme that proofreads the daughter strand of replicated DNA and corrects any base
pairing errors
DNA Polymerase III
DNA replication (holoenzyme = 9 subunits)
DNA Polymerase alpha
contains primase activity and initiates DNA synthesis by synthesizing an RNA primer,
followed by a short string of DNA nucleotides.
(4 subunits)
DNA Polymerase delta
Lagging strand synthesis
Also nucleotide and base excision repair
DNA Polymerase epsilon
Leading strand synthesis
Also nucleotide and base excision repair
Sliding Clamp
ring-shaped protein that holds the DNA polymerase on the DNA strand
- Loaded by Clamp Loader using ATP
origin recognition complex (ORC)
A protein complex that initiates DNA replication at eukaryotic origins
DNA error rate
, 1 in 10,000, but 1 in a billion go unfixed
Intrinsic cellular processes that cause DNA damage
- DNA replication
- rNTPs used instead of dNTPs
- Spontaneous hydrolysis of covalent bonds (depurination, depyrimidation, deamination
etc)
- Metabolic biproducts (e.g. O2- in H2O2 breakdown)
External factors for DNA damage
- Environmental (UV, ionisation)
- Alkylating agents (add CH3 etc groups to backbone)
- Intercalating agents (e.g. EtBr)
- Base analogues being incorporated
- Genotoxic substances (e.g. Phthalates)
Nucleotide Excision Repair (NER) - Eukaryotes
1) XPE, XPC, RAD23B recognise distortions
2) XPB, XPD open DNA around lesion (helicase activity)
3) XPG, RPA unwind and stabilise DNA
4) XPF cuts 5' upstream of lesion
5) XPG cuts 3' downstream of lesion
- Gives 24-50 bp region long
6) Gap sealed by DNA polymerase and ligase
Single Stranded DNA Repair Mechanisms
