MICR 271 Module Questions with Correct
Answers
What do archaea protein complexes involved in DNA replication resemble?
those of eukaryotes compared to those of bacteria
even though both archaea and bacteria contain circular chromosomes
What do studies prove about the mechanisms involved in archaeal DNA replication?
they correlate with their positioning in the tree of life as related to bacteria but as antecedents
of eukaryota
What are antecedents?
thing or event that existed before or logically precedes another
What is the direction of replication processes?
bi directional
Where does DNA replication begin in prokaryotes?
origin or ori C
specific site on chromosome
What is the origin rich in?
AT rich, easier to separate then GC rich regions
What happens after double stranded DNA is opened?
replication forks proceed in opposite directions until they meet at termination site
What drives the replication forks?
activity of replisome
,What is replisome?
molecular machine composed of multiple components that carries out DNA replication
What happens for replication forks in rapidly growing cells?
additional rounds of replication initiate at the origin before prior rounds reach termination site
allows for multiple copies of chromosome to be ready for partitioning into daughter cells
What does replication of circular chromosome result in?
two interlocked (catenated) daughter chromosomes
What happens to the interlocked daughter chromosomes?
one chromosome is cleaved by topoisomerase to resolve the two chromosomes
What happens if the strands dont separate?
cell death
What problem is alleviated with circular chromosomes?
problems in DNA replication associated with having free ends
What have eukaryotic organisms with linear chromosomes evolved to have?
telomeres
Steps of bacterial replication fork?
1. helicase unwinds DNA and the lagging strand is coated with single stranded DNA binding
(SSB) proteins to protect sDNA while an RNA primer is synthesized by primase
2. DNA polymerase III holoenzyme is tethered to the DNA via B clamp and is loaded into the
complex by t clamp loader
,3. one core enzyme of Pol III carries out leading strand synthesis, synthesizes DNA
continuously
4. two additional Pol III enzymes carry out lagging strand synthesis, synthesizes pieces of
DNA called okazaki fragments
5. core enzyme reaches completed region, released from DNA and okazaki fragments joined
together. done by DNA polymerase I removing RNA primer filling in the gap with DNA and
DNA ligase joins strands
What is a holoenzyme?
active form of an enzyme, consisting of an enzyme as well as its cofactor
Steps of eukaryotic replication fork?
1. helicase must be complexed with additional proteins to be activated to unwind DNA.
single stranded DNA is protected by replication protein A
2. helicase associates indirectly with a primase which synthesizes an RNA primer
3. polymerase engages in leading strand synthesis while a different polymerase carriers out
lagging strand synthesis. these polymerases are loaded onto DNA via proliferating cell
nuclear antigen which is carried to the DNA by replication factor C
4. okazaki fragments generated are much shorter than those of prokaryotes. RNA primer is
removed by strand displacement and filled in by polymerase and the single strand gap is
repaired by ligase
Speed of replication in eukaryotes
15-30 times slower than prokaryotes. have multiple initiation sites
Why is eukaryotic replication slower than prokaryotic?
, 1. eukaryotic replisomes are subject to cell cycle-dependent regulation of replication
initiation and termination and must deal with displacing nucleosomes during passage of
replication fork
2. many of the enzymes in eukaryotic replisome are subject to post-translational
modifications that activate or inactivate them
What are nucleosomes?
form of DNA packaging, where a section of DNA is wrapped around a core of proteins
What are the two DNA repair approaches that function during replication process?
1. proofreading: some DNA polymerases possess the ability to repair replication error. if an
error is made while these DNA polymerases replicating DNA, enzymes are able to reverse,
excise the incorrect base and insert correct base
2. repair only: other polymerases engage only in repair. important at the replication fork in
order to repair breaks in double stranded DNA if fork becomes "stalled"
DNA polymerase families important notes
1. eukaryotes evolved to have several different polymerases in each family
2. bacteria and archaea tend to have one specific polymerase for a very defined function.
translesion repair accomplished by Pol V in bacteria and Pol Y in archaea
3. archaeal ancestor of eukaryotes encoded three DNA polymerases; two family BDNA
polymerases and a family DDNA polymerase. contributed to evolution of eukaryotic
replication machinery
4. main function of Pol I in bacteria is that of repair, joining okazaki fragments by deleting
RNA primers to replacing them with DNA
5. family B polymerases responsible for leading and lagging strand synthesis and are highly
accurate. ability to recognize and repair mispaired bases at the replication fork
Answers
What do archaea protein complexes involved in DNA replication resemble?
those of eukaryotes compared to those of bacteria
even though both archaea and bacteria contain circular chromosomes
What do studies prove about the mechanisms involved in archaeal DNA replication?
they correlate with their positioning in the tree of life as related to bacteria but as antecedents
of eukaryota
What are antecedents?
thing or event that existed before or logically precedes another
What is the direction of replication processes?
bi directional
Where does DNA replication begin in prokaryotes?
origin or ori C
specific site on chromosome
What is the origin rich in?
AT rich, easier to separate then GC rich regions
What happens after double stranded DNA is opened?
replication forks proceed in opposite directions until they meet at termination site
What drives the replication forks?
activity of replisome
,What is replisome?
molecular machine composed of multiple components that carries out DNA replication
What happens for replication forks in rapidly growing cells?
additional rounds of replication initiate at the origin before prior rounds reach termination site
allows for multiple copies of chromosome to be ready for partitioning into daughter cells
What does replication of circular chromosome result in?
two interlocked (catenated) daughter chromosomes
What happens to the interlocked daughter chromosomes?
one chromosome is cleaved by topoisomerase to resolve the two chromosomes
What happens if the strands dont separate?
cell death
What problem is alleviated with circular chromosomes?
problems in DNA replication associated with having free ends
What have eukaryotic organisms with linear chromosomes evolved to have?
telomeres
Steps of bacterial replication fork?
1. helicase unwinds DNA and the lagging strand is coated with single stranded DNA binding
(SSB) proteins to protect sDNA while an RNA primer is synthesized by primase
2. DNA polymerase III holoenzyme is tethered to the DNA via B clamp and is loaded into the
complex by t clamp loader
,3. one core enzyme of Pol III carries out leading strand synthesis, synthesizes DNA
continuously
4. two additional Pol III enzymes carry out lagging strand synthesis, synthesizes pieces of
DNA called okazaki fragments
5. core enzyme reaches completed region, released from DNA and okazaki fragments joined
together. done by DNA polymerase I removing RNA primer filling in the gap with DNA and
DNA ligase joins strands
What is a holoenzyme?
active form of an enzyme, consisting of an enzyme as well as its cofactor
Steps of eukaryotic replication fork?
1. helicase must be complexed with additional proteins to be activated to unwind DNA.
single stranded DNA is protected by replication protein A
2. helicase associates indirectly with a primase which synthesizes an RNA primer
3. polymerase engages in leading strand synthesis while a different polymerase carriers out
lagging strand synthesis. these polymerases are loaded onto DNA via proliferating cell
nuclear antigen which is carried to the DNA by replication factor C
4. okazaki fragments generated are much shorter than those of prokaryotes. RNA primer is
removed by strand displacement and filled in by polymerase and the single strand gap is
repaired by ligase
Speed of replication in eukaryotes
15-30 times slower than prokaryotes. have multiple initiation sites
Why is eukaryotic replication slower than prokaryotic?
, 1. eukaryotic replisomes are subject to cell cycle-dependent regulation of replication
initiation and termination and must deal with displacing nucleosomes during passage of
replication fork
2. many of the enzymes in eukaryotic replisome are subject to post-translational
modifications that activate or inactivate them
What are nucleosomes?
form of DNA packaging, where a section of DNA is wrapped around a core of proteins
What are the two DNA repair approaches that function during replication process?
1. proofreading: some DNA polymerases possess the ability to repair replication error. if an
error is made while these DNA polymerases replicating DNA, enzymes are able to reverse,
excise the incorrect base and insert correct base
2. repair only: other polymerases engage only in repair. important at the replication fork in
order to repair breaks in double stranded DNA if fork becomes "stalled"
DNA polymerase families important notes
1. eukaryotes evolved to have several different polymerases in each family
2. bacteria and archaea tend to have one specific polymerase for a very defined function.
translesion repair accomplished by Pol V in bacteria and Pol Y in archaea
3. archaeal ancestor of eukaryotes encoded three DNA polymerases; two family BDNA
polymerases and a family DDNA polymerase. contributed to evolution of eukaryotic
replication machinery
4. main function of Pol I in bacteria is that of repair, joining okazaki fragments by deleting
RNA primers to replacing them with DNA
5. family B polymerases responsible for leading and lagging strand synthesis and are highly
accurate. ability to recognize and repair mispaired bases at the replication fork
