DNA REPLIC and REPAIR Flashcards
DNA is duplicated in what phase of the cell cycle?
S Phase
Replication occurs in the __’–>__’ direction
Takes place in the 5′ → 3′ direction
A free 3′-OH group of an existing single-strand attaches to the phosphate group of the next nucleotide.
For simultaneous replication of both parent strands, DNA replication occurs continuously on the _______________________strand and discontinuously on the _________________ strand in a 5′→3′ direction.
For simultaneous replication of both parent strands, DNA replication occurs continuously on the leading strand and discontinuously on the lagging strand in a 5′→3′ direction.
__________________catalyzes the formation of phosphodiester bonds in a section of double-stranded DNA, typically after DNA repair or during lagging strand synthesis. It does not have RNA exonuclease activity.
DNA ligase
_____________________ elongates both the leading strand and lagging strand during bacterial DNA replication. Although it proofreads added DNA nucleotides with its intrinsic 3’→5’ exonuclease activity, it does not have RNA exonuclease activity.
DNA polymerase III
_______________adds DNA hexamers to the end of chromosomes to avoid the loss of genetic material that occurs during DNA replication. Although it does have uracil in its internal RNA template, it does not have RNA exonuclease activity. Moreover, telomerase is neither expressed nor needed in prokaryotic cells, which do not experience loss of genetic material during DNA replication because of their circular genomes.
Telomerase
_______________________________ uses intrinsic 5’→3’ exonuclease activity to remove RNA primers added by primase during bacterial DNA replication and to remove damaged DNA before filling the gaps with DNA nucleotides through its 5’→3’ polymerase activity. ___________________also proofreads added DNA nucleotides with its intrinsic 3’→5’ exonuclease activity.
In eukaryotes, RNA exonuclease activity is performed by RNase H and flap endonuclease-1.
DNA polymerase I
It uses intrinsic 5’→3’ exonuclease activity to remove RNA primers added by primase during bacterial DNA replication and to remove damaged DNA before filling the gaps with DNA nucleotides through its 5’→3’ polymerase activity. DNA polymerase I also proofreads added DNA nucleotides with its intrinsic 3’→5’ exonuclease activity.
In eukaryotes, RNA exonuclease activity is performed by RNase H and flap endonuclease-1.
______________________ cut through single- and double-stranded DNA molecules in order to relieve the supercoiling created during DNA replication.
DNA topoisomerases
In eukaryotes, RNA exonuclease activity is performed by __________________ and ____________________
RNase H and flap endonuclease-1.
This disease is a rare, autosomal-recessive disease in which the ability to repair UV-induced DNA damage is defective. Individuals who suffer from this have mutations that impact excision endonucleases resulting in impaired function of ssDNA repair from UV exposure.
xeroderma pigmentosum
UV radiation results in dimer formation of neighboring pyrimidine bases, most commonly thymine. These bulky pyrimidine dimers induce helix distortion and can disrupt DNA replication. Dimers are usually repaired by nucleotide excision repair in the G1 phase of the cell cycle, in which the damaged oligonucleotides are first recognized and then excised. The process is carried out by excision endonucleases. DNA polymerase and ligase then fill and reseal the resulting gap. Mutations in any of these endonucleases can lead to extreme UV sensitivity and xeroderma pigmentosum.
What are the three major methods of ssDNA repair?
Nucelotide excision
Base excision
Mismatch
Of the three major methods of ssDNA repair, which method or methods emply the use of endonucleases?
All of them at some point in the process!
UV radiation results in dimer formation of neighboring pyrimidine bases, most commonly thymine. These bulky pyrimidine dimers induce helix distortion and can disrupt DNA replication. Dimers are usually repaired by _________________________ in the G1 phase of the cell cycle.
nucleotide excision repair
A mechanism of double-stranded DNA repair in which DNA ligase connects two ends of the break without a homologous template (which can lead to lost DNA). Defective in patients with ataxia telangiectasia.
nonhomologous end joining
What are the methods of dsDNA repair?
Nonhomologous end joining and homologous recombination
______________ in DNA are caused by free radicals that are created by exposure to ionizing radiation (e.g., x-rays and background radiation).
Double-strand breaks
RNA primer removal is achieved by ___________________ and occurs on both the leading and lagging strands of DNA.
DNA polymerase I
Ionizing radiation causes ionization of water to this reactive oxygen species. It will attack the DNA backbone and bases. These reactions cause DNA single-strand breaks and, most deleteriously, DNA double-strand breaks, which are very difficult for the cell to repair, leading to cell death.
Hydroxyl radicals
UV radiation leads to the formation of __________________ repaired by ____________________ while ionizing radiation leads to the formation of _________________________ repaired by ____________________.
UV radiation leads to the formation of pyrimidine dimers repaired by nucleotide excision repair while ionizing radiation leads to the formation of ss breaks, dsbreaks, and free radicals repaired by mutliple methods but ds breaks in this case likely are repaired by NHEJ.
A form of single-stranded DNA repair in which replications errors in newly synthesized DNA (e.g., base-base mismatches and mispairings caused by erroneous base insertion or deletion) are recognized and removed. The gap is then filled and resealed. Occurs primarily during S phase. Defective in patients with ……
This is DNA mismatch repair, LYNCH SYNDROME
DNA that has undergone a double-stranded break is repaired by what enzyme?
DNA ligase IV
An autosomal recessive disease caused by a mutation in the ATM gene, a tumor suppressor gene that assists in the repair of double strand breaks. Affected individuals have severe humoral immunodeficiency (decreased IgA, IgG, and IgE), ataxia due to cerebellar atrophy, and capillary malformations (i.e., telangiectasia). They also have an increased risk of developing lymphomas and leukemias.
Ataxia telangiectasia, mutations in ATM impacting NHEJ
Which dsDNA repair has higher fidelity and is less prone to error?
Homologous recombination repair. This method requires a (nearly) identical sequence (such as the complementary strand) to serve as a template for repair
No DNA is lost in the process. NHEJ has no template and so it is more prone to error.
BRCA1 and 2 lead to dysfunction in what DNA repair mechanism?
dsDNA repair via homologous recombination repair
Mismatched base pairs are recognized by MSH proteins. Mutations in these proteins leads to dysfunction of this mechanism and can lead to this syndrome.
it leads to dysfunction of DNA mismatch repair and can lead to lynch syndrome
What does an endonuclease do?
Endonucleases sever the pentose-phosphate backbone and remove a segment of DNA from double-stranded DNA, usually in relation to some DNA damage, so DNA polymerase can fill in the gap, repairing the DNA.
Fluoroquinolones are a first-line empiric treatment of uncomplicated pyelonephritis. They interfere with bacterial DNA replication by inhibiting bacterial ___________________________-
Fluoroquinolones are a first-line empiric treatment of uncomplicated pyelonephritis. They interfere with bacterial DNA replication by inhibiting bacterial topoisomerase II and topoisomerase IV.
are responsible for cleaving DNA to relieve supercoils.
