DNA repair
Homologous recombination repair of a double-strand break A. uses the sister chromatid as a template to repair the damage with a sequence mutation. B. can only occur during meiosis. C. can only occur in diploid organisms. D. physically attaches the broken end on to the sister chromatid.
A
At which phase of the cell cycle do sister chromatids exist? A. G1 B. S C. Anaphase
B
examples of homologous recombination
BRCA1 AND BRCA2
Mismatch repair in E. coli distinguishes between old and new strands of DNA on the basis of A. differences in the base composition of the two strands. B. modification of histone proteins. C. base analogs on the new strand. D. methyl groups on the old strand.
D
____________ repair removes one nucleotide, and ___________. A. Nucleotide excision / replaces it with a random base B. Base excision / replaces it with a random base C. Nucleotide excision / uses the opposite strand as a template D. Base excision / uses the opposite strand as a template
D
nucleotide excision repair
DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers
type of damage repaired in nucleotide excision
DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers
ligation
DNA ligase seals the nick left in the sugar-phosphate backbone of the repaired strand
ex of mismatch repair
DNA replication errors
Nucleotide- and Base-excision repair:
Enzymes recognize and remove damaged bases. DNA polymerase + ligase restore a copy of the template strand.
homologous recombination can only occur in the ____ so the break must have occurred _____ DNA replication
S phase after
ex of nucleotide excision repair
UV light damage
For a direct repair list: The type of DNA damage repaired The process involved in repair. How the damaged strain is identified by the repair enzymes (where discussed)
UV-induced pyrimidine dimers photolyase- uses energy captured by light to break covalent bonds that link pyrimidines in a dimer
in base excision and mismatch repair, a _____ is made in the sugar phosphate backbone on one side of the damage
a single nick
base excision repair
abnormal bases, modified bases, and pyrimidine dimers
type of damage repaired in base excision
abnormal bases, modified bases, and pyrimidine dimers
types of damage
break in both strands of the double helix complete chromosome breakage
unregulated cell division
cancer
For a base-excision repair list: The type of DNA damage repaired The process involved in repair. How the damaged strain is identified by the repair enzymes (where discussed)
catalyzed by a group of enzymes called DNA glycosylases, each recognizes and removes a specific type of modified base by cleaving the bond that links that base to the sugar After the modified base has been removed, AP endonuclease cuts the phosphodiester bond and DNA polymerase adds one or more new nucleotides to the 3' OH group
ex of base excision repair
chemical damage to a base
detection
damaged DNA is recognized
in mismatch repair, the old nucleotides are
degraded
List the four basic steps that are common to all forms of single-stranded DNA damage repair.
detection, excision, polymerazation, and ligation
in nucleotide excision repair, the old nucleotides are
displaced by helicase enzymes
damage is either
endogenous or exogenous
excision
endonucleases nick the sugar phosphate backbone on one or both sides of the DNA damage, and one or more nucleotides are removed
What kind of problem does Direct Repair fix?
enzymes identify and return the damaged nucleotide to its original structure
senescence
hibernation (irreversible)
double strand damages
ionizing radiation
Nucleotide Excision Repair: A complex process involving _______ (but you just need to know that it is just what it sounds like)
many enzymes.
in base excision repair, DNA polymerase displaces the old nucleotides and adds:
new nucleotides to the 3' end
in nucleotide excision repair, _____ is made on ____ sides of the damage
nicks both
3 types of single strand repari
nucleotide excision repair base excision repair mismatch repair
in direct repair enzymes identify and return the damaged nucleotide to its
original structure
homologous recombination
pairs a broken DNA molecule by using the identical genetic information contained in another molecule the same mechanism for crossing over begins with the removal of some nucleotides at the broken ends, followed by invasion, displacement, and replication
apoptosis
programmed cell death
type of damage repaired in direct
pyrimidine dimers
direct repair
pyrimidine dimers; other specific types of alterations
Nucleotide (or Base)-excision repair: Enzymes ______ and ______ damaged bases. DNA polymerase + ligase restore a copy of the template strand.
recognize remove
During replication, mismatched base pairs are recognized, removed, and replaced with a correct nucleotide prior to the continuation of replication ("proofreading"). What two enzymatic activities are required for DNA polymerase to remove and replace a mismatched base? Choose two. A. Ligase B. De-methylase C. Acytelase D. 3'-to-5' Exonuclease
A, D
What is the distinguishing feature of 'nucleotide excision repair'? A.Damaged nucleotides are removed (excisized) B.Damaged nucleotides are chemically altered back to their normal form C.DNA Polymerase uses the non-damaged strand to replace the damaged bases
A.
endonuclease
An enzyme that cleaves its nucleic acid substrate at internal sites in the nucleotide sequence.
Why would homologous repair of a double-strand break only be available during late S-phase or G2? A. Because cyclin-dependent kinases are required B. Because there must be a sister chromatid to act as the template C. Because non-homologous end-joining is preferable at other times D. Because the cell must be nearly ready to divide.
B
What is the distinguishing feature of 'direct repair'? A.Damaged nucleotides are removed (excisized) B.Damaged nucleotides are chemically altered back to their normal form C.DNA Polymerase uses the non-damaged strand to replace the damaged bases
B.
If DNA Polymerase makes a single-nucleotide mistake during replication (inserting the wrong nucleotide), which of the following is most likely? A.The incorrect nucleotide will base-pair with the complementary strand B.The incorrect nucleotide will undergo chemical changes to allow it to base-pair C.The incorrect base pair will form a bulge in the DNA structure D.The template nucleotide will undergo a conformational change to allow it to base-pair with the new nucleotide
C.
In what parts of the cell cycle can homologous recombination be used to repair damaged DNA? A.S B.G1 C.S and G2 D.S and Metaphase
C.
polymerization
DNA polymerase adds nucleotides to the newly exposed 3'-OH group by using the other strand as a template and replacing damaged nucleotides
What are the two error-correction processes that are "intrinsic to the replication process"?
Proofreading and base repair
Differentiate between the two types of repair pathways used in repairing double-stranded breaks, and describe how the cell 'knows' which repair pathway to use.
homologous recombination and nonhomologous end joining
For mismatch list: The type of DNA damage repaired The process involved in repair. How the damaged strain is identified by the repair enzymes (where discussed)
incorrectly inserted nucleotides that escape detection by proofreading the mismatch-repair enzymes cut out a section of the newly synthesized strand and fill the gap with new nucleotides by using the original DNA strand as a template. the proteins that carry out mismatch repair in e coli differentiate between old and new strands by the presence of methyl groups on certain sequences of the old strand
type of damage repaired in mismatch
replication errors such as mispaired bases and strand slippage
mismatch repair
replication errors, including mispaired bases and strand slippage
homologous recombination uses the _______ as a template for repair
undamaged homologous double helix
type of damage repaired in homologous recombination
double strand breaks
type of damage repaired in nonhomologous end joining
double stranded breaks
double strand repair mechanisms
non-homologous end joining microhomology-mediated end joining homologous recombination
For a nucleotide excision repair list: The type of DNA damage repaired The process involved in repair. How the damaged strain is identified by the repair enzymes (where discussed)
removes bulky DNA lesions (pyrimidine dimers) enzymes scan DNA and find distortion enzymes separate the two nucleotide strands at the damaged region and SSBP stabilize strands sugar-phosphate backbone of damaged strand is cleaved on both sides and part of the damaged strand is peeled away by helicase enzymes DNA polymerase fills gap and ligase seals it
nonhomologous end joining
repairs double strand breaks.connects broken ends of DNA without replacing original sequences, causes deletions in chromosomes. quicker than HRR but more error-prone
During replication, mismatched base-pairs are recognized, removed, and replaced with a correct nucleotide prior to continuation of replication ("proofreading"). In the image below, a mismatched base has been added to the growing strand ('green' instead of 'blue'). What activities would be required for DNA polymerase to remove and replace the mismatched base? Choose all that apply. A.Intrinsic ligase activity of DNA Polymerase B.Intrinsic exonuclease activity of DNA Polymerase C.Intrinsic de-methylase activity of DNA Polymerase D.Intrinsic acytelase activity of DNA Polymerase
A. b.
Photoreactivation
The enzyme photolyase binds to the pyrimidine dimer and cleaves the cyclobutane ring.