10/30
Depurination results in an abasic site. Is this the same thing as a deletion?
NO
homologous recombination can only occur in the ____ so the break must have occurred _____ DNA replication
S phase after
chemical modification of normal bases Can cause ______, or other effects - includes the same modifications as spontaneous chemical damage - plus a lot more kinds
deamination
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
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
Which of the following is most likely to result in a base-substitution mutation? A.Polymerase slippage B.Deamination of Cytosine to Uracil C.UV light
B.
examples of homologous recombination
BRCA1 AND BRCA2
5-bromouracil is a Thymine base analog. It ___________ A.creates an apurinic site. B.pairs just like Thymine. C.pairs like Thymine, but also with Guanine. D.will not pair with anything.
C.
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.
A polypeptide has the wild-type sequence Met-Ser-Pro-Arg-Leu-Gly-GluThe mutant polypeptide Met-Ser-Pro was most likely created by a ___________ mutation. A.nonsense B.missense C.synonymous D.inversion
A.
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.
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.
endonuclease
An enzyme that cleaves its nucleic acid substrate at internal sites in the nucleotide sequence.
'Indel' is an abbreviation for A.independently deleterious. B.insertion or deletion. C.indivisible lineage. D.individual elevation.
B.
At which phase of the cell cycle do sister chromatids exist? A. A.G1 B.S C.Anaphase
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.
Base analogs are mutagenic because of what characteristic? A.They induce a change in the enzymatic function of DNA polymerase. B.They distort the structure of DNA. C.They chemically modify the base they are analogous to. D.They are similar in structure but have different pairing characteristics to the base they are analogous to.
D.
Mutations in an exon that do not change the protein's amino-acid sequence are called __________ mutations. A.permissive B.suppressor C.reverse D.silent
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
polymerization
DNA polymerase adds nucleotides to the newly exposed 3'-OH group by using the other strand as a template and replacing damaged nucleotides
Depurination often causes a base substitution, when the missing base is replaced by
DNA repair machinery
ex of mismatch repair
DNA replication errors
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 homologous recombination
double strand breaks
type of damage repaired in nonhomologous end joining
double stranded breaks
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
intercalating agents cause
frameshift mutations
senescence
hibernation (irreversible)
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
•If the cell takes up a base analog, it can be_______
incorporated into DNA during replication
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
Spontaneous Chemical Mutations: Depurination (= loss of a purine)- sugar phosphate backbone remains:
intact
double strand damages
ionizing radiation
Spontaneous Chemical Mutations: Depurination (= loss of a purine)- is/is not an indel
is not
Nucleotide Excision Repair: A complex process involving _______ (but you just need to know that it is just what it sounds like)
many enzymes.
in alkylating agents, they donate methyl and ethyl groups causing
mispairing
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
double strand repair mechanisms
non-homologous end joining microhomology-mediated end joining homologous recombination
The U results in a G to A mutation in one of the new DNA daughter strands -- is this a transition or a transversion?
transition
homologous recombination uses the _______ as a template for repair
undamaged homologous double helix
Spontaneous deamination of cytosine results in _____:
uracil
deaminating chemicals deaminate cytosine to _____ which pairs with _____
uracil adenine
"a mammalian cell in culture loses approximately ______ purines every day." (text p. 528)
10,000
type of damage repaired in base excision
abnormal bases, modified bases, and pyrimidine dimers
in base analogs, a thymine analog can pair with ___ or _____
adenine or guanine
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
Depurination results in either _______ (if the abasic site originally had an A) or a ______
correction base-change mutation
hydroxylamine causes hydroxylated ______ which ______ with adenine
cytosine mispairs
UV light causes ____ dimers and ____ dimers which cause errors in _____
cytosine thymine replication
detection
damaged DNA is recognized
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
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