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