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93 Cards in this Set
- Front
- Back
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True or false: E. coli have one site of initiation.
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true
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True or false: rate of replication is faster in eukaryotes than in E. coli.
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false, but multiple origins enable it to take the same amount of time as E. coli
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What do large number of replication forks at opposite ends of "bubbles" of duplicated DNA suggest?
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multiple origins of replication
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free end of linear DNA |
telomere
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What are susceptible to damage by nucleases?
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telomeres
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What occurs to one strand due to the nature of DNA synthesis?
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shortens upon each round
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Why can't DNA polymerase fill in the terminal gap? |
there is no free 3' end
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What do telomeres do?
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protect the end from degradation
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What is the end of the leading strand rich in? |
guanine
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What contains hundreds of tandem repeats? |
end of the leading strand
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What can the stretch of guanine-rich single-strand DNA form and why does it do this? |
loop structure to protect the end of the chromosome
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What express telomerase? |
germ, stem, and early embryonic cells; not somatic
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What are the three steps of telomere DNA replication? |
Telomerase adds repeats of TTGGGG sequences, which form a hairpin turn. Gap is filled by RNA polymerase, adding on to the 3' end of the hairpin structure. Gap sealed and hairpin cleaved to yield lengthened telomere. |
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Why is telomerase called a reverse transcriptase when it is adding deoxynucleotides? |
It is a RNA-dependent DNA polymerase with its own RNA template complementary to the telemeric repeat sequence so it REVERSE transcribes DNA from the RNA template.
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True or false: nuclease is a reverse transcriptionase. |
false, telomerase is
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What are two complications of short telomeres? |
premature greying bone marrow diseases |
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What does secondary hit plus short telomeres cause? |
idiopathic pulmonary fibrosis (scarring or thickening of the lungs)
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About how many billion base pairs are in the human genome?
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3 billion
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True or false: DNA polymerase III holoenzyme possesses 3' to 5' exonuclease activity for "proofreading". |
true
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What can catalyze both chain elongation and degradation? |
DNA polymerase III
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What recognizes distortion in the DNA caused by incorrectly paired bases? |
DNA polymerase III
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What removes mispaired nucleotide before polymerization continues? |
exonuclease activity of DNA polymerase III
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What would happen if E. coli DNA polymerase III had a mutation which inactivated the 3' to 5' exonuclease activity? |
the error rate of polymerization would increase
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True or false: DNA is the only cellular macromolecule that can be repaired. |
true
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What are seven examples of DNA damage? |
alkylation methylation deamination deletions insertions cross-linking breakage of phosphodiester backbone |
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What recognize mismatched bases and/or modified nucleotides? |
specific repair enzymes
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What may lesions be fixed by? |
direct repair
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does not require breaking the phosphodiester backbone of DNA |
direct repair
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What are three examples of indirect DNA repair? |
mismatch repair base-excision repair nucleotide-excision repair |
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What is common after damage by ultraviolet light? |
dimerization of adjacent pyrimidines in a DNA strand
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What are the main cause of melanomas?
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thymine dimers
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small percentage of skin cancer, but responsible for 75% of skin cancer deaths |
melanoma
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True or false: replication cannot proceed in the presence of thymine dimers. |
true, template strand distorted
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True or false: many organisms can directly repair thymine dimers. |
true, but not humans
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What repairs thymine dimers and how? |
DNA photolyase by photoreactivation
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What in mismatch-repair recognizes the error? |
MutS
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What is mismatch-repair recruits an exonuclease to cleave the DNA? |
MutL
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What in mismatch-repair cleaves the DNA? |
MutH
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How does mismatch-repair machinery recognize the correct base? |
Parent strand may be "marked" by methylation of adenines.
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What synthesizes new strand in mismatch-repair? |
DNA polymerase III
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What combines pieces together in mismatch repair? |
DNA ligase
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What mechanism repairs thymine dimers in humans?
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mismatch-repair
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What does the exonuclease activity of MutH do? |
excises bases
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What is the most common nucleotide deamination? |
hydrolytic deamination of cytosine to uracil
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What does uracil in place of cytosine cause? |
incorporation of an incorrect base during replication
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What hydrolyze base-sugar N-glycosidic bonds? |
DNA glycosylases
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What happens to deaminated bases? |
removed and replaced
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How are deaminated bases removed? |
base-excision repair
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What corrects the most common point mutations in humans? |
base-excision repair
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What in base-excision repair hydrolyzes the glycosidic bond leaving an AP site? |
AlkA glycosylase
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What in base-excision repair detects AP site and nicks the sugar-phosphate backbone? |
AP endonuclease
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What in base-excision repair excises the deoxyribose phosphate? |
deoxyribose phoshpodiesterase
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What in base-excision repair fills the gap?
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DNA polymerase I
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What is base-excision repair seals the nick? |
DNA ligase
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What are the four steps of base-excision repair?
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creation of AP site nick backbone gap filled nick sealed |
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What breaks the glycosidic bond between base and sugar? |
glycosylase
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What breaks the phosphodiester bond between 3' OH and 5' phosphate? |
endonuclease
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What are the three steps of nucleotide excision-repair? |
excision of a 12-nucleotide fragment DNA synthesis by DNA polymerase I joining by DNA ligase |
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What enzyme excises nucleotides in the nucleotide excision-repair pathway?
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UvrABC excinuclease
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What is "exci" Latin for? |
to cut out
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True or false: the nucleotide excision-repair pathway can be used to remove thymine dimers. |
true
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What play a role in base-excision repair? (5) |
glycosylase endonucleases deoxyribose phosphodiesterase DNA polymerase DNA ligase |
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What are often genes that encode DNA-repair proteins? |
tumor suppressor genes
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genetic disorder in DNA nucleotide excision repair genes |
xeroderma pigmentosum (XP)
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What genes are faulty in XP?
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UvrABC genes
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Patients of this disease have extreme sensitivity to the sun, much greater risk of skin cancer. |
XP
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What lack DNA repair systems?
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tumors
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Damaging the DNA with chemicals such as what is a strategy to prevent cancer growth? |
cyclophosphamide cisplatin |
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How are carcinogens detected?
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bacteria (Ames test)
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simple, sensitive means of determining if a chemical is mutagenic |
Ames test
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How does the Ames test work? (3)
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Salmonella bacteria that require histidine because of a mutation in its biosynthetic pathway are treated with the chemicals. Salmonella are plated on a plate lacking histidine. Salmonella growth (appearance of colonies) suggest that the chemical caused a mutation which restored histidine synthesis. |
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exchange or transfer of pieces of DNA from one chromosome to another or within a chromosome
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recombination
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occurs between pieces of DNA that have closely related sequences (e.g. exchange between paired chromosomes during meiosis) |
homologous recombination
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True or false: transposons are examples of homologous recombination. |
false, nonhomologous
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True or false: most recombination events are homologous. |
true
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Why is recombination needed? (3) |
Mutation gives new genetic variation. Parent chromosomes not the same as progeny chromosomes. Important role in repair of DNA. |
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How can recombination be used in repair? |
Severe lesions in DNA can be repaired by strand exchange from intact daughter chromosome to defective daughter.
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What can result when replication machinery falls apart upon encountering a nick? |
double-stranded break
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How are double-strand breaks repaired? |
recombination
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What happens once double-strand break is recognized?
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5' ends are digested and single-strand regions are bound by RAD 51
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What is strand invasion? |
single strand from damaged DNA replaces a strand in undamaged DNA, forming a three-stranded structure
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three-stranded structure formed by strand invasion |
displacement loop
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What are the five steps in double-strand break repair by recombination? |
5' end digested and single-strands bound by RAD 51 strand invasion DNA synthesis second strand invasion, forming Holliday junction cleavage and ligation to yield two intact helices |
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How does DNA synthesis occur in double-strand break repair by recombination? |
using the undamaged DNA as a template
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How is double-strand break repair completed after DNA synthesis? |
second strand invasion occurs forming Holliday junction, then cleavage and ligation
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unique structure in dsDNA repair |
Holliday junction
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What are required for recombination repair of ds breaks in human DNA? |
BRCA1 and BRCA2
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What do BRCA1 and BRCA2 form a complex with? |
RAD51
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What may serve to deliver RAD51 to the site of DNA damage? |
BRCA2
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True or false: conserved C-terminus of BRCA2 appears to bind dsDNA. |
true, and ssDNA
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What is the directionality of DNA polymerase I exonuclease activity?
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3' to 5' and 5' to 3'
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What is the directionality of DNA polymerase III exonuclease activity? |
3' to 5'
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What is the difference between deoxynucleotides and dideoxynucleotides?
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3' position of their sugars
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