Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
59 Cards in this Set
- Front
- Back
What are transition and transversion mutations? |
Transition = purine-to-purine or pyrimidine-to-pyrimidine |
|
Sets of mutation-prone sequences with simple di-, tri-, or tetra-nucleotide sequences are known as _______ _______. |
DNA microsatellites |
|
The _______ removes wrongly incorporated nucleotides through a proofreading mechanism. |
3'-5' exonuclease component of the replisome |
|
The DNA _______ _______ _______ increases the accuracy of DNA synthesis by an additional two to three orders of magnitude. |
mismatch repair system |
|
In _______, mismatches are detected by the _______ mismatch repair protein MutS. |
E. coli, dimerized |
|
How does MutS recognize nucleotide mismatches? |
By the distortion they cause in the DNA backbone. |
|
After binding to the mismatched DNA, MutS... |
...exhibits a conformational change, kinking the DNA and recruiting MutL to the DNA strand via ATPase activity. |
|
What is the role of MutH? |
MutH is an endonuclease activated by MutL that excises DNA during mismatch repair. |
|
After nicking during mismatch repair... |
...a helicase (UvrD) and one of three nucleases digest the mutated strand; DNA polymerase and ligase repair the gap. |
|
How does E. coli distinguish the mutated vs. the original strand during DNA mismatch repair? |
The template strand is methylated by Dam methylase. |
|
Dam methylase methylates _______ residues in the sequence 5'-_______-3'. |
adenine (A), 5'-GATC-3' |
|
In E. coli, how long is DNA hemimethylated immediately following DNA replication? |
A few minutes (until Dam methylase catches up). During this time, mismatch repair occurs. |
|
_______ protein binds at such hemimethylated sites, but remains latent until bound by the _______ complex. |
MutH, MutS-MutL |
|
In E. coli DNA is methylated every few _______ base pairs. |
hundred |
|
During mismatch repair in E. coli, |
VII or RecJ (5' → 3') |
|
The most frequent and important kind of hydrolytic damage to DNA is... |
...the deamination of cytosine to form uracil. |
|
What forms when adenine and guanine undergo spontaneous deamination, respectively? |
adenine → hypoxanthine (bonds w/ C) |
|
What is depurination? |
The spontaneous hydrolysis of the N-glycosyl linkage, producing an abasic site |
|
This nucleic acid forms hotspots for spontaneous mutations in vertebrate DNA: |
5-methylcytosine |
|
This modified base plays a role in transcriptional silencing: |
5-methylcytosine. |
|
One of the most vulnerable sites of alkylation on a nitrogenous base is... |
...the oxygen attached to C-6 of guanine |
|
O6-methylguanine often mispairs with _______. |
thymine |
|
Guanine, when oxidized to _______ (____), can base-pair with _______ or _______. |
7,8-dihydro-8-oxoguanine (oxoG), cytosine or adenine. |
|
The most common carcinogenic mutation is... |
...the G:C to T:A conversion (e.g. via guanine oxidation to oxoG) |
|
Radiation with a wavelength of ~____ nm forms thymine dimers |
260 nm (UV) |
|
The thymine dimer is comprised of... |
...a cyclobutane ring generated by links between carbon atoms 5 and 6 of adjacent thymines. |
|
Under UV radiation, when a thymine is adjacent to a cytosine... |
...they attach between the C-4 of cytosine and the C-6 of thymine, forming a thymine-cytosine adduct. |
|
These mutagens cause double-strand breaks in DNA. |
γ-radiation and X-rays (ionizing radiation) |
|
Compounds that substitute for normal bases are called _______. |
base analogs. |
|
One of the most mutagenic base analogs is _______. |
5-bromouracil |
|
What are 3 examples of intercalating agents? |
Proflavin, acridine, and ethidium. |
|
What kinds of mutations do intercalating agents like ethidium cause? |
Addition or deletion of a single or a few DNA base pairs. |
|
What process is involved with DNA excision repair? |
Removal of a damaged nucleotide or stretch of damaged DNA (lesion). |
|
What is another name for double-strand break repair? |
Recombinational repair. |
|
This DNA repair mechanism does not depend on base-pairing. |
Translesion DNA synthesis |
|
What are two examples of direct reversal of DNA damage? |
1. Photoreactivation (via photolyase on T-T dimers) |
|
In base excision repair, an enzyme called a _______ recognizes and removes the damaged base by hydrolyzing the glycosidic bond. |
<img src="https://lh5.googleusercontent.com/-MazIu_3lkC8/VRRuF1jNNAI/AAAAAAAAF3s/36vDFH8khIM/s1024/Base%2520Excision%2520Repair.png"/> |
|
DNA glycosylases are _______. |
lesion-specific. |
|
How do glycosylases "scan" for specific damaged bases? |
Through base flipping. |
|
What do the fail-safe glycosylases do? |
Removes the incorrect adenine base-paired to oxoG. |
|
Nucleotide excision repair is selective to... |
...distortions to the shape of the DNA double-helix. |
|
Nucleotide excision repair is largely accomplished by these four proteins: |
UvrA, UvrB, UvrC, and UvrD |
|
Please list the functions of each of the following: |
A) Recognizes lesion and recruits UvrB to site. |
|
Some of the proteins involved with nucleotide excision repair are denoted with a(n) _______. |
XP (Xeroderma pigmentosum) |
|
What is transcription-coupled repair? |
The rescuing of a stalled RNA polymerase by nucleotide excision repair proteins on a lesion in the DNA structure. |
|
TFIIH is responsible for these two separate functions: |
1) Its strand-separating helicases XPA and XPD to melt DNA lesions |
|
Genetic information from _______ _______ is used during double-strand break (DSB) repair. |
sister chromatids |
|
_______ is a backup DSB repair system in yeast, but in higher cells, it is widely used. |
Nonhomologous end joining (NHEJ) |
|
These two polypeptides are the most fundamental components of NHEJ: |
Ku70 and Ku80 |
|
Ku70 and Ku80 form a heterodimer with _______, forming the _______ complex |
DNA-PKcs, Artemis |
|
What is Artemis? |
Both a 5' to 3' exonuclease and a latent endonuclease that is activated by phosphorylation by DNA-PKcs. |
|
During NHEJ, ligation is carried out by _______ in a complex with _______ and _______. |
Ligase IV, XRCC4, Cernunnos-XLF |
|
This organism relies on NHEJ rather than the DSB repair pathway because it has only one chromosome. |
Spores of B. subtilis. |
|
Translesion synthesis in E. coli is carried out by a complex of the proteins _______ and _______. |
UmuC and UmuD'. |
|
The genes encoding the translesion polymerase are expressed as part of a pathway known as the _______. |
SOS response. |
|
What does ROS stand for? |
Reactive Oxygen Species |
|
What does DNA pol H (pol η) do? |
Conducts translesion repair synthesis. |
|
These three types of lesions are corrected by DSB repair: |
Double-strand breaks (mainly) |
|
DSB repair occurs between _______ chromatids during _______ phases of _______. |
sister chromatids, S and G2, mitosis |