Molecular Biology - Ch. 10 (The Mutability And Repair Of Dna)

Front 1

What are transition and transversion mutations?

Back 1

Transition = purine-to-purine or pyrimidine-to-pyrimidine

Transversion = purine-to-pyrimidine & vice versa

Front 2

Sets of mutation-prone sequences with simple di-, tri-, or tetra-nucleotide sequences are known as _______ _______.

Back 2

DNA microsatellites
(e.g. CA)

Front 3

The _______ removes wrongly incorporated nucleotides through a proofreading mechanism.

Back 3

3'-5' exonuclease component of the replisome

Front 4

The DNA _______ _______ _______ increases the accuracy of DNA synthesis by an additional two to three orders of magnitude.

Back 4

mismatch repair system

Front 5

In _______, mismatches are detected by the _______ mismatch repair protein MutS.

Back 5

E. coli, dimerized

Front 6

How does MutS recognize nucleotide mismatches?

Back 6

By the distortion they cause in the DNA backbone.

Front 7

After binding to the mismatched DNA, MutS...

Back 7

...exhibits a conformational change, kinking the DNA and recruiting MutL to the DNA strand via ATPase activity.

Front 8

What is the role of MutH?

Back 8

MutH is an endonuclease activated by MutL that excises DNA during mismatch repair.

Front 9

After nicking during mismatch repair...

Back 9

...a helicase (UvrD) and one of three nucleases digest the mutated strand; DNA polymerase and ligase repair the gap.

Front 10

How does E. coli distinguish the mutated vs. the original strand during DNA mismatch repair?

Back 10

The template strand is methylated by Dam methylase.

Front 11

Dam methylase methylates _______ residues in the sequence 5'-_______-3'.

Back 11

adenine (A), 5'-GATC-3'

Front 12

In E. coli, how long is DNA hemimethylated immediately following DNA replication?

Back 12

A few minutes (until Dam methylase catches up). During this time, mismatch repair occurs.

Front 13

_______ protein binds at such hemimethylated sites, but remains latent until bound by the _______ complex.

Back 13

MutH, MutS-MutL

Front 14

In E. coli DNA is methylated every few _______ base pairs.

Back 14

hundred

Front 15

During mismatch repair in E. coli,
if the DNA is nicked on the 5' side of the mismatch, exonucleases _______ or _______ are recruited.
If the DNA is nicked on the 3' side of the mismatch, ________ is recruited.

Back 15

VII or RecJ (5' → 3')
Exonuclease I (3' → 5')

Front 16

The most frequent and important kind of hydrolytic damage to DNA is...

Back 16

...the deamination of cytosine to form uracil.

Front 17

What forms when adenine and guanine undergo spontaneous deamination, respectively?

Back 17

adenine → hypoxanthine (bonds w/ C)
guanine → xanthine (bonds to C w/ only 2 H-bonds)

Front 18

What is depurination?

Back 18

The spontaneous hydrolysis of the N-glycosyl linkage, producing an abasic site

Front 19

This nucleic acid forms hotspots for spontaneous mutations in vertebrate DNA:

Back 19

5-methylcytosine

Front 20

This modified base plays a role in transcriptional silencing:

Back 20

5-methylcytosine.

Front 21

One of the most vulnerable sites of alkylation on a nitrogenous base is...

Back 21

...the oxygen attached to C-6 of guanine

Front 22

O6-methylguanine often mispairs with _______.

Back 22

thymine

Front 23

Guanine, when oxidized to _______ (____), can base-pair with _______ or _______.

Back 23

7,8-dihydro-8-oxoguanine (oxoG), cytosine or adenine.

Front 24

The most common carcinogenic mutation is...

Back 24

...the G:C to T:A conversion (e.g. via guanine oxidation to oxoG)

Front 25

Radiation with a wavelength of ~____ nm forms thymine dimers

Back 25

260 nm (UV)

Front 26

The thymine dimer is comprised of...

Back 26

...a cyclobutane ring generated by links between carbon atoms 5 and 6 of adjacent thymines.

Front 27

Under UV radiation, when a thymine is adjacent to a cytosine...

Back 27

...they attach between the C-4 of cytosine and the C-6 of thymine, forming a thymine-cytosine adduct.

Front 28

These mutagens cause double-strand breaks in DNA.

Back 28

γ-radiation and X-rays (ionizing radiation)
(AKA clastogenic agents)

Front 29

Compounds that substitute for normal bases are called _______.

Back 29

base analogs.

Front 30

One of the most mutagenic base analogs is _______.

Back 30

5-bromouracil

Front 31

What are 3 examples of intercalating agents?

Back 31

Proflavin, acridine, and ethidium.

Front 32

What kinds of mutations do intercalating agents like ethidium cause?

Back 32

Addition or deletion of a single or a few DNA base pairs.

Front 33

What process is involved with DNA excision repair?

Back 33

Removal of a damaged nucleotide or stretch of damaged DNA (lesion).

Front 34

What is another name for double-strand break repair?

Back 34

Recombinational repair.

Front 35

This DNA repair mechanism does not depend on base-pairing.

Back 35

Translesion DNA synthesis
(a special polymerase continues DNA replication across lesions or apurinic sites)

Front 36

What are two examples of direct reversal of DNA damage?

Back 36

1. Photoreactivation (via photolyase on T-T dimers)
2. Methyltransferase activity on O6-methylguanine

Front 37

In base excision repair, an enzyme called a _______ recognizes and removes the damaged base by hydrolyzing the glycosidic bond.

Back 37

<img src="https://lh5.googleusercontent.com/-MazIu_3lkC8/VRRuF1jNNAI/AAAAAAAAF3s/36vDFH8khIM/s1024/Base%2520Excision%2520Repair.png"/>

Front 38

DNA glycosylases are _______.

Back 38

lesion-specific.

Front 39

How do glycosylases "scan" for specific damaged bases?

Back 39

Through base flipping.

Front 40

What do the fail-safe glycosylases do?

Back 40

Removes the incorrect adenine base-paired to oxoG.
Removes the incorrect thymine base-paired to G.
(remember 5-methylcytosine → thymine)

Front 41

Nucleotide excision repair is selective to...

Back 41

...distortions to the shape of the DNA double-helix.

Front 42

Nucleotide excision repair is largely accomplished by these four proteins:

Back 42

UvrA, UvrB, UvrC, and UvrD

Front 43

Please list the functions of each of the following:
UvrA
UvrB
UvrC
UvrD

Back 43

A) Recognizes lesion and recruits UvrB to site.
B) Melts DNA surrounding the lesion; recruits UvrC
C) Cuts DNA 8 nucleotides from 5' side and 4-5 nucleotides from 3' side of lesion
D) Provides helicase activity to access exposed single strand

Front 44

Some of the proteins involved with nucleotide excision repair are denoted with a(n) _______.

Back 44

XP (Xeroderma pigmentosum)

(XPA, XPC, XPD, XPF, XPG)

Front 45

What is transcription-coupled repair?

Back 45

The rescuing of a stalled RNA polymerase by nucleotide excision repair proteins on a lesion in the DNA structure.

Front 46

TFIIH is responsible for these two separate functions:

Back 46

1) Its strand-separating helicases XPA and XPD to melt DNA lesions
2) Its helicase activity during initiation of transcription

Front 47

Genetic information from _______ _______ is used during double-strand break (DSB) repair.

Back 47

sister chromatids

Front 48

_______ is a backup DSB repair system in yeast, but in higher cells, it is widely used.

Back 48

Nonhomologous end joining (NHEJ)

Front 49

These two polypeptides are the most fundamental components of NHEJ:

Back 49

Ku70 and Ku80

Front 50

Ku70 and Ku80 form a heterodimer with _______, forming the _______ complex

Back 50

DNA-PKcs, Artemis

Front 51

What is Artemis?

Back 51

Both a 5' to 3' exonuclease and a latent endonuclease that is activated by phosphorylation by DNA-PKcs.

Front 52

During NHEJ, ligation is carried out by _______ in a complex with _______ and _______.

Back 52

Ligase IV, XRCC4, Cernunnos-XLF

Front 53

This organism relies on NHEJ rather than the DSB repair pathway because it has only one chromosome.

Back 53

Spores of B. subtilis.

Front 54

Translesion synthesis in E. coli is carried out by a complex of the proteins _______ and _______.

Back 54

UmuC and UmuD'.

Front 55

The genes encoding the translesion polymerase are expressed as part of a pathway known as the _______.

Back 55

SOS response.

Front 56

What does ROS stand for?

Back 56

Reactive Oxygen Species

Front 57

What does DNA pol H (pol η) do?

Back 57

Conducts translesion repair synthesis.
Synthesizes two adenines across from a thymine dimer.

Front 58

These three types of lesions are corrected by DSB repair:

Back 58

Double-strand breaks (mainly)
Single-strand nicks (sometimes)
Thymine dimers (sometimes)

Front 59

DSB repair occurs between _______ chromatids during _______ phases of _______.
DSB recombination repair occurs between _______ chromatids during _______ phase of _______.

Back 59

sister chromatids, S and G2, mitosis
non-sister chromatids, prophase (after G2), meiosis