Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MBG > Genome integrity > Flashcards

Genome integrity Flashcards

1
Q

six basic forms of DNA repair

A

nucleotide excision repair, base excision repair, recombination (NHEJ), direct reversal repair, mismatch repair, recruit mutagenic pols to get through stalled fork

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what is most frequent form of spontaneous damage?

A

spontaneous depurination of guanine to O6-methylguanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

how to tell which strand is newly synthesized in bacteria?

A

methylation patterns, newly synthesized is unmethylated, recognized by MutSHL proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how do photolyases work?

A

use light energy to become activated, break up thymidine dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

for what are XP genes named?

A

Xeroderma pigmentosum

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what are some ways you can get mispairing?

A

misincorporation, tautomer incorporation, spontaneous hydrolysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is translesion DNA synthesis?

A

process that permits synthesis across unrepaired lesions, carried out by error prone polymerases. Members of polymerase Y family

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is translesion DNA synthesis?

A

process that permits synthesis across unrepaired lesions, carried out by error prone polymerases. Members of polymerase Y family

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

how do you repair double stranded breaks?

A

two broad pathways - non-homologous end joining and homology directed repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

which DSB repair pathway is highly preferred by the cell?

A

NHEJ > HDR, although it is almost always an imprecise join

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

T/F. Homology directed repair has a strong cell cycle dependence

A

True, it is almost completely absent during G1, pops up in S phase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

T/F. NHEJ and Crispr knockouts are related

A

True, you cut with Crispr and rely on the cell to repair the break via NHEJ, which introduces mutations at the site and often causes a frameshift

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are the NHEJ mammalian proteins and what do they do?

A

Ku binds broken ends, recruits DNA-PKcs, Artemis nuclease which trims single stranded tails, DNA ligated by ligase 4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

synthesis dependent strand annealing is the mechanism for what repair pathway?

A

homology-directed repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

strand exchange in homologous recombination is mediated by what types of proteins?

A

specialized recombinases, RecA in Ecoli, Rad51 in eukaryotes, and Dmc1 in meiosis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

how does stretching/underwinding of DNA by specialized recombinases affect melting temperature

A

it lowers it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

how are single stranded tails at DSBs generated?

A

by RecBCD, is a bidirectional helicase that melts/separates DNA strand while the RecB degrades both strands, hits a chi site that induces RecBCD to only chew up one strand, leaving the tail which is the invading entity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

T/F. In ecoli as much as half cells require replication fork restoration in each round of chromosome duplication

A

True, they requires homology directed repair to rescue them

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

holliday junction

A

formed and resolved during homologous recombination, due to reciprocal exchange of strands between homologous DNA duplices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

how can homologous recombination occur?

A

between plasmid, viral and host chromosomes, during mitosis, transformation, and most importantly ) meiosis in eukaryotes, during transduction/conjugation etc in prokaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what are two ways holliday junctions can resolve and what are their consequences?

A

horizontal, no exchange and non-recombinant product

vertical, exchange and recombinant product

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

T/F. Homologous recombination involves formation of a single Holliday junction

A

False, you need a double junction in reality

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

why is sliding of holliday junction energetically possible?

A

because you pair a base for every one you break, driving the reaction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

loss of heterozygosity can be caused by (2)

A

homologous recombination or break induced replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

types of chromosomal rearrangements produced by homologous recombination

A

deletion, unequal crossing over between sister chromatids or homologs, or translocation between non-homologous chromosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

T/F. Mobile genetic elements are found in all 3 domains of life.

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Effects of genetic elements?

A

genome plasticity, impact on structure/function, evolution

28
Q

T/F. Genetic element mobility is always programmed.

A

False, it can be stochastic or programmed

29
Q

How can mobile elements be harnessed for experiments?

A

Examples - Tnseq, gene transfer, **

30
Q

what is transposition?

A

movement of a discrete DNA element into diverse target sites

31
Q

what mediates mobile element movement?

A

proteins specific to that element

32
Q

what are two different ways mobile elements can be integrated into a new site?

A

cut and paste, or copy and paste

33
Q

how do transposable elements create genetic diversity? (4)

A

gene disruption, gene mobilization, gene expression mobilization, substrates for homologous recombination

34
Q

the first active human transposon was discovered at Hopkins, what’s that story?

A

two unrelated boys with hemophilia and no family history, found they had inserted sequences in a non-LTR LINE element

35
Q

T/F. Mutation rate due to transposition varies by organism

A

True

36
Q

what are 4 criteria used to group TEs?

A

element or transposase structure, mechanism of transposition, and effects of transposition on donor site

37
Q

what are the TE groups based on element structure?

A

DNA only, and RNA intermediates

38
Q

DNA only transposons - two groups

A

autonomous, non-autonomous

39
Q

what kinds of DNA seqs do DNA-only transposons act on

A

terminal inverted repeats

40
Q

LTR elements distinctive feature

A

long terminal repeats at ends that support the conversion of RNA copy to cDNA, which is then integrated into the host genome

41
Q

non-LTR elements

A

transpose RNA intermediate, but don’t carry long terminal repeats. LINEs and SINEs. Typically nonfunctioning, although some do still transpose. LINEs 21% human genome, SINEs 13%

42
Q

Differences between LINEs and SINEs (3)

A

abundance, autonomy, and proteins required for transposition

43
Q

why is the collection of genetic material between TEs relevant?

A

a mechanism in bacteria for the integration of sandwiches antibiotic resistance genes to other parts of genome

44
Q

what are the components of composite bacterial transposons?

A

insertion sequences which flank other genes (ex drug resistance)

45
Q

when a cut and paste element is removed from the genome, what happens to the place it was removed from?

A

you have a DSB which needs to be healed

46
Q

DNA-only cut and paste transposition strategy

A

be able to draw loop - remember excision exposes 3’ OH is important, since its attack on DNA region you’re inserting within is catalyzed by a transposase

47
Q

what do all pathways for excision have in common?

A

all create a 3’ OH

48
Q

what are the unique features of nick and paste transposition?

A

result in a co-integrate structure which result in an insertion flanks by transposable elements

49
Q

nick and paste transposition draw

A

draw it

50
Q

resolvase

A

involves in co-integrate resolution, catalyzes recombination between res sites. Cre is a form of resolvase

51
Q

LTR elements two groups

A

LTR retrotransposons (only intracellular) and retroviruses (intracellular and extracellular stages)

52
Q

components of LTR elements

A

GAG nucleic acid binding domain, protease and RT domains, RNase H. Retroviruses have these plus an integrase and envelope component

53
Q

how are cDNA intermediates integrated into their target site?

A

be able to draw/describe**

54
Q

T/F. LTR target joining is chemically identical to that of DNA only elements.

A

True

55
Q

Important shared feature of DNA-only transposases and retroviral integrates

A

Catalytic cores, spatially clustered DDE or DDD which binds Mg2+, essential

56
Q

how many LINE families are in the human genome, and how many are active?

A

3 families, only L1 active, but only a portion of L1

57
Q

transposition of non-LTR elements

A

be able to draw/describe** - looks like a carabiner

58
Q

what are group II mobile introns?

A

catalytic self-splicing RNAs, might be progenitors of our introns - present in bacteria, mitochondria, and chloroplast

59
Q

what are the 3 functions of the single enzyme within group II mobile introns?

A

RT, endonuclease, and maturase function

60
Q

4 features of conservative site specific recombination

A

recombination supported by 10s of bp specific DNA sites, catalyzes by recombinases, and you don’t lose or add nucleotides or involve DNA pols

61
Q

tyrosine recombinases

A

conserved tyrosine residue involved in DNA cleavage, Cre recombinase is the most famous member

62
Q

what is Cre’s native role?

A

resolution of loxP dimers into monomeric genomes

63
Q

features of Cre/Lox

A

inverted recombinase binding elements of 34bp in Lox, holliday junction intermediate

64
Q

Cre-mediated recombination/holliday junction model

A

be able to draw

65
Q

how does the Cre-activated transposon mutagenesis work?

A

sleeping beauty transposase under conditional control by Cre (stop site flanked by loxP needs to be excised by Cre in order to activate transposase), Cre transgene under control of tissue-specific promoter, find with PCR

MBG (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions