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Molecular Biology > DNA replication, repair and recombination 3 (lecture 5) > Flashcards

DNA replication, repair and recombination 3 (lecture 5) Flashcards

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1
Q

Can crossing over and gene conversion occur in the same chromosome

A

yes

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2
Q

Meiotic recombination occurs with paired ____ and _____ chromosomes

A

maternal and paternal homologous

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3
Q

Meiotic recombination begins with a _______ by enzymes ____ and ____

A

double strand break, Spo11 (yeast), which breaks the ends, and Mre11 which process the ends

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4
Q

DNA intermediate containing four DNA strands from two different helices

A

Holliday junction

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5
Q

Homologous recombination is a means to generate DNA molecules of ____ sequence

A

novel

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6
Q

Holliday junctions are present only

A

transiently

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7
Q

Resolution of Holliday junctions is when strands of the helices are cleaved by ______

A

endonuclease (RuvC)

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8
Q

Resolution of Holliday junctions results in 2 outcomes

A
  • Crossing over

- Gene conversion

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9
Q

90% of Holliday junctions in humans resolve in

A

gene conversion

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10
Q

_____ are rare events with only 1-2 per chromosome

A

Crossing over

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11
Q

If both strands in each holliday junction are cut in the same way, they will separate with

A

minimal exchange of sequences

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12
Q

If both strands in each Holliday junction are cut in opposite directions,

A

portions of each chromosome upstream and downstream are swapped, yielding crossover

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13
Q

in branch migration, base pairs are continually ____ and ___ as the branch point moves

A

broken and reformed

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14
Q

Once strand invasion occurs, the point of exchange can move through _____

A

branch migration

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15
Q

in branch migration ____ region of one single strand displaces a ____ region on the other

A

unpaired, paired

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16
Q

Branch migration happens _____ in both directions or can be catalyzed by ____ to move in one direction

A

spontaneously, special helicase (use of helicase requires energy)

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17
Q

Meiotic recombination results in regions of _____ DNA

A

heteroduplex

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18
Q

what is a strand with the DNA sequence of the paternal homolog is base-paired with a strand from the maternal homolog is called

A

Heteroduplex region

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19
Q

In meiosis, each parent should make _____ contribution to the genetic material of the offspring. This may not be the case due to ____

A

an equal, gene conversion

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20
Q

Divergence form the expected distribution of alleles during meiosis

A

gene conversion

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21
Q

How do gene conversions occur

A
  • DNA synthesis during homologous recombination
  • Repair of mismatches in regions of heteroduplex DNA. As a consequence of repair, one allele is lost, the other duplicated, resulting in “conversion” of one to the other
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22
Q

What are the two types of homologous recombination that do not require substantial regions of DNA homology

A
  • Transpositional recombination

- Conservative-site-specific recombination

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23
Q

Transpositional Recombination

A
  • DNA-only transposons
  • Retroviral-like retrotransposons
  • Nonretroviral retrotransposons
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24
Q

Conservative site- specific recombination

A
  • Bacteriophage lambda
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25
Q

Mobile genetic elements

A

Transposons

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26
Q

Transposable elements are also called

A
  • Selfish DNA

- Jumping genes

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27
Q

specialized segments of DNA that move form one position in the genome to another

A

Transposons

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28
Q

Transposons range in size form ____ to ______ of nucleotide pairs

A

100s to tens of thousands

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29
Q

Each transposon has ____ set of genes and encode enzymes that catalyzes ______ of transposon

A

unique, movement

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30
Q

Transposons can provide benefits to the cell such as in ____ in bacteria

A

antibiotic resistance

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31
Q

Transposons produce ______ variation by occasionally rearranging neighboring ___ of host and can induce _________

A

genetic, DNA, Spontaneous mutations

32
Q

Do Transposons require sequence homology

A

No!!! They can insert anywhere in the genome

33
Q

Transposons move ______. one in every ____ cell divisions in bacteria

A

infrequently. 10^5

34
Q

Enzyme encoded by the transposon itself

A

Transposase

35
Q

Functions of Transposase

A
  • Acts on specific DNA sequence on each end of the transposon
  • Allows insertion into a target DNA site
36
Q

Transposons are grouped into ___ large classes: which are?

A
  • 3
  • DNA-only transposons
  • Retroviral-like retrotransposons
  • nonretroviral retrotransposons
37
Q

What is the specialized enzyme required for the movement of DNA-only transposons

A

Transposase

38
Q

What is the specialized enzymes required for the movement of Retroviral-like retrotransposons

A

Reverse transcriptase and Integrase

39
Q

What is the specialized enzymes required for the movement of nonretroviral retrotransposons

A

Reverse transcriptase and endonuclease

40
Q

Mode of movement for DNA-only transposons

A

moves as DNA, either by cut-and-paste or replicative pathways

41
Q

Mode of movement for retroviral-like retrotransposons

A

Moves via an RNA intermediate whose production is driven by a promotor in the LTR

42
Q

nonretroviral retrotransposons mode of movement

A

moves via an RNA intermediate that is often synthesized from a neighboring promotor

43
Q

DNA only transposons exist only as ____ in their movement

A

DNA

44
Q

DNA only transposons are predominate in _____ and are largely responsible for

A

bacteria, and are largely responsible for the spread of antibiotic resistance

45
Q

DNA only transposons use ________ or ______ forms of movement

A
  • cut-and-paste transposition

- replicative transposition

46
Q

DNA only transposons contain

A
  • gene encoding transposase

- sequences recognized by the enzyme necessary for movement

47
Q

explain cut-and-paste transposition

A
  • begins when transposase brings the two inverted DNA sequences of the DNA-only transposon together forming a DNA loop
  • insertion into the target chromosome, also catalyzed by the transposase, occurs at a random site through the creation of staggered breaks in the target chromosome
  • following the transposition reaction, the single-stranded gaps created by the staggered breaks are repaired by DNA polymerase and ligase
  • the insertion site is marked by a short direct repeat of the target DNA sequence
  • The break in the donor chromosome is repaired (note that this often alters the DNA sequence causing a mutation at the original site of the excised transposable element
48
Q

DNA-only transposons can be recognized in chromosomes by the

A

inverted repeat DNA sequences present at their ends

49
Q

Two transposase molecules come together forming a loop juxtaposing two ends of element this is referred to as the

A

Transpososome

50
Q

After the transpososome is formed transposase introduces cuts at base of loop then_____ and ____

A

removes element and forms central intermediate

51
Q

The central intermediate of DNA only transposons catalyzes ________ creating a ______

A

direct attack on random site of target DNA, create a staggered break (breaks 2 phosphodiester bonds, creates new ones as it joins DNA together

52
Q

Staggered breaks produce gaps that are repaired by _____ and sealed by ____. Resulting in

A

DNA polymerase and sealed by ligase. Resulting in duplication of the target DNA’s insertion site

53
Q

The hole in the donor chromosome after DNA only transposon is removed is repaired by

A
  • double-stranded break repair, if chromosome has just been replicated and there is an identical copy thus Transposon will be restored
  • homologous recombination using homologous chromosome (transposon will not be restored)
  • Nonhomologous end joining (will produce a mutation at the break site)
54
Q

Retrovirus-like transposons resemble a retrovirus but lack a

A

coat

55
Q

Retrovirus-like transposons move in and out of chromosome the same way but

A

they are unable to leave the resident cell

56
Q

what is the first step in retroviral-like retrotransposons transposition

A

is the transcription of the entire transposon, producing an RNA copy of the element that is typically serval thousand nucleotides long.

57
Q

What is the second step in retroviral-like retrotransposons transposition

A

The translation of the RNA transcript as messenger RNA by the host cell, encodes a reverse transcriptase enzyme

58
Q

What is the third step in retroviral-like retrotransposons transposition

A

Reverse transcriptase makes a double strand DNA copy of the RNA molecule via an RNA-DNA hybrid intermediate. This double strand DNA can then integrates onto a site of the chromosome using the enzyme integrase which is encoded by the element as well

59
Q

The entire Retrovirus-like transposon is transcribed by the

A

host

60
Q

Explain how integrase integrates retrovirus or retroviral-like transposon

A
  • integrase cuts on strand at each end of viral sequence
  • Each exposed 3’ OH end attacks a phosphodiester bond of target DNA
  • This inserts viral DNA into target, leaving gaps to be filled/ligated
  • leaves short repeats on each side of integrated DNA segment
61
Q

Nonretroviral transposons make up ____% of human genome

A

40%

62
Q

Nonretroviral transposons comprise a large portion of

A

our genome

63
Q

a significant fraction of many vertebrate chromosome is made up of repeated DNA sequences. In human chromosomes, these repeats are mostly mutated and truncated versions of _______

A

nonretroviral retrotransposons

64
Q

Relatively recent movements of _____ (a nonretroviral retrotransposons) have been identified, some of which result in human disease, for example a particular type of hemophilia results from an L1 insertion into the gene encoding the blood-clotting protein Factor VIII

A

L1 element

65
Q

Most nonretroviral Transposons are ____ but few retain the ability to ____

A

immobile, move

66
Q

Nonretroviral transposons require ____ and ____ to move

A

endonuclease and reverse transcriptase

67
Q

Nonretroviral transposons _____ the endonuclease and reverse transcriptase they need to move instead they

A

do not encode thrown enzymes

instead they use enzymes form other transposons

68
Q

Explain Transposition by nonretroviral retrotransposons

A
  • endonuclease and reverse transcriptase bind to L1 RNA
  • Endonuclease nicks the target DNA at insertion point
    • this releases 3’OH to serve as primer in reverse transcription step
  • Single-Stranded DNA copy of L1 directly linked to target DNA
  • Insertion of double-stranded DNA copy of L1 at target site
69
Q

Conservative site specific recombination mediates rearrangements of other types of ______

A

mobile DNA elements (not transposons)

70
Q

Conservative site-specific recombination can _____ rearrange DNA

A

Reversibly

71
Q

in conservative site-specific recombination breakage and joining occur at ____ special sites, ____ on each participating DNA molecule

A

2 , 1

72
Q

Depending on position and relative orientations of recombination sites Conservative site-specific recombination can lead to

A
  • DNA integration
  • DNA excision
  • DNA inversion
73
Q

Conservative site-specific recombination differs from transposition by

A
  • need special sites on each DNA that serve as recognition sites for recombinase, which will catalyze there rearrangement (only transposon sequence is required for transposition and they can use any sequence)
  • Recombinases resemble topoisomerases in the sense that they form transient high energy covalent bonds and use this energy to complete DNA rearrangement (No covalent protein/DNA intermediate in transposition and Gaps must be filled by DNA polymerase and ligase)
74
Q

______ recombination is often used by DNA viruses to move their genomes in and out of the genomes of their host cells ex. ____

A

conservative site-specific recombination. Ex. Bacteriophage lambda

75
Q

Conservative site specific recombination can produces two types of DNA rearrangements

A
  • if sites are in same orientation, DNA sequence can be integrated or excised
  • If sites are inverted in orientation, DNA sequence is inverted instead of excised
76
Q

salmonella uses conservative site-specific recombination to control the expression of ______ genes

A

flagellin

Molecular Biology (14 decks)

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