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Genetics > Exam 2: Transposable Elements > Flashcards

Exam 2: Transposable Elements Flashcards

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Biology 101 flashcards
1
Q

define transposable element

A

seqs that can move about the genome (mobile DNA seqs found in the genomes of all organisms)

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2
Q

transposition

A

movement of the transposons

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3
Q

transposable element features (2)

A
  1. flanking direct repeats (3-12 bp)

2. terminal inverted repeats

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4
Q

transposons make up at least _ of human DNA

A

45%

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5
Q

transposons often cause _

A

mutations

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6
Q

the short flanking repeat feature of transposons do not _ and are regenerated _

A

do not travel with the transposable element and regenerated at the point of insertion

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7
Q

what kind of cuts are made with transposons

A

staggered cuts are made in the target DNA, leaving short, single stranded pieces of DNA on either side of the transposable element (3’ overhang = sticky end want something to adhere to ie transposon)

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8
Q

what creates the flakinking direct repeats

A

replication of single-stranded DNA

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9
Q

terminal, inverted repeats are how many bp long and found where?

A

9 to 40 bp long and are found at ends of many transposable elements

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10
Q

common features of terminal, inverted repeats (3)

A
  1. seqs are inverted and complimentary on same strand (mirror image)
  2. recognized by enzymes that catalyze transposition
  3. rqd for transposition to take place
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11
Q

flanking direct repeats are generated when a _

A

transposable element inserts into DNA after a staggered cut (the staggered cuts leave short, single-stranded pieces of DNA and replication of this single-stranded DNA creates the flanking direct repeats)

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12
Q

t/f: transposable elements have common characteristics

A

true; generate flanking direct repeats on each side of the point of insertion into target DNA and also possess terminal inverted repeats

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13
Q

how do transposons cause mutations

A

-inserting into another gene
-promoting DNA rearrangements
(insert at random and can land on a valuable gene and either turn off or change the function of the gene in an unpredictable manner)

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14
Q

prok transposons are found in _

A

only DNA transposons are found in bacteria

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15
Q

prok transposons include: (2)

A
  1. insertion seqs

2. composite transposons

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16
Q

what are feats of a insertion seq

A

(proks)

  • common in bacteria but also infect plasmids and viruses
  • carry only the ifo rqd for movement
  • typically include 1/2 genes that encode transposase
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17
Q

what are the feats of composite transposons

A

(proks)

  • complex DNA segment flanked by 2 copies of an insertion seq
  • DNA seqs not directly related to transposition
  • designated by Tn then a number
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18
Q

why is a bacterial insertion sequence seen as autonomous

A

has only enough info to facilitate moving (moves around and amplifies itself)

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19
Q

a bacterial composite transposon retains enough _

A

information to transpose

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20
Q

Tn10

A

bacterial composite transposon that carries the tetracycline resistance seq)

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21
Q

Mu is a transposing _

A

bacteriophage

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22
Q

mechanisms of transposition (3)

A
  • staggered breaks are made in the target DNA
  • transposable element is joined to single-stranded ends of the target DNA
  • DNA is replicated at the single-strand gaps
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23
Q

replicative transposition, why is this process referred to as “copy and paste” transposition?

A

-new copy of the transposable element is introduced at a new site while old copy remains at the original site incr frequency in genome

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24
Q

replicative transposition can be either between _

A

2 different DNA molecules or between two parts of the same DNA molecule

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25
Q

events necessary for co-integrate formation of replicative transposition (4)

A
  • single copy of the transposable element is on one DNA molecule
  • 2 DNA molecules are joined
  • transposable element is replicated
  • results in the production of a cointegrate structure: 2 DNA molecules plus 2 copies of the transposable element
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26
Q

in replicative transposition, crossing over at regions w/in the copies of the transposable element produces

A

2 molecules, each with a single copy of the transposable element = resolution of the cointegrate

27
Q

enzymes involved in replicative transposition (2)

A
  1. transposase

2. resolvase

28
Q

fcn of transposase

A

enzyme that binds to the end of a transposon and catalyzes the movement

29
Q

transposase is encoded by

A

cellular gene or often by transposable element

30
Q

transposase mechanism

A

makes single-strand breaks at each end of the transposable element and on either side of the target seq where insertion occurs

31
Q

fcn of resolvase

A

enzyme which brings about the separation of 2 transposons contained in a cointegrate during the process of replicative transposition

32
Q

resolvase encoded by

A

either by cellular genes or by transposable element (responsible for resolution)

33
Q

non-replicative transposition, why is this process referred to as “cut and paste” transposition?

A

-transposable element is excised from old site and inserted into a new site does not incr number of copies

34
Q

cleavage in non-replicative transposition rqs

A

a transposase enzyme produced BY THE transposable element

35
Q

joining of the transposable element in non-replicative transposition is carried out by

A

normal replication and repair enzymes

36
Q

original site where non-replicative transposon was is typically repaired using

A

homologous template on sister chromatid

37
Q

the 2 groups of euk transponsons

A
  1. those structurally similar to transposable elements found in bacteria (typical end in short inverted repeats and transpose as DNA)
  2. retrotransposons
38
Q

euk transposon similar to transposable elements found in bacteria include:

A

P elements (Drosophila) and Ac and Ds elements (maize)

39
Q

retrotransposons are similar to _ and include _

A

(reverse transcribed)

similar to retroviruses and include Ty elements (yeast) and Copia elements (Drosophila) and Alu elements (humans)

40
Q

retrotransposons are elements that transpose through an _

A

RNA intermediate (in contrast to DNA transposons)

41
Q

retrotransposon mechanism

A
  • RNA is transcribed from an DNA transposable element

- RNA is copied back to another DNA site using reverse transcriptase

42
Q

retrotransposons are only done through _

A

replicative transposition

43
Q

retrotransposons are more common than _

A

DNA transposons in euks

44
Q

SINEs transposon constitute about _ of the human genome and includes _

A

11% of the human genome and includes Alu

*short interspersed nuclear elements)

45
Q

LINEs transposon approximate _ copies in human genome and constitute about _ of the total human DNA

A

approximately 900,000 copies of LINEs in the human genome and constitute about 21% of the total human DNA

46
Q

chromosomal arrangements are consequences of

A

transposed sequences

47
Q

transposition increases

A

chromosomal breaks, which incr variation, and improper healing

48
Q

transposable elements were thought (back then) to be genomic parasites, provide no benefit to the cell, and may be harmful. why is this refuted?

A

DNA replication rqs immense energy and would be selectively advantageous to rid of these elements than to continue replicating their seqs

49
Q

what are the “benefits” of transposable elements NOW? (3)

A
  • may exist bc they generate genetic diversity
  • may be useful to the cell ex co-opted by the vertebrate immune sys as a means of producing antibody diversity
  • relationship w/ telomeres; telomeric structure is reminiscent of transposon structure
50
Q

class I of euk transposable elements

A

retrotransposons

51
Q

structure of class I transposons

A

long terminal direct repeats; short flanking direct repeats at target site

52
Q

genes encoded by class I transposons

A

reverse-transcriptase gene

53
Q

transposition of class I transposon happens via

A

RNA intermediate

54
Q

structure of class II transposons

A

short terminal inverted repeats; short flanking direct repeats at target site

55
Q

genes encoded by class II transposons

A

transposase gene (sometimes others)

56
Q

transposition of class II transposon happens via

A

through DNA (replicative or nonreplicative)

57
Q

who is barbara mcclintock

A

McClintock discovered transposition (transposons) and used it to demonstrate that genes are responsible for turning physical characteristics on or off
transposition resulted in variegated maize kernels

58
Q

variegated corn kernels resulted

A

the excision of DS elements from genes controlling pigment production during development

59
Q

real world example: Rider caused a piece of DNA from chromosome 10 to duplicate and move to chromosome 7. Within this duplicated region is gene IQD12; movement of IQD12 results in

A

IQD12 is overexpressed resulting in elongated tomato

60
Q

real world example: retrotransposons inactivation of factor 8 (blood clotting enzyme)

A

de novo case of hemophilia; a LINE element had become activated and jumped into factor 8 gene and inactivated it causing lack of blood clotting

61
Q

transposons and mammalian uterus/developmental pathways

A

evidence that developmental pathways have been synchronized bc of transposons; transposons in the promoter elements in many of the genes that are important in controlling the development of uterus

62
Q

transposons in evolution: transposons may have coordinated _ responsiveness that led to the evolution of pregnancy in mammals

A

progesterone; progesterone responsive uterus due to transposons
allowing old genes to be expressed in a new location, the uterus, during pregnancy
“genes need some way of knowing when and where to be expressed”

63
Q

retrosponsons in variation and disease

A

retrotransposons have real world consequences of jumping into a gene and causing clinical phenotypes (pose a threat to individuals who have mobile genetic elements)

64
Q

transposons and p53

A

half of all cancers have p53 turned off
p53 is a tumor suppressor and perhaps suppresses transposon activity. when p53 is turned off, you get a transposon storm so now these jumping genes are jumping around genome; can progress cancer (hyper-growth) by finding a cell that can handle them

Genetics (37 decks)

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