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Genetics > Exam 2: Transposable Elements > Flashcards

Exam 2: Transposable Elements 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
events necessary for co-integrate formation of replicative transposition (4)
- 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
26
in replicative transposition, crossing over at regions w/in the copies of the transposable element produces
2 molecules, each with a single copy of the transposable element = resolution of the cointegrate
27
enzymes involved in replicative transposition (2)
1. transposase | 2. resolvase
28
fcn of transposase
enzyme that binds to the end of a transposon and catalyzes the movement
29
transposase is encoded by
cellular gene or often by transposable element
30
transposase mechanism
makes single-strand breaks at each end of the transposable element and on either side of the target seq where insertion occurs
31
fcn of resolvase
enzyme which brings about the separation of 2 transposons contained in a cointegrate during the process of replicative transposition
32
resolvase encoded by
either by cellular genes or by transposable element (responsible for resolution)
33
non-replicative transposition, why is this process referred to as "cut and paste" transposition?
-transposable element is excised from old site and inserted into a new site *does not incr number of copies*
34
cleavage in non-replicative transposition rqs
a transposase enzyme produced BY THE transposable element
35
joining of the transposable element in non-replicative transposition is carried out by
normal replication and repair enzymes
36
original site where non-replicative transposon was is typically repaired using
homologous template on sister chromatid
37
the 2 groups of euk transponsons
1. those structurally similar to transposable elements found in bacteria (typical end in short inverted repeats and transpose as DNA) 2. retrotransposons
38
euk transposon similar to transposable elements found in bacteria include:
P elements (Drosophila) and Ac and Ds elements (maize)
39
retrotransposons are similar to _ and include _
(reverse transcribed) | similar to retroviruses and include Ty elements (yeast) and Copia elements (Drosophila) and Alu elements (humans)
40
retrotransposons are elements that transpose through an _
RNA intermediate (in contrast to DNA transposons)
41
retrotransposon mechanism
- RNA is transcribed from an DNA transposable element | - RNA is copied back to another DNA site using reverse transcriptase
42
retrotransposons are only done through _
replicative transposition
43
retrotransposons are more common than _
DNA transposons in euks
44
SINEs transposon constitute about _ of the human genome and includes _
11% of the human genome and includes Alu | *short interspersed nuclear elements)
45
LINEs transposon approximate _ copies in human genome and constitute about _ of the total human DNA
approximately 900,000 copies of LINEs in the human genome and constitute about 21% of the total human DNA
46
chromosomal arrangements are consequences of
transposed sequences
47
transposition increases
chromosomal breaks, which incr variation, and improper healing
48
transposable elements were thought (back then) to be genomic parasites, provide no benefit to the cell, and may be harmful. why is this refuted?
DNA replication rqs immense energy and would be selectively advantageous to rid of these elements than to continue replicating their seqs
49
what are the "benefits" of transposable elements NOW? (3)
- 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
class I of euk transposable elements
retrotransposons
51
structure of class I transposons
long terminal direct repeats; short flanking direct repeats at target site
52
genes encoded by class I transposons
reverse-transcriptase gene
53
transposition of class I transposon happens via
RNA intermediate
54
structure of class II transposons
short terminal inverted repeats; short flanking direct repeats at target site
55
genes encoded by class II transposons
transposase gene (sometimes others)
56
transposition of class II transposon happens via
through DNA (replicative or nonreplicative)
57
who is barbara mcclintock
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
variegated corn kernels resulted
the excision of DS elements from genes controlling pigment production during development
59
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
IQD12 is overexpressed resulting in elongated tomato
60
real world example: retrotransposons inactivation of factor 8 (blood clotting enzyme)
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
transposons and mammalian uterus/developmental pathways
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
transposons in evolution: transposons may have coordinated _ responsiveness that led to the evolution of pregnancy in mammals
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
retrosponsons in variation and disease
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
transposons and p53
*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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