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LIFESCI 2G03 > Module 9 - Part 2 > Flashcards

Module 9 - Part 2 Flashcards

1
Q

Transposable Elements

A

fragment of DNA that can be excised and then moved elsewhere

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2
Q

Genetic elements that move are called: (5)

A
  1. controlling elements
  2. jumping genes
  3. mobile genes
  4. mobile genetic elements
  5. transposons
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3
Q

Barbara McClintock (1902-1992)

A
  • discovered TEs in 1940/50s
  • ignored for 20 years because…
    1. it was too different
    2. didn’t fit w the accepted understanding of the genome
    3. other scientists didn’t understand
    4. it was the 1950s and she was a women
  • her work eventually recognized w a Nobel prize in physiology in 1983
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4
Q

2 genetic factors that are required for chromosome breakage (in maize):

A
  1. dissociation factors (DS): always at site of breakage (cis factor)
  2. activator factor (Ac): at an unlinked locus, but was required to activate or cause breakage (trans factor)
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5
Q

Ac factor is considered

A

mobile (& resides in different location in different individual plants)

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6
Q

Abrupt changes associated with the activity of Ac and DS factors were given the name

A

controlling elements

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7
Q

Transposase

A

an enzyme that has a “cut and paste” mechanism that removes the DNA element from one locus and inserts it into another

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8
Q

Mechanism of transposition (3 steps)

A
  1. transpose makes a staggered cut in the host DNA molecule (creates overhang)
  2. transposon inserts between ends of cut
  3. host DNA repair machinery joins host DNA & transposon at each end using overhangs as templates
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9
Q

Ds is _______ in the absence of a func. Ac

A

stable

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10
Q

Ac is….

A

unstable

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11
Q

Ds is a _________ variant of Ac

A

deletion

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12
Q

Ac

A

autonomous element (encodes all info necessary for movement)
- transposase & IR = inverted repeats

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13
Q

Ds

A

non-autonomous element (requires a related autonomous element to move)
- no transposase

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14
Q

Class 1: retrotransposons

A
  • related to retrovirus
  • use an RNA intermediate
  • they encode a reverse transcriptase that makes a DNA copy of the RNA that can be encoded into the genome
  • found in eukaryotes only
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15
Q

Class 2: DNA transposons

A
  • DNA element that moves directly from one position in genome to another (cut & paste)
    or may be copied & moved as a DNA molecule
  • found in both eukaryotes and prokaryotes
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16
Q

Common characteristics of TEs

A
  • have direct repeats - short repeated seq flanking the element (arise by transposition)
  • carry a gene coding for an enzyme that catalyzes transposition
    1. transposase: elements use DNA intermediate
    2. reverse transcriptase: elements use RNA intermediate
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17
Q

Retrovirus

A

single-stranded virus, uses a double stranded DNA intermediate for replication

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18
Q

Retroviral genes

A

gag, pol, env
genes encoding proteins required for transposition

19
Q

Gag

A

maturation of viral RNA genome

20
Q

Pol

A

reverse transcriptase + integrase

21
Q

Env

A

structural protein surrounding virus

22
Q

LTR

A

long terminal repeat; recognition site for transposition

23
Q

How do TEs cause mutations

A
  • insert themselves in coding regions & disrupt protein func
  • when DNA transposons move = cause a deletion or DSB
24
Q

TEs can ______ gene expression by influencing….

A

increase, neighbouring promotor or replacing nascent promotor

25
Q

______ can bind to TEs and can _______

A

insulators, block enhancer-promotor communication
- repress gene expression

26
Q

TEs can turn gene expression ____ by blocking ________

A

on, inhibitory sequences (like repressive chromatin)

27
Q

Maize

A

49-78% of genome is made up of retrotransposons

28
Q

Wheat

A

90% of genome consists of repeated sequences
68% of TEs

29
Q

Mammel

A

45-48% genome comprised of transposons or remnants of transposons
>45% genome made up of retrotransposons
DNA transposons accounts for 2-3%

30
Q

SINEs

A

Short interspaced nuclear elements
- Alu - 300bp

31
Q

LINEs

A

long interspaced nuclear elements (avg. length 6.5kb retrotransposons

32
Q

Minisatellites

A

aka VNTRs
- regions 10-100bp long, repeated variably

33
Q

Microsatellites

A

aka STRP
- regions 2-5bp repeated 10-30X

34
Q

Alu elements

A
  • found dispersed throughout the human genome
  • > 11 mil elements in human genome (approx 11% of genome)
35
Q

TEs impact on human genome

A
  • increase metabolic burned on the cell (replication)
  • leave a copy behind after transposition, therefore increase in number
  • increase genome diversity
36
Q

Where do TEs insert

A

mostly 5’ end of gene (regulatory region)

37
Q

Are TEs mobile

A

most are not, maybe 0.05% can

38
Q

Are TEs transcribed

A

yes

39
Q

Do TEs impact chromosome structure

A

yes

40
Q

Diseases caused by TEs (7)

A
  • hemophilia A & B
  • severe combined immunodeficiency
  • porphyria
  • predisposition to cancer
  • Duchenne muscular dystrophy
  • BRCA1
  • neurofibromatosis
    (deleterious insertions associated with Alu elements)
41
Q

do SINEs (Alu seq) and LINEs causes mutations responsible for human genetic diseases

A

yes

42
Q

HERV

A

human endogenous retrovirus

43
Q

HERV-H

A
  • subfamily most common
  • expressed preferentially in embryonic SCs
  • promote genome instability through non-allelic homologous recombination
    “HERV susceptibility regions”
44
Q

Case study HERV-H finding

A

deletion near 4 potential HERV-H loci on chromosome 3

LIFESCI 2G03 (17 decks)

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