Exam 2: Transposable Elements

Question 1

define transposable element

Answer 1

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

Question 2

transposition

Answer 2

movement of the transposons

Question 3

transposable element features (2)

Answer 3

1. flanking direct repeats (3-12 bp)

2. terminal inverted repeats

Question 4

transposons make up at least _ of human DNA

Answer 4

45%

Question 5

transposons often cause _

Answer 5

mutations

Question 6

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

Answer 6

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

Question 7

what kind of cuts are made with transposons

Answer 7

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)

Question 8

what creates the flakinking direct repeats

Answer 8

replication of single-stranded DNA

Question 9

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

Answer 9

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

Question 10

common features of terminal, inverted repeats (3)

Answer 10

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

Question 11

flanking direct repeats are generated when a _

Answer 11

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)

Question 12

t/f: transposable elements have common characteristics

Answer 12

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

Question 13

how do transposons cause mutations

Answer 13

-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)

Question 14

prok transposons are found in _

Answer 14

only DNA transposons are found in bacteria

Question 15

prok transposons include: (2)

Answer 15

1. insertion seqs

2. composite transposons

Question 16

what are feats of a insertion seq

Answer 16

(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

Question 17

what are the feats of composite transposons

Answer 17

(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

Question 18

why is a bacterial insertion sequence seen as autonomous

Answer 18

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

Question 19

a bacterial composite transposon retains enough _

Answer 19

information to transpose

Question 20

Tn10

Answer 20

bacterial composite transposon that carries the tetracycline resistance seq)

Question 21

Mu is a transposing _

Answer 21

bacteriophage

Question 22

mechanisms of transposition (3)

Answer 22

• 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

Question 23

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

Answer 23

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

Question 24

replicative transposition can be either between _

Answer 24

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

Question 25

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

Answer 25

- 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

Question 26

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

Answer 26

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

Question 27

enzymes involved in replicative transposition (2)

Answer 27

1. transposase | 2. resolvase

Question 28

fcn of transposase

Answer 28

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

Question 29

transposase is encoded by

Answer 29

cellular gene or often by transposable element

Question 30

transposase mechanism

Answer 30

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

Question 31

fcn of resolvase

Answer 31

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

Question 32

resolvase encoded by

Answer 32

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

Question 33

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

Answer 33

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

Question 34

cleavage in non-replicative transposition rqs

Answer 34

a transposase enzyme produced BY THE transposable element

Question 35

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

Answer 35

normal replication and repair enzymes

Question 36

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

Answer 36

homologous template on sister chromatid

Question 37

the 2 groups of euk transponsons

Answer 37

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

Question 38

euk transposon similar to transposable elements found in bacteria include:

Answer 38

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

Question 39

retrotransposons are similar to _ and include _

Answer 39

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

Question 40

retrotransposons are elements that transpose through an _

Answer 40

RNA intermediate (in contrast to DNA transposons)

Question 41

retrotransposon mechanism

Answer 41

- RNA is transcribed from an DNA transposable element | - RNA is copied back to another DNA site using reverse transcriptase

Question 42

retrotransposons are only done through _

Answer 42

replicative transposition

Question 43

retrotransposons are more common than _

Answer 43

DNA transposons in euks

Question 44

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

Answer 44

11% of the human genome and includes Alu | *short interspersed nuclear elements)

Question 45

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

Answer 45

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

Question 46

chromosomal arrangements are consequences of

Answer 46

transposed sequences

Question 47

transposition increases

Answer 47

chromosomal breaks, which incr variation, and improper healing

Question 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?

Answer 48

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

Question 49

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

Answer 49

- 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

Question 50

class I of euk transposable elements

Answer 50

retrotransposons

Question 51

structure of class I transposons

Answer 51

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

Question 52

genes encoded by class I transposons

Answer 52

reverse-transcriptase gene

Question 53

transposition of class I transposon happens via

Answer 53

RNA intermediate

Question 54

structure of class II transposons

Answer 54

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

Question 55

genes encoded by class II transposons

Answer 55

transposase gene (sometimes others)

Question 56

transposition of class II transposon happens via

Answer 56

through DNA (replicative or nonreplicative)

Question 57

who is barbara mcclintock

Answer 57

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*

Question 58

variegated corn kernels resulted

Answer 58

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

Question 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

Answer 59

IQD12 is overexpressed resulting in elongated tomato

Question 60

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

Answer 60

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

Question 61

transposons and mammalian uterus/developmental pathways

Answer 61

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

Question 62

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

Answer 62

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"

Question 63

retrosponsons in variation and disease

Answer 63

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

Question 64

transposons and p53

Answer 64

*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