transposable elements

Question 1

Transposons

Answer 1

“jumping genes”
- segments of DNA that integrate into new locations on the chromosome
- make up about 40% of human genome
- major source of mutations
- bacterial transposons can carry antibiotic-resistant genes

Question 2

Cut and paste transposons

Answer 2

• element that is physically cut out of one site in a chromosome and pasted into a new site, “switch”
• catalyzed by transposase
• DNA transposon
• both prokaryotes and eukaryotes

Question 3

Replicative transposons

Answer 3

• replicated with one copy inserted at a new site and one remains original
• catalyzed by transposase
• DNA transposon
• only in prokaryotes

Question 4

Retrotransposons

Answer 4

• DNA copy of element made by reverse transcription from its RNA and then inserted into a new chromosomal site
• catalyzed by reverse transcriptase
• 2 kinds: retrovirus-like elements and retroposons

Question 5

bacterial transposons

Answer 5

• move within and between chromosomes and plasmids
• cut and paste types: insertion sequences (IS elements) and composite transposons
• replicative transposons: Tn3 elements

Question 6

General structure of Cut-and-Paste DNA transposons

Answer 6

• gene that encodes a transposes: protein required for transposition
• terminal inverted repeats: identical or nearly identical inverted sequences at both ends of element
• target site duplication: short directly repeated sequences at both ends, result from staggered cleavage of the double-stranded DNA

Question 7

IS elements

Answer 7

• simplest bacterial transposons
• compactly organized and contain only genes whose products are involved in transposition
• inverted terminal repeats are found at the ends
• some IS elements encode transposase

Question 8

How does insertion of an IS element cause target site duplication

Answer 8

• staggered cuts are made in the target DNA
• a transposable element inserts itself into the DNA
• the staggered cuts leave short, single-stranded pieces of DNA
• replication of this single-stranded DNA creates the flanking direct repeats

Question 9

Multiple IS elements

Answer 9

• bacterial chromosome may contain many copies of an IS element
• when a particular IS element is found in both a plasmid and chromosome, homologous recombination may occur inserting the plasmid into the chromosome

Question 10

conjugative and non-conjugative plasmid

Answer 10

conjugative: donor of DNA
non-conjugative: acceptor of DNA

Question 11

Homologous recombination of IS elements

Answer 11

• involve a non-conjugative resistant (R) plasmid and a conjugative plasmid
• mobilize antibiotic resistance genes
• needs an RTF component to promote conjugation between bacteria

Question 12

composite transposons

Answer 12

• created when 2 IS elements insert near each other “capturing” a DNA sequence
• IS element excision through transposase cleavage at each end of the transposons can mobilize the entire captured DNA, which may mobilize antibiotic-resistant genes

Question 13

Tn3 elements

Answer 13

• Tn3 elements are larger than the simple IS elements
• often contain additional genes not involved in transposition
• have simple inverted repeats at each end

Question 14

replicative transposons

Answer 14

• transposase encoded by Tn3 catalyzes the formation of cointegrate between the donor and recipient plasmids
• Tn3 is replicated so there is an element at each junction
• recombination separates the co-integrate into 2 DNAs each with a copy of Tn3

Question 15

the discovery of transposons

Answer 15

• found in eukaryotes (corn)
• found by Barbra McClintock

Question 17

Cut-and-paste transposons in eukaryotes

Answer 17

dependent on Ac and Ds elements
Ac = fully active transposon (activator)
Ds = have elements they can’t transpose without help from Ac (dissociation)
- 2 versions of the same transposon

Question 18

The Ac/Ds system in corn

Answer 18

• Ds is located at a site on chromosome 9 in mosaic kernels where chromosome breakage occurs
• Ds cannot induce breakage by itself so Ac stimulates chromosome breakage at the site of Ds

Question 19

Activities of the Ac/Ds elements

Answer 19

• similar to cut-and-paste in prokaryotes
• the Ac element encodes a transposase that is responsible for excision, transposition, mutation and chromosome breakage
• the Ac transposase interacts with sequences at the ends of Ac and Ds elements and catalyzes their movement
• deletions or mutations in the Ac gene abolish its catalytic function

Question 20

similarities between 3 types of transposons

Question 21

differences between 3 types of transposons

Question 22

retroviruses

Answer 22

• use reverse transcriptase to copy the retroviral-like RNA into DNA
• unique to eukaryotes

Question 23

retrotransposons

Answer 23

• use reverse transcriptase to copy the retroviral-like RNA into DNA
• do not have terminal inverted repeats
• resemble the reverse transcripts of poly A+ mRNA

Question 24

general structure of retroviruses

Answer 24

• genes that encode reverse transcriptase and integrase
• terminal inverted repeats
• target site duplication

Question 25

general structure of retroposons

Answer 25

• genes that encode reverse transcriptase and endonuclease activities
• 5’ and 3’ untranslated regions and poly A tail
• create a target site duplication but have no terminal inverted repeats

Question 26

long interspersed nuclear elements (LINES)

Answer 26

example L1
- LINES are the most abundant class of transposable elements in humans
- retroposon
- have an internal promoter, 2 open reading frames that encode a nucleic acid binding protein and a protein with endonuclease and reverse transcriptase activities

Question 27

short interspersed nuclear elements (SINES)

Answer 27

• second most abundant class of transposable elements
• only Alu elements are transpositional-active
• less than 400 base pairs long
• reverse transcriptase required for SINE is provided by LINE-type element

Question 28

genetic evolutionary significance or transposons

Answer 28

• they are mutagens
• can mobilize foreign genes
• change in genome organization

Question 29

transposons and chromosome rearrangements

Answer 29

• pairing by looping and crossing over between 2 transposons oriented in the same direction leads to deletion
• pairing by bending and crossing over between 2 transposons oriented in opposite directions leads to an inversion
• misalignment and unequal exchange between transposons on sister chromatids leads to one chromosome with a deletion and one with a duplication