Chapter 17_Recombination And Transposition At The Molecular Level

Question 1

Transposable Elements

Answer 1

The DNA segments that transpose themselves. TEs have sometimes been referred to as “jumping genes” because they are inherently mobile.

Question 2

Mutable Site

Answer 2

Locus where chromosomes break at a fairly high rate.

Question 3

Simple Transposition

Answer 3

• (Conservative Transposition) The TE is removed from its original site and transferred to a new target site.
• This mechanism is also called a cut-and-paste mechanism because the element is cut out of its original site and pasted into a new one.
• Widely found in bacterial and eukaryotic species.

Question 4

Replicative Transposition

Answer 4

• Involves the replication of the TE and insertion of the newly made copy into a second site.
• One of the TEs remains in its original location, and the other is inserted at another location.
• Relatively uncommon and found only in bacterial species.

Question 5

Transposons

Answer 5

• Move as a DNA molecule from one site to another.

- This describes simple and replicative transposition.

Question 6

Retro-Transposition

Answer 6

• Moves via an RNA intermediate.
• Found in eukaryotic species, where it is very common.
• The element is transcribed into RNA. An enzyme called reverse transcriptase uses the RNA as a template to synthesize a DNA molecule that is integrated into a new region of the genome.
• Like replicative transposons, retro-transposons increase in number during retrotransposition.

Question 7

Retrotransposons

Answer 7

• (retro-elements, retro-posons) Transposable elements that move via retro-transposition.

Question 8

All TEs are flanked by…

Answer 8

…direct repeats (DRs), also called target-site duplications, which are identical nucleotide sequences that are oriented in the same direction and repeated.

Question 9

Insertion Sequence

Answer 9

• The simplest TE, which is commonly found in bacteria.
• It has two important characteristics:
  
  • Both ends of the insertion sequence contain inverted repeats (IRs). They are DNA sequences that are identical (or very similar) but run in opposite directions
  • Insertion sequences may contain a central region that encodes the enzyme transposase, which catalyzes the transposition event.

Question 10

Composite Transposons

Answer 10

• Contain additional genes that are not necessary for transposition “per se”. They commonly contain genes that confer a selective advantage to the organism under certain growth conditions.
• Prevalent in bacteria, where they often contains genes that provide resistance to antibiotics or toxic heavy metals.

Question 11

Replicative Transposons

Answer 11

• Elements that move by replicative transposition
• Have a sequence organization that is similar to insertion sequences except that replicative transposons have a resolvase gene that is found between the inverted repeats.

Question 12

LTR Retrotransposons

Answer 12

Evolutionarily related to known retroviruses. These TEs have retained the ability to move around the genome, though, in most cases, they do not produce mature viral particles.

Question 13

Long Terminal Repeats

Answer 13

• (LTRs) LTR retrotransposons are so named because they contain LTRs at both ends of the element.
• They are typically a few hundred nucleotides in length.
• Like their viral counterparts, LTR retrotransposons encode virally related proteins such as reverse transcriptase and integrase that are needed for the retrotransposition process.

Question 14

non-LTR retrotransposons

Answer 14

• Appear less like retroviruses in their sequence.

- They may contain a gene that encodes a protein that has both reverse transcriptase and endonuclease function.

Question 15

Autonomous Elements

Answer 15

Transposable elements that contain all of the information necessary for transposition or retrotransposition to take place.

Question 16

Nonautonomous element

Answer 16

Typically lacks a gene such as transposase or reverse transcriptase that is necessary for transposition.

Question 17

What is the problem with the ligation of the transposable element into its new site?

Answer 17

It leaves short gaps in the target DNA. The DNA sequences in these gaps are complementary to each other. Therefore, when they are filled in by DNA gap repair synthesis, this produces direct repeats that flank both ends of the TE.

Question 18

Replicative transposition requires…

Answer 18

…both transposase and resolvase.

Question 19

The movement of LTR retrotransposons requires two key enzymes:

Answer 19

Reverse transcriptase and integrase.

Question 20

Reverse transcriptase

Answer 20

Uses RNA as a template to synthesize a double-stranded DNA molecule.

Question 21

Integrase

Answer 21

Catalyzes the insertion of the DNA into the target chromosomal DNA.

Question 22

Target-Site Primed Reverse Transcription (TPRT)

Answer 22

• The currently accepted model for the replication and integration of non-LTR retrotransposons.
• The retrotransposon is first copied into RNA with a polyA tail.
• The target DNA site is recognized by an endounclease, which may be encoded by the retrotransposon.
• This endonuclease recognizes a consensus sequence and initially cuts just one of the DNA strands.
• The 3’-polyA tail of the retrotransposon RNA can bind to this nicked site due to AT base pairing.
• Reverse transcriptase then uses the target DNA as a primer and makes a DNA copy of the RNA.

Question 23

Selfish DNA Hypothesis

Answer 23

TEs exist because they contain characteristics that allow them to multiply within the chromosomal DNA of living cells.
- They resemble parasites in the sense that they inhabit a cell without offering any selective advantage to the organism.

Question 24

Exon Shuffling

Answer 24

Transposition may cause the insertion of exons from one gene into another gene, thereby producing a new gene with novel function(s).

Question 25

Possible Consequences of Transposition (Chromosome Structure)

Answer 25

• Chromosome breakage: Excision of a TE.

- Chromosome rearrangements: Homologous recombination between TEs located at different positions in the genome.

Question 26

Possible Consequences of Transposition (Gene Expression)

Answer 26

• Mutation: Incorrect excision of TEs.
• Gene Inactivation: Insertion of a TE into a gene.
• Alteration in Gene Regulation: Transposition of a gene next to regulatory sequences or the transposition of regulatory sequences next to a gene.
• Alteration in the Exon Content of a Gene: Insertion of exons into the coding sequence of a gene via TEs. This phenomenon is called exon shuffling.
• Gene Duplications: Creation of a composite transposon that transposes to another site the genome.