HRR: DNA rearrangements

Question 1

what are the 4 major types of gene rearrangements

Answer 1

homologous recombination, site-specific, transposition, and retrotransposition

Question 2

define homologous recombination

Answer 2

Breaking and joining of two separate DNA molecules. Their alignment is dependent on complementary base pairing

Question 3

describe the process of homologous recombination

Answer 3

• Both strands get nicked
• Strand invasion and complementary base pairing
• Ligation (holiday junction 4 strand intermediate)
• Cleavage and re-ligation

Question 4

Define heteroduplex DNA and describe how it is generated by the Holliday model.

Answer 4

Region of chromosome where the DNA strands are derived from different DNA molecules. Seen as the product of homologous recombination

Question 5

what are the main proteins involved in homologous recombination in prokaryotes? eukaryotes?

Answer 5

prokaryotes: RecA, RuvA, RuvB, RuvC

eukaryotes: Rad51/dmc1, Gen1

Question 6

specify the role of RecA/Rad51

Answer 6

binds to a single strand of DNA and non-specifically binds it to double stranded DNA. Base pairing occurs between the RecDNA and the complementary double stranded DNA. Strand exchange occurs via displacement of the homologous strand, which is then nicked

Question 7

specify the role of RuvA

Answer 7

catalyze branch migration of crossed strands

Question 8

specify the role of RuvB

Answer 8

catalyze branch migration of crossed strands

Question 9

specify the role of RuvC/Gen1

Answer 9

endonuclease that catalyzes rotation and cleavage of crossed strands

Question 10

what is Gen1

Answer 10

a eukaryotic endonuclease that resolves holiday junctions

Question 11

what processes is homologous recombination important in?

Answer 11

meiosis: occurs during prophase I and allows for genetic diversity

DNA repair: occurs during recombinatorial repair so we can repair strand breaks without losing genetic material

Question 12

define site-specific recombination

Answer 12

Occurs Between specific DNA sequences to which we bind proteins and create programmed rearrangements. it is used in VDJ recombination of immunoglobulins to create antibody diversity

Question 13

describe the process of site-specific recombination

Answer 13

• Rag1 and Rag2 bind to recombination signal sequence (RSS) next to the V and adjacent to the DJ and cleave the intervening DNA
• The nonhomologous ends become ligated to form VDJ

Question 14

define transposition

Answer 14

Move transposons (mobile genetic elements) from one part of the genome to another. No specific sequence is required.

Question 15

“juming genes” and “cut and paste” refers to….

Answer 15

transposons

Question 16

what are the three types of transponsons?

Answer 16

insertion sequences, simple transponsons, and composite transponsons

Question 17

describe insertion sequences

Answer 17

DNA segment with a transposase gene and two inverted terminal repeat sequences (ITRs) on either side. Transposase recognizes and binds to the ITR and cuts out the whole insertion sequence. It’ll then find a random target sequence, cut into it, and insert itself into the new site

Question 18

describe simple transposons

Answer 18

they’re like insertion sequences but have additional genes besides the transposase. the most relevant are antibiotic resistance genes.

Question 19

describe composite transposons

Answer 19

a segment of DNA with multiple insertion sequences and antibiotic resistance genes. they have the same mechanism as insertion sequences.

Question 20

define plasmids

Answer 20

mobile elements of DNA that carry genes and replicate independently of the bacterial chromosome

Question 21

give the types of plasmids

Answer 21

F: fertility (conjugation)
R: resistance (drug resistance)
Col: colicinogenic (genes for bacterial toxins)

Question 22

what is bacterial conjugation

Answer 22

enables simultaneous replication and transmission of a plasmid between bacteria via a sex pillus

Question 23

describe how transposons relate to antibiotic resistance

Answer 23

transposons jump onto an R factor in a plasmid and get transferred from one bacteria to another via conjugation. long-term antibiotic use results in selecting fir the strain that carries an R factor with the resistance gene.

Question 25

define retrotransposition

Answer 25

Move retrotransposons through an RNA intermediate. They involve reverse transcription of retrotransposon mRNA to cDNA and insertion into new sites of the genome (RNA to cDNA to protein)

Question 26

what are LTR elements

Answer 26

class of retrotransposons; human retroviruses in the genome that are not active and do not cause human disease

Question 27

what are non-LTR elements? what are the two main kinds?

Answer 27

class of retrotransposons; LINE-1 and alu elements

Question 28

describe LINE-1

Answer 28

a non-LTR element that can be capable of autonomous replication and mobilization; it has target site duplication sequences, endonuclease, and reverse transcriptase

Question 29

describe alu elements

Answer 29

do not code for proteins and are non-autonomous. they require LINE-1 for transcription and insertion.

Question 30

which rearrangement is also known as copy and paste?

Answer 30

retrotransposons

Question 31

which rearrangement is known as cut and paste

Answer 31

transposition