lecture 29

Question 1

what is a base analog(antimetabolite) of uracil that can replace thymine in a strand of DNA?

Answer 1

5-bromouracil

Question 2

what are very unstable and quick reacting molecules that “steal” electrons from nearby stable molecules?

Answer 2

free radicals

Question 3

what type of environmental factor causes pyrimidine dimers by the formation of covalent linkages localized on cysteine double bonds?

Answer 3

UV light

Question 4

what does ectopic recombination cause?

Answer 4

chromosome duplication

Question 5

in terms of evolution, what role do transposons have?

Answer 5

they increase the genome size as they generate some type of mutation when they move

Question 6

what class of TEs require reverse transcriptase in order to move?

Answer 6

class 1

Question 7

what class of TEs do NOT require reverse transcriptase in order to move?

Answer 7

class 2

Question 8

what protein do all DNA transposons(class 2) code for?

Answer 8

transposase

Question 9

what class of transposons moves through the genome in a “cut and paste” mechanism?

Answer 9

class 2 - DNA transposons

Question 10

what does TIR stand for?

Answer 10

terminal inverted repeats

Question 11

what recognizes the TIRs at the ends of the TE?

Answer 11

transposase

Question 12

what does (F)DR stand for?

Answer 12

(flanking) direct repeats

Question 13

are (F)DR a part of the TE?

Answer 13

no

Question 14

what provides a marker for the excision site of the TE once it has been removed?

Answer 14

(F)DRs

Question 15

what allows retrotransposons to function?

Answer 15

RNA intermediates

Question 16

do retrotransposons code for transposase?

Answer 16

no

Question 17

what class of TEs move throughout the genome in a “copy and paste” mechanism?

Answer 17

class 1 - retrotransposons

Question 18

what do retrotransposons produce?

Answer 18

RNA transcripts

Question 19

what must happen in order for a retro-transposon to bind?

Answer 19

reverse transcriptase must reverse transcribe the RNA into DNA sequence PRIOR to insertion into target DNA

Question 20

what are LTRs?

Answer 20

long terminal repeats; located on each end of TE

Question 21

what are the only active class of transposons in humans?

Answer 21

non-long terminal repeats

Question 22

what must non-autonomous transposons borrow to move?

Answer 22

reverse transcriptase

Question 23

what are LINEs?

Answer 23

long interspersed elements, a type of autonomous retrotransposon

Question 24

what proteins do FUNCTIONAL L1 elements encode?

Answer 24

endonuclease and reverse transcriptase

Question 25

what does endonuclease do?

Answer 25

cuts DNA

Question 26

what does reverse transcriptase do?

Answer 26

makes a DNA copy of an RNA transcript

Question 27

what do NON-functional L1 elements do?

Answer 27

play a role in regulating the efficiency of transcription of the gene in which they reside

Question 28

what are SINEs?

Answer 28

short interspersed elements, a type of non-autonomous retrotransposon

Question 29

what are short DNA sequences that represent reverse transcribed RNA molecules originally transcribed by RNA polymerase II?

Answer 29

SINEs

Question 30

what are the most abundant SINEs?

Answer 30

Alu elements

Question 31

Alu elements consist of a sequence that contains a site that is recognized by Alu1 which is what?

Answer 31

restriction enzyme

Question 32

where do Alu elements normally occur?

Answer 32

introns

Question 33

how does an Alu element end up being translated into the protein product if it begins in an intron?

Answer 33

it can be spliced into mRNA, thereby creating a new exon which is translated

Question 34

what does alternative splicing allow for in terms of Alu elements?

Answer 34

nature can try out new proteins without losing the original, functioning one

Question 35

what is the main factor for transposable element function?

Answer 35

where it lands

Question 36

if a transposable elements lands in a non-coding region, what effect does it have?

Answer 36

not much

Question 37

if a transposable element lands in a gene, what effect does it have?

Answer 37

mutation, leading to genetic diversity

Question 38

assume the V gene regulates anthocyanin pigment production in black grapes. when a G retrotransposon is added to the V gene, what is the phenotypic result?

Answer 38

white grapes

Question 39

what effect does the G retrotransposon have on the V gene in grapes?

Answer 39

it disrupts anythocyanin synthesis, thereby preventing color from being made, resulting in white grapes

Question 40

assume a white grape undergoes a second mutation wherein the G retrotransposon is removed; however a piece is left behind. what is the phenotypic result and why?

Answer 40

red grapes, because anthocyanin production is partially restored