[Lec 4] Key Terms: Genome Structure, Chromatine, and the Nucleosome

Question 1

Genome

Answer 1

the complete haploid genetic complement of a typical cell

Question 2

Genome annotation

Answer 2

identifies location and function of genes

Question 3

DNA transposons

Answer 3

moves through DNA intermediate

Question 4

Retrotransposons

Answer 4

moves through RNA intermediate; 1. always increases in numbers when they move, 2. are closely related to retroviruses

Question 5

Pseudogenes

Answer 5

copies of coding regions with no regulatory sequences

Question 6

heterochromatin

Answer 6

appears dark and dense; typically low levels of gene expression

Question 7

euchromatin

Answer 7

appears less dense; typically shows higher levels of gene expression

Question 8

chromatin

Answer 8

1. compacts DNA, 2. protects DNA from damage; 3. facilitates segregation into daughter cells; 4. inhibits processes that require unwinding of DNA (i.e. transcription, replication, or recombination)

Question 9

heterochromatin

Answer 9

higher-order chromatin structure

Question 10

negative supercoiling

Answer 10

DNA twisted in opposite direction of double helix; easier to unwind; when nucleosomes create left-handed toroidal writhe

Question 11

positive supercoiling

Answer 11

DNA twisted in same direction of double helix; harder to unwind; very hard to add new nucleosome to positively supercoiled DNA

Question 12

Type I Topoisomerase

Answer 12

make single stranded breaks

Question 13

Type II Topoisomerase

Answer 13

makes double stranded breaks

Question 14

gyrase

Answer 14

prokaryotic type II typoisomerase; uses ATP to introduce negative supercoiling into relaxed DNA (prokaryotes don’t have nucleosomes)

Question 15

histones

Answer 15

small basic proteins that have same general fold (histone fold)

Question 16

histone fold motif

Answer 16

folded in all four histones; functions primarily as dimerization motif

Question 17

phosphorylation

Answer 17

creates a negative charge (-)

Question 18

acetylation

Answer 18

neutralizes a charge (+)

Question 19

methylation

Answer 19

does not change a charge

Question 20

bromodomain

Answer 20

containing proteins interact with acetylated histone N-terminal tails (these regions typically associated with active transcription; higher levels of acetylation; lower amount of 30 nm fibers)

Question 21

chromodomain

Answer 21

containing proteins interact with methylated histone tails (that are associated with either transcriptionally inactive chromatin depending on which amino acid is modified)