18: Genomic Regulation

Question 1

Major bond stabilizing DNA

Answer 1

H bonds between complementary bases

Question 2

Bonds between A /T and C/G

Answer 2

A/T: 2 H bonds

G/C: 3 H bonds

Question 3

Nt per turn for B DNA

Answer 3

10nt per turn

Question 4

How A DNA and Z DNA are different from B

Answer 4

A: 11nt per turn
Z: left haded form

Question 5

Nucleosome

Answer 5

Core of 8 histones + DNA

Question 6

Charge of histones and DNA

Answer 6

Histones: positive
DNA: negative

Question 7

Histone H1

Answer 7

Linker histone - separates each nucleosome

Question 8

Chromatin in G1 vs M phase of cell cycle

Answer 8

G1: loose
M: tight

Question 9

Exon vs intron

Answer 9

Exon: coding region
Intron: non-coding

Question 10

Four characteristics of DNA replication

Answer 10

1. Semiconservative
2. Bi-directional (multiple ORIs)
3. Primed by RNA
4. Semi-discontinuous while synthesizing

Question 11

Topoisomerases

Answer 11

Remove supertwisting in DNA

Question 12

SsDNA binding proteins

Answer 12

Prevents premature annealing of single stranded DNA to double stranded DNA

Question 13

DNA primase

Answer 13

Adds RNA primers

Question 14

DNA ligase

Answer 14

Seals breaks/nicks in DNA after DNA Pol fills gaps

Question 15

Most frequent type of DNA damage

Answer 15

Spontaneous DNA damage

Question 16

What can takes care of epoxides that cause issues?

Answer 16

Cytochrome P450 enzymes

Question 17

Two types of epigenetics modifications

Answer 17

1. Gene methylation

2. Histone mods by acetylation and deacetylation

Question 18

Major site of DNA methylation

Answer 18

A cytosine base, especially the 5’ C next to a G (5’ CG 3’)

Question 19

What does methylation of 5’ CG 3’ areas do?

Answer 19

Cause steric hindrance of TFs in promoter region

Question 20

What process is gene methylation important for?

Answer 20

Tissue-specific gene expression

Question 21

What syndrome is caused by gene methylation

Answer 21

Fragile X syndrome

Question 22

Mutation in fragile X syndrome

Answer 22

Addition of CGG nt repeats -> hypermethylation -> inactivating FMRI gene (fragile X MR 1 gene)

Question 23

Symptoms of Fragile X Syndrome

Answer 23

Intellectual disability, problems with social interaction, delayed speech, long and narrow face, large ears, flexible fingers, large testicles

Question 24

What does histone modification by acetylation and deacytlation do?

Answer 24

Makes DNA more or less accessible to TFs

Question 25

Enzymes that acetylate and deacytlate histones

Answer 25

Acetylate: histone acetyltransferases (HATs)
Deacetylate: HDAC

Question 26

What type of gene silencing can lead to cancer?

Answer 26

Silencing tumor suppressor genes

Question 27

Clinical associations of Xeroderma Pigmentosa

Answer 27

High photosensitivity, pigment changes, prone to melanoma and squamous cell carcinomas

Question 28

Cockayne Syndrome clinical associations

Answer 28

Neurologic delay, photosensitivity, progeria (premature aging), common hearing loss and eye abnormalities