Genomic Regulation

Question 1

How many hydrogen bonds b/w DNA and histone octamer

Answer 1

142

Question 2

What AAs make up 20% of the histone protein AA content

Answer 2

Lysine and arginine- lots of ++ charge to attract to – charged DNA

Question 3

Which histone AA is the primary target of post translational modifications

Answer 3

Lysine

Question 4

Chromatin is made up of

Answer 4

Protein + nuclear DNA

Question 5

Heterochromatin vs Euchromatin

Answer 5

Euchromatin makes up 92% of total chromatin. It consists of many genes that are frequently active. Heterochromatin is tightly packed and has very few active genes

Question 6

What percentage of total DNA sequence is coding sequences

Answer 6

1.5%

Question 7

Comparative genome hybridization

Answer 7

Used to detect copy number variants, can also detect deletions

Question 8

Long terminal repeats

Answer 8

Found at either end of retrotransposons
Formed by reverse transcription of retroviral RNA
Used by viruses to insert their genetic material into host genome

Question 9

15% of all mutations affect _____

Answer 9

RNA splicing

Question 10

Nucleoside analog inhibitors of DNA synthesis

Answer 10

Nucleoside analogs typically lack a 3’ OH, which interferes with DNA replication. Acyclovir is a nucleoside analog inhibitor

Question 11

DNA polymerase requires a primer with a free _____ to begin processing

Answer 11

Primer must have a free 3’ OH

Question 12

What type of DNA replication do we have (conservative/non-conservative/semi-conservative)

Answer 12

Semi-conservative

Question 13

DNA helicase function

Answer 13

Unwind DNA

Question 14

Topoisomerase function

Answer 14

Relieve supercoiling

Question 15

ssDNA binding protein

Answer 15

Binds exposed single-strand DNA to stabilize it, prevent formation of hairpins
-DNA bases remain exposed while ssDNA BP is bound

Question 16

Ionizing radiation vs non-ionizing

Answer 16

Ionizing can cause DS-breaks, modifications of bases, DNA-protein cross-links (e.g. thymine-tyrosine link)
Non-ionizing radiation causes thymine dimers

Question 17

Depurination vs Deamination

Answer 17

Depurination- adenine/guanine lost from strand

Deamination- cytosine–>uracil, adenine–>hypoxanthine, guanine–>xanthine

Question 18

CpG islands and methylated cytosine

Answer 18

Associated with inactive genes

Deamination of methyl-cytosine produces T mismatched with G

Question 19

Cross linking agents include

Answer 19

Nitrogen mustard
Cisplatin
Mitomycin C
Carmustine

Question 20

Alkylating agents include

Answer 20

Dimethyl sulfate (DMS)
Methyl methanesulfonate (MMS)

Question 21

Intercalating agents include

Answer 21

Thalidomide

Question 22

Base excision repair enzymes/functions

Answer 22

DNA glycosylase cuts bad base out
AP endonuclease/phosphodiesterase remove sugar phosphate
DNA polymerase adds new base, ligase seals

Question 23

Nucleotide excision repair enzymes/functions

Answer 23

Excision nuclease makes cuts
DNA helicase removes section of DNA
Polymerase and ligase repair

Question 24

Defects in NER can cause what diseases

Answer 24

Xeroderma pigmentosum
Cockayne syndrome (transcription coupled repair)

Question 25

Mismatch excision repair

Answer 25

Removes most errors missed by DNA polymerase proofreading
MutS binds DNA while MutL scans for nicks and triggers degradation
In bacteria, methylation distinguishes new strand from old, in humans- SS breaks reveal okazaki fragment

Question 26

Defects in mismatch repair cause what disease

Answer 26

Hereditary nonpolyposis colorectal cancer

Question 27

Transcription coupled repair

Answer 27

Used for sequences that urgently need repair because they are being actively transcribed
RNA polymerase guides DNA repair proteins to sequence
NER or BER are typically used
-defects can lead to cockaynes syndrome

Question 28

Xeroderma pigmentosum

Answer 28

Defect in nucleotide excision repair
Individuals are extremely sensitive to sunlight and have higher risk of melanomas
Sunlight causes thymine dimers which are usually repaired by NER

Question 29

BRCA mutations and breast cancer

Answer 29

Tumor suppressor gene, mutation causes 5x increase in breast cancer risk