Symes DNA Structure and Function

Question 1

B-form DNA

Answer 1

Hydrated, 10 bp/turn
- right handed
- wider major groove (allows access for proteins)

Question 2

A form DNA

Answer 2

Low humidity, 11 bp/turn
- right handed
- narrower, deeper major groove

Question 3

Z form DNA

Answer 3

GCGCGCGC, 12 bp/turn
- left-handed
- spreads out actively transcribing genes

Question 4

2º DNA stabilizing factors

Answer 4

H bonds, vDw interactions, ions

Question 5

2º DNA destabilizing factors

Answer 5

electrostatic repulsions, PO4- (at pH 7)

Question 6

What wavelength do NTs and nucleic acids absorb light at

Answer 6

260 nm

Question 7

Does single or double stranded DNA absorb more light

Answer 7

Single-stranded absorbs more light because the bases are exposed
- still the same wavelength

Question 8

What is the Tm

Answer 8

Temperature at which 50% of DNA is denatured

Question 9

5 HAART Inhibitors

Answer 9

1) Nucleoside Reverse Transcriptase Inhibitors (NRTIs)
2) Non-nucleoside RTIs
3) Protease Inhibitors
4) Entry Inhibitors
5) HIV Integrase Inhibitors

Question 10

How do Nucleoside Reverse Transcriptase Inhibitors work?

Answer 10

Inhibit addition of NTs to a chain using a nucleoside analog
- AZT, Acyclovir (only uses the viral kinase)

Question 11

A supercoil which is underwound is positive or negative

Answer 11

Negative

Question 12

A supercoil which is overwound is positive or negative

Answer 12

Positive

Question 13

Is natural DNA negatively or positively supercoiled

Answer 13

Negative (underwound)

Question 14

Topoisomerase 1 function

Answer 14

Breaks one strands and changes it by +1 or -1 supercoils
- requires the DNA to be strained (overwound or underwound)

Question 15

Topoisomerase 2 function

Answer 15

Cuts 2 strands, changes the number of supercoils by 2
- removes supercoiling 2 twists at a time
- in prokaryotes, it can add supercoils to new DNA

Question 16

How do topoisomerase inhibitors work?

Answer 16

Inhibit the re-ligation function of the enzyme

Question 17

Are the topoisomerases the same in prokaryotes and eukaryotes

Answer 17

Nahh bb diff versions

Question 18

3º structure of DNA in eukaryotes

Answer 18

Histones (small, positive proteins)

Question 19

H1 function

Answer 19

Linker DNA for higher-order structures

Question 20

H2A function

Answer 20

Combined with H2B, H3 and H4 in the nucleosome core
- DNA wrapped around core is same length as Okazaki fragment

Question 21

What are highly repetitive sequences

Answer 21

Short, tandem, AT-rich sequences found in eukaryotes
- greater than 300k copies/genome
- 10% of genome
- ex. telomeres

Question 22

What is a solenoid

Answer 22

Complex of nucleosomes that causes a 35-40x shortening of DNA
- 6 nucleosomes per turn

Question 23

What are moderately repetitive sequences?

Answer 23

Code for highly-used genes in eukaryotes
- SINES/LINES space out actively transcribing genes

Question 24

What are unique/single-copy sequences

Answer 24

40-60% of eukaryotic genome
- grouped in families
- includes pseudogenes: genes which are never transcribed
- housekeeping genes

Question 25

Whats special about the beta-globin family of genes

Answer 25

They are spreading out on different chromosomes, and are expressed in different tissues at different ages

Question 26

Myotonic Dystrophy Type 1

Answer 26

Results of CTG-repeats
- increased number increases severity by decreasing onset age
- due to the polymerase slipping on trinucleotide repeats

Question 27

Concept of anticipation

Answer 27

Severity of a disease increases with each successive generation