DNA structure

Question 1

What force contributes the most stability to DNA?

Answer 1

Hydrophobic interactions between adjacent stacked base pairs (van der Waals)

Question 2

How many hydrogen bonds form between G and C?

Answer 2

3

Question 3

How many hydrogen bonds form between A and T?

Answer 3

2

Question 4

What end is the phosphate attached to?

Answer 4

5’

Question 5

What is the destabilizing force in DNA structure?

Answer 5

Repulsion between the negative charges of the phosphate backbone.

Question 6

What is the complementary sequence to ACCGTATTC?

Answer 6

5’-GAATACGGT-3’

Question 7

What forms are the adenine and cytosine bases in order for correct base pairing to occur?

Answer 7

Amino (as opposed to imino)

Question 8

What form at the guanine and thymine bases?

Answer 8

Keto (as opposed to enol)

Question 9

How wide is the secondary structure of DNA?

Answer 9

2 nm

Question 10

How tall is each turn (B form)? How many base pairs per turn?

Answer 10

3.4 nm and 10 base pairs per turn (.34 nm between adjacent stacked base pairs)

Question 11

What handedness is the DNA helix (B form)

Answer 11

right-handed

Question 12

How are base pairs oriented to the helix axis (B form)?

Answer 12

Flat and perpendicular

Question 13

What does the major groove allow when DNA needs to be used?

Answer 13

Proteins to gain access to the bases

Question 14

What environment is A form DNA found in?

Answer 14

Dehydrated

Question 15

How many base pairs per turn of A form DNA?

Answer 15

11

Question 16

What is the structure for dsRNA and RNA-DNA hybrid?

Answer 16

A form

Question 17

How is the backbone oriented in Z DNA? Why?

Answer 17

Zig zag due to alternating purine and pyrimidine sequences (first isolated as repeating dGdC)

Question 18

How is the helix oriented in Z DNA (handedness)?

Answer 18

Left handed

Question 19

How many base pairs per turn in z DNA?

Answer 19

12

Question 20

Where do other forms of DNA involving 3 or 4 strands appear?

Answer 20

Sites important for initiation or regulation of DNA metabolism, such as replication and transcription.

Question 21

What is hyperchromicity?

Answer 21

The phenomenon of increased UV absorption as strands of the double helix separate. Bases absorb UV light at 260 nm

Question 22

What occurs at the Tm?

Answer 22

Half of DNA has melted (denatured)

Question 23

What factor of DNA composition influences Tm?

Answer 23

Concentration of AT to GC. More GC pairs will make DNA more stable so it will have a higher melting point.

Question 24

Where is circular DNA found in eukaryotes?

Answer 24

mitochondria

Question 25

What are 4 ways to interrupt the HIV life cycle (HAART therapy)?

Answer 25

Inhibit: 1) reverse transcriptase; 2) HIV entry into the host cell; 3) protease that cleaves proteins HIV needs to make new viral particles; 4) inhibit integrase

Question 26

What is AZT?

Answer 26

An NRTI. It is a thymidine analogue that lacks a 3' hydroxyl group. Terminates chain elongation.

Question 27

What does acyclovir do?

Answer 27

It goes through a series of conversions to eventually resemble dGTP, but it lacks a 3' OH group so it prevents attachment of additional nucleosides.

Question 28

What type of drug is Cipro and what does it inhibit?

Answer 28

Antibiotic. Topoisomerase inhibitor.

Question 29

What other type of therapy uses topoisomerase inhibitors?

Answer 29

Antineoplastic (chemotherapy)

Question 30

What supercoiled state is DNA normally in? How is this advantageous for transcription?

Answer 30

Negative. This rotation opposes the double helix twisting, so DNA is easier to open and utilize.

Question 31

How do type Ia topoisomerases work?

Answer 31

Cut one strand and passes the unbroken strand through the cut, then rejoins. Strand must have tension from a supercoiled state to provide energy.

Question 32

How to type Ib topoisomerases work?

Answer 32

Cuts one strand and lets the other strand rotate around before rejoining.

Question 33

What type of supercoil can type Ia TI relax?

Answer 33

negative

Question 34

What type of supercoil can type Ib TI relax?

Answer 34

- or +

Question 35

How do prokaryotes introduce negative supercoiling into newly synthesized DNA?

Answer 35

Type II topoisomerase

Question 36

What can type II topoisomerases relax?

Answer 36

Negative or positive supercoils

Question 37

What do eukaryotes use to introduce negative supercoils?

Answer 37

Histones. We don't use topoisomerase II for nuclear DNA.

Question 38

What amino acids are histones rich in?

Answer 38

Lysine and arginine. so basic

Question 39

What is the full structure of nucleosome?

Answer 39

Octamer of two identical tetramers (H2A, H2B, H3, and H4)x2. DNA wrapped around 1 and 3/4 time.

Question 40

Where does histone 1 come in?

Answer 40

Associated with linker DNA. Helps form higher order structures.

Question 41

What is the level of structure above nucleosome?

Answer 41

Solenoid

Question 42

How many nucleosomes per solenoid turn? What is the shortening ration?

Answer 42

6. Provides 35-40 fold shortening of DNA.

Question 43

How many turns are taken out of DNA by wrapping around a histone?

Answer 43

one

Question 44

What is the packing efficiency of condensed DNA?

Answer 44

10,000 times shorter

Question 45

Highly repetitive sequences

Answer 45

Not transcribed, tandem repeats, usually 10% or less of genome

Question 46

Moderately repetitive sequences

Answer 46

Derived from transposon, usually transcribed but not translated, 25-45% of genome

Question 47

How frequently repeated are sequences for histones, tRNA, rRNA?

Answer 47

Moderately

Question 48

Single copy DNA

Answer 48

Most genes, 40-60% of genome, one type of unique gene exists with gene families