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Biochemistry > DNA structure > Flashcards

DNA structure Flashcards

1
Q

What force contributes the most stability to DNA?

A

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

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2
Q

How many hydrogen bonds form between G and C?

A

3

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3
Q

How many hydrogen bonds form between A and T?

A

2

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4
Q

What end is the phosphate attached to?

A

5’

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5
Q

What is the destabilizing force in DNA structure?

A

Repulsion between the negative charges of the phosphate backbone.

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6
Q

What is the complementary sequence to ACCGTATTC?

A

5’-GAATACGGT-3’

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7
Q

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

A

Amino (as opposed to imino)

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8
Q

What form at the guanine and thymine bases?

A

Keto (as opposed to enol)

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9
Q

How wide is the secondary structure of DNA?

A

2 nm

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10
Q

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

A

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

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11
Q

What handedness is the DNA helix (B form)

A

right-handed

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12
Q

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

A

Flat and perpendicular

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13
Q

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

A

Proteins to gain access to the bases

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14
Q

What environment is A form DNA found in?

A

Dehydrated

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15
Q

How many base pairs per turn of A form DNA?

A

11

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16
Q

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

A

A form

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17
Q

How is the backbone oriented in Z DNA? Why?

A

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

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18
Q

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

A

Left handed

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19
Q

How many base pairs per turn in z DNA?

A

12

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20
Q

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

A

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

21
Q

What is hyperchromicity?

A

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

22
Q

What occurs at the Tm?

A

Half of DNA has melted (denatured)

23
Q

What factor of DNA composition influences Tm?

A

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

24
Q

Where is circular DNA found in eukaryotes?

A

mitochondria

25
Q

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

A

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

26
Q

What is AZT?

A

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

27
Q

What does acyclovir do?

A

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.

28
Q

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

A

Antibiotic. Topoisomerase inhibitor.

29
Q

What other type of therapy uses topoisomerase inhibitors?

A

Antineoplastic (chemotherapy)

30
Q

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

A

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

31
Q

How do type Ia topoisomerases work?

A

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

32
Q

How to type Ib topoisomerases work?

A

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

33
Q

What type of supercoil can type Ia TI relax?

A

negative

34
Q

What type of supercoil can type Ib TI relax?

A
  • or +
35
Q

How do prokaryotes introduce negative supercoiling into newly synthesized DNA?

A

Type II topoisomerase

36
Q

What can type II topoisomerases relax?

A

Negative or positive supercoils

37
Q

What do eukaryotes use to introduce negative supercoils?

A

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

38
Q

What amino acids are histones rich in?

A

Lysine and arginine. so basic

39
Q

What is the full structure of nucleosome?

A

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

40
Q

Where does histone 1 come in?

A

Associated with linker DNA. Helps form higher order structures.

41
Q

What is the level of structure above nucleosome?

A

Solenoid

42
Q

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

A
  1. Provides 35-40 fold shortening of DNA.
43
Q

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

A

one

44
Q

What is the packing efficiency of condensed DNA?

A

10,000 times shorter

45
Q

Highly repetitive sequences

A

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

46
Q

Moderately repetitive sequences

A

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

47
Q

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

A

Moderately

48
Q

Single copy DNA

A

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

Biochemistry (6 decks)

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