Chapter 4 - Nucleic Acids

Question 1

What is a nucleic acid?

Answer 1

Polymers of nucleotides (nitrogenous base, pentose sugar, phosphate)
Strong acids
Capable of conversion between tautomeric forms

Question 2

What are the kinds of bases?

Answer 2

(1) Pyrimidines (CTU)

2) Purines (AG

Question 3

What spectrum is the absorbance of nucleic acids?

Answer 3

UV region. Conjugated double bonds of the nitrogenous bases.

Question 4

Metastability

Answer 4

Thermodynamically favored to break down, but do so only very slowly unless the reaction is catalyzed.

Question 5

DNA hydrolysis is thermodynamically ______.

Answer 5

Favored.

Question 6

What catalyzes the hydrolysis of DNA phosphodiester bonds?

Answer 6

Acid catalysis, nucleases

Question 7

Phosphodiester bonds

Answer 7

Links between nucleotide monomers

Question 8

Glycosidic bond

Answer 8

Bond between C1 of sugar and the base nitrogen

Question 9

What is the difference between RNA and DNA structure?

Answer 9

RNA has a 2’-OH group whereas DNA has a 2’-H group on the pentose sugar (ribose vs deoxyribose).

Question 10

What gives RNA the capacity for information as well as catalysis?

Answer 10

2’-OH group on pentose sugar

Question 11

Tautomers

Answer 11

Structural isomers differing only in location of H-atoms and double bonds

Question 12

Adenine is what kind of base?

Answer 12

Purine

Question 13

Guanine is what kind of base?

Answer 13

Purine

Question 14

Cytosine is what kind of base?

Answer 14

Pyrimidine

Question 15

Thymine is what kind of base?

Answer 15

Pyrimidine

Question 16

Uracil is what kind of base?

Answer 16

Pyrimidine

Question 17

A bonds with?

Answer 17

T

Question 18

G bonds with?

Answer 18

C

Question 19

C bonds with?

Answer 19

G

Question 20

U bonds with?

Answer 20

A

Question 21

T bonds with?

Answer 21

A

Question 22

What is Chargaff’s Rule?

Answer 22

[A] = [T] and [G] = [C]

Question 23

What are nucleases?

Answer 23

Enzymes that catalyze the hydrolysis of phosphodiester bonds in both RNA and DNA

Question 24

Describe DNA primary structure

Answer 24

• Directionality 5’ vs 3’

- Individuality (via nucleotide sequence)

Question 25

Describe DNA secondary structure

Answer 25

• DNA double helix

Question 26

Describe DNA secondary structure

Answer 26

(1) DNA double helix (A, B**, Z)
(2) Hairpins
(3) Cruciforms
(4) Triple-helices (H-DNA)
(5) G-Quadruplex

Question 27

B-DNA

Answer 27

• Aqueous environment
• “Normal” / most common
• Perpendicular bases
• Right-handed

Question 28

A-DNA

Answer 28

• Tilted bases
• Major = Minor groove
• Typically for double-stranded RNA and DNA-RNA hybrids
• Right-handed

Question 29

Z-DNA

Answer 29

• Zig-zag phosphates
• Very, very narrow
• Left-handed

Question 30

H-DNA

Answer 30

Triple-helices, Hoogsten-type base pairing

Question 31

What are some secondary structures for double-stranded DNA?

Answer 31

(1) DNA double helix (A, B**, Z)
(2) Hairpins
(3) Cruciforms
(4) Triple-helices (H-DNA)
(5) G-Quadruplex

Question 32

H-DNA

Answer 32

Triple-helices, Hoogsten-type base pairing

Question 33

What are some secondary structures for single-stranded DNA?

Answer 33

(1) Random coil (high temps)
(2) Single-chain, stacked-base helix
(3) Hairpin

Question 34

What is the formula for determining thermodynamic stability?

Answer 34

∆G = ∆H - T∆S

Question 35

What is the formula for determining thermodynamic stability?

Answer 35

∆G = ∆H - T∆S

Question 36

What are some destabilizing forces of the DNA double-helix?

Answer 36

(1) Electrostatic repulsion

2) Entropy (random coil, ∆S>0

Question 37

What are some stabilizing forces of the DNA double-helix?

Answer 37

(1) Hydrogen-bond between base-pairs

(2) van der Waal stacking interaction

Question 38

What are some stabilizing forces of the DNA double-helix?

Answer 38

(1) Hydrogen-bond between base-pairs

(2) van der Waal stacking interaction

Question 39

What are some stabilizing forces of the DNA double-helix?

Answer 39

(1) Hydrogen-bond between base-pairs

(2) van der Waal stacking interaction

Question 40

What is the melting temperature?

Answer 40

Temperature at which ∆G=0. Tm = ∆H / ∆S, for DNA ~95ºC

Question 41

Supercoiling ∆L?

Answer 41

∆L = ∆T + ∆W