biochem: nucleotides and nucleic acids

Question 1

DNA VS RNA

Answer 1

1. stores genetic info
2. carries genetic info, catalytic rxn

Question 2

nucleoside vs nucleotides

Answer 2

1. sugar (pentose), and purine or pyrimidine base
2. same but with phosphate (1,2,or 3)

Question 3

what rxn is binding DNA

Answer 3

anabolic.
creates order, need energy

Question 4

name the bases of ribonucleotides and deoxynucleotides

Answer 4

1. adenylate, guanylate, cytidylate, and uridylate
2. deoxyadenosine deoxyguanosine, deoxythymidine, deoxycytidine

Question 5

nucleotide units held together by

Answer 5

phosphodiester bonds

Question 6

Base stacking

Answer 6

Hydrophobic base pairs stack on eachother to create a hydrophobic interior. They interact w/ VdW (cheap but useful when many) and weak dipole dipole bonds

Stacking=important as H-bonding stabalizing the helical structure of dna (drawing at pg 181)

Question 7

Major and minor grooves

Answer 7

Wind along molecule parallel to the phosphodiester backbones. Proteins can bind to specific nucleotide sequences in these grooves. Allows control of gene expression

Question 8

Nucleic acid flexibility

Answer 8

Sugar phosphate backbone flexible and can rotate in many bonds- many combos

7 bonds total

Diff conformations allows for secondary and tertiary nucleic acids

Question 9

DNA denturation

Answer 9

Heat= rapid reforming of h-bonds base pairs and stacking

Increase on temp= more thermal motion which shift equilibrium to strand separation

Question 10

What causes dentures in dna strand

Answer 10

Heat, enzymes (replication), ph extremes

Question 11

Base pairs have what bonds

Answer 11

H-binding w/ eachother

G&C have 3 h-bonds
A-T have 2

Question 12

Monitoring denturation of dna

Answer 12

• by using changes in absorption of uv light

Mononucleotides (when dna by itself) absorb UV light (260 nm often used) due to their aromatic ring structure.

Base stacking in DNA decreases this ability to absorb light (hypochromic effect).

Melting causes increased absorption of UV light since base pairs are no longer stacked and interacting with each other

Question 13

Tm in graph of dna denturation

Answer 13

melting temperature where half of the base pairs in DNA are denatured (single stranded) and half are still double stranded. Higher tm= harder yo denture the dna

Question 14

Relationship between G-C content and melting

Answer 14

DNA with increasing
%GC has higher Tm since

(i) GC base pairs have 3 H-bonds versus the 2 for AT and

ii) GC base pairs have stronger stacking interactions than AT
base pairs.

The straight line means that the Tm is proportional to the base composition of DNA.

Question 15

what enzyme can replicate the genome via strand separation and synthesis of a daughter strand

Answer 15

DNA polymerases

Question 16

Why rna is less stable

Answer 16

Ribose sugar, not deoxyribose

due to the hydroxyl group’s presence, which makes it more prone to hydrolysis and destruction.

DNA is resistant since it lacks OH on the 2’C.

Question 17

How does rna acquire double stranded character

Answer 17

RNA
* RNA is single stranded but it can fold back on itself to form base-paired regions such as hairpins, therefore acquiring double stranded character (secondary structure)

Question 18

how is RNA like proteins

Answer 18

an example of tertiary structure

like protein, very complex folding

• like protein, some of these structures have catalytic properties (makes activation E lower since structure can engage with favourably w/ substrate)
• unusual base pairs (see G-U base)

Question 19

why do we want maximized h-bonds

Answer 19

help the proteins and nucleic acids form and maintain specific shapes