Lecture 3

Question 1

What is a nucleobase?

Answer 1

Heterocycle

Question 2

What is a nucleoside?

Answer 2

Base + Ribose

Question 3

What is a nucleotide?

Answer 3

Base + ribose + PO4

Question 4

On what carbon is the variable OH and H (for RNA and DNA)?

Answer 4

2

Question 5

Nucleobases are ___ structure, ribose rings are ___

Answer 5

Flat
Puckered

Question 6

Are all the nucleobases neutral at pH 7?

Answer 6

Yes

Question 7

When are nucleic acid modifications done?

Answer 7

After DNA synthesis

Question 8

What kind of linkages form the backbone of nucleic acid polymers?

Answer 8

Phosphodiester linkages

Question 9

What are long chains of nucleic acid polymers called?

Answer 9

Oligonucleotides

Question 10

Sequences are read from the _’ to _’

Answer 10

5 to 3

Question 11

What is more stable, DNA or RNA?

Answer 11

DNA (half life of 100,000 years versus 1 day)

Question 12

How is RNA cleaved?

Answer 12

RNAses and self cleaving

Question 13

Which bonds cannot rotate in DNA?

Answer 13

The ones that make up the ribose

Question 14

How many rotatable bonds are there in DNA?

Answer 14

7

Question 15

How many bonds do not rotate freely?

Answer 15

4

Question 16

What does the limited rotation of 4 bonds give rise to?

Answer 16

Ring pucker (exo vs endo)

Question 17

What are the two backbone conformations?

Answer 17

C-2 exo and endo
C-3 exo and endo

Exo is a phantom position and endo is the lifted ring carbon

Question 18

What is Chi in the context of DNA?

Answer 18

torsion angle around N-glycosidic bond

Question 19

What is Chi for syn conformation?

Answer 19

0 degrees

Question 20

What is Chi for anti conformation?

Answer 20

180 degrees

Question 21

What conformation is found in B-form DNA?

Answer 21

Anti conformation

Question 22

Based on Watson-Crick base pairing, what is stronger, a GC or AT bond?

Answer 22

GC based on there being 3 H bonds

Question 23

How many base pairs per helical turn?

Answer 23

10.5 base pairs

Question 24

___ ___ ___ dominated electrostatics in DNA

Answer 24

Negatively charged phosphate backbone dominates electrostatics

Question 25

Where do proteins often bind to the DNA?

Answer 25

The major and minor grooves

Question 26

What is the difference of the major and minor grooves?

Answer 26

They have different acceptors and donors of H-bonds on each face

Question 27

How does sequence specific protein binding happen?

Answer 27

Electrostatic and H-bonding interactions with polar groups in the DNA grooves

Question 28

What is [Zt]?

Answer 28

Total single strand DNA

Question 29

dH0u and dS0u are ___ for a given DNA double helix

Answer 29

Constant

Question 30

DNA melting is ___-dependent because it involves dimerization

Answer 30

Concentration

Question 31

Describe DNA synthesis (the lab kind)

Answer 31

- Nucleoside protected at 5' hydroxyl - Attach resin to a nucleoside at the 3' hydroxyl - Protecting group removed - Next nucleotide protected at the 3' hydroxyl is added (that new nucleotide's protection is removed) - Oxidation to form triester - Remove protecting groups from bases - Remove cycloethyl groups from phosphates - Cleave chain from silica support

Question 32

How do you clone bacteria in DNA?

Answer 32

- EcoRI restriction endonuclease (sticky end) and Pvull restriction endonuclease (clean cut) create a segment of DNA that will create a plasmid cloning vector - DNA ligase then attaches that vector to a plasmid with a ampicillin resistance gene - let the bacteria duplicate - select for colonies containing plasmid by introducing them to ampicillin - purify plasmid - analyze by gel

Question 33

What happens first in DNA replication?

Answer 33

Strand separation

Question 34

After strand separation, how are new strands made?

Answer 34

Each strand will serve as a template for the synthesis of a new strand

Question 35

What catalyzes the DNA unwinding and synthesis?

Answer 35

DNA polymerases which are complexes of many protein subunits

Question 36

How do NTPs build DNA? (dXTP)

Answer 36

Nucleophillic attack of the 3' OH of the growing strand displaced P2O7 from an incoming NTP to form the phosphodiester backbone

Question 37

DNA polymerase 1 requires ___ and ___

Answer 37

Template strand and primer strand

Question 38

Triphosphate hydrolysis is catalyzed by _?

Answer 38

Mg2+, the ions stabilize the pentavalent transition state

Question 39

How does DNA Polymerase prevent non-cognate base pairs to H-bond? (i.e. A-G pairing)

Answer 39

Steric fits which DNA polymerase uses to be very specific with base pairing

Question 40

What is supercoiling good for?

Answer 40

Relieves strain derived from underwinding

Question 41

What is a topoisomer?

Answer 41

Two forms of circular DNA that differ only in linking number

Question 42

What do topoisomerases do?

Answer 42

Unwind and rewind DNA during transcription and replication (cleaves one strand by using a tyrosine to attack the phosphate and fold the other side over before reconnecting the strand)

Question 43

What are nucleosomes?

Answer 43

DNA wrapped around histone proteins

Question 44

What are chromatin fibers made of?

Answer 44

Further wrapped nucleosomes

Question 45

What are histones?

Answer 45

Heterooctamers with many basic residues in their exteriors (leading to + charge)

Question 46

The interaction of histones' basic residues with the phosphate groups are regulated by

Answer 46

Reversible acetylation

Question 47

What is the dominant form of DNA in free DNA and chromosomal DNA?

Answer 47

B form

Question 48

When does A form DNA occur?

Answer 48

When water content of solution decreases and it becomes the more compact A form

Question 49

What is the Z form of DNA?

Answer 49

A rarer form of DNA caused by stretches of alternating purines and pyrimidines

Question 50

What can palindromic DNA do?

Answer 50

Hybridize with itself

Question 51

What are G-quadruplexes? Where do they occur? What do they bind to? Intramolecularly, intermolecularly, or both?

Answer 51

Occur in telomeres 4 guanines that form H-bonds with one another and surround a cation (usually K+) Can occur both intra and intermolecularly

Question 52

How do telomeres act as a molecular clock?

Answer 52

They are shortened with each cell cycle until they either cause apoptosis or cancer

Question 53

RNA is unstable under ___ conditions

Answer 53

Basic, it will cause cleavage

Question 54

When RNA does adopt a double stranded configuration, it adopts an ___ form helix

Answer 54

A

Question 55

Backbone cleavage is usually catalyzed by

Answer 55

Enzymes (RNAse A)

Question 56

What kind of secondary structure does RNA usually have?

Answer 56

A complex one with secondary structure motifs

Question 57

How do cations interact with RNA?

Answer 57

They can bind to lone pairs on Ns and Os, phosphate backbone and ribose OH so it can change structure depending on ion concentration

Question 58

___ nucleic acids, non-watson-crick nucleobase interactions, and backbone-nucleobase interactions lead to __ structure

Answer 58

Modified tRNA

Question 59

What are Aptamers?

Answer 59

RNA molecules that can fold up to bind small molecules like ATP

Question 60

Can RNAs act as enzymes?

Answer 60

Yes they can do self cleavage and it often involved bound metal ions

Question 61

What can self-splicing introns do?

Answer 61

They can turn into catalytically active 3D structures that cleave RNA backbones and form a lariat

Question 62

What is the ribosome mainly composed of?

Answer 62

RNA