Nucleic Acids

Question 1

What do the major and minor grooves do?

Answer 1

Provide access for binding of regulatory proteins along the DNA chain

Question 2

What does it mean to be antiparallel?

Answer 2

5’ end of one strand is paired with 3’ end of other strand

The two strands are opposite in direction

Question 3

Two key features of Z-DNA?

Answer 3

Left handed and high GC content (also rare)

Question 4

Most common structural form of DNA?

Answer 4

B-DNA (Watson and crick form); right handed

Question 5

Another word for renaturation

Answer 5

Reannealing

Question 6

DNA with more ___ bonds will denature slowest

Answer 6

CG

Question 7

What type of interaction between stacked bases?

Answer 7

Hydrophobic

Question 8

Difference in structure between DNA and RNA?

Answer 8

RNA has -OH attached to carbon 2, DNA does not (just H)

Question 9

Structural difference between Uracil and Thymine?

Answer 9

Thymine is exactly same as Uracil except with an added methyl group

Question 10

What provides the energy necessary for nucleic acid synthesis?

What makes these compounds high energy?

Answer 10

Nucleotide triphosphates (NTPs) such as ADP and ATP

The energy associated with anhydride bonds

Question 11

What is attached to carbon 3?

Answer 11

OH group (in both DNA and RNA) required for polymerization of nucleic acids, joined to the 5’ carbon through a phosphodiester bond

Question 12

1. Free ___ group at 3’ end

2. Free ___ group at 5’ end

Answer 12

1. Hydroxyl

2. Phosphate

Question 13

Complementary means?

By what kind of bonds?

Answer 13

A always pairs with T; G always pairs with C

Hydrogen bonds

Question 14

5’-AGGTCCTTAGG-3’

What is complementary strand of above?

Answer 14

5’-CCTAAGGACCT-3’

Question 15

What is the name of the rule that allows you to determine the % of each of the 4 nucleotides

Answer 15

Chargaff’s Rule

Question 16

1. Denaturation breaks____ but does not break _____

2. What does denaturation result in?

Answer 16

1. Denaturation breaks hydrogen bonds between base pairs but does not break phosphodiester bonds linking the nucleotides
2. Single stranded DNA (ssDNA)

Question 17

What does Tm represent?

When will you have a higher Tm?

Answer 17

Temperature required to melt 50% of the DNA in a sample

When there are high GC content DNA

Question 18

1. DNA gyrase is a type of ____ that is inhibited by ____

2. DNA gyrase promotes ___

Answer 18

1. DNA gyrase is a type of topoisomerase II that is inhibited by quinolones
2. Supercoiling (quinolones inhibit supercoiling)

Question 19

If DNA is relaxed, what cannot happen?

Answer 19

Division (needs to be condensed)

Question 20

Quinolones function as ___ but?

Answer 20

Antibiotics but are toxic in high concentrations (because they inhibit supercoiling)

Question 21

Histones are rich in __ and ___; so they bind strongly to ____

Answer 21

Lysine and arginine (+ charged, basic amino acids); so they bind strongly to negatively charged DNA

Question 22

1. Histones help DNA to ____

2. Answer from 1. Is good for?

Answer 22

1. Condense

2. Condensation is good for division (beads on a string is good for gene expression; decondensed a bit)

Question 23

What is “beads on a string”?

What is it sensitive to?

What is it necessary for?

Answer 23

A group of free nucleosomes (without H1)

Sensitive to nuclease degradation

Necessary for gene expression

Question 24

Type of RNA that can base pair back on itself?

Answer 24

TRNA

Question 25

2 features that eukaryotic mRNA have that prokaryotic mRNA do not have?

Answer 25

M7G-cap on 5’ terminus and a poly-a tail on 3’ terminus

Question 26

1. Function of rRNA? 2. Sizes of eukaryotic and prokaryotic sub units of rRNA? 3. Antibiotics usually target which sub unit? 4. What does the S unit mean?

Answer 26

1. Combine with proteins to form ribosomes 2. Pro: 50S + 30S = 70S Eu: 60S + 40S = 80S 3. 30S 4. Means you’re talking about the ability of this component to pass through a gradient when being centrifuged

Question 27

Where is the amino acid attachment site on tRNA?

Answer 27

CCA-3’ terminus

Question 28

Why is tRNA considered to have unusual bases?

Answer 28

It’s the only RNA that contains a T

Question 29

Differences in tRNA lie where?

Answer 29

In the anti codon region

Question 30

What is the function of the anticodon loop?

Answer 30

Determines amino acid specifically by base pairing with mRNA during translation

Question 31

1. SnRNA (small nuclear RNA) is only located where? | 2. Function?

Answer 31

1. In the nucleus of eukaryotes | 2. Combine with certain proteins to form snRNPs used for splicing hnRNA to form mRNA

Question 32

What are ribozymes?

Answer 32

RNAs that act as enzymes