DNA/RNA Basics

Question 1

Purines

Answer 1

2 rings

Adenine, Guanine

Question 2

Pyrimidines

Answer 2

1 ring

Thymine, Cytosine, Uracil

Question 3

Nucleoside = ?

Answer 3

Sugar + base

Question 4

Nucleotide = ?

Answer 4

sugar + base + phosphate (mono, di, tri)

Question 5

Solubility rules for bases/nucleotides

Answer 5

pyrimidine > purine

Nucleotide > nucleoside > bases

Question 6

Gout and Lesch Nyhan disease

Answer 6

build up of purines of low solubility in tissues

Question 7

Phosphodiester Linkage

Answer 7

5’ phosphate group attaches to 3’ carbon of adjacent nucleotide

Question 8

AZT drug

Answer 8

• Inhibits reverse transcriptase
• Nucleoside analog does not have a 3’OH, so reverse transcriptase can’t make phosphodiester bond –> terminates the chain

Question 9

Avery, McCloud and McCarty Experiment

Answer 9

• Established DNA as the genetic material
• Encapsulated bacteria that killed mice deactivated. Then mixed with benign unencapsulated bacteria.
• Transformed benign R strain into killer S strain

Question 10

Chargaff’s Rules

Answer 10

• Discovered base pairing

- Proportion of G=C, and A=T

Question 11

Watson and Crick 3-D model traits (6)

Answer 11

• Double Stranded
• right handed helix
• antiparallel
• phosphodiester backbone
• base pairing favored by bonding
• hydrophobic stacking in interior

Question 12

Stability of Double Helix from…

Answer 12

• H-bonds

- Hydrophobic interactions between stacked bases inside

Question 13

Melting Temperature

Answer 13

When 50% of the dsDNA separates

Question 14

If you increase salt concentration you ______ Tm

Answer 14

increase

salt ions neutralize charge on phosphates

Question 15

If you increase chain length you _________ Tm

Answer 15

increase

Question 16

If you increase G:C content you ________ Tm

Answer 16

increase

G:C has 3 H-bonds

Question 17

Forms of DNA Damage (5)

Answer 17

1. Methylation
2. Deamination
3. Depurination
4. UV Crosslinking
5. Alkylation

Question 18

Methylation

Answer 18

• add CH3 group
• does not effect base pairing
• impacts gene regulation

Question 19

5-methylCytosine

Answer 19

methylation of 5 carbon in Cytosine

Question 20

Deamination

Answer 20

• loss of amino group on base (replaced by oxygen)

- impacts DNA structure

Question 21

Deamination of 5-methylCytosine –> ?

Answer 21

Thymine

Question 22

Deamination of Cytosine –> ?

Answer 22

Uracil

Question 23

Depurination

Answer 23

• cleavage of bond between base and sugar

- makes phosphate backbone sensitive to breakage

Question 24

UV Crosslinking

Answer 24

• UV light causes covalent cross-links between adjacent thymines
• Kinks DNA structure, can block replication enzymes

Question 25

Alkylation

Answer 25

Alkyl group added to the N on the bases

Question 26

Actinomycin D

Answer 26

• naturally occurring antibioitc
• intercalating agent
• has aromatic rings that interact with DNA similar to normal stacking interaction of base pairs
• interferes with DNA function

Question 27

Doxorubicin

Answer 27

blocks DNA replication by intercalation

Question 28

DNA vs. RNA

Answer 28

DNA - no hydroxyl group on 2’ position of ribose
-more stable, less prone to hydolyzation by nucleophilic attack
RNA- hydrolyzed, usually single stranded, uses Uracil instead of thymine

Question 29

3 classes of RNA

Answer 29

Structural RNA
Regulatory RNA
Information containing RNA

Question 30

Structural RNAs (4)

Answer 30

rRNA
tRNA
snRNA
snoRNA

Question 31

Regulatory RNAs (2)

Answer 31

miRNA

snoRNA

Question 32

Information containing RNA (1)

Answer 32

mRNA

Question 33

puromycin

Answer 33

• naturally occurring antibiotic
• interferes with translation
• mimics amino-acyl tRNA to terminate translation