Nucleic Acids

Question 1

Distinguish purines and pyrimidines bases

Answer 1

purines have two rings: PURe As Gold (adenine, guanine)

pyrimidines have one ring: CUT PYe. (Cytosine, Urasil, Thymine)

Question 2

Distinguish ribose and deoxyribose

Answer 2

deoxyribose does not have a OH group at the 2’ carbon on the ring.

Question 3

distinguish nucleotides, nucleosides di and tri phosphates

Answer 3

nucleotide- base, sugar, phosphate

nucleoside- base, sugar

Question 4

discuss solubility of components of nucleotides and related diseases

Answer 4

solubility- pyrimidines > purines. Nucleotides>nucleosides>bases.

Gout and Lesch-Nyhan disease are caused by accumulation of purines.

Question 5

Discuss chemistry in phosphodiester linkage of DNA and RNA polynucleotide strands.

Answer 5

phosphodiester linkage between 5’ phosphate of one nucleotide to 3’OH of another. enzymes add nucleotide 5-3

Question 6

What drug fights HIV by lacking a 3’OH and acts like a nucleotide, preventing polymerization of virus?

Answer 6

DDI

Question 7

Chargaffs rules

Answer 7

Molar amts of Pur and Pyr was always equal in any cellular DNA sample. Led to base-pairing idea

Question 8

Describe Watson-Crick Model model

Answer 8

Double Helix- 2strands intertwined in right-handed turn
Anti-Parralel stands- stand 1 is 5-3 and other is 3-5
Phosphate Backbone- outside of the helix with one (-) per phosphate. Geometry only allows for AT and GC pairing.
Base Pairing- through H-bonds in the center of the helix and stacking (hyrdophobic interactions).
Melting Temp- when 50% of molecules are separated. GC has 3 H-bonds, AT has 2. So more GC is more stablility.

Question 9

Describe basis for stability of double helix in solution

Answer 9

higher salt concentration helps stability by neutralizing phosphate (-).
extremes of pH- alter base ionization states
increase in DNA length increases melting temp.

Question 10

Discuss DNA melting/annealing is weakened by a mismatch. This is diagnosed by a complementary ‘probe’.

Answer 10

.

Question 11

DNA and RNA similarities and differences

Answer 11

Ribose has 2’OH, which makes it more susceptible to hydrolysis. Allows cell to regulate [RNA] thus gene expression. RNA has Uracil instead of thymine.
Usually is single stranded

Question 12

3 classes of RNA in humans

Answer 12

Informational- mRNA (translated into protiens)
Structural- tRNA, rRNA, snRNA.
Regulatory- microRNA, small interfering RNA, long noncoding RNA.

Question 13

How does puromycin mimic amino-acyl tRNA to terminate translation?

Answer 13

it mimics, the ‘acceptor’ 3’end in tRNA, and it binds in the ribosome during translation and terminates it. Streptomuces makes puromycin and also an inhibitor for it.

Question 14

DNA damage-Base Alkylation:

Answer 14

caused by benzene from coal and cig smoke, forms large covalent adducts to DNA. Not easily repaired and blocks replication and transcription. used against cancer.

Question 15

DNA damage- De-purination

Answer 15

low pH can break bond between base and sugar

Question 16

DNA damage- oxidative damage

Answer 16

oxygen free radicals from mitochondria can disrupt DNA stx, by adding OH groups

Question 17

DNA damage- Thymine Dimers

Answer 17

UV light causes covalent bonding of adjacent thymines on same strand.

Question 18

DNA damage- Deamination of bases-

Answer 18

nitrous acid from nitrosamine in cigarrete smoke, cleave the amines. If a nromally methylated C loses amine group, it becomes T. causes mismatch and point mutation. Mismatch is fixed, but eh point is often missed.

Question 19

DNA damage- Methylation of Adenine-

Answer 19

in bacteria helps repair enzymes identify older strands.

Question 20

DNA damage- Methylation of Cytosine-

Answer 20

in eukaryotes C’s adjacent to G’s (CpG) are methylated in the 5’ position, silencing transcription.

Question 21

Drugs-Cisplatin

Answer 21

base akylating agent

Question 22

Drugs- Actinomycin D

Answer 22

natural antibiotic. “intercalates” (inserts ring stx into DNA sirupting stx.) prevents replication and transcription.

Question 23

Drugs- Doxorubicin

Answer 23

similar to Actinomycin

Question 24

Drugs- Etoposide and Camptothecin

Answer 24

chemotherapuetics that target topoisomerases (prevent supercoiling). Leaves breaks in DNA that aren’t repaired.