Lecture 15

Question 1

Distinguish between purines, pyrimidines; ribonucleosides, deoxyribonucleosides; ribonucleotides and deoxyribonucleotides.

Answer 1

Purines: A + G
Imidazole ring

Pyrimidines: T + C + U
N at c1,3,6

nucleoside:
- nitrogenous base and a ribose or deoxyribose sugar

Nucleotide
Nitrogenous base + ribose or deoxyribose sugar + phosphate group
- base attached via b n glycosidic bind attached to nitrogen #1 of pyrimidine and #9 of purine

Question 2

Describe the phosphodiester bond

Answer 2

Phosphodiester Bond:
DNA/RNA polymerase catalyze a the formation of a phosphodiester bond between 3OH group of deoxyribose /ribose and the 5 phosphate of dNTP/NTP precursor

Because synthesisis from 5-3 we are adding to the 3OH

Cleaved triposphate is the energy source for the phosphodiester bond formation

Question 3

List and describe the important features of the Watson-Crick DNA double helix (complementary, antiparallel, and forces stabilizing the helix).

Answer 3

Complementary:
Nucleotide bases are complementary held together by h bonds
- bases are perpendicular to axis of symmetry
A-T 2 h bonds
G-C 3 h bonds

Groove

• major groove: DNA binding protein interact with protein and make contact with the bases
• minor groove

Antiparallel
The two right handed chains are antiparallel so that one chain is 5-3 and the other is 3-5

Question 4

Discuss some of the physicochemical properties of DNA

Answer 4

Physicochemical properties of DNA:
B DNA
Right handed
Variation depending on nucleotides present

Z DNA
Left hand
Alternating pyrimidines and purines

A DNA
Right hand
Dehydrated state

Question 5

Describe the basic structures and roles of the major classes of RNA (mRNA, tRNA, rRNA, snRNA, miRNA)

Answer 5

mRNA: codon info for translation

tRNA: stem loop structure formed by intramolecular h bonds
- carries amino acid to ribosome during translation

rRNA: complexes with protein to form ribosome
- overall structure of ribosome
- catalytic activity; form covalent peptide bonds
82-% of total RNA

snRNA: involved in spicing; remove non coding information /introns in RNA
- involved in reg of transcription factors, RNA pol 2 activity and telomere maintenance

miRNA: silencing of gene expression

• translation is repressed
• target mENA are degraded

Question 6

Discuss the medical significance and mechanism of action of nucleoside and nucleotide analogs used as drugs listed below.

Anti-viral nucleosides: Azidothymidine (AZT), Didanosine (ddI), acyclovir

Answer 6

Anti-Viral NucleoSides:

1. AZT viral transcriptase inhibitor
   - no phosphate on 5 phosphate group and we want nucleoside triposphate so we can cleave triposphate to get energy. Without the 3OH group we cannot add more synthesis stops
   - Azt uses host cellular kinase to phosphorylate and then use viral reverse transcriptase to incorporate into ds DNA
   - doesn’t have the 3oh instead has 3n

• prolongs life of HIV patients
• reduce mom to baby transmission

2. DDL viral reverse transcriptase inhibitor
   - same mechanism and instead of 3oh has nothing
   - drug has. 100-300 greater affinity for reverse transcriptase than euk DNA polymerase

• HIV combo drug

3. Acyclovir viral DNA polymerase inhibitor
   - uses viral thymidine kinase to phosphorylate acyclovir then uses host cellular kinase for chain termination
   - acyclovir is activated only in infected cells because only infected cells have girls kinase

Question 7

Discuss the medical significance and mechanism of action of nucleoside and nucleotide analogs used as drugs listed below.

Anti-viral nucleotides: Tenofovir

Answer 7

Anti-viral nucleotides:

Tenofovir

• no 3oh again
• does have phosphate but the other two phosphates needed to make ATP to drive phosphodiester bond are coming from the host cellular kinase

Question 8

Discuss the medical significance and mechanism of action of nucleoside and nucleotide analogs used as drugs listed below.

Anti-cancer agents: cytosine arabinoside (Cytarabine), adenosine arabinoside
(Vidarabine)

Answer 8

Anti-cancer agents:

1. Cytosine arabinoside
   Cystosine nucleoside analogue
   - no phosphate
   - does have a 3oh but the 2oh is stereohinderance due to linear formation
2. Adenosine arabinoside
   Adenosine nucleoside analogue
   - same exception that it has 3oh group but the 2oh is steric hinders de so prevents DNA elongation
   - has adenosine in the 1c

• anti neoplastic agent; relapsed childhood acute lymphoblastic leukemia
  Herpes simplex infections

Question 9

Discuss the medical significance and mechanism of action of nucleoside and nucleotide analogs used as drugs listed below.

DNA hypomethylation agents: 5-azacytidine, 5-aza-2’-deoxycytidine (Decitabine)

Answer 9

DNA hypomethylation agents:

1. Cytidine analogue
   DNA hypo methylation agents
   - hypo methylation = active
   - when incorporated into DNA and RNA cause hypo methylation because cannot add n to position 5
   - bind and inhibit DNA methyl transferase enzymes
   P 15 inhibits CDK and prevents cell growth

• meylodysplastic syndrome
• acute myeloid leukemia