Lecture 30: DNA Structure/Function

Question 1

Structural features of DNA

Answer 1

Double helix, negatively charged sugar-Pi backbone, R hand helix w/ major and minor grooves

Question 2

DNA primary structure

Answer 2

5’ end: Pi group (neg. charge)
3’ end: OH group
3’-5’ phosphodiester bonds join NTs in chain

Question 3

DNA secondary structure

Answer 3

Complimentary base pairs:
- A/T 2 H-bonds, G/C 3 H-bonds
Unstrained: ~10 base pairs/turn in helical rise; different number = strained DNA

Question 4

DNA forms

Answer 4

1. B form (hydrated, normal)
2. A form (more dehydrated, narrower)
3. Z form (contains GCGCGC repeat regions, L handed helix often separating active genes)

Question 5

Stabilizing factors for DNA strands

Answer 5

• H-bonds between base pairs (G/C more stable)
• van der Waals forces
• Cellular cations (interactions w/ neg. backbone)

Question 6

Destabilizing factors for DNA strands

Answer 6

• Electrostatic repulsion between neg. charged Pi groups; denaturation often through heat

Question 7

Tm of DNA

Answer 7

Temperature at which 1/2 of DNA sample is denatured; depends on AT/GC content

Question 8

HIV life cycle

Answer 8

1. Cell entry via CD4/CCR5
2. Reverse transcriptase activity creates dsDNA from viral RNA
3. Integrase inserts viral dsDNA into cell genome
4. Transcription of viral mRNA + translation to viral proteins
5. Viral protein maturation via proteases

Question 9

Highly Active Anti-Retroviral Therapies

Answer 9

HAART = therapies for HIV
1. Nucleoside reverse transcriptase inhibitors (NRTIs)
2. Non-nucleoside reverse transcriptase inhibitors (NNRTIs, same effect as 1 but diff. mechanism)
3. Protease inhibitors (prevent HIV virion maturation)
4. Entry inhibitors (prevent HIV entry to cell)
5. HIV integrase inhibitors (prevent HIV DNA integration)

Question 10

DNA tertiary structure

Answer 10

Aka supercoiling; regulated by topoisomerases (Type I/II)

Question 11

Type I topoisomerases

Answer 11

Require energy aka strained DNA.
2 mechanisms, change # of supercoils by 1:
1. Pass through
2. Rotation

Question 12

Type I topoisomerase pass through mechanism

Answer 12

1. Break 1 DNA strand
2. Pass unbroken strand through break
3. Re-ligate

Question 13

Type I topoisomerase rotation mechanism

Answer 13

1. Break 1 DNA strand
2. Broken strand strain → rotation around unbroken strand
3. Re-ligate

Question 14

Type II topoisomerases

Answer 14

Can work on relaxed DNA; used on prokaryotes to introduce supercoils to newly synth. DNA. Changes # of supercoils by 2 via pass through mechanism

Question 15

Topoisomerase inhibitors

Answer 15

Inhibit religation, resulting in nicks/breaks in DNA. Used as anti-neoplastic/anti-microbial agents.

Question 16

Histones

Answer 16

Small, positively charged protein complexes that DNA associates with to form chromatin complexes in eukaryotes.

Question 17

Nucleosome structure

Answer 17

2x (H2A, H2B, H3, H4) tetramers form histone core.
H1 DNA linker keeps DNA wrapped around nucleosome.
Removes 1 DNA turn (negative supercoiling)

Question 18

Eukaryotic DNA tertiary structure

Answer 18

DNA packing with histones forming nucleosomes forming solenoids forming loops; DNA overall shortens by ratio of 10^4.

Question 19

Prokaryotic vs eukaryotic NT sequence and gene organization

Answer 19

Prokaryotes:
1. DNA + protein are colinear (no introns/exons)
2. Gene sequences are all unique or single copy
3. Size of genome = # of genes

Eukaryotes:
1. Only 10% of genome encodes protein
2. Most eukaryotic DNA non-functional or not unique
3. Size of genome doesn’t correspond to # of genes

Question 20

Highly repetitive sequences

Answer 20

• Not transcribed
• Usually short tandem AT rich repeats
• More than 300k copies per genome
• Some functional e.g. telomeres

Question 21

Moderately repetitive sequences

Answer 21

• 2-300k copies per genome
• Usually transcribed, not always translated
• Short/long interspersed sequences (SINES/LINES)
• Highly used genes, interspersed w/ single copy DNA

Question 22

Unique/single copy genes

Answer 22

• All unique, some grouped in families
• Pseudogenes: certain unique non-func. sequences