Lecture 30: DNA Structure/Function Flashcards
Structural features of DNA
Double helix, negatively charged sugar-Pi backbone, R hand helix w/ major and minor grooves
DNA primary structure
5’ end: Pi group (neg. charge)
3’ end: OH group
3’-5’ phosphodiester bonds join NTs in chain
DNA secondary structure
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
DNA forms
- B form (hydrated, normal)
- A form (more dehydrated, narrower)
- Z form (contains GCGCGC repeat regions, L handed helix often separating active genes)
Stabilizing factors for DNA strands
- H-bonds between base pairs (G/C more stable)
- van der Waals forces
- Cellular cations (interactions w/ neg. backbone)
Destabilizing factors for DNA strands
- Electrostatic repulsion between neg. charged Pi groups; denaturation often through heat
Tm of DNA
Temperature at which 1/2 of DNA sample is denatured; depends on AT/GC content
HIV life cycle
- Cell entry via CD4/CCR5
- Reverse transcriptase activity creates dsDNA from viral RNA
- Integrase inserts viral dsDNA into cell genome
- Transcription of viral mRNA + translation to viral proteins
- Viral protein maturation via proteases
Highly Active Anti-Retroviral Therapies
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)
DNA tertiary structure
Aka supercoiling; regulated by topoisomerases (Type I/II)
Type I topoisomerases
Require energy aka strained DNA.
2 mechanisms, change # of supercoils by 1:
1. Pass through
2. Rotation
Type I topoisomerase pass through mechanism
- Break 1 DNA strand
- Pass unbroken strand through break
- Re-ligate
Type I topoisomerase rotation mechanism
- Break 1 DNA strand
- Broken strand strain → rotation around unbroken strand
- Re-ligate
Type II topoisomerases
Can work on relaxed DNA; used on prokaryotes to introduce supercoils to newly synth. DNA. Changes # of supercoils by 2 via pass through mechanism
Topoisomerase inhibitors
Inhibit religation, resulting in nicks/breaks in DNA. Used as anti-neoplastic/anti-microbial agents.
Histones
Small, positively charged protein complexes that DNA associates with to form chromatin complexes in eukaryotes.
Nucleosome structure
2x (H2A, H2B, H3, H4) tetramers form histone core.
H1 DNA linker keeps DNA wrapped around nucleosome.
Removes 1 DNA turn (negative supercoiling)
Eukaryotic DNA tertiary structure
DNA packing with histones forming nucleosomes forming solenoids forming loops; DNA overall shortens by ratio of 10^4.
Prokaryotic vs eukaryotic NT sequence and gene organization
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
Highly repetitive sequences
- Not transcribed
- Usually short tandem AT rich repeats
- More than 300k copies per genome
- Some functional e.g. telomeres
Moderately repetitive sequences
- 2-300k copies per genome
- Usually transcribed, not always translated
- Short/long interspersed sequences (SINES/LINES)
- Highly used genes, interspersed w/ single copy DNA
Unique/single copy genes
- All unique, some grouped in families
- Pseudogenes: certain unique non-func. sequences
