DNA/RNA Basics Flashcards
Purines
2 rings
Adenine, Guanine
Pyrimidines
1 ring
Thymine, Cytosine, Uracil
Nucleoside = ?
Sugar + base
Nucleotide = ?
sugar + base + phosphate (mono, di, tri)
Solubility rules for bases/nucleotides
pyrimidine > purine
Nucleotide > nucleoside > bases
Gout and Lesch Nyhan disease
build up of purines of low solubility in tissues
Phosphodiester Linkage
5’ phosphate group attaches to 3’ carbon of adjacent nucleotide
AZT drug
- Inhibits reverse transcriptase
- Nucleoside analog does not have a 3’OH, so reverse transcriptase can’t make phosphodiester bond –> terminates the chain
Avery, McCloud and McCarty Experiment
- 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
Chargaff’s Rules
- Discovered base pairing
- Proportion of G=C, and A=T
Watson and Crick 3-D model traits (6)
- Double Stranded
- right handed helix
- antiparallel
- phosphodiester backbone
- base pairing favored by bonding
- hydrophobic stacking in interior
Stability of Double Helix from…
- H-bonds
- Hydrophobic interactions between stacked bases inside
Melting Temperature
When 50% of the dsDNA separates
If you increase salt concentration you ______ Tm
increase
salt ions neutralize charge on phosphates
If you increase chain length you _________ Tm
increase
If you increase G:C content you ________ Tm
increase
G:C has 3 H-bonds
Forms of DNA Damage (5)
- Methylation
- Deamination
- Depurination
- UV Crosslinking
- Alkylation
Methylation
- add CH3 group
- does not effect base pairing
- impacts gene regulation
5-methylCytosine
methylation of 5 carbon in Cytosine
Deamination
- loss of amino group on base (replaced by oxygen)
- impacts DNA structure
Deamination of 5-methylCytosine –> ?
Thymine
Deamination of Cytosine –> ?
Uracil
Depurination
- cleavage of bond between base and sugar
- makes phosphate backbone sensitive to breakage
UV Crosslinking
- UV light causes covalent cross-links between adjacent thymines
- Kinks DNA structure, can block replication enzymes
Alkylation
Alkyl group added to the N on the bases
Actinomycin D
- naturally occurring antibioitc
- intercalating agent
- has aromatic rings that interact with DNA similar to normal stacking interaction of base pairs
- interferes with DNA function
Doxorubicin
blocks DNA replication by intercalation
DNA vs. RNA
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
3 classes of RNA
Structural RNA
Regulatory RNA
Information containing RNA
Structural RNAs (4)
rRNA
tRNA
snRNA
snoRNA
Regulatory RNAs (2)
miRNA
snoRNA
Information containing RNA (1)
mRNA
puromycin
- naturally occurring antibiotic
- interferes with translation
- mimics amino-acyl tRNA to terminate translation