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What is the central dogma of DNA?
DNA is an informational molecule
genes are composed of DNA
genes code for proteins
transcription -- RNA using DNA template
RNA processed to mRNA
mRNA translated into protein by ribosome
Describe the characteristics of B-DNA.
Double-stranded uniform polymer
Right handed double helix
Two DNA strands of double helix antiparallel
Directionality 5’ --> 3’
Monomers are nucleotides (A, T, G, C)
Core of stacked base-pairs with edges exposed
10 base pairs per turn
Highly negatively charged phosphodiester backbone
H-bonds, hydrophobic and VDW contribute to stability
Major Groove - Width (13.6 Å) & Depth (5.8 Å)
Minor Groove - Narrow (9.6 Å) & Depth (6.7 Å)
Persistence length of DNA ~150 base pairs
Bending preference of A-T stretches (4-6 nucleotides)
List the 2 types of protein DNA interactions.
1. Non specific DNA interactions
2. Specific DNA interactions
Describe Non specific DNA interactions.
Protein interacts with phosphate or sugar of DNA without selecting a specific site on the strand.
Describe specific DNA interactions.
Proteins interact with specific nucleotides in the DNA strand.
Describe direct readout (base readout) interactions.
proteins discriminate between different bases in a DNA sequence via direct interactions with the DNA bases.
Describe indirect readout (shape readout) interactions.
sequence dependent deformability or structural differences between DNA molecules that contribute to their discrimination by proteins.
Describe Higher Order Multi-protein Recognition Codes.
mechanisms by which genomic targeting is encoded in multi-protein complexes.
Compare A-DNA to B-DNA.
wider and shorter
wider and deeper major groove
more narrow and shallower minor groove
RNA-DNA & RNA-RNA duplexes
What functional groups are found in major and minor grooves?
H bond donor
H bond accepter
Where does the name nucleic acid come from?
It is due to the acid character of the phosphate group, which is deprotonated at the neutral pH, producing H+.
What makes make DNA more stable than RNA?
The 2' hydrogen makes DNA more stable than RNA.
True or false: the 2' OH in RNA results in slow hydrolysis of phosphodiester bond.
Can DNA function as a catalytic molecule?
No, but RNA can due to the 2' OH.
What are the 3 methods utilized in denaturation of DNA?
Increasing temperature, breaks H bonds
Agents that destabilized H bonds (formamide or urea)
extreme pH changes, this causes repulsions between bases.
How do high cation concentrations stabilize duplex DNA?
They shields negative charges of the DNA backbone.
DNA is ___ in water.
DNA is ___ in alcohol.
DNA molecules longer than ___ kb tend to break if not handled gently.