Molecular and Cellular Biology (1)

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

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)

1. Non specific DNA interactions

2. Specific DNA interactions

Protein interacts with phosphate or sugar of DNA without selecting a specific site on the strand.

Proteins interact with specific nucleotides in the DNA strand.

proteins discriminate between different bases in a DNA sequence via direct interactions with the DNA bases.

sequence dependent deformability or structural differences between DNA molecules that contribute to their discrimination by proteins.

mechanisms by which genomic targeting is encoded in multi-protein complexes.

wider and shorter

wider and deeper major groove

more narrow and shallower minor groove

RNA-DNA & RNA-RNA duplexes

H bond donor

H bond accepter 

Methyl

Hydrogen

It is due to the acid character of the phosphate group, which is deprotonated at the neutral pH, producing H+.

The 2' hydrogen makes DNA more stable than RNA.

True

No, but RNA can due to the 2' OH.

Increasing temperature, breaks H bonds

Agents that destabilized H bonds (formamide or urea)

extreme pH changes, this causes repulsions between bases.

They shields negative charges of the DNA backbone.

Soluble

Insoluble

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