CHEM 237 - Nucleic acids

nucleic acids

linear polymers of nucleotide monomers

nucleotides

base, sugar and phosphate

purine

2 fused rings (A,G)

pyrimidines

1 ring (C,T)

linkage between nucleotides

phosphodiester linkages between C5 of ribose and C3 carbon of next

why is RNA less stable

more susceptible to nuc attacks by OH on the phosphate

can form more complicated structures due to 2’OH

structure of DNA

2 strands in antiparallel orientation

A + T = 2 H-bonds

C + G = 3 H-bonds

read 5’-3’

B DNA

Major group is wide and deep

minor group is narrow and deep

n = 10

p = 34

Right handed

center is tightly packed

A DNA

major groove is narrow and deep

minor groove is wide and shallow

n = 11.6

p = 24

right handed

centre is not closely packed

Z DNA

real, but less common

Left handed

stacking interactions

Pi orbital overal

solvent exclusion effects: bases associate and exclude water in centre of double helix

Ionic interactions

between phosphate groups can cations to stabilize nucleic acids

Duplex DNA “melts”

2 strands separate, dsDNA to ssDNA

can be monitored by UV absorbance

Duplex denaturation

highly cooperative

all or none response, either folded or unfolded

Measure of Tm

measures helix stability of transition

50% dsDNA

50% ssDNA

Tm trends

1) Tm increases as helix length increases

2) Tm increases as GC (3-Hbonds) content increases

supercoiling

when circular DNA is underwound and causes supercoiling

DNA separated by gel electrophoresis

travels from (-) to (+)

highly supercoiled travels the furthest as it is most compact

how does DNA become underwound

topoisomerases cut and religate DNA

RNA structure

A helices

Secondary structures:

1. duplex

2. stem loop

3. bulge

4. loop

has 2’OH that forms Hbonds to stabilize tertiary structure

tRNA structure

carriers covalently bound amino acid

anticodon loop pairs with codon on mRNA on ribosome

cloverleaf structure

tertiary structure

rRNA structure

features are determined by RNA

protein components are peripheral

• interface between 30S and 50S determined by RNA

ribozyme increases peptide bond formation

small subunit (30s)

composed of 16s rRNA

has 4 domains

large subunit (50s)

composed of 23S and 5S rRNA

what holds the ribosome together

Watson Crick base pairs

non standard base pairs

stacking energy of bases

H bonding between bases, OH, and phosphate

Entropy trap of ribosome

activation energy decreases by immobilizing and orienting substrates in active site

decreases motion and entropy of substrates