12. Nucleic Acid

nucleic acids are linear polymers of nucleotide monomers

1. ribonucleotides (ribose)

2. deoxyribonucleotides (2’deoxyribose)

each nucleotide consists of

base, sugar, and phosphate

bases can be

purines (a,g) or pyrimidines (c, t/u)

nucleotides are linked via

phosphodiester linkage between the C5’ carbon of one ribose and the C3’ carbon of next

DNA is much less susceptible to hydrolysis than RNA, which

hydrolyzes relatively easily due to base catalyzed attack by the C2’OH on the phosphate

DNA is more stable for storage of genetic information, RNA can form

more complicated structures due to 2’OH (can make extra H-bonds)

two strands of DNA associate in an antiparallel orientation with

A bases interacting with T (2 H bonds) and G bases interact with C bases (3 H bonds)

DNA sequences read

5’ → 3’

B DNA grooves

major groove is wide and deep, minor groove is narrow and deep

B DNA n and p

1. n=10 base pairs/turn

2. pitch 34 armstrongs/turn

3. right handed (5’ → 3’)

centre of B-DNA

close packed, base pairs centred on helix

B-DNA is thought to be the

native (biologically functional) form of DNA

A DNA grooves

major groove is narrow and deep, minor groove wide and hsallow

A-DNA n and p

1. n= 11.6 base pairs/turn

2. 34 armstrongs/turn

3. right handed

centre of A-DNA

not closely packed, base pairs off centre

Z-dna strange looking, real, less common

left handed

H-bonds with the base pairs: important for

structural specificity (similar to effects of H-bonding in specificity of folded protein structure), relatively small energy contribution

what are stacking interactions

1. pi orbital overlap

2. solvent exclusion effects: different thermodynamics than the hydrophobic but similar result → bases associate and exclude water in centre of double helix

ionic interactions between ____ also important

phosphate groups (-) and bound cations (+) especially Mg2+ stabilize nucleic acids

forces that hold dna strands together

1. h bonds

2. base stacking: stacking energy

   • pi orbital overlap

   • solvent exclusion effects

3. ionic interactions

Duplex stability depends on

sequence

DNA “melts” 2 strands separate

melting can be monitored by UV absorbance

as for protein denaturation, duplex DNA denaturation is

highly cooperative (all-or-none, 2 state) and can be reversible

Temperature for midpoint of transition (or melting temp) is a

measure of helix stability

Tm increases as

1. helix length increases (more bp)

2. GC content increases (more H bonding)

circular DNA forms

highly twisted structures

circular DNA is underwound which causes

supercoiling, this is important in transcription and translation

equivalent topologically:

interconvertible without breaking any covalent bonds

how does dna become underwound

topoisomerases: cut, turn, and religate DNA

supercoiling creates strain which

helps to unwind and separate the duplex strands for DNA replication, RNA transcription etc

RNA helices are A type helices, there is no room

for the 2’OH group in the B type helix

DNA-RNA hybrid helices adopt

the A-type conformation

RNA secondary structures (4)

1. duplex

2. stem-loop

3. bulge

4. loop

RNA has 2’OH that can

form H bonds to stabilize tertiary structure

e.g of 2’oh forming h bonds to stabilize h bonding

• trna carries covalently bound amino acid: anticodon loop base pairs with mRNA on the ribosome

has many bases, and non-standard H bonding, folds into cloverleaf structure

(nonstandard) interactions between bases that are far apart in linear sequence but are close in space

tertiary interactions

e.g of tertiary interactions

• ribosomal RNA (rRNA) ribozyme

catalytic RNA accelerates rate of peptide bond formation and supports proposal of original RNA world

structure of ribosome determined by

combination of cryo-electron microscopy and x0ray crystallography to ~5.5A resolution

main features determined by RNA

protein components peripheral

rRNA: interface between 30S particle and 50S particle is determined

mainly by (specific) RNA interactions

16S rRNA is part of

30S particle, consists of ~ 1542 nucleotides

16s has 4 domains (compact structures) and ~ ____ are base-paired

54% (linear), and non base-paired regions may be well structured

23S and 5S rRNA are part of

50S particle, consist of ~2904 and ~120 nuceotides

what holds rRNA structure together

1. watson-crick base pairs

2. non-standard base pairs

3. stacking energy of bases (pi-orbital overlap, solvent exclusion)

4. h-bonding, between bases, 2’OH, and phosphate

MANY NON COVALENT INTERACTIONS

the ribosome functions as an entropy trap (mode of catalysis decrease in entropy of transition)

activation energy decreased by immobilizing and orienting substrates ina ctive site

how is activation energy decreased in ribosome function

decrease motion, therefore decrease entropy of substrates so more similar to entropy of entropy in transition state, and entropy will decrease

trna, nucleophilic attack of amino group is concerted with

proton shuttle involving ribose 3’O and 2’OH