Nucleic Acids Slides

base A

base G

base T

base C

base U

DNA structure

one OH group one H

nucleoside vs nucleotide

tide= has phosphate group

purine

A + G

pyrimidines

C, T, U

nomenclature for nucleotides

nucleoside + phosphate derivative ex: adenosine triphosphate (ATP)

nucleoside names

-adenosine

-guanosine

-cytidine

-thymidine

-uridine

nucleotide names

-adenylate

-guanylate

-cytidylate

-thymidylate

-uridylate

name?

Adenosine 3’, 5’ cyclic monophosphate

cAMP- reguklatory nucleotide

second messenger, mediates cells response to extracellular signals espically in energy + metabolism

name?

Adenosine 2’, 3’- cyclic monophosphate

regulatory molecules

-CoA: coenzyme A= inmportant in metabolism citirc acid cycle

-NAD+/NADH= oxidation/reducation

-cAMP= second messanger

why is DNA more stable than RNA?

RNA is readily hydrolyzed by aqueous basic conditions

what is this reaction?

RNA being hydrolzyed, result is cyclic monophosphate + shortened RNA

Chargaff Base Rules

%A=%T

%G=%C

total purine= total pyrimidine

DNA double helix

-B form

-2 antiparallel strands wrapping around common axis

-bases occupy the core of the helix

-sugar phosphate backbone= outside

what factors stabilize DNA structure

-hydrophobic effect

-base stacking

-sugar phosphate backbone = highly soluble

why is bare DNA unstable

electrostatic repulsions of phosphate groups

watson crick A+T

watson crick G+C

ways to purify nucleic acids

-chromatography- ikon exchange

-phenol-chlorofrom extraction (solubility based)

ways to synthesize nucleic acids

solid phase chemical synthesis

ways to analyze nucleic acids

fragment then sequence short sections, electrophoresis ob agarose gel visulized with ethidium bromide intercalation into stacked bases

why use ethidium bromide

-flat planar aromatic rings

-hydrophobic surface

-can fit between 2 bases

common DNA damage

-abasic lesions-guanine leaves residue

-pyrimidine dimers

pyrimidine dimers

causes kink in DNA, altes both physical + chemical structure, adjacent thymines + UV light cause crosses between bases

partial renaturation is cuased by

DNA is cooled too quickly + gets trapped in local energy minimia causing hairpins + intermolecular aggration

DNA with higher concentration of A + T bases is slightly less stbale than C + G, why

C + G have an additional H-bond

A form DNA

-typical RNA structure

-compact

-dehydrated DNA, well paired double helix

Z form DNA

used in gene regulation

-left handed

Hoogsteen Pairing

a nonstandard base-pairing geometry in DNA+ RNA using a different hydrogen-bonding face of the bases.

hoogsteen pairing guanosine tetraplex

hoogsteen pairing possibilties

• TAT

• C=G-C+

• guanosine tetraplex

ribosome

ribonucloprotein complex that assembles protein