Biochem Ch 8

nucleic acid functions

store info (DNA), transmit info (mRNA), protein synthesis (tRNA, rRNA), process pre-mRNA

nucleotide functions

energy for metabolism (ATP), coenzymes (NAD+), signal transduction (cAMP)

cytosine

thymine

uracil

adenine

guanine

structures and properties of nitrogenous bases (4)

nitrogen aromatic amines, planar, absorb UV light (260 nm peak), good H bond donors and acceptors

how to determine nucleotide purity

absorbance at 260 nm - 280 nm

nucleobases

nitrogenous base only

nucleosides

nitrogenous base and pentose sugar

nucleotides

nitrogenous base, pentose sugar, and phosphate

nucleoside names

(deoxy)adenosine, guanosine, cytindine, thymidine, uridine

ribose vs deoxyribose

OH vs H on 2’ carbon

prime carbons

in the sugar (normal is in base)

glycosidic bond

bond between base and sugar

conformation of nucleotide favored in DNA

anti conformation (allows more interactions/ H bonds)

how DNA is read

5’ to 3’

phosphodiester bonds

connect nucleotides in phosphate backbone (3’ and 5’ OH)

type of reaction that forms phosphodiester bonds

condensation reaction (between two OH groups)

oligo and poly nucleotides

short and long chains of nucleotides

charge on backbone

negative

RNA structure

single stranded; can adopt 2 and 3 structures by interacting with self (ex. hairpin loops)

number of H bonds between A and T/U

2

number of H bonds between G and C

3

number of H bonds between G and U (soemtimes formed)

2

RNA in basic conditions

faster breakdown

rapid hydrolysis (RNA)

2’ OH group makes RNA unstable (breaks down on its own)

enzaymatic RNA (RNases)

very reactive, very stable (tight cross links); can catalyze reactions

base stacking

bases (planar) in DNA stack together through hydrophobic interactions and van der Waals forces

cause of major and minor grooves

sugar phosphate backbones are not equally spaced along the helix

benefit of major groove

allows specific protein-DNA interactions; can fit an alpha helix from a protein

why additional forms of DNA helix exist

conformational variations of sugar residues, orientations of planes of the bases between the two strands

A form (DNA)

right handed helix, more base tilt (twisted), bases cluster toward backbone

B form (DNA)

right handed helix, mostly planar, bases cluster toward middle

Z form (DNA)

left handed helix, mostly planar, bases cluster toward middle, zigzag backbone

major DNA conformation

B form

what makes melting temp higher in DNA

higher G+C content

hyperchromic effect

allows monitoring of denaturing/renaturing by looking at UV light absorption (closer bases don’t absorb as well)

DNA denaturation process (simple)

high temp/pH causes strands to separate (no covalent bonds broken)

Annealing process (combining strands)

normal temp/neutral pH causes a slow alignment of DNA strands, then quick rebuilding when lined up

factors that cause DNA strands to break (become ssDNA)

disruption of hydrogen bonds via temp, pH, or ionic strength

absorption when DNA is heated (above 80 C)

UV absorbance increases 30-40% (due to strands separating)

hyperchromic shift (purpose; think of other cards)

reflects unwinding of DNA double helix

what happens when temp is lowered

absorption drops (because strands renature)

factors affecting DNA denaturation (and Tm)

DNA length (longer DNA has higher Tm), pH and ionic strength (high salt increases Tm- charges from salt stabilize neg backbone), GC content

Tm

midpoint of melting

Tm if everything is the same

Tm depends on base composition; high CG increases it

cancer cell sensitivity

more sensitive than normal cells to inhibitors of making nucleotides

analogs of glutamine

used to synthesize nitrogenous bases (converted to purines w an enzyme)

azaserine

a drug that inhibits (competitively) enzyme in purine synthesis

truvada

inhibits reverse transcriptase