molecular exam one

nucleic acids and proteins

covalent bonds

very strong, electrons shared

non-covalent bonds

weak, play role in molecular structure and stabilization

can be easily formed and broken allowing for flexibility

van de walls radius

atoms that come closer than their radius are repulsed from one another

hydrophobic interractions

drive molecular folding

hydrophobic areas interact to exclude water and vice versa for hydrophillic

dna vs. rna

dna: OH and H group

rna: OH OH group

purines

double ringed

adenine:NH2 group

guanine: NJ2 and O group

pyrimidines

single ringed

cytosine: NH2 and N group

thymine: NH3 and H3C group

uracil: only NH3 group

protonated

ph below pka

gaining H+

deprotonated

ph above pka, loosing H+

tautomers

when H+ move around bases, migrate to different positions

not very common, affects pairing, dna repliation, and can change bases

b dna

most common structure

10.5 bases per turn

wide major groove

dna

H bonds and van de waals stabilize

protein interractions can change dna structure

base pairing arrangement thermodynamically favorable

proteins interact with major groove- reach in with helix

a dna

wide, 11 bases per turn

narrow major groove

induced by dna binding, proteins, dehydrated

z dna

left handed helix

narrow, 12 bases per turn

flat major groove

denaturing dna

splitting apart

longer dna- more base pairs- harder to split apart

Tm

temp at which ½ dna sample is denatured

primers need to have similar melting temps

ds dna

A260= 1 for 50 ug/ml

ss dna

A260= 1 for 40 ug/ml

primers

A260=1 for 33 ug/ml

dna ratios

260/280= 1.8-1.9

below 1.8= lots of protein

above 1.9= lots of rna

rna rations

260/280= 2+

below 2= lots of dna and/or protein

hybridization

everything needs to be single stranded

factors affecting: tm of probe/dna, gc content, single vs double stranded

slipped structure

tandem repeats, slipping during replication

polymerase skips tandem repeat, creating a loop

cruciform structure

palindromes, negative super coiling

several inverted repeats that bind

triple helices

rare, affect transcription

areas of mirror repeats that allow 3rd strand to slip in

supercoiled

circular dna is cut, held at one end while the other is twisted

closed, circular sna can be supercoiled

relaxed

2 ends stuck back together, dna twists to restore preferred amt. of bases per turn

open, uncoiled dna is relaxed

positive SC

counterclockwise, left helix

negative SC

clockwise, right helix

linking number

number of times 1 strande of dna wrapse around echother

twist

number of turns in a fragment of dna

writhe

describes Sc

relaxed: wr=0

pos. sc: positive wr=counterclockwise

neg. sc: negative wr=clockwise

rna

singled stranded

alot of modified bases, leads to alot of 2nd structures

bases modified after synthesis

rna helix

wider and flatter than b dna, similar to a dna

can form 2nd structures: t loop, stem loop

mrna

carries genetic instructions to ribosomes to make proteins

trna

brings AA to ribosomes during protein synthesis

rrna

forms integral parts of ribosomes

proteins

polymers of covalently bonded AA

central c (C), amino group (-NH3+), carboxylate (-COO-), side R chain

pka of carboxyl group

2

pka of amino group

9-9.5

different r chains affect polypeptides configurations

glycine, small, found in tight turns- v, small side chain making it flexible

proline, big, in wider turns- unusual structure inducying kinks in chain

protein folding

driven by hydrophobic interractions'

-folding based on thermodynamics

-folding energetically favorable, entropy increases

-internal protein structures tightly packed with few gaps

protein and dna interractions

-chem groups exposed in major and minor grooves

-dna binding proteins reach in and bind with major groove

-binding in minor groove induces distortion to dna to benefit certain rxns

interractions determined by dna sequence, protein shape, and available binding groups

lamba cro

protein that interracts with dna

binds 3 operator sites, competes with lamba repressor

each cro monomer has 3 strands B sheets and 3 a helices

cro binds in two places