when folding in one area initiates folding in another area.  sequential process

1. hydrophobic interactions

2. ionic

3. H-bond

4. hydrophobic cluster

5. van der waals

what is meant by saying a protein has resilience and flexibility?

resilience - combination of many, many weak forces gives overall stability (resilience)

flexibility - b/c forces are weak, able to change shape

1. ring (virus protein coat)

2.  helix (actin)

3. cylinder (microtubule)

1. Cofactors - ions, etc. that are not fixed, can move from protein to protein (Fe, Cu)

2. Prosthetic groups - fixed to a protein (heme, vitamins such as B-3)

3. Large biomolecules - nucleic acids, carbohydrates, lipids. make up conjugated proteins.

1. enzymes

2. structural (microtubules, flagella)

3. Binding

4. Mechanical

5. Information processing

1. transport

2. carrier

3. storage

1. hydrolase (nuclease, protease)

2. synthase (polymerase, ligase)

3. transferase (kinase)

4. isomerase

5. oxidoreductase

binds to hydrophobic side chains

1. phosphorylation/dephosphorylation - certain enzymes only acitive with or w/out phosphate

2. precursor enzymes - must be cleaved to be active

1. binding regions - palindromic sequeces (usually)

2. binding domains - motifs

1. helix turn helix

2. helix loop helix

3. leucine zipper

4. zinc finger

1. consecutive leucines - hydrophobic attraction

2. basic region (+) that binds to dna

1. zinc atom

2. 2 histidine aa

3. 2 cysteine aa

1. heat - break covalent bonds

2. pH - neutralizes charges on side chains

3. chemical reagants - ex. SDS

pyrimidine - 6 member ring. N on 1, 3

purine - 6 ring and 5 ring N. on 1,3,7,9

adenine, guanine, cytosine, thymine, uracil

nucleotide w/out the phosphate.

add -osine to purines

add -idine to pyrimidines

how are nucleotides linked?

B dna

Right-handed

2 nm across

10 bp/turn

Translated RNA (mRNA)

Non-translated RNA

ribosomal

transfer

small nuclear

guide

regulatory

antisense

recognition

ribozymes

1 - attaches to N-base and O linking ring

2 - attaches to aa in tRNA

3 - attached to OH

4 - attache to O linking ring

5 - attaches to phosphate

smaller subunit - 1 RNA type, 21 proteins

larger subunit - 2 RNA types, 32 proteins

Transcription

Introns spliced out - mRNA

Translation

moderately repetitive sequences scattered t/o genome. make up 25% of human genome

what is satellite DNA

tandem repeats (no gaps between)

highly variable among organisms

non-coding

make up heterochromatin (tightly coiled form of DNA & proteins around centromere)

what are VNTRs?

where found?

minisatellites

Variable Number of Tandem Repeats

short tandem repeats

usually found in telomeres

Viruses

Transposons

may have been inserted, then mutated, making them junk

what are the 2 types of palindrome sequences?

which type is more popular

mirrorlike

inverted repeats - more common

hairpin

stem & loop

cruciform structure

how do cruciform structures form?

why are they important?

when DNA unwinds, if there are palindrome sequences the single strands wind into cruciform structures

important b/c regulation and expression of genes often involve binding of proteins to cruc.structures

negative - twist in opp.direction of helix

positive - twist in same direction as helix (rt handed)

removes excess negative supercoiling

cuts one strand to do this

what does topoisomerase II do?

what is another name for it?

removes positive supercoiling, adds negative

aka - DNA gyrase

cuts both strands to do this

different conformations of a circular DNA molecule (supercoiled, open circle, etc.)

covalently closed circular DNA

most compact topoisomer form

has 11bp/turn

shorter, fatter than B-DNA

12 bp/turn

left-handed

skinnier, longer than B

DNA and associated proteins (histones)

eukaryotes

what is a nucleosome?

what are the two main parts?

subunit of chromatin

1) core

2)linker DNA

160 bp DNA

8 histone proteins (2 each):

H2A

H2B

H3

H4

40 bp DNA

1 H1 histone protein

euchromatin - 'sting with pearls' - dna wrapped around nucleosomes

- still active, can be expressed

heterochromatin - higly compact. inactive. can't be expressed

coil-coil-fold-coil

eu after first coil

heter after fold

native - dsDNA

denatured - ssDNA

want the DNA denatured but not hydrolyzed to work with it

dna will be hydroyzed

1. High pH

2. High salt concentration

3. Heat

A-T bonds

less H-bonds

renaturation - same parental molecules formed

hybridization - similar but not identical strands recombine

what sequences are conserved in most species?

which ones mostly variable?

coding regions conserved

non-coding variable