MCBL MIDDY 2

sigma 70

keeps transcription on all the time

basic promoter sequence

TTGACAT —17bp— TATAAT

transcription initiation

sigma factor binds DNA

córę enzyme unwinds

sigma factor released

elongation

core polymerase adds nucleotides

rho dependent/independent

uses rho/doesnt use rho

rho

helices binds to mRNA and breaks off RNA polymerase - transcription over

rho independent termination

pause site, U-A base pairs unstable and breaks off DNA

codon

triplet of nucleotides

open reading frame (ORF)

3 possible reading frames, between start and stop codon

tRNA

binds individual amino acids

anticodon

exact opposite of codon you’re reading - knows which amino acids its carrying

ribosomes

large RNA/protein complexes

30S - small

50S - large

1 mRNA + 3 tRNA

multiple ribosomes bind to each mRNA so transcrip/transl coupled

initiation

shine dalgarno site bind to 30S

IF3 brings ribosome and dalgarno together

IF1 blocks A site

IF2 brings tRNA to start codon

50s docks to 30s subunit

elongation

aminoacyl tRNA binds to A site (acceptor)

peptide bond formed between new aa site and P site

ribosome shifts down mRNA one codon - tRNA gets taken out of exit site

termination

stop codon on mRNA enters A site

protein releasing factor enters A site

EFG and ribosome recycling enter A and ribosome falls apart

bacterial genomes

extensive gene loss and gain

large deletions/insertions

plasmids

extrachromosomal DNA

own origin of replication

transferred by transformation and conjugation

pluck eye from neighbor and take it

defense against transferred DNA

cut foreign DNA using restriction endonuclease - use methyl for own DNAC

CRISPR

immune system against viruses and viral DNA

when infected, cut up viral and DNA and insert into own genome - bacteria remembers for future generations

mutations

heritable change in nucleic acid bases in genome

point - single base

transition - purine to purine

transversion - purine to pyrimidine

insertion/deletion - addition/removal of 1+ base pairs

inversion - DNA flipped in orientation

reversion - DNA mutates back to original sequence

point mutations

silent - does not change amino acid because of degeneracy

nonense - mutation produces stop codon

missense - changes amino acid

frameshift mutations

insertions or deletions that disrupt reading frame

not multiple of 3

physical mutagen

radiation

cause two adjacent pyrimidine bases to dimerize

prevents DNA rep and transcrip

chemical mutagens

base analogs are similar to natural bases - leads to point mutation because of incorrect base pairing

DNA modifying agents - changes bases structure and pairing characteristics

transposons

jumping genes - Barbara McClintock

hop from one place of DNA to another

mutagen in molecular genetics - all living things

ames test

examines ability of chemical substance to cause mutations

commonly used for cancer

bacterial mutant that can’t synthesize histidine

mutation causes reversion of hisG

more colonies = stronger mutagen

DNA repair

proofreading - correction of mismatch by DNA poly

photo reactivation - photolyze enzyme cleaves

excision repair

fixes mutations that changes shape of DNA

cut, copy, and paste mechanism

SOS response

extensive DNA damage induces SOS

LexA represses SOS

repair DNA rapidly, but numerous mutations

double stranded break repair

ligases recruited to fix break

no longer circle

causes chromosomal instability, causes problems with replication

horizontal gene transfer

from one organism to another

transformation, conjugation, transduction

transformation

conjugation

transfers between bacteria and eukaryotes

phage transduction

transduction

transformation discovery

lac operon

digest lactase

lacY

lactose permease

bring lactose into cell

lacZ

B-galactosidase

convert to allolactose (inducer)

break lactose to galactose and glucose (eat)

absence of lactose

lacI binds to operon

glucose over lactose

glucose inhibits cAMP production

will always choose glucose > lactose

if a lot of glucose, little bit of cAMP around

trp operon

repressed by TrpR

makes top

inactive aporepressor

regulate genes encoding biosynthetic enzymes

holorepressor

aporepressor complex

bind to operator sequence upstream

blocks RNA poly

attenuation

terminate transcription after already started

important where end products are low