BIOL 303 Ch. 13 stuff you dont know

core genome

set shared amongst all/most strains

dispensable genome

set shared amongst few strains

unique genome

strain specific

phenotype is influenced by what 2 things

genotype and enviornment

plasmids found in which domains?

bacteria and archea

bacteria and archaea ploidy

haploid 1 chromosome

eukaryotes ploidy

diploid

what is the Nucleoid made of?

1 closed circular , double stranded dna molecule

Nucleoid associated protiens, what type of bonding does it use?

aid in bending nucleoid dna snd structure through electrostatic interactions (no covalent bonds)

nucleoid structures are organized into ____ _____ that are further divided into _____ _____ _____

1 Mbp macrodomains, chromosome interacting domains

bacterial chromosomes have how many orgins of replication and eukaryotes have how many?

bacterial- 1 (oriC)

eukaryotes- many

what happens to dna without an orgin

it wont be replicated

terminus

the terminating site that both sides of the replicating fork will ultimately meet

semiconservative replication

dna contains 1 original, one new synthesized strand

oriC orgin

bacteria- a 245 bp sequence that includes a series of repeats

DnaA

triggers replication, a protein that increases in concentration during cell growth, causes bending and separation of strands until it can recruit DnaB

DnaA binds to _____ and recruits ____

oriC and recruits Helicases (DNAB) and gyrase which bind to the orgin

helicase disrupts _____ to expose ssDNA

H bonding

Gyrase

unwinds dna, relieves twist generated by the rapid unwinding of the double helix by transiently breaking and then releasing DNA strands

DNA Primase

synthesizes small strands of RNA that serve as a primer to initiate dna synthesis so that dna pol 3 can attach to in order to begin dna synthesis

dna pol only synthesizes in which direction

5->3

what removes primers once replication is complete?

pol 1 and ligase

what enzyme sythesizes new dna in replication

pol 3

how does dna ligase work?

forms a phosphodiester bond between 3'-OH of the growing strand and the 5'-phosphate of an Okazaki fragment

How many terminator sequences are on the E. coli chromosome?

as many as 10

Tus

terminus utilization substance, a protien that binds to termination sequences to ensure that the replisome does not escape and continue replicating dna

chromosomes that are linked

catenated

decatenated chromosomes form when... and how?

gyrase (topoisomerase) produces a double-strand break and rejoins dna strands to form 2 daughter chromosomes after replication

3 types of rna

mrna, tuna, rrna

what is the role of messanger rna

carries the message from dna to ribosome which is primarily made of rRNA

polycistronic, and which organisms are like this

several genes for multiple protiens of one strand usually found in prokaryotes

monocistronic and which domain

one gene for one protien, eukaryotes

rna pol can initiate without what andhow?

a primer, by binding to a promoter with the help of sigma factors

rna polymerase is a what and its composed of

core enzyme composed of 5 polypeptides (2 a subunits, B, B prime, and w) this catalyzes rna synthesis

sigma factor

has no catalytic activity but helps the core enzyme recognize the start gene (promoter)

rna polymerase holoenzyme

core enzyme and sigma fator

only holoenzyme can begin transcription

leader sequence

transcribed into mRNA but is not translated into amino acids (shine delgarno)

shine delgarno

The initial ribosome attachment site on bacterial mRNA

stop codon is immediately followed by what?

trailer sequence which prepares rna polymerase for the terminator sequence

what is the purpouse of the promoter sequence and where is it found?

dictates direction of transcription and which strand is used and a template. found -10 to -35 bp upstream of where transcription starts

-35 promoter sequence (template strand)

TTGACA, sigma factor recognizes and directs holoenzyme to settle here

-10 promoter sequence (template strand)

TATAAT where dna strands start to seperate

when doessigma detach

detaches from rna pol after binding to promoter is complete

how is transcription bubble formed in transcription?

rna polymerase denatures a short stretch of dna exposing nucleotides of dna to form a transcription bubble

the cell controls what genes ae expressed by doing what?

controlling the availability of specific sigma factors

ecoli has how many main sigma factors?

7

RpoD

sigma 70 , the housekeeping sigma factor that trascribes most genes in growing cells

RpoH

sigma 32, heat shock sigma factor turned on when bacteria are exposed to heat , expresses heat shock protiens which enable the cell to survive highere temperatures

sigma factors are unique to what?

prokaryotes

sigma factors are homologous to :

archaea-

eukaryote-

transcription factor B

transcription factor 2 B

which strand is the + and which is the - strand in transcription?

- (minus ) is the template

+ (plus) is the non template strand

elongation of transcription is fueled by what energy source?

hydrolyzing high energy phosphate bond from incoming nucleotide

rho dependent

a rho protein follows RNA pol and pops it off the DNA when it reaches a termination sequence (typiclly a GC rich sequence)

rhos RNA-DNA ____ ___ causes everything to dissociate

helicase activity

rho independent

g c rich repeats terminator sequence results into hairpin loops in RNA transcript

hairpin along with ____ CAUSES NEWLY SYNTHESIZED Mrna TO BE RELAEASED and rna polymerase to disassociate

NusA

how many differnt codons are there?

64

universal codons

used by all living things

degenrate codons

up to 6 differnt codons that code for the same amino acid

start codon and the amino acid it codes for

aug, codes for methionine

sense codons

the 61 codons that specify amino acids

nonsense codon

stop codons UAA, UAG, UGA, dont encode amino acids, recognized by release factors

16s rRNA

needed for initiation of translation

binds to shine delgarno sequence (ribosome binding site), binds to 3'CCA end of aminocyyl tRNA

23S rRNA

ribozyme that catalyses peptide bond formation

streptomycin affect on translation

bactericidal arrow-spectrum (G- bacteria) drug that inhibits 70s ribosome formation byb binding to rRNA. SIDE EFFECTS- CAN BIND TO HOST RIBOSOMES

Tetracycline affect on translation

bacteriostatic , broad spectrum drug, inhibits aminoacyl - tRNA binding to the A site

where does transcription occur in eukaryotes?

in he nucleus and then mRNA is translated in the cytoplasm making it impossible for transcription and translation to occur at the smae time. preMRNA must be processed before transcription

whAT IS DIFFERNT ON THE EUKARYOTE TAILS AND HEADS OF Mrna

5' end methlyated cap, 3' end polyadelation tail

eukaryote ribosomes and their subunits

80s

40s and 60 s

coupled transcription and translation

occurs in prokaryotes when protiens are transcribed as rna is being translated

polysomes

several ribosomes that are attached to the same mRNA at one time.