biology ch 8 & 9 final

Initiation, elongation, termination

3 stages of translation

70s

bacterial ribosome

Shine-Dalgarno sequence

bacterial sequence for small ribosomal subunit to bind to

16s subunit

portion of 30s bacterial ribosome that Shine-Delgarno sequence is complementary to

fMet

first amino acid brought by initiator tRNA

mRNA, 30s ribosomal subunit, Initiation factors 1 & 3 bound to 16s, tRNA carrying fMet and initiation factor 2 carrying GTP

30s initiation complex

GTP hydrolyzation

stimulates the release of initiation factors 1, 3, and 2

1. small ribosomal subunit binds to Shine-Dalgarno
2. Translation begins, 30s complex
3. large ribosomal subunit binds
4. 70s complex

3 steps of bacterial translation

final complex with fMet-tRNA in the P site bound to the start codon

70s initiation complex

30s

bacterial small ribosomal subunit

50s

bacterial large ribosomal subunit

binding, bond building, and movement

3 steps of elongation

aminoacid-tRNA-EF-Tu-GTP

complex that brings the new amino acid to the A site to form a bond with the mRNA codon

peptidyl transferase

catalyzes the formation of peptide bonds, also cleaves completed polypeptide from its tRNA

1. break bone between fMet and its tRNA in the P site
2. form peptide bond between free fMet and next amino acid still attached to tRNA in the A site

2 steps in breaking and lengthening amino acid chain

ribozyme

RNA molecule capable of catalyzing a reaction

EF-G-GTP complex

binds to the ribosome during translocation of amino acids, its GTP gets hydrolyzed to provide the energy for movement

A site

Site where new amino acid attached to a tRNA will enter the ribosome

UAG, UAA, UGA

stop codons

release factors 1, 2, 3

proteins that read the stop codon and initiate polypeptide chain termination

RF 1

release factor that recognizes UAA and UAG

RF2

release factor that recognizes UAA and UGA

RF3

release factor that stimulates termination events

RF3-GDP

complex that stimulates the release of the releases factors 1 and 2 from the ribosome

they are recycled

what happens to tRNA and ribosome when translation is over

ribosome recycling factor

binds to ribosomal A site in order to dissociate the ribosomal subunits from the mRNA

ribosome translocation

phenomenon initiated by EF-G-GTP’s GTP hydrolysis to move ribosome for dissociation

alpha helixes and beta pleated sheets

characteristic formations of secondary polypeptide structure

3D shape

characteristic of tertiary polypeptide structure

interactions between R-groups

characteristic of quaternary polypeptide structure

\-initiation factors 1, 2, 3

\-elongation factors EF-G and EF-Tu

\-fMet

bacterial translation components

EF-G

bacterial elongation factor that promotes translocation

EF-Tu

bacterial elongation factor that adjusts tRNA in the A-site

\-initiation factors 1, 1A/4, 5, & 3

\-elongation factors EF-2 and EF 1

\-Met

eukaryotic translation components

eEF-2

eukaryotic elongation factor that promotes translocation

eEF-1

eukaryotic elongation factor that adjusts tRNA in the A-site

Svedberg units

velocity of sedimentation after centrifugation: based on size, shape, and hydration state

charge

ribosomal protein identification via 2D gel electrophoresis isoelectric fusing along with pH gradient to separate fragments based on ______

mass

addition of SDS separates ribosomal subunits by ____

preinitiation complex

1st stage of translation initiation in eukaryotes is the formation of the _______ ______

eIF proteins and uncharged tRNA with Met

preinitiation complex (eukaryotic)

eIF-4

eukaryotic initiation factor that helps preinitation complex recruit small ribosomal subunits and charged tRNA with Met to the 5’ cap for binding

40s

eukaryotic small ribosomal subunit

scanning

process whereby eukaryotic initiation complex searches mRNA for a START codon

Kozak sequence

eukaryotic sequence where start codon is found

80s initiation complex

final ribosome assembly helped by eIFs

1. 40s RNA with charged tRNA binds to 5’cap
2. tRNA scans mRNA for Kozak sequence

2 eukaryotic steps of translation initiation

1

number of eukaryotic release factors

monocistronic mRNA

only type of mRNA that can be produced by eukaryotes

operon

group of bacterial genes controlled by a single promoter

polycistronic mRNA

type of mRNA that can only be produced by prokaryotes

A,G

purines

C, U, T

pyrimidines

isoaccepting tRNA

tRNA molecules with different anticodons for the same amino acids

third base wobble

relaxation of strict base pairing at the 3’ most nucleotide of the codon or 5’ most nucleotide of the anticodon

aminoacyl-tRNA-synthetases

enzyme that catalyzes the addition of the correct amino acid to tRNAs

kinases

protein responsible for phosphorylating a protein by adding phosphate group to an individual amino acid post-translation

signal sequence

specialized region at the N-terminal end of a polypeptide that contains an address label to direct the protein to the correct final destination

C terminal

end of the polypeptide

splicesome

snRNA-protein complex that removes introns

snRNA

RNA found in eukaryotic nuclear RNA, come together to form splicesomes

telomerase RNA

RNA that acts as a template to maintain and elongate telomere length in eukaryotic chromosomes

telomerase ribonucelomprotein complex

location where telomerase RNAs are held

polyribosomes

group of ribosomes all actively translating the same mRNA, in prokaryotes or eukaryotes

\-35 and -10

location of bacterial consensus sequences before the transcription initiation site

pribnow box

name of bacterial consensus sequence at -10

RNA polymerase 2

which RNA polymerase binds to promoter to initiate transcription

holoenzyme

RNA polymerase plus a sigma subunit that fulfills transcription in prokaryotes

sigma 70

Most common sigma subunit that is used for housekeeping genes (bacteria)

sigma 32

sigma subunit that is useful for heat tolerance (bacteria)

TATA box, CAAT box, GC-rich box

3 most common eukaryotic consensus sequences

sequences within the promoter

what are consensus sequences

\-25

location of TATA box

\-80

location of CAAT box

\-90

location of GC-rich box

band shift assay

assay used to confirm that DNA is the piece that binds protein, because DNA with proteins bound doesn’t travel as far in gel

DNA footprint protection assay

assay used to identify location of protein binding sequence in DNA by labelling with 32P and cleaving DNA with DNase

blank space in the gel because the promoter is protected from cleavage by bound transcriptional proteins

How do you know which region is the promoter with the DNA footprint protection assay

RNA polymerase 1, 2, and 3

Eukaryotic RNA polymerases

RNA pol 1

RNA polymerase responsible for transcribing several ribosomal RNA genes

RNA pol 2

RNA polymerase responsible for transcribing protein coding genes and most snRNA genes

RNA pol 3

RNA polymerase responsible for transcribing tRNA genes, the promoters often have an internal control region

RNA pol 2 and 3

RNA polymerases that transcribe miRNA and siRNA

TF2

Transcription factor required by RNA pol 2

TF2D, TF2A, TF2B, TF2F

Order of TF proteins that bind during eukaryotic transcription initiation

TF2D, TATA sequence, TATA binding protein (TBP), and the TBP associated factor

components of the initial committed complex for eukaryotic transcription initiation

TF2A, TF2B, RNA pol 2, and TF2F in addition to components of initial complex

components of the minimal initiation complex

TF2E and TF2H in addition to components of initial and minimal complexes

components of preinitiation complex

initial committed, minimal ignition, and preinitiation

Order of 3 eukaryotic initiation complexes

Enhancer sequences

eukaryotic DNA sequence that attracts activator proteins to drive transcription

activator proteins

eukaryotic proteins that are drawn to enhancer DNA sequence

silencer sequence

eukaryotic DNA sequence that binds proteins that induce beds in DNA to reduce transcription via shielding from RNA Pol 2

intrinsic termination

method of bacterial transcription termination that relies on inverted repeats and the formation of a stem-loop to derail RNA polymerase

stem-loops

string of uracils at the end of mRNA template that derails RNA polymerase

Rho-dependent termination

method of bacterial termination that involves a stem-loop and a rho-protein that binds to a rho-utilization site

guanylyl transferase

eukaryotic enzyme responsible for adding modified guanine monophosphate to 5’ end of premRNA

protection of the mRNA strand and marker so the mRNA can be easily found by ribosomes

purpose of 5’ cap

CPSF

protein that is attracted to polyadenylation signal sequence that helps with polyadenylation

polyadenylation sigal sequence

DNA sequence downstream of stop codon that attracts CPSF for function in poly-A tail addition

polyadenylate polymerase (PAP)

actual protein that adds 20-200 adenine nucleotides to 3’ end of mRNA strand