Chapter 8: Protein Synthesis, Processing, and Regulation

translation

protein synthesis from mRNA templates

direction in which mRNA reads

5’ to 3’

length of tRNAs

70 - 80 nucleotides

type of RNA with codons

mRNA

type of RNA with anticodons

tRNA

complementary base pairing

method by which the anticodon loop binds to the appropriate codon

sequence at the 3’ terminus of tRNA

CCA

aminoacyl tRNA synthetase

enzyme that attaches an amino acid to its specific tRNA

1st step of amino acid attachment to tRNA

the amino acid joins AMP to form aminoacyl AMP

2nd step of amino acid attachment to tRNA

the amino acid is transferred to the 3’ terminus of the tRNA and AMP is released

number of amino acids

20

number of different tRNAs

40

wobble

nonstandard base pairing at the 3rd codon position

prokaryotic ribosomal subunit sizes

50S (large subunit) and 30S (small subunit)

components of prokaryotic large ribosome subunit

23S RNA + 5S RNA = 34 proteins

components of prokaryotic small ribosome subunit

16S RNA = 21 proteins

eukaryotic ribosomal subunit sizes

60S (large subunit) and 40S (small subunit)

components of eukaryotic large ribosome subunit

28S RNA + 5.8S RNA + 5S RNA (~46 proteins)

components of eukaryotic small ribosome subunit

18S RNA (33 proteins)

type of RNA responsible for catalyzing peptide bond formation

rRNA

do eukaryote mRNAs encode a single protein or multiple proteins

a single protein

do prokaryote mRNAs encode a single protein or multiple proteins

multiple proteins

methionine

start signal for translation

AUG

methionine codon sequence

Shine-Dalgarno sequence

initial binding site for translation in prokaryotic mRNA, upstream of methionine

7-methylguanosine cap

initial binding site for translation in eukaryotic mRNA, upstream of methionine

location of the 7-methylguanosine cap

5’ terminus

initiation

1st stage of translation

elongation

2nd stage of translation

termination

3rd stage of translation

1st step of initiation (prokaryotes and eukaryotes)

methionyl tRNA and the mRNA bind to the small ribosomal subunit

polysome

a group of ribosomes bound to an mRNA molecule

what type of translation factor is IF1

prokaryotic initiation factor

what type of translation factor is EF-Tu

prokaryotic elongation factor

what type of translation factor is RF1

prokaryotic termination factor

what type of translation factor is eIF1

eukaryotic initiation factor

what type of translation factor is eEF1α

eukaryotic elongation factor

what type of translation factor is eRF1

eukaryotic termination factor

function of eIF2

binds and delivers methionyl tRNA to the complex

function of eIF4E

delivers mRNA to the complex

function of eIF5

triggers the hydrolysis of GTP bound to eIF2 (after identification of AUG)

result of the release of the initiation factors from the complex

the large subunit (60S) joins the complex

methionyl tRNA binds to this ribosomal binding site

P site

the next aminoacyl tRNA binds to this ribosomal binding site

A site

function of EF-Tu

brings the aminoacyl tRNA to the ribosome in prokaryotes

function of eEF1α

brings the aminoacyl tRNA to the ribosome in eukaryotes

forms when 2 amino acids are at the P site and the A site

peptide bond

translocation

movement of the next codon into the empty A site, the peptidyl tRNA from A to P, and the uncharged tRNA from P to E

function of EF-G

translocation in prokaryotes

function of eEF2

translocation in eukaryotes

translocation is coupled to this process

GTP hydrolysis

function of eEF1ßγ

converts GDP back to GTP on elongation factor eEF1α

is eEF1α bound to GDP active or inactive

inactive

is eEF1α bound to GTP active or inactive

active

termination signal for elongation

a stop signal is translocated into the A site

release factors

recognize the stop signal and terminate protein synthesis

RNA interference (RNAi)

experimental tool to block gene expression at the translation level

RNAs that mediate RNA interference

siRNA and miRNA

production of siRNA

formed by the nuclease Dicer from double-stranded RNA

production of miRNA

transcribed by RNA polymerase II, then cleaved by the nucleases Drosha and Dicer

siRNA function

inhibits translation by pairing perfectly with its target and inducing cleavage of mRNA

miRNA function

inhibits translation by forming a mismatch pairing

function of protein kinases

inhibit translation by phosphorylation of initiation factors, blocking exchange of GDP to GTP

chaperones

proteins that facilitate the folding of other proteins, and stabilize unfolded polypeptide chains during transport

heat-shock proteins (Hsp)

chaperones that are subjected to high temperatures

chaperonin

double-chambered structure in which protein folding takes place

protein disulfide isomerase (PDI)

catalyzes disulfide bond formation in the ER

peptidyl prolyl isomerase

catalyzes a conformational change of peptide bonds that involve proline residues

proteolysis

cleavage of the polypeptide chain to remove portions (like methionine) to maintain the functional portion

4 ways to regulate proteins

regulation by small molecules, kinases/phosphatases, protein-protein interactions, protein degradation by ubiquitin-proteasome