Translation

Three steps of elongation

(1) A charged tRNA binds to the A site (2) The formation of a peptide bond between the amino acids that are attached to tRNAs in the P and A sites. Peptide bond formation occurs within the peptidyl transferase center, which is part of the large subunit of the ribosome. (3) translocation - Movement of ribosome along mRNA in the course of translation. This step positions the ribosome over the next codon and requires elongation factor G (EF-G) and the hydrolysis of GTP to GDP.

Key differences between initiation in eukaryotes and prokaryotes

(1) There is no Shine-Dalgarno sequence in eukaryotes, instead the 5' cap is a key element in the initiation of translation- the initiation complex binds at the cap (2) Eukaryotic initiation requires at least seven initiation factors, bacteria only requires three (3) Poly(A) tail also help initiate translation: proteins that attach to the poly(A) tail interact with proteins that bind to the 5′ cap, enhancing the binding of the small subunit of the ribosome to the 5′ end of the mRNA

Three sites that a tRNA can occupy on a ribosome

(1) aminoacyl or A site - Where the charged tRNA anticodon binds to the mRNA codon, thus lining up the correct amino acid to be added to the growing polypeptide chain. (2) peptidyl or P site- In the elongation stage of protein synthesis, tRNAs move from the aminoacyl (A) site into the P site, initiator tRNA immediately occupies the P site (3) exit or E site - is where the tRNA, having given up its amino acid, resides before being released from the ribosome and going back to the cytosol to pick up another amino acid and begin the process again.

Four stages of translation

(1) tRNA charging - in which tRNAs bind to amino acids (2) initiation - in which the components necessary for translation are assembled at the ribosome (3) elongation - in which amino acids are joined, one at a time, to the growing polypeptide chain (4) termination - in which protein synthesis halts at the termination codon and the translation components are released from the ribosome.

What is required for elongation to occur?

(1) the 70S complex (2) tRNAs charged with their amino acids (3) several elongation factors (4) GTP

What does the intiator complex look like before the large subunit ribosome? (30S initiator complex)

(1) the small subunit of the ribosome; (2) the mRNA; (3) the initiator tRNA with its amino acid (fMet-tRNAfMet); (4) one molecule of GTP; and (5) several initiation factors. These components are collectively known as the 30S initiation complex

Amino Acids bind to which part of the tRNA?

3' end

Shine Dalgarno

A consensus sequence upstream of promoter in prokaryotes that the small ribosomal subunit binds to

cap-binding complex

A group of proteins in eukaryotes that binds to the 5′ cap and initiates translation. Aids in exporting mRNA from the nucleus to the cytoplasm and promotes the initial (pioneer) round of translation.

no go decay (NGD)

A mRNA surveillance system in eukaryotes that helps remove stalled ribosomes resulting from secondary structures in mRNA, chemical damage to mRNA, premature stop codons, and ribosomal defects. A series of proteins bring about termination, recycling of the ribosomes, and degradation of the mRNA.

Termination of translation

A protein called release factor is required for the termination of translation; because there is no tRNA anticodon for the stop codon it binds to a ribosome when a stop codon is reached and stimulates the release of the polypeptide chain, the tRNA, and the mRNA from the ribosome. Eukaryotic cells require two release factors (eRF-1 and eRF-2), whereas E. coli requires three (RF-1, RF-2, and RF-3).

tRNA charging

Chemical reaction in which an aminoacyl-tRNA synthetase attaches an amino acid to its corresponding tRNA.

What are some posttranslation modifications of proteins

Cleavage and trimming of enzymes, attachment of carbohydrates, modification of amino acids- acetylation of amino end in eukaryotes, and addition of ubiquitin which targets the protein for degredation, removal of signal sequence after it has arrived it its destination.

aminoacyl tRNA synthetase

Enzyme that attaches an amino acid to a tRNA. Each aminoacyl-tRNA synthetase is specific for a particular amino acid, therefore each cell has a specific twenty.The reaction uses ATP, forming a high-energy bond between the amino acid and the tRNA, which is later used in the formation of peptide bonds between amino acids in a growing polypeptide chain.

70S initiator complex

Final complex formed in the initiation of translation in bacterial cells; consists of the small and large subunits of the ribosome, mRNA, and initiator tRNA charged with fMet.

signal sequence

From 15 to 30 amino acids that are found at the amino end of some eukaryotic proteins and direct the protein to specific locations in the cell; usually cleaved from the protein

Kozak sequence

Helps iniation translation in eukaryotes by helping facilitate the recognition of the first start codon- AUG

transfer-messanger RNA

In bacteria is is an RNA molecule that has properties of both mRNA and tRNA; functions in rescuing ribosomes that are stalled at the end of mRNA. Functions by being delivers EF-Tu to the stalled A site, tmRNA then acts like a surrogate tRNA and add a amino acid that tags the protein for degradation. The ribosome then continues on the mRNA portion of the tRNA until a stop codon is reached.

Antibiotics and translation

Many antibiotics target translation because it is required by all living things, but do so without harming the host.

nonstop RNA decay

Mechanism in eukaryotic cells for dealing with ribosomes stalled at the 3′ end of an mRNA that lacks a termination codon. A protein binds to the A site of the stalled ribosome and recruits other proteins that degrade the mRNA from the 3′ end.

mRNA surveillance

Mechanisms for the detection and elimination of mRNAs that contain errors that may create problems in the course of translation. Mechanisms like these keep the cell from wasting resources translating aberrant mRNAs and prevent the production of truncated proteins, which may be toxic to the cell.

Polyribosome

Messenger RNA molecule with several ribosomes attached to it.

molecular chaperones

Molecule that assists in the proper folding of protein initially, some are associated with ribosomes.

nonsense-mediated mRNA decay

Process that brings about the rapid elimination of mRNA that has a premature stop codon in eukaryotic cells, this stops the synthesis of truncated proteins.

IF2

Protein required for the initiation of translation in bacterial cells; forms a complex with GTP and the charged initiator tRNA and then delivers the charged tRNA to the initiation complex.

Does protien synthesis recognize the anticodon of the tRNA or the amino acid attached?

Protein synthesis machinery recognizes the anticodon of the charged tRNA, not the amino acid attached to it. This is exemplified by the experiment by Seymour Benzer when he chemicallt modified the cystosine in a cys-tRNA molecule into alanine and alanine was delivered to the ribosome.

Elongation factor tu

Protein taking part in the elongation stage of protein synthesis; forms a complex with GTP and a charged amino acid and then delivers the charged tRNA to the ribosome.

wobble phenomenon

The cell gets by with about two-thirds of the number of codons of tRNA species because the specificity for the base at the 3′ end of the codon (and the 5′ end of the anticodon) is not always strictly observed

Where on the mRNA does the ribosome bind during initiation of translation?

There are key sequences where it binds, intending to stall the mRNA from synthesis, it usually binds at the Shine-Dalgarno consensus sequence. During initiation, the nucleotides in the Shine-Dalgarno sequence pair with their complementary nucleotides in the 16S rRNA, allowing the small subunit of the ribosome to attach to the mRNA and positioning the ribosome directly over the initiation codon.

How does ribosome fidelity occur

When a charged tRNA with the correct anticodon binds to the appropriate codon in mRNA, hydrogen binding occurs between paired bases; if hydrogen binding does not occur that tRNA is ejected from the ribosome

nonsense mutation

When a codon that codes for an amino acid is altered into a stop codon, this leads to early termination of translation and a truncated protein

tRNA charging formula

amino acid + tRNA + ATP → aminoacyl-tRNA + AMP + PPi

3'

carboxyl group

Progress of tRNA through elongation

cytoplasm → A site → P site → E site → cytoplasm

Initiator tRNA

fMet-tRNA^(fMet)

What are all the components necessary for protein synthesis?

mRNA, the small and large subunits of the ribosome, a set of three proteins called initiation factors, initiator tRNA with N-formylmethionine attached (fMet-tRNAfMet), and GTP