Chapter 40 The Mechanism of Protein Synthesis

Two kinds of interactions determine where protein synthesis starts in bacteria

1. the pairing of mRNA bases with the end of 16S rRNA 2. The pairing of the initiator codon on mRNA with the anticodon of an initiator tRNA molecule.

30S subunit

16S rRNA and 21 proteins The small subunit of the bacterial 70S ribosome; composed of 21 different proteins and a 16S RNA molecule.

Protein Targeting

A means by which proteins are directed to specific cellular compartments or processed for secretion. Also called protein sorting.

elongation factor G (EF-G) (Translocase)

A member of the G-protein family required for protein synthesis in eukaryotes. The hydrolysis of GTP by EF-G causes the tRNAs and mRNA to move through the ribosome a distance corresponding to one codon.

Translocon

A multisubunit assembly of integral and peripheral membrane proteins constituting the machinery that translocates a nascent protein across the endoplasmic reticulum; forms a protein-conducting channel that opens when the translocon and ribosome bind to each other.

Accommodation

A process that rotates the aminoacyl-tRNA in the A site so that the amino acid is brought into proximity with the aminoacyl-tRNA in the P site on the ribosome.

signal sequence

A sequence of 9 to 12 hydrophobic amino acid residues, sometimes containing positively charged amino acids and usually near the amino terminus of a nascent polypeptide chain. The presence of the signal sequence identifies the nascent peptide as one that must cross the endoplasmic reticulum membrane The sequence within a protein that directs the protein to a particular organelle.

iron-response element (IRE)

A stem-loop structure found in the mRNAs for ferritin and transferrin receptor that interacts with the IRE-binding protein and regulates the translation of the mRNAs.

signal peptidase

An enzyme that cleaves signal sequences in mature proteins on the lumenal side of the endoplasmic reticulum membrane. cleaves signal sequence

SRP receptor

An integral membrane protein consisting of two subunits to which a complex consisting of a signal- recognition particle and a ribosome binds.

IRE-binding protein (IRE-BP)

An iron-sensitive protein that regulates the translational capability of ferritin mRNA and the stability of transferrin-receptor mRNA by binding to a stem-loop structure called an iron-response element (IRE) in the mRNA molecule.

50S subunit

Contains 28S and 5S RNA The large subunit of the bacterial 70S ribosome; the site of peptide-bond synthesis, it contains 34 different proteins, a 5S RNA species, and a 23S RNA species.

microRNAs (miRNAs)

Belongs to a class of noncoding RNAs found in plants, invertebrates, and vertebrates. These ~21-nucleotide-long RNA molecules are excised from longer double-stranded RNAs and play a role in post-transcriptional regulation

peptidyl transferase center

Component of the large ribosomal subunit which is responsible for the formation of peptide bonds

Binding sites for transfer RNA

E Site P Site A Site

Polypeptide-chain growth

Ester bond of amino acid in P site is cleaved to undergo a condensation reaction to form a peptide bond with the amino acid in the A site. P site is amino acid is now transferred and bonded to A site thus the chain grows until a stop codon lands in the P site.

70S initiation 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.

Ferritin

Iron-storage protein found primarily in the liver and kidneys. found in the liver, spleen, and red bone marrow

Protein synthesis in bacteria

It starts with the modified amino acid N-formylmethionine (fMet) -70s ribosomes -formyl-methionine

Formylmethionyl-tRNAf Is Placed in the P Site of the Ribosome in the formation of the 70S Initiation Complex

Messenger RNA and must be brought to the ribosome for protein synthesis to begin.

Shine-Dalgarno sequence

Named after John Shine and Lynn Dalgarno, who first described the sequence In bacterial messenger RNA, a purine-rich region about 10 nucleotides on the 5' side of an initiator codon that pairs with the 3' end of 16S RNA in the 30S ribosomal subunit; helps to determine where translation is initiated on an mRNA molecule.

initiation factors (IF)

One of a set of proteins that assist in the association of the ribosome, mRNA, and initiator tRNA to initiate the process of protein synthesis. assist in the assembly of the protein-synthesizing machinery

release factors (RFs)

One of a set of proteins that recognize Stop codons on mRNA at the A site on the ribosome, which leads to the release of the completed protein from the tRNA in the P site of the ribosome.

methionyl-tRNA

Picture

elongation factor Tu (EF-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.

signal recognition particle (SRP)

Recognizes the signal sequence and binds the sequence and the ribosome as soon as the signal sequence exits the ribosome. SRP then shepherds the ribosome and its nascent polypeptide chain to the endoplasmic reticulum membrane.

RNA interference (RNAi)

Refers to the regulation of gene expression post-transcriptionally by small molecules of RNA.

Polycistronic

The coding pattern of prokaryotes, in which one mRNA may code for multiple proteins.

Protein Synthesis Decodes the Information in Messenger RNA

The first step in protein synthesis is initiation. Protein-synthesis initiation requires the cooperation of the ribosome, tRNA, mRNA, and various protein factors.

ADP-ribose

The portion of NAD+ that is transferred to the Gαs subunit of a G-protein. This action contributes to the inhibition of the GTPase activity and the increased activity of adenyl cyclase. (see cholera)

Ribosomes Have Three tRNA- Binding Sites That Bridge the 30S and 50S Subunits

The three tRNA-binding sites on ribosomes are arranged to allow the sequential formation of peptide bonds between amino acids encoded by the codons on mRNA. The mRNA fragment being translated at a given moment is bound within the 30S subunit. Each of the tRNA molecules is in contact with both the 30S subunit and the 50S subunit.

iron response element (IRE)

a cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration

Transferrin receptor (TfR)

a membrane protein that binds iron-loaded transferrin and facilitates its entry into cells by the process of receptor mediated endocytosis Cell surface receptor required for iron uptake

Tranferrin

a transport protein that carries iron in the blood serum. iron-binding blood plasma glycoproteins that control the level of free iron in biological fluids

mRNA Molecule

carries the coded message that directs the process All known mRNA molecules contain signals that define the beginning and the end of each encoded polypeptide chain

Streptomycin

inhibits 70S ribosome formation

fMet

mRNA start codon (AUG) codes for N-formylmethionine in proks that stimulates neutrophil chemotaxis

Elongation factor Ts

protein that regenerates elongation factor Tu in the elongation stage of protein synthesis

Transferrin Receptor mRNA

transferrin protein delivers iron from ingested food to cells via the transferrin receptor (TfR) on the surface of cells -3'UR of TfR mRNA contains a destabilizing AU-rich regions that promotes its rapid deggradation when iron conc. is hgih -3'UTR also contain 3 IREs 1 of which overlaps the AU-rich region -low iron allows IRE-BP binding to the IREs and blocks degradation