Biology: Chapter 15.5- Ribosomes and Protein Synthesis

shine-dalgarno sequence

(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30s ribosome

translation complex

- 30s and 50s subunit join in prokaryotes - 40s and 60s and ATP in eukaryotes

initiation complex

- initiator tRNA interacts with the start codon - binding of fmet (formyl carboxyl group) to the tRNA (attached to the amino group of methionine) --> initiation complex formed

recap of translation

- begins when an initiator tRNA anticodon recognizes a start codon on mRNA bound to a small ribosomal subunit - the large ribosomal subunit joins the small subunit (translation complex), and a 2nd tRNA is recruited - as the mRNA moves relative to the ribosome, successive tRNAs move through the ribosome and the polypeptide chain is formed - entry of a release factor into the A site terminates translation and components dissociate

ribosomes and translation

- dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation - bacteria: 30s and 50s for 70s - mammals: 40s and 60s for 80s - small unit is responsible for binding the mRNA template - large unit sequentially binds tRNAs - each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction --> reading the mRNA from 5'-3' and synthesizing the polypeptide from the N terminus to C terminus

protein synthesis machinery

- in addition to mRNA template, many molecules and macromolecules contribute to translation - translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors

initiation of translation in prokaryotes

- in mRNA, a sequence upstream of the first AUG codon (shine-dalgarno) interacts with the rRNA molecules that compose the ribosome - this interaction anchors the 30s ribosomal subunit at the correct location on the mRNA template - GTP acts as an energy source during translation --> at the start of elongation and ribosome's translocation (also using IF-III)

initiation of translation in eukaryotes

- instead of depositing at the shine-dalgarno sequence, initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA - cap-binding protein (CBP) and other IFs assist the movement of the ribosome to the 5' cap at the mRNA - once at the cap, the initiation complex tracks along the mRNA in the 5'-3' direction, searching for the AUG start codon --> kozak's rules

termination of translation

- occurs when a nonsense codon is encountered - upon aligning with the A site, these nonsense codons are recognized by protein release factors that resemble tRNAs - the releasing factors instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid --> this reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released - the small and large ribosomal subunits dissociate from the mRNA and from each other --> they are recruited almost immediately to another translation initiation complex - after many ribosomes have complete translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction

tRNA

- structural RNA molecules transcribed by RNA polymerase III - serve as adaptor molecules --> each carries a specific amino acid and recognizes 1 or more of the mRNA codons that define the order of amino acids in a protein - aminoacyl-tRNAs bind to the ribosome and add the corresponding amino acid to the polypeptide chain --> tRNA molecules translate the language of RNA into the language of proteins - each tRNA anticodon can base pair with 1 or more of the mRNA codons for its amino acid --> matches more than 1 codon

overview of translation

- synthesis of proteins consumes more of a cell's energy than any of metabolic process; proteins account for more mass and perform virtually every function in the cell - involves the decoding of an mRNA message into a polypeptide product - amino acids are covalently strung together by interlinking peptide bonds ---> polypeptides are formed when the amino group of 1 amino acid forms a peptide bond with the carboxyl group of another amino acid - reaction is catalyzed by ribosomes and generates 1 molecule - each amino acid has an amino group (NH2) and carboxyl (COOH) group

elongation in prokaryotes and eukaryotes

- the mRNA template provides a tRNA specificity - as the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured - without mRNA not present in the elongation complex, the ribosome would bind to tRNA randomly and nonspecifically - proceeds with charged tRNAs sequentially entering and leaving the ribosome as each new amino acid is added to the polypeptide chain - movement of tRNA from A-P-E site is induced by conformational changes that advance the ribosome by 3 bases in the 3' direction --> energy for each step along the ribosome is donated by elongation factors that hydrolyze GTP --> energy required for both the binding of a new aminoacyl-tRNA to the A site and for its translocation to the P site after the formation of the peptide bond

compartments of the ribosome

- when the translation complex is formed, the tRNA binding region of the ribosome consists of 3 compartments: - A (aminoacyl) site binds incoming charged aminoacyl tRNAs - P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA --> the initiating methionyl-tRNA occupies the P site at the beginning of the elongation phase - E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids -

tRNA specificity

1) they must be recognized by the correct aminoacyl synthetase 2) they must be recognized by ribosomes 3) they must bind to the correct sequence in mRNA

consensus

DNA sequence that is used by many species to perform the same of similar functions

peptidyl transferase

RNA-based enzyme that is integrated into the 50s ribosomal subunit and catalyzes the formation of peptide bonds - peptide bond is formed between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA - energy for each peptide bond formation is derived from the high-energy bond linking each amino acid to its tRNA - after peptide bond formation, the A-site tRNA that now holds the growing peptide chain moves to the P site, and the P site tRNA that is now empty moves to the E site and is expelled from the ribosome

ribosome

complex macromolecule composed of structural and catalytic rRNAs and many distinct polypeptides (not protein enzyme --> nucleic acid) - a cell must invest energy to build them before an mRNA is translated - nucleolus (eukaryotes) is completely specialized for synthesis and assembly of rRNAs - exist in the cytoplasm of prokaryotes and both cytoplasm and rough endoplasmic reticulum of eukaryotes - mitochondria and chloroplasts have their own matrix and stroma

kozak's rules

determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5'-GCC (puring)CCAUGG-3'; the bolded bases are most important - the nucleotides around the AUG indicate whether it is the correct start codon - the closer the sequence is to this consensus, the higher the efficiency of translation - once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60s subunit binds to the complex of met-tRNA, mRNA, and the 40s subunit --> completes the initiation

protein folding, modification, and targeting

during and after translation: - individual amino acids may be chemically modified - signal sequences appended - the new protein folded into a distinct 3D structure as a result of intramolecular interactions

aminoacyl tRNA synthetase

enzyme that "charges" tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid - occurs when the tRNA is processed and exported to the cytoplasm and the corresponding amino acid is added - enzymes bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and AMP --> the activated amino acid is then transferred to the tRNA and AMP is released - charging: high-energy bond that attaches to an amino acid to its tRNA is later used to drive the formation of the peptide bond

chaperone

helper molecule that prevents proteins from aggregating during the complex process of folding

initiator tRNA

in prokaryotes, called tRNA met; in eukaryotes, called rRNA; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain

overview of initiation complex

in prokaryotes, involves the small 30s ribosome, mRNA template, 3 initiation factors, and a special initiator tRNA

polysome

mRNA molecule simultaneously being translated by many ribosomes all going in the same direction - complete mRNA/polyribosome structure

signal sequence

short tail of amino acids that directs a protein to a specific cellular compartment - protein's "train ticket" to its ultimate destination (mitochondria or chloroplast) - recognized by signal-recognition proteins that act as conductors - once the protein reaches its cellular destination, the signal sequence is clipped off