Ch. 13: Translation of mRNA

proteins

• the building blocks of all organisms

• have many different functions

alkaptonuria

• what Archibald Garrod studied

a missing enzyme

• What Garrod proposed alkaptonuria was caused by

• he knew it followed a recessive pattern in inheritance

• he proposed a relationship between the inheritance of the trait and the inheritance of a defective enzyme

• described the disease as an inborn error of metabolism

a single gene controlled the synthesis of a single enzyme

• Beadle and Tatum’s conclusion

• their genetic model was Neurospora crassa

  • in normal strains, they could live on minimal media

  • in the mutant strains, a genetic defect in one gene prevent the synthesis of one amino acid preventing them from living on minimal media

• by supplementing minimal media with individual amino acids, they were able to identify which amino acid the mold could no longer synthesize

modifications of the One Gene-One Enzyme theory

• enzymes are only one category of proteins

• some proteins are composed of two or more different polypeptides

  • polypeptides denote structure

  • protein denotes function

• many genes have been identified that do not code polypeptides

  • function RNA molecules (tRNA, rRNA)

• one gene can code multiple polypeptides through alternative splicing

translation

• involves an interpretation of one language into another

  • the nucleotide language of mRNA is converted into the amino acid language of proteins

  • the process relies on the genetic code

AUG

• start codon

• specifies methionine

UAA, UAG, UGA

stop codons

degeneracy

• a trait the genetic code possesses

• more than one codon can specify the same amino acid

  • ex: GGU, GGC, and GGG all code for glycine

reading frame

• a series of nonoverlapping codons beginning with the start codon

• goes from a start codon to a stop codon

tRNA

• molecules that play a role in establishing the relationship between the series of codons in mRNA, and the series of amino acids in a polypeptide

• also called anticodons which are antiparallel to mRNA and run in the 3’ to 5’ direction

amino acids

• the building blocks of all proteins

• 20 different ones that have different properties

  • nonpolar, polar, aromatic, positively charges, negatively charged

nonpolar

• type of amino acids that are hydrophobic

• they are often buried within the interior of a folded protein

polar and charged

• type of amino acids that are hydrophilic

• more likely to be on the surface of a protein

peptide bonds

• type of bonds that join amino acids together

ribosome

• molecule that catalyzes the reaction between the carboxyl end of a growing peptide and the amino end of the incoming amino acid, forming peptide bond

5 to 3

• directionality of polypeptide synthesizes

• corresponds to the N to C orientation of the polypeptide

primary structure

• sequence of amino acids

secondary structure

• alpha helix of beta pleated sheets

tertiary structure

• 3-D conformation

quaternary structure

• two or more polypeptides may associate with each other

functions performed by proteins

• transport and movement

• cell shape and organization

• cell signaling and cell surface recognition

• enzymes that accelerate chemical reactions within a cell

structure and function of tRNA

• the binding between mRNA and tRNA obeys the AU/CG rule

  • A bonds to U and G bonds to C

  • the binding between mRNA and tRNA is anti-parallel

third position

• where degeneracy in codons always occurs except for serine, arginine and leucine

Wobble rule

• in the codon/anti-codon recognition process, the first two positions pair strictly according to the Au/GC rule

• the third position can move a bit

  • it can tolerate certain types of mismatches due to degeneracy

large and small subunits

• the structures that compose a ribosome

• each structure is formed from the assembly of proteins and rRNA

nucleolus

• where ribosomal protein and rRNA assembly occurs in eukaryotic cells

discrete sites of a ribosome

• P sit

• A site

• E site

Peptidyl site (P site)

• one of the discrete sites on a ribosome

• where the peptide bond is catalyzed

Aminoacyl site (A site)

• one of the discrete sites on a ribosome

• where new tRNA comes in

Exit site (E site)

• one of the discrete sites on a ribosome

• where tRNA leaves

translation initiation

• the small ribosomal subunit binds the mRNA facilitated by Poly-A and 5’-Methyl cap binding proteins

• scans the mRNA until it finds a start codon surrounded by a Kozak sequence

Kozak sequence

• the start codon and sequence around it that signify to start translation instead of just another AUG codon being recognized

translation elongation

• a charged tRNA brings a new amino acid to the ribosome so that it can be attached to the end of the growing polypeptide

  • a charged tRNA carrying a single amino acid bind to the A site

• Peptidyl transfer: the polypeptide is removed from the tRNA and the P site and transferred to the amino acid at the A site

  • the 23S rRNA (a component of the large subunit) is the actual peptidyl transferase

• the ribosome the moves, or translocates, to the next codon in the mRNA, moving the tRNAs at the P and A sites to the E and P sites

termination of translation

• occurs when a stop codon is reached in the mRNA

• these codons are not recognized by tRNAs, but by proteins called release factors