Translation and protein synthesis

Abstract

Gene expression is the process by which genetic information flows from DNA to RNA to the protein. The translation of DNA into RNA is termed transcription; protein synthesis from RNA templates is called translation. Details on gene expression and transcription can be found in a separate learning card.

Translation is carried out by ribosomes, which are large molecular complexes of ribosomal RNA (rRNA) and proteins. Ribosomes bind to RNA templates, also termed messenger RNA (mRNA), and catalyze the formation of a polypeptide based on this template. In the process, a charged transfer RNA (tRNA) recognizes a nucleotide triplet of mRNA that matches a specific amino acid (AA). The new AA is then linked to the next AA of the growing polypeptide on the ribosome. Translation ends once a specific nucleotide sequence of the mRNA is reached (a stop codon). The ribosome subsequently dissociates and the mRNA and newly synthesized protein are released.

Before proteins are functional, a proper shape and destination are both necessary. Proteins begin to fold into their three-dimensional structure during translation according to the AA sequence and local chemical forces and reactions. Various specialized proteins (folding catalysts, chaperones) also help the newly formed proteins to fold properly and reach their correct destinations (e.g., cytosol, organelles, extracellular matrix) via protein modifications. The translation rate of proteins is adjusted to the current conditions of the cell and bodily demands, and is affected by the presence or absence of certain nutrients.

Genetic code

The genetic code

To help remember the stop codons UGA, UAG, and UAA: U Go Away, U Are Gone, and U Are Away!

tRNA charging

Translation process

Translation occurs in three phases in a functional ribosome: initiation, elongation, and termination. It requires mRNA, tRNA, and rRNA (see RNA section from nucleic acids: DNA and RNA).

Ribosome binding sites

Eukaryotes have Even-numbered ribosomal subunits (40S + 60S → 80S); PrOkaryotes have Odd-numbered ribosomal subunits (30S + 50S → 70S).

For binding sites, think of an “APE” party: 1. A site → Arrival with Aminoacyl-tRNA 2. P site → Growing (GTP) Party of Peptides 3. E site → party Ends and is EmptytRNA Exits; Growing stands for GTP as energy source

1. Initiation

  • Description: assembly of functional ribosomes with the help of initiation factors (IFs): and recognition of the start codon (AUG) on the mature mRNA by the initiator methionyl-tRNA (met-tRNA)
  • Process

  1. Initiator met-tRNA, eukaryotic IF2 (eIF2), and GTP bind to the small ribosomal subunit to form a preinitiation complex; (initially a 43s preinitiation complex).
  2. mRNA is recognized by eIF4 and binds to the preinitiation complex; , leading to the formation of the 48s preinitiation complex. eIF4 recognizes mRNA: Initiator met-tRNA recognizes the start codon (typically the first AUG triplet after the 5' cap of the mRNA) and binds the P site.
  3. GTP hydrolysis provides energy for the release of eIF2, allowing the large and small ribosomal subunits to assemble into a functional ribosome (the final initiation complex; 80S in eukaryotes, 70S in prokaryotes).

2. Elongation

  • Directions of processes
    • mRNA is read in a 5' to 3' direction
    • Elongation occurs in an N-terminus to C-terminus direction: The N-terminus of the growing protein also initially leaves the ribosome.
  • Process

3. Termination

ATP for Activating (charging) tRNA; GTP for tRNA Gripping and Going through the ribosome (translocation) for Growing a polypeptide

Protein folding and misfolding

Protein folding

  • Description: The process by which a protein goes from an unfolded native state to form a three-dimensional structure via progressive stabilization of the intermediate states until the most favorable energy level is achieved.
    • Correct protein folding begins during translation and is required for a protein to perform its function within the cell or organism.
  • Intrinsic factors
    • The spatial structure is specified in the AA sequence of the protein (see protein structure for more details).
    • Largely driven by hydrophobic interactions, Van der Waals forces, H+-bonds, salt bridges, disulfide bonds
  • Regulatory proteins: proteins that help other proteins to form their native structure
    • Chaperone
      • Protein complexes that prevent protein aggregation during synthesis (thus prevent making proteins nonfunctional) and permit refolding of misfolded proteins in a protected environment
      • Assist in transporting (precursor) proteins
      • ATP is consumed in the process.
      • Examples: heat shock proteins (e.g., Hsp70, Hsp60, Hsp90) prevent denaturation or misfolding at high temperatures or when under chemical stress
    • Folding catalysts: : enzymes that accelerate rate-limiting steps during protein folding
      • Protein disulfide-isomerase: Catalyzes the formation of thermodynamically favorable disulfide bonds within proteins (in proteins that possess more than two cysteine residues), if less energetically favorable disulfide bonds are formed.
      • Prolyl isomerase: Assists in finding the energetically favorable conformation of a peptide bond with the AA proline.
        • Usually a trans confirmation; however, the cis conformation is at times more favorable.

Protein misfolding

Post-translational modification

Many proteins require specific covalent alterations (co- or post-translational modifications) in addition to correct folding to function properly. Examples include glycosylation, lipid anchors, phosphorylation, acetylation, ubiquitination, ADP-ribosylation, biotinylation, carboxylation, methylation and hydroxylation.

Protein glycosylation

N-linked glycosylation O-linked glycosylation
Site
% of all glycosylations ∼ 90% ∼ 10%
Attached by N-glycosidic bonds O-glycosidic bonds
Amino acids involved Asparagine

Serine or threonine

Carbohydrate side chains Complex oligosaccharides Less complex oligosaccharides
Sugar residues involved
  • Glucose
  • Mannose
  • Fucose
  • Galactose
  • N-Acetylglucosamine
  • N-Acetylneuraminic acid
  • Galactose
  • N-Acetylgalactosamine
  • N-Acetylglucosamine
  • N-Acetylneuraminic acid
Enzymes/molecules involved
  • Specific glycosyltransferases: oligosaccharyltransferase
  • Dolichol phosphate (in the membrane)
  • Other enzymes, e.g., flippases
  • Specific glycosyltransferases

N-linked glycosylation, the attachment of sugar to the asparagine residue of proteins, begins in the rough ER! Enzymatic glycosylation should not be mistaken with nonenzymatic glycation. In glycation, aldoses (e.g., glucose) spontaneously bind to the amino groups of proteins and may influence their function! (A classic example is HbA1c, whose function is unaffected by glycation.)

Lipid anchors

Reversible covalent alterations

Enzymatic reversible protein modification alters the protein's spatial structure (conformation), thereby allowing its activity to be regulated. For example, a protein may interact with other proteins and/or become recognizable as a substrate. Reversible protein modification essentially allows the protein to be switched on or off. Additionally, the durability of proteins may be influenced.

Protein trimming

  • Description: the excision of N- or C-terminal propeptides to create a mature protein (from an inactive state)
  • Examples:

Protein sorting

Protein transportation

A protein's intended final destination depends on its signal sequence (if it has one) at the N-terminus and determines if translation is concluded on free ribosomes or ribosomes on the rough ER.

Destination Signal sequence? Ribosome
Cytosol No Free ribosomes
Mitochondria, peroxisomes, or nucleus Yes Free ribosomes
Cell membrane, lysosomes, or extracellular (secretory proteins) Yes Rough ER ribosomes

Translocation of ribosomes on the rough ER

Proteins that leave the cell (secretory proteins); , as well as membrane and lysosomal proteins, are initially synthesized on free ribosomes of the cytosol. However, their synthesis is paused shortly after starting and the ribosome is transported to the cytosolic side of the rough ER. Protein synthesis then recommences and the protein is directly synthesized into the ER lumen.

Mechanism

  1. Initiation of translation on the free ribosomes in the cytosol
  2. If a signal sequence (specific amino acid sequence of 9–12 amino acids) is synthesized, it is bound to a signal recognition particle (SRP, a ribonucleoprotein):
  3. SRP induces a pause in translation and transports the ribosome with the peptide chain across the ER membrane.
  4. SRP facilitates binding of the ribosome with the signal peptide to the SRP receptor on the ER membrane.
  5. SRP and the SRP receptor are both bound to GTP, which is hydrolyzed to GDP. → SRP is released and can bind to a new signal sequence.
  6. The ribosome is transferred to a translocon, a protein-lined channel composed of a complex of proteins spanning the ER membrane, with opening of the translocon channel. This translocon is termed the sec61 channel.
  7. Translation resumes and the protein is synthesized in the ER lumen.
  8. The signal sequence is cut off from the growing protein by a signal peptidase.
  9. After termination of translation, the ribosome is released into the cytosol.
  10. The translocon channel closes and the synthesized protein is left in the ER.
    • During translation, the protein is folded into its native conformation.

Other processes

Translational regulation

  • Main component: initiation phase of translation (regulation via initiation factors)
  • Regulation mechanisms
    • Decreased formation of the ternary complex of eIF2, GTP, and initiating tRNA through phosphorylation of the initiation factor eIF2
      • Phosphorylated eIF2 in the GDP-bound form can no longer be converted to its active GTP-bound form. The ternary complex necessary for initiating translation can no longer be formed and the translation rate is reduced.
        • Example: synthesis of globin in red blood cells
          • If there are insufficient levels of heme available to be incorporated in the globin protein, globin synthesis is inhibited by phosphorylation of eIF2.
    • Regulation of the cap recognition process by eIF4
last updated 11/22/2018
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