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Translation (Protein Synthesis)

Notes

Translation (Protein Synthesis)

Sections

PROTEIN SYNTHESIS

Translation

Conversion of mRNA to protein

Codon

Group of three mRNA nucleotides that encode one amino acid

Ribosomal Structure

  • 2 subunits each made of protein and RNA:
  1. Small ribosomal subunit - has mRNA binding site
  2. Large ribosomal subunit
  • E-site (Exit site)
  • P-site (Peptidyl-tRNA binding site)
  • A-site (Aminoacyl-tRNA binding site)

PROTEIN SYNTHESIS STEPS

Initiation

  • Initiator t-RNA (methionine) binds to small ribosomal subunit (with help from initiation factors)
  • Small ribosomal subunit/initiator t-RNA complex binds mRNA (using 5' cap to bind the 5' end)
  • Complex scans towards the 3' end until it locates the start codon (AUG which sets the appropriate reading frame) and the large ribosomal subunit arrives

Elongation

  • Current tRNA in the P-site
  • New tRNA added to A-site
  • Growing peptide chain added to amino acid bound to A-site tRNA
  • Large ribosomal subunit shifts 3' one codon
  • Small ribosomal subunit follows - tRNA that was in P-site now in E-site and tRNA that was in A-site now in P-site
  • E-site tRNA ejected and new A-site tRNA added

Termination

  • When codon in A-site is stop codon (UAG, UAA, or UGA) a release factor is added to the A-site
  • Release factor binding releases the peptide chain and causes ribosome to dissociate

Full-Length Text

  • Here we will learn about protein synthesis, the second step in the two-step process in which DNA's code is used to generate protein.
  • Let's start a table to explore key concepts of protein synthesis.
  • Denote that translation is the term for conversion of mRNA to protein.
  • Denote that a codon is a group of three mRNA nucleotides that encode one amino acid.

First, we'll look at ribosomal structure.

  • Draw a molecule of mRNA.
  • Label the 5' and 3' ends.
  • Then, draw the two parts of the ribosome:
    • The small ribosomal subunit.
    • And large ribosomal subunit.
  • Label the mRNA binding site on the small ribosomal subunit, only.
  • Write that ribosomes are large protein/RNA complexes, which are the key protein synthesis machinery.
  • Label the E-site, P-site and A-site.
    • Each represents an important site for protein synthesis:
    • E for Exit site,
    • P for Peptidyl-tRNA binding site,
    • A for Aminoacyl-tRNA binding site.

Next, let's learn about the concept of the reading frame.

  • Write out a short string of nucleotides, UAGGCUUAA, three times.

For each row, let's see what codon combinations we can make:

  • Starting with the leftmost uracil first, we make three codons: UAG, GCU, and UAA.
  • Start one acid to the right (at the first) adenosine, we make: AGG and CUU.
  • Start two acids to the right (at the first guanine), we make: GGC and UUA.

Having the wrong amino acids could ruin the protein, so how does a ribosome know where to start?

  • As we'll see, the reading frame set with the start codon: AUG.
  • Now let's look at the three-step process of protein synthesis:
    • Initiation
    • Elongation
    • Termination.

Begin with initiation.

  • Draw the small ribosomal subunit.
  • Draw the initiator transfer RNA (tRNA) attached to the P-site.
  • We'll see that tRNAs are adaptors with a three nucleotide "anti-codon" section that binds to mRNA codons and also bind amino acids.
  • Now, attach the amino acid methionine to the tRNA.
  • Write that each tRNA is specific, it only binds one amino acid at the amino acid's carboxyl end.
  • Indicate that multiple initiation factors stabilize this interaction as part of initiation (we group them for simplicity).
    • Write that the initiation factors also stabilize the initiator tRNA binding to mRNA.
  • Now, redraw the small ribosomal subunit and tRNA complex.
  • Then, draw a strand of mRNA.
  • Label a single codon, AUG, in the middle of the strand.
    • Write that it is the start codon.
  • Label the 5' cap to show that the tRNA complex binds to the 5' end of the mRNA.
    • Write that the 5' cap signals the location of the 5' end of the mature mRNA.
  • Indicate that the small ribosomal subunit complex scans from 5' to 3'.
  • Again, redraw the mRNA.
  • Draw the small ribosomal subunit such that the tRNA is now bound to the AUG codon.
  • Write that start codon (AUG) signals for the large ribosomal subunit to arrive, and thus, it sets the appropriate reading frame for synthesis.
  • So now, bring in the large ribosomal subunit.
  • Show a new tRNA (with bound amino acid) added to the A-site.

Next, elongation.

  • Draw the ribosomal subunits bound to mRNA.
  • Show that our new tRNA molecule shifts from the A-site to the P-site and now has growing chain of amino acids bound to it.
  • Write that ribosomes add amino acids to the carboxyl end of the growing peptide chain.
  • Then, draw a new tRNA (with amino acid) in the A-site.

Just what happened to our initiator tRNA…? We'll find out in these next steps.

  • Redraw the ribosome bound to the mRNA with the two tRNAs.
  • But, here, shift the peptide to the amino acid in the A-site and indicate the newly formed peptide bond.
  • Write that the ribosome catalyzes the peptide chain to shift from the P-site to the A-site.
  • Then, with an arrow, show that the large ribosomal subunit shifts in the 3' direction.

Illustrate this next step as follows:

  • Redraw the mRNA, tRNAs, and large ribosomal subunit.
  • Indicate that the tRNAs have both shifted within the large ribosomal subunit:
    • The P-site tRNA is now in the E-site.
    • The A-site tRNA is now in the P-site.
  • Then, show that the small ribosomal subunit is unmoved from its prior position and thus there is an open space above it (the large subunit is now shifted to the right).
  • Indicate with an arrow that the small subunit now shifts in the 3' direction.

Illustrate this next step as follows:

  • Redraw the mRNA and the ribosome.
  • Redraw the P-site tRNA with the bound peptide chain.
  • Show the E-site tRNA ejected from the E-site without a peptide.
  • Then, draw a new tRNA (which matches the codon) in the A-site.
  • So what happened to our initiator tRNA…?
    • It entered the E-site and was ejected.

This is the cycle of protein elongation.

Now, termination.

  • Draw an mRNA molecule.
  • Draw the ribosomal subunits bound to it.
  • Shift the tRNA from the last step to the P-site from the A-site and show that its bound peptide chain has grown.
  • Then, label the mRNA bases under the A-site as UAG, which is one of three stop signal codons.
    • Write that the other two are UAA and UGA.
  • Draw a release factor bound to the stop codon.
    • Write that release factor binding to the stop codon releases the peptide chain from the P-site tRNA, which causes the ribosome to dissociate.
  • Finally, show the dissociated components:
    • Empty tRNA
    • Release factor
    • mRNA
    • Ribosomal subunits
    • And the released protein product.

UNIT CITATIONS:

  1. Campbell, N. A. & Reece, J. B. Biology, 7th ed. (Pearson Benjamin Cummings, 2005).
  1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. Molecular Biology of the Cell, 5th ed. (Garland Science, 2008).
  1. Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. Essential Cell Biology, 3rd ed. (Garland Science, 2010).
  1. Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., Ploegh, H. & Matsudaira, P. Molecular Cell Biology, 6th ed. (W. H. Freeman and Company, 2008).
  1. Marieb, E. N. & Hoehn, K. Human Anatomy & Physiology, 10th ed. (Pearson, 2016).
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