Protein synthesis

Protein synthesis is the fundamental biological process by which cells create proteins (also known as polypeptides). This process is essential for all living organisms as proteins dictate the structure and function of cells. The instructions for making proteins are encoded in the cell's DNA. The entire process can be summarized as "DNA makes RNA and RNA makes protein".

Protein synthesis occurs in two main stages: transcription and translation.

I. Transcription

Transcription is the first stage where the DNA code is copied into a messenger RNA (mRNA) molecule.

• Location: In eukaryotic cells, transcription takes place in the nucleus. In prokaryotic cells, which lack a nucleus, it occurs directly in the cytoplasm.

• Process:

  1. The enzyme RNA polymerase attaches to the beginning of a gene on the DNA double helix.

  2. In eukaryotes, DNA helicase (attached to RNA polymerase) breaks the hydrogen bonds between the two DNA strands within the gene, causing the DNA molecule to unwind and uncoil, exposing the bases.

  3. One of the DNA strands, known as the template strand (or transcribed strand), is used to create the mRNA copy.

  4. Free RNA nucleotides in the nucleus line up opposite their complementary bases on the template DNA strand. According to complementary base pairing, adenine (A) on DNA pairs with uracil (U) on RNA (instead of thymine), and guanine (G) pairs with cytosine (C).

  5. RNA polymerase then joins these RNA nucleotides together, forming the sugar-phosphate backbone of the new mRNA strand.

  6. As RNA polymerase moves along the DNA, the unwound DNA strands re-form hydrogen bonds and coil back into a double helix.

  7. Transcription stops when RNA polymerase reaches a stop codon on the DNA template strand and detaches from the DNA.

• Product:

  • In eukaryotes, the initial RNA molecule produced is pre-mRNA, which contains both coding sequences (exons) and non-coding sequences (introns). The introns are then removed by a process called splicing, leaving only the exons, which are joined together to form the mature mRNA.

  • In prokaryotes, mRNA is produced directly from the DNA, as their DNA does not contain introns.

• Post-Transcription: The mature mRNA molecule then leaves the nucleus (in eukaryotes) through a nuclear pore and travels to the cytoplasm, where it attaches to a ribosome for the next stage.

II. Translation

Translation is the second stage, where the mRNA sequence is used to synthesize a polypeptide chain (protein).

• Location: Translation occurs at the ribosomes in the cytoplasm in both eukaryotic and prokaryotic cells.

• Key Molecules Involved:

  • mRNA: Carries the genetic code from the DNA to the ribosomes. Its sequence of codons (three adjacent bases) dictates the order of amino acids.

  • tRNA (transfer RNA): Molecules that carry specific amino acids to the ribosome. Each tRNA molecule has a specific sequence of three bases called an anticodon, which is complementary to an mRNA codon.

  • Ribosomes: Composed of ribosomal RNA (rRNA) and proteins. They have a small and a large subunit. Ribosomes are the sites where amino acids are linked together to form polypeptides.

• Process:

  1. The mRNA molecule attaches to a ribosome.

  2. A tRNA molecule with an anticodon complementary to the start codon (usually AUG) on the mRNA attaches itself to the mRNA by complementary base pairing. The start codon codes for the amino acid methionine.

  3. A second tRNA molecule attaches to the next codon on the mRNA in the same way.

  4. The two amino acids brought by the tRNA molecules are then joined together by a peptide bond, catalyzed by an enzyme within the ribosome.

  5. The first tRNA molecule moves away, leaving its amino acid behind, and the ribosome moves along the mRNA to the next codon.

  6. This process of tRNA binding, peptide bond formation, and ribosome movement continues, adding amino acids one by one, forming a lengthening polypeptide chain.

  7. The elongation stops when a stop codon (UAA, UAG, or UGA) is reached on the mRNA, signaling the termination of protein synthesis. The completed polypeptide chain then detaches from the ribosome.

  8. Often, several ribosomes translate the same mRNA molecule simultaneously, forming a structure called a polysome.

• Energy Requirement: ATP provides the energy needed for the bond formation between the amino acid and its specific tRNA molecule, allowing the tRNA to carry the amino acid to the ribosome.

III. Genetic Code and Protein Structure Link

• The genetic code is the sequence of base triplets (codons) in mRNA that precisely codes for specific amino acids [Genetic Code Summary, 146, 242, 330, 515, 603, 717]. Each amino acid is coded for by a sequence of three bases.

• The genetic code is universal (the same codons code for the same amino acids in almost all organisms), degenerate (most amino acids are coded for by more than one triplet), and non-overlapping (each triplet is read distinctly and sequentially).

• The sequence of amino acids in the polypeptide chain determines its primary structure, which in turn largely determines the protein's overall 3D structure (secondary, tertiary, and quaternary structures) and ultimately its specific function.

IV. Post-Translation and Cellular Structures

• After translation, proteins may undergo further modification within the cell. Proteins synthesized on ribosomes attached to the rough endoplasmic reticulum (RER) are folded and processed, and then transported to the Golgi apparatus in vesicles.

• In the Golgi apparatus, proteins may undergo further processing, such as adding or trimming sugar chains to form glycoproteins.

• Finally, these processed proteins are packaged into vesicles and transported to their final destination, including secretion out of the cell via exocytosis.