A

Protein Synthesis Notes ( in depth )

Proteins and Their Roles

  • Proteins build all living materials: muscles, hair and nails, feathers, wool, claws, scales, horns, and hooves. A protein called alpha-keratin forms hair and fingernails, and is a major component of feathers, wool, claws, scales, horns, and hooves.
  • Actin and myosin are proteins that enable muscular movement (e.g., blinking, breathing, rollerblading).
  • Hemoglobin is a protein that carries oxygen in the blood to every part of the body.
  • Ion channel proteins control brain signaling by allowing small molecules into and out of nerve cells.
  • Receptor proteins stud the outside of cells and transmit signals to partner proteins on the inside of cells.
  • Antibodies are proteins that defend the body against foreign invaders (bacteria, viruses).
  • Enzymes are proteins in saliva, stomach, and small intestine that help digest food.
  • Cellular construction workers: large clusters of proteins form molecular machines that perform heavy cellular work (e.g., copying genes during cell division and making new proteins).

Building Blocks: Amino Acids and Protein Structure

  • Proteins are composed of amino acids – there are 20 amino acids.
  • Different proteins are made by combining these 20 amino acids in different combinations.

The Ribosome and Protein Synthesis Machinery

  • Proteins are manufactured by the ribosomes (ribosomal proteins, ribosomal RNA (rRNA)).
  • Ribosomes are composed of large and small subunits and can be associated with the Rough Endoplasmic Reticulum (RER) or be free in the cytoplasm.
  • A newly formed protein chain grows as amino acids are added by transfer RNA (tRNA) bringing amino acids to the ribosome.
  • Components involved: tRNA, mRNA, ribosome (with large and small subunits), and the ribosome’s A site and P site where tRNA binds.
  • Rough Endoplasmic Reticulum (RER) houses ribosomes that synthesize proteins destined for membranes or secretion.

Function of Proteins

  • 1) Help fight disease.
  • 2) Build new body tissue.
  • 3) Enzymes (proteins) catalyze digestion and other chemical reactions; enzymes speed up reaction rates.
  • 4) Components of all cell membranes.

Step 1: Transcription (DNA to RNA)

  • First Step: Copying of genetic information from DNA to RNA is called Transcription.
  • Why transcription exists: DNA contains the genetic code for the needed protein, but ribosomes (where proteins are made) are outside the nucleus in the cytoplasm.
  • DNA is too large to leave the nucleus (double-stranded), but RNA can leave the nucleus (single-stranded).
  • Part of DNA temporarily unzips and is used as a template to assemble complementary nucleotides into messenger RNA (mRNA).

Step 2: Translation (RNA to Protein)

  • Second Step: Decoding of mRNA into a protein is called Translation.
  • Transfer RNA (tRNA) carries amino acids from the cytoplasm to the ribosome.
  • Amino acids come from the food we eat; proteins in food are broken down into amino acids and rearranged into new proteins according to the needs and directions of our DNA.

mRNA, tRNA, and Codons

  • A codon is a series of three adjacent bases in an mRNA molecule that codes for a specific amino acid.
  • Each tRNA has 3 nucleotides that are complementary to the codon in mRNA (the anticodon).
  • Each tRNA carries a different amino acid.

Start and Stop in Translation

  • Start codon: AUG signals the start of translation; translation begins at AUG.
  • Translation proceeds by matching codons on mRNA with corresponding anticodons on tRNA and adding the proper amino acids to the growing polypeptide chain.
  • Stop codons: UAA, UAG, UGA terminate translation; when the ribosome hits a stop codon, the polypeptide is released as a complete protein.

The Polypeptide Assembly Line (Polypeptide Synthesis)

  • The ribosome joins amino acids to build a growing polypeptide chain.
  • Example during one cycle: Methionine (start) and Phenylalanine are joined; the bond between methionine and its tRNA is released; the ribosome binds another tRNA and amino acid.
  • The ribosome moves along the mRNA, binding new tRNA molecules and amino acids.
  • Translation continues until a stop codon is reached, yielding a complete polypeptide.
  • Polypeptide = Protein.

Reading the Genetic Code: Codon Chart (Overview)

  • Codons are read in groups of three; there are 64 possible codons.
  • Each codon maps to an amino acid or a stop signal.
  • Start codon: AUG codes for Methionine.
  • Stop codons: UAA, UAG, UGA terminate translation.
  • The genetic code is degenerate: multiple codons can code for the same amino acid.

Practice Translations: Example Sequences

  • Example 1: CAC/CCA/UGG/UGA → Histidine − Proline − Tryptophan (Stop)
    • Translation proceeds until the Stop codon (UGA) is encountered; the resulting polypeptide is Histidine-Proline-Tryptophan.
  • Example 2: AUG/AAC/GAC/UAA → Methionine − Asparagine − Aspartic acid (Stop)
    • Start with Methionine, then Asparagine, then Aspartic acid, until the Stop codon.

Reading the Genetic Code (Expanded View)

  • A subset of codon-to-amino-acid mappings (examples):
    • UUU → Phenylalanine
    • UCU → Serine
    • UAU → Tyrosine
    • UGU → Cysteine
    • UUC → Phenylalanine
    • UCC → Serine
    • UAC → Tyrosine
    • UGC → Cysteine
    • UUA → Leucine
    • UCA → Serine
    • UUG → Leucine
    • UCG → Serine
    • UGG → Tryptophan
    • CUU → Leucine
    • CCU → Proline
    • CAU → Histidine
    • CGU → Arginine
    • CUC → Leucine
    • CCC → Proline
    • CUA → Leucine
    • CCG → Proline
    • CAC → Histidine
    • CAA → Glutamine
    • CAG → Glutamine
    • CGC → Arginine
    • CGA → Arginine
    • CGG → Arginine
    • AUU → Isoleucine
    • AUC → Isoleucine
    • AUA → Isoleucine
    • ACC → Isoleucine
    • ACA → Threonine
    • AAU → Asparagine
    • AAC → Asparagine
    • AAA → Lysine
    • AAG → Lysine
    • AGU → Serine
    • AGC → Serine
    • AGA → Arginine
    • AGG → Arginine
    • GUU → Valine
    • GCU → Alanine
    • GAU → Aspartic acid
    • GGU → Glycine
    • GUC → Valine
    • GCC → Alanine
    • GAC → Aspartic acid
    • GGC → Glycine
    • GUA → Valine
    • GCA → Alanine
    • GAA → Glutamic acid
    • GGA → Glycine
    • GUG → Valine
    • GCG → Alanine
    • GAG → Glutamic acid
    • GGG → Glycine
  • Note: The table shows how different codons map to amino acids; many codons encode the same amino acid (degeneracy).

From Gene to Protein: Process Overview (Central Dogma)

  • DNA transcription produces mRNA.
  • mRNA translation produces a polypeptide, which folds into a functional protein.
  • Flow: DNA -> RNA -> Protein.

Real-World Relevance and Implications

  • Protein synthesis explains how genes influence traits and diseases.
  • Diet provides amino acids; the body can reuse amino acids from digested proteins to build new proteins.
  • Proteins perform essential roles in membranes, signaling, immune defense, metabolism, and more.

Ethical, Philosophical, or Practical Implications

  • The transcript provided does not discuss ethical or philosophical implications directly.
  • General considerations in biology and biotechnology apply (gene expression control, biotechnology applications, protein engineering, and their societal impact).

Summary

  • The core idea: DNA carries the genetic code; transcription copies this code into mRNA; translation uses mRNA codons and tRNA anticodons at the ribosome to assemble amino acids into a growing polypeptide, which becomes a functional protein.
  • Key components: DNA, mRNA, tRNA, ribosome (large and small subunits; A and P sites), and, for many proteins, Rough Endoplasmic Reticulum.
  • Important numbers and signals: 20 amino acids; codons are groups of 3 bases; start codon AUG (Methionine); stop codons UAA, UAG, UGA; there are 64 possible codons.
  • Practical examples provided illustrate how codons map to amino acids and how translation terminates at stop signals.