Protein Structure and Function Quiz

Biochemistry Science Course: EBA 1300

• Course code: EBA 1300

Fundamental Biochemistry of Proteins (Lec. 7)

• Classification of amino acids: Based on the properties of the R group.
  • Electrochemical polarity
  • Structural classification
  • Physiological classification
  • Metabolic classification

Metabolic Classification

• Glucogenic amino acids: Converted into glucose via gluconeogenesis.
  • Form glucose precursors
  • Important in gluconeogenesis
  • Include most essential and non-essential amino acids
• Ketogenic amino acids: Form acetyl CoA or acetoacetyl CoA.
  • Form precursors for ketone bodies
  • Important in ketogenesis
  • Include exclusively lysine and leucine
• Mixed: Isoleucin and 3 aromatic amino acids

Catabolism of Amino Acids

• Figure: Depicts a cyclic pathway with various amino acids (e.g., alanine, aspartate, etc.) and intermediates (e.g., Acetyl-CoA, Citrate, Isocitrate). Different amino acids enter at various points and their breakdown leads to intermediates that are utilized in other metabolic pathways, like the citric acid cycle.

Function of Amino Acids

• Building blocks of proteins

• Functional: Neurotransmitters

  • Glutamate and aspartate (excitatory)
  • Glycine (inhibitory)

• Note: Glycine and proline contribute to 57% of total amino acids (AAs) in collagen.

• Precursors to other molecules:

  • Neurotransmitters (serotonin, melatonin, dopamine)
  • GABA
  • Thyroxine
  • Indole acetic acid
  • Epinephrine
  • Porphyrins (e.g., heme)
  • Histamine
  • Nucleotides
  • Nitric oxide

How Amino Acids are Joined Together

• Amino acids are linked by peptide bonds.
• Polymers of fewer than 50 amino acids are oligopeptides; more than 50 are polypeptides.
• The bond formation involves the carboxyl group of one amino acid and the amino group of another, releasing a water molecule.

Peptide Bonds Link Amino Acids

• The peptide bond is formed through a condensation reaction.
• Nucleophilic addition-elimination reaction between the amino group of one amino acid and the carboxyl group of another.

Amino Acid (1) and (2)

• Shows the N-terminus and C-terminus of amino acids (1) and (2). Formation of a peptide bond.

Condensation and Hydrolytic Reactions

• Peptide bonds form by condensation.
• Broken down by hydrolysis.
• Requires energy, derived from ATP.

Structure of the Protein

• Four levels of structure:

  • Primary
  • Secondary
  • Tertiary
  • Quaternary

• Any alteration of structure or sequencing alter shape and function of the protein.

1. Primary Structure

• Unique sequence of amino acids in a polypeptide chain.
• Basic level.
• Amino acids linked covalently (peptide bonds).
• Starts from N-terminus to C-terminus.
• Example: Insulin has two polypeptide chains (A and B).

2. Secondary Structure

• Polypeptide chain folding.
• Hydrogen bonds form between backbone atoms.
• Two main types:
  • α-helix
  • β-pleated sheet

3. Tertiary Structure

• 3D shape of a protein.
• Further folding of secondary structures.
• Due to interactions between R-groups of amino acids.
  • Hydrogen bonding
  • Ionic bonding
  • Hydrophobic interactions
  • Disulfide bonding (covalent linkage between cysteine residues)

4. Quaternary Structure

• Proteins with more than one polypeptide chain (subunits).
• Subunits held together by bonds.
• Heteromeric: formed from different subunits.
• Homomeric: formed from identical or similar subunits. Example (hemoglobin and ferritin)

Determination of Tertiary Structure (PDB)

• X-ray crystallography
• Nuclear Magnetic Resonance (NMR)
• Atomic coordinates stored in a database (Protein Data Bank).
• Analyze and compare structures.

Denaturation

• Process where a protein loses its native shape and biological activity.
• Disruption of weak chemical bonds.
• Loss of secondary, tertiary, and quaternary structure.
• Primary structure remains unchanged.
• Examples affecting denaturation: Temperature, pH, solvents, enzymes.
• A protein's function depends on its three-dimensional shape, and losing that structure means the protein loses its function.