Biological Molecules - Amino Acids and Proteins

Amino acid description

  • Absolute configuration at the alpha position
    • L and D amino acid configuration
    • L and D is different from R and S. L is not always S, and D is not always R.
    • If the priority of NH2 > COOH > R, then L=S and D=R. For example, L-Alanine = S-Alanine.
    • If the priority of NH2 > R > COOH, then L=R, and D=S. For example, L-Cysteine = R-Cysteine.
    • L-amino acids are the more common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins.
  • Amino acids as dipolar ions classification
    • zwitterion
    • At low pH, amino acids exist in the cationic form.
    • At high pH, amino acids exist in the anionic form.
    • At pH = pI, amino acids exist in the zwitterion form, which is overall neutral.
  • Classification
    • Acidic or basic
      • If the R group contains carboxylic acid, then it's an acidic amino acid. There are two acidic amino acids: aspartic acid and glutamic acid.
      • If the R group contains an amine group, then it's a basic amino acid. There are three basic amino acids: lysine, arginine, and histidine.
    • Hydrophobic or hydrophilic
      • Hydrophobic: If the R group doesn't contain any of the stuff below.
      • Hydrophilic: If the R group contains acids, bases, amines or alcohols.

Amino acid reactions

  • Sulfur linkage for cysteine and cystine
    • Cysteine = side chain with the thiol group
    • cystine = 2 cysteines forming a disulfide bond
  • Peptide linkage
    • peptide bond
    • Peptide bond = amide bond.
    • The peptide bond is formed by the amine group attacking the carbonyl carbon.
  • Hydrolysis
    • hydrolysis of the peptide bond
    • The peptide bond is very difficult to hydrolyze. It requires a strong base, or a biological enzyme.

Protein structure

  • Primary structure of proteins
    • Primary structure = sequence.
    • The primary structure of proteins is read from the N-terminus to the C-terminus.
  • Secondary structure of proteins
    • Secondary structure = repetitive motifs formed by backbone interactions.
    • Backbone interactions = hydrogen bonding between the NH and C=O
    • The two most common secondary structures are α helices and β pleated sheets.
    • The α helix is right-handed, with the R groups sticking outward.
    • In β sheets, R groups stick out above and below the sheet.
  • Tertiary structure
    • 3D structure of proteins
    • Caused electrostatic side chain - side chain interactions
  • Quaternary structure
    • Separate chains/subunits joining together
    • Caused by covalent disulfide bonding of cysteine side chains

Protein conformational stability

  • Folding = chain -> 3D structure
  • Many proteins fold spontaneously, some require the assistance of chaperone proteins
  • Denaturing = loss of the native 3D structure such that it no longer function
  • Extreme heat, salt concentration, or pH denatures proteins

Separation techniques

  • Isoelectric point
    • pH at which the molecule is neutral
    • Acidic amino acids and proteins with lots of acidic side chains have have a lower isoelectric point
    • Basic amino acids and proteins with lots of basic side chains have a higher isoelectric point
  • Electrophoresis
    • Protein is charged
    • An electric field forces protein to travel through a gel
    • Larger charge = more electrical force = travels faster
    • Smaller protein = squeezes through easier = travels faster
    • Structure plays no role because SDS is usually added to denature the protein

Non-enzymatic protein function

  • Binding: the active site binds the substrate
  • Stronger binding = lower Kd value
  • Stronger binding doesn't necessarily mean a more efficient enzyme (if it binds the substrate and not let go, then it can't catalyze a new substrate)
  • Stronger binding = better antibody
  • Immune system
    • Antibody = proteins that bind antigen on pathogens, which promote their destruction by the immune system
    • Antigen = proteins expressed by pathogens. They can either directly bind to antibodies, or be presented by antigen presenting cells (such as macrophages and dendritic cells)
    • Complement = proteins that punch holes in cells to be destroyed by the immune system
  • Motors: uses ATP/GTP as energy to create motion
    • Flagella (bacteria, sperm)
    • ATP synthase (mitochondria, chloroplasts)
    • Motile cilia (trachea)
    • Myosin (muscle)
    • Kinesin/Dynein (intracellular transport)
    • Actin polymerization (Listeria)

Old topic, no longer tested

  • synthesis of amino acids
    • Strecker synthesis
      • starting material: R-aldehyde
      • reagents: cyanide (KCN), ammonium (NH4Cl)
      • product: amino acid with the -R group originally on the aldehyde
    • Gabriel synthesis
      • starting material: R-halide
      • reagents: 1. phthalimide, 2. NH2-NH2
      • product: amino acid with the -R group originally on the halide