Protein and Amino Acids Flashcards

Proteins and Amino Acids

• Proteins are the most abundant and diverse organic molecules, made of amino acids.

Types of Proteins

• Enzymes: Catalyze biochemical reactions, making them faster.
  • Enzymes bind to a substrate (starting material) to react.
  • Enzyme names often end with "-ase".
• Hormones: Long-distance chemical signaling molecules released by endocrine cells.
  • Peptide hormones: Protein-based, e.g., insulin.
  • Steroid/lipid hormones: Made from lipids (steroids) but act as hormones.
• Other Functions:
  • Transport: Hemoglobin (carries O2).
  • Structure: Actin, tubulin, keratin.
  • Defense: Antibodies.
  • Contraction: Myosin.
  • Storage: Legume storage proteins, albumin (egg white).

Shapes of Proteins

• Globular: Hemoglobin.
• Fibrous: Collagen (in skin).

Amino Acids

• Amino acid: Monomer of a protein.
• Polypeptide: One or more linear chains of amino acids.
• Basic Structure of Amino Acid: NCC (like the inverse of CNN news channel).
  • N terminus: NH_2 (amino group).
  • Central (alpha) carbon: Has a side chain (R group) and a hydrogen group.
    • Alpha carbon: The carbon nearest to a functional group; subsequent carbons are beta, gamma, etc.
  • C terminus: COOH (carboxyl group).
• pK_a: Measures the strength of an acid or base.
  • Lower pK_a = stronger acid = more H+ = lower pH value.
  • High Ka= low pka

All Amino Acids

• R group: Unique to each amino acid, determines its identity and properties.

Peptide Bond Formation

• Protein synthesis: The C terminus of one amino acid binds with the N terminus of the next, releasing water.
• Always read N terminus to C terminus.
• Peptide bond: The bond between two amino acids.

Amino Acids in the Body

• Essential amino acids: Obtained from diet.
  • His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val.
• Non-essential amino acids: Created by the body.
  • Ala, Asn, Asp, Glu, Ser, Arg, Cys, Gln, Gly, Pro, Tyr.

Post-translational Modifications on Amino Acids

• Phosphorylation: Add a phosphate (P) group, commonly to Ser, Thr, or Tyr.
• Glycosylation: Add a carbohydrate group.
• Acetylation: Add an acetyl group.
• Methylation: Add a methyl group (alkyl).
• Ubiquitination: Add ubiquitin to lysine for tagging and degradation.
  • Ubiquitin: A protein that tags other proteins for degradation or alteration.

Protein Structure

• Primary structure: The sequence of amino acids.
  • Determined by DNA inside a gene.
  • Change in DNA sequence leads to change in amino acid sequence, polypeptide, and protein.
  • Medical example: Substitution of Glu to Val at the 6th position in hemoglobin causes sickle cell anemia.
    • Sickle cell Anemia: Hemoglobin molecules form long fibers, causing disc-shaped RBCs to become crescents or "sickled".
• Secondary structure: Hydrogen bonding between backbone interactions (polypeptide/sequence interaction) forming alpha-helices or beta-pleated sheets. Only between N-H and C-O
  • Alpha helix: 1 turn in helix = 3.6 amino acids. R groups face outward.
    • Proline: Alpha helix breaker as it introduces bends and is incompatible.
  • Beta-pleated sheet: Two polypeptide chains line up with R groups above and below the plane.
    • Parallel: NCC, NCC for each chain.
    • Antiparallel: NCC, CCN for each chain.
    • Amino acids incorporated: Trp, Tyr, Phe (due to space for rings).
• Tertiary structure: R group interactions. All non-covalent bonds (hydrogen bond, ionic, dipole-dipole, Van der Waals forces), except peptide bonds, within ONE subunit. Hydrophobic interactions. One covalent bond: disulfide between cysteines.
• Quaternary structure: Has subunits (1+ polypeptide chains). Interactions are the same as tertiary but occur between subunits.

Tip for Structures

• Primary: Peptide bond between amino acids.
• Secondary: Backbone interaction, hydrogen bonds resulting in alpha-helices or beta-sheets (or both or neither).
• Tertiary: R groups, all non-covalent, no peptide bonds, yes disulfide bonds within 1 subunit.
• Quaternary: Same as tertiary but between subunits.

Types of Bonds Involved in Protein Folding (Tertiary Structure)

• Hydrophobic interactions: Non-polar amino acids cluster together, avoiding water.
  • Nonpolar aggregate in center -> Water is sent to the environment -> system entropy increases.
• Hydrogen bonding: Forms between polar side chains and the backbone or side chain and side chain.
• Ionic bond/salt bridge: Positive charged (basic) + negative charged (acidic) side chain.
  • Example: Na^+Cl^-.
• Disulfide: Cysteine-cysteine, i.e., S-S.
• Van der Waals/London dispersion forces: Weak, require close proximity.

Entropy Change Due to Bonds

• Entropy: Measure of disorder in a system.
• Conformational entropy: Higher protein folding = more order = less conformational entropy.
• Solvent entropy: More hydrophobic aggregation = more H_2O released to the outside = high solvent entropy in other water molecules = drives folding.

Bonds in Quaternary Structure

• Hydrophobic: Entropy helps minimize hydrophobic regions of subunit exposure to water.
• Hydrogen bond: In between subunits.
• Ionic bonds: Between charged residues of different subunits.
• Disulfide: Different subunits connect by cysteine.

Chaperones

• Chaperones help in protein folding.

Denaturation

• Denaturation: Native conformation (original) becomes a non-native state (altered shape).
  • Temperature: High temp = high K.E. = non-covalent interactions disrupted.
  • pH: Acidic or basic side chains affected by pH changes.
  • Chemical agents: Urea or guanidine hydrochloride affect H-bonds or hydrophobic reactions.
• Reversible denaturation: Possible due to removal of denaturing agent/restoration of suitable environment AND primary sequence intact; loss of structure occurs but not broken peptide bonds.
• Irreversible denaturation: Covalent modifications, aggregation leads to permanent loss.
  * Albumin (white part) in eggs.