Biology Proteins and Peptides Quiz

Proteins and Peptide Bonds

• Proteins are the most abundant organic molecules in the human body.
• Composed of carbon, hydrogen, oxygen, nitrogen, and some contain sulfur and phosphorus.
• Monomer unit of proteins is an amino acid.
• Peptide bonds (amide bonds) form between amino acids.
• Peptide: unbranched chain of amino acids.
• Oligopeptide: 10-20 amino acid residues.

Functions of Proteins

• Structural support
• Enzymes
• Hormones and receptors
• Immunity
• Fluid and acid-base balance

Amino Acid

• Building block of protein.
• Contains both an amino group and a carboxyl group.
• α-amino acid: amino group and carboxyl group are attached to the α-carbon atom.
• R denotes a side chain group.

Amino Acid Classification

• Non-polar amino acids:
  • Zero net charge
  • Form hydrophobic interactions
  • Found in the interior of the protein
  • Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
• Polar uncharged amino acids:
  • Zero net charge
  • Form hydrogen bonds
  • Found on the surface of the protein
  • Serine, Threonine, Tyrosine (contain -OH), Cysteine (-SH), Asparagine, Glutamine (amides)
• Charged amino acids:
  • Positive (acidic) or negative (basic) net charge
  • Form ionic interactions
  • Found on the surface of the protein
  • Acidic: Aspartate, Glutamate
  • Basic: Arginine, Lysine, Histidine

Essential Amino Acids

• Cannot be synthesized in the body.
• Semi-essential amino acids: required for growth in children, but not for adults.
• Barone Essential Amino Acid Mnemonic: PVT.TIM HALL
  • Phenylalanine, Valine, Tryptophan
  • Threonine, Isoleucine, Methionine
  • Histidine, Arginine, Lysine (ketogenic), Leucine (ketogenic)

Zwitterion

• Has a positive charge on one atom and a negative charge on another atom with no net charge.
• Amino acids can serve as buffers in aqueous solutions.

Types of Conjugated Proteins

• Hemoproteins:
  • Prosthetic group: heme unit
  • Hemoglobin, myoglobin
  • Carrier of O2 in blood, oxygen binder in muscles

Protein Stability

• Chemical Factors:
  • Disulfide bonds
  • Hydrophobic interactions (predominant)
  • Hydrogen bonding
  • Van der Waals interactions
  • Increase in IMF, more stable due to decreased Gibbs free energy change (ΔG)

Peptide Bond

• Rigid planar trans configuration
• Partial (about 40%) double bond character between α-amino nitrogen of one amino acid to the carbonyl carbon of the next.
• Keeps peptide links relatively resistant to conformational change

Torsional Angles

• Ψ (psi): allowed rotation for –Cα–C=O
• Ф (phi): allowed rotation for –N–Cα–
• Limited rotation due to steric and torsional strains
• Ramachandran diagram indicates allowed conformations of polypeptides

Conformation & Configuration

• Conformation: Spatial relationship of every atom in a molecule.
  • Interconversion between conformers occurs with retention of configuration.
• Configuration: Geometric relationship between a given set of atoms.
  • Interconversion of configurational alternatives requires breaking and reforming covalent bonds.

Protein Conformation

• Spatial arrangement of atoms in a molecule (protein).
• Native proteins: functional and folded conformation.
• Folding must achieve a decrease in Gibbs free energy change for a protein to be stable.
• Stability is the tendency to maintain a native conformation.

Secondary Structure

• Conformation of the polypeptide backbone
• Spatial arrangement of the polypeptide backbone.
• Alpha helix:
  • Right-handed coiled spring shape (helix).
  • Stabilized by intramolecular hydrogen bonds.
  • Hydrogen bonds are parallel to the axis of the helix.
  • 3.6 amino acid residues per turn.
  • Pitch: 5.4 Å (0.54nm) rise per turn.
  • Amino acid side chains (R groups) project outward from the helix.
• Beta pleated sheet:
  • Highly extended polypeptide backbone.
  • Zigzag or pleated pattern.
  • R groups of adjacent amino acid residues project in opposite directions.
  • Hydrogen bonds occur between neighboring polypeptide chains.
  • Parallel β sheet: H-bonded chains run in the same direction.
  • Antiparallel β sheet: H-bonded chains run in the opposite direction.
• β-Loops:
  • Short segments of amino acids that join two units of the secondary structure (e.g., two adjacent strands of an antiparallel β sheet).
  • 180° turn involving 4 amino acid residues.
  • Structural role.
• β-Bulge:
  • Irregularity in antiparallel β-sheets.
  • Hydrogen bonding between 2 residues from one strand with 1 residue from the other.

Super Secondary Structure

• Also known as motifs.
• Intermediate in scale between secondary and tertiary structures.
• A recognizable folding pattern involving 2 or more elements of secondary structure and the connection/s between them.
• Examples:
  • β-α-β loop
  • α-α unit (helix-turn-helix)
  • β-meander
  • Greek key motif

Fibrous and Globular Proteins

• Fibrous: - Long narrow rod. - Structural role. - Mostly insoluble in water. - Repetitive amino acid sequence. - Examples: collagen, keratin
• Globular: - Rounded/spherical. - Functional role. - Mostly water soluble. - Irregular amino acid sequence. - Examples: hemoglobin, enzymes, immunoglobulins

Keratin

• Occurs in all higher vertebrates.
• Found in hair, nails, claws, wool, quills, feathers, horns, hooves, and skin.
• α-Keratins: found in mammals.
  • Right-handed α-helix.
  • Two α-helices coil each other to form a left-handed supercoil.
  • Rich in Cys residues that form disulfide bonds, linking filaments.
  • Hard keratin: hair, horn, nail (less pliable).
  • Soft keratin: skin, callus.
• β-Keratins: occur in birds and reptiles.
  • Provides waterproofing and prevents drying.
  • β-sheet pattern in native state.

Permanent Wave in Hair

• Forces Involved in 3° Structure:
  • Disulfide bonds.
  • Hydrophobic interactions.
  • Hydrogen bonding.
  • Van der Waals interactions.