Amino Acids, Proteins, and Enzymes - Vocabulary

Proteins and Amino Acids

• Proteins are polymers of 20 different amino acids.
• Functions:
  • Structural components (cartilage, muscles, hair, nails)
  • Enzymes: regulate biological reactions
  • Transport oxygen (hemoglobin, myoglobin)

Amino Acids

• Building blocks of proteins.
• Central α-carbon bonded to:
  • Ammonium group (-NH_3 ^+)
  • Carboxylate group (-COO^-)
  • Hydrogen atom
  • R group (side chain).

Classification of Amino Acids

• Nonpolar (hydrophobic): hydrocarbon side chains.
• Polar (hydrophilic): polar or ionic side chains.
• Acidic: R group is a carboxylic acid.
• Basic: R group is an amine.

Amino Acid Stereoisomers

• All α-amino acids except glycine are chiral.
• D or L enantiomers based on NH_3 ^+ group position on the chiral carbon.

Essential Amino Acids

• 9 amino acids that must be obtained from the diet.
• Complete proteins (eggs, milk, meat, fish) contain all essential amino acids.
• Incomplete proteins (plants) are deficient in one or more essential amino acids.

Amino Acids as Acids and Bases

• Isoelectric point (pI): the pH at which an amino acid is neutral in charge.

Ionized Forms of Amino Acids

• At pI, amino acid has both carboxylate anion (-COO^-) and ammonium cation (-NH_3 ^+).
• At pH < pI, carboxyl group gains H^+.
• At pH > pI, ammonium group loses H^+.

Proteins: Primary Structure

• Peptide bond: amide bond between the -COO^- group of one amino acid and the -NH_3 ^+ group of the next.
• Linking amino acids forms a peptide.
  • Dipeptides (2 amino acids).
  • Tripeptides (3 amino acids).
  • Tetrapeptides (4 amino acids).
• Polypeptide: intermediate chain length polymer, less than 50 amino acids
• Protein: polymer with more than 50 amino acids
• Amino acid residue: an amino acid that is part of a polymer

Formation of Peptides

• N-terminal residue on the left, C-terminal residue on the right.

Naming Peptides

• All amino acids end in yl except the C-terminal amino acid.

Primary Structure of Proteins

• Sequence of amino acids held together by peptide bonds.

Proteins: Secondary, Tertiary, and Quaternary Structures

• Secondary Structure:
  • Alpha helix (α helix): hydrogen bonds between C=O and N-H groups.
  • Beta-pleated sheet (β-pleated sheet): hydrogen bonds between carbonyl oxygen and amide hydrogen atoms.
  • Triple helix: three polypeptide chains woven together.

Tertiary Structure

• Overall 3D shape due to interactions between R groups.
  • Hydrophobic interactions, hydrophilic interactions, salt bridges, hydrogen bonds, disulfide bonds.

Quaternary Structure

• Combination of two or more protein units.

Protein Structural Levels

• Primary, secondary, tertiary, and quaternary.

Denaturation of Proteins

• Disruption of bonds in secondary, tertiary, and quaternary structures.
  • Caused by heat, organic compounds, acids, bases, heavy metal ions, agitation.

Enzymes

• Proteins that act as biological catalysts.
• Active site: region on enzyme that binds substrate.

Enzyme Names

• Replace end of reaction/reacting compound name with -ase.
• Describes reaction (e.g., oxidase).

Classification of Enzymes

• Oxidoreductases: oxidation-reduction.
• Transferases: transfer groups of atoms.
• Hydrolases: hydrolysis.
• Lyases: add/remove atoms to/from a double bond.
• Isomerases: rearrange atoms.
• Ligases: use ATP to combine small molecules.

Active Site

• Binds substrate.
• Contains amino acid R groups that bind substrate.
• Releases products when reaction is complete.

Enzyme-Catalyzed Reaction

• Substrate attaches to active site.
• Enzyme-substrate (ES) complex forms.
• Reaction occurs, products are released.

Enzyme Action: Lock-and-Key Model

• Active site has a rigid shape.
• Enzyme binds only substrates that exactly fit.

Enzyme Action: Induced-Fit Model

• Enzyme structure is flexible and adjusts to fit substrate.

Factors Affecting Enzyme Activity

• Temperature: Optimum temperature, denaturation above 50°C.
• pH: Optimum pH, loss of activity at low/high pH.

Enzyme Inhibition

• Substances that decrease enzyme activity.

Competitive Inhibition

• Inhibitor similar to substrate, competes for active site.
• Reversed by increasing substrate concentration.

Noncompetitive Inhibition

• Inhibitor binds to enzyme at a site other than the active site.
• Distorts enzyme shape, prevents substrate binding.
• Not reversed by adding more substrate.

Irreversible Inhibition

• Destroys enzyme activity.
• Often a toxic substance, forms covalent bond.

Regulation of Enzyme Activity

• Allosteric Enzymes
• Feedback Control

Enzyme Regulation: Covalent Modification and Genetic Control

Enzyme Cofactors

• Cofactor: A nonprotein part of an enzyme that is essential to the enzyme’s catalytic activity; a metal ion or a coenzyme.
• Coenzyme: An organic molecule that acts as an enzyme cofactor.

Vitamins

• Water soluble
• Fat soluble

Water-Soluble Vitamins

• Soluble in aqueous solutions.
• Cofactors for many enzymes.
• Not stored in the body.

Fat-Soluble Vitamins

• Vitamins A, D, E, and K.
• Are soluble in lipids, but not in aqueous solutions.
• Are important in vision, bone formation, antioxidants, and blood clotting.
• Are stored in the body.