Biochemistry: Macromolecules and Amino Acids

Macromolecules

• Insulin is a protein
• Proteins are one of the four major classes of biological molecules

Amino Acids

• The titration curve of an amino acid shows two pKa values
• The first pKa represents the protonation or deprotonation of the carboxyl group
• Glycine is the only amino acid that is not optically active, because its side chain is only a hydrogen atom
• Cysteine and Methionine are the only two amino acids containing sulfur
• Aside from proline, all other amino acids contain a primary amino group, a carboxyl group, and a hydrogen atom bonded to the alpha carbon
• The chirality of an amino acid derives from the alpha carbon, which is bonded to four different chemical groups
• Glutamate (Glu) has a side chain that can act as an acid or base and participate in acid-base catalysis.

Protein Structure

• Amino acids are joined by peptide bonds through condensation reactions, forming a polypeptide chain
• There are 20 proteinogenic amino acids incorporated into proteins
• Proteins can be modified after translation, including acetylation of lysine
• Protein structure is stabilized by hydrogen bonds, hydrophobic effects, electrostatic interactions, and disulfide bonds.
• The peptide bond can rotate around the Cα – C and the Cα – N bonds, which creates a pivot point at the peptide bond
• Parallel beta-sheets occur when adjacent polypeptide chains are oriented with the N-terminus of one aligned with the C-terminus of the other
• Phosphorylation of a protein is a posttranslational modification that often regulates the function of the protein
• Quaternary structure describes the arrangement of multiple polypeptide chains (subunits) into a functional oligomer
• Primary, secondary, and tertiary protein structures are formed and maintained predominantly by noncovalent bonds
• Protein tertiary structure folds into a specific conformation due to the amino acid sequence and sometimes with the help of chaperones
• Proteins can unfold (denature) due to changes in temperature or pH.

Protein-Ligand Binding

• Myoglobin is a single polypeptide chain that lacks quaternary structure.
• Mutations, like changing an Asp to Met in hemoglobin, can alter the binding affinity for oxygen, changing the binding constants of the protein
• sigmoidal binding curves indicate positive cooperativity. Positive cooperativity means that the binding of one ligand molecule to a protein increases the affinity of the protein for subsequent ligand molecules.
• Heme binds to the protein by noncovalent interactions with the pyrrole groups of the porphyrin ring.
• The porphyrin ring binds ferrous iron (Fe^2+^).
• Heme functions as an oxidation-reduction cofactor during oxygen transport.
• When hemoglobin transitions from the T to the R state, the oxygen ligand is not transferred from one subunit to another. Instead, iron moves into the heme plane, causing a movement of the α-helix containing the proximal His.

Enzyme Structure/Function

• In the induced-fit model, the substrate must bind to the enzyme's active site to induce a conformational change that facilitates the catalytic reaction.
• Enzymes are catalysts that increase the rate of a chemical reaction without being consumed themselves.
• Enzymes are highly specific for their substrates.
• Enzymes lower the activation energy of a reaction.
• The catalytic mechanism of RNase does not involve metal ion catalysis.
• The mechanistic step for chymotrypsin involves covalent catalysis and acid-base catalysis.
• Coenzyme A participates in acyl group transfer reactions
• Zinc ions can stabilize negative charges in the substrate to aid in binding and help stabilize negative charge developed during the transition state.

Inhibitors and Enzyme Kinetics

• Organophosphorus compounds such as sarin are examples of covalent irreversible inhibitors, because they form a stable covalent bond with the enzyme.
• At very high substrate concentrations, the reaction rate approaches the maximum velocity (Vmax) for the enzyme.
• Competitive inhibitors increase the apparent K_M, because the substrate is competing with the inhibitor for binding to the active site.
• Noncompetitive inhibitors decrease the apparent V_max, because they bind to the enzyme at a site other than the active site, altering its activity.
• Allosteric inhibitors bind to the enzyme at a site other than the active site, changing the conformation of the enzyme and reducing its activity.
• β-lactams are a class of antibiotics that inhibit bacterial cell wall synthesis. They do not directly bind to the active site but inhibit the enzyme by blocking the formation of the peptide cross-links in peptidoglycan.