Biochem Final

• Amino acids in humans are L (chiral, counterclockwise)
• General structure of an amino acid


  Contains an amino group, a carboxyl group, and a side chain (R group) attached to an α-carbon
• With the exception of glycine, all amino acids have at least one chiral center (the α-carbon) and are chiral
• All amino acids have at least two charged groups
• Amino acid classifications


  • Nonpolar
  • Polar uncharged
  • Polar charged
• Zwitterions


  Twin ions carrying equal and opposite charges, lack a charged side chain
• pH


  Relates to pK of ionizable groups on proteins
• Predicting overall charge on peptide at given pH

  1. If R group is not ionizable

  2. Both groups are protonated, acidic

  3. Zwitterionic form, neutral

  4. Both groups are deprotonated, basic
• Isoelectric point (pI)


  Calculated as (pKa1 + pKa2)/2 if amino acids have two ionizable groups
• Nonessential amino acids


  • alanine, cysteine, aspartic acid, glutamic acid, glycine, asparagine, proline, glutamine, arginine, serine, tyrosine
• Essential amino acids


  • phenylalanine, histidine, isoleucine, lysine, leucine, methionine, threonine, valine, tryptophan
• Proteins


  • Unbranched polymers of amino acids
  • Peptide bonds have 6 molecules and are planar
  • Usually trans to separate bulky groups
  • N terminus connects to C terminus
• Main chain, side chains, and disulfide bonds in polypeptides

  • Main chain is the amino acid backbone
  • Side chains are variable and distinctive
  • Disulfide bond is a covalent bond formed by the oxidation of two cysteines
• Knowing the amino acid sequence of a protein is important because it determines protein structure and structure dictates biochemical function
• Levels of protein structure

  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Forces involved in protein structure

  • Primary- peptide bonds
  • Secondary- hydrogen bonds
  • Tertiary- hydrophobic forces
  • Quaternary- noncovalent forces
• Factors that can disrupt an alpha helix

  • Proline bend
  • Strong electrostatic repulsion
  • Steric crowding
  • Competition for hydrogen bonds
• Amino acids commonly found in reverse turns

  • Proline
  • Glycine
• Denaturation


  Unraveling of the 3-D structure of a macromolecule caused by the breakdown of noncovalent interactions
• Protein misfolding and aggregation are associated with some neurological diseases
• First-order, second-order, and zero-order reactions

  • First order- velocity proportional to reactant concentration
  • Second order- velocity proportional to reactant concentration squared
  • Zero order- rate does not depend on substrate concentration
• At low substrate concentrations, reaction is first order. At high substrate concentrations, reaction is zero order.
• Steady State Kinetics


  • Concentrations of intermediates stay the same even though substrate and product concentrations are changing
  • Enzyme-substrate complex stays constant throughout the reaction
• Relationship between velocity and substrate concentration

  Hyperbolic curve
• Km


  • Substrate concentration that yields 1/2vmax
  • Indicates affinity between enzyme and substrate
  • Michaelis constant
• Vmax, K2, and Kcat/Km


  • Vmax- maximum velocity
  • K2/Kcat- rate constant for decomposition of ES to E+P
  • Kcat/Km- measure of catalytic efficiency
• Michaelis-Menten model


  Measuring initial velocity early in the reaction when [P] is negligible
• Lineweaver-Burk equation


  • Straight line curve, double reciprocal of MM equation
  • Useful for analyzing inhibitor effects
• Allosteric enzymes and allosteric effectors

  • Allosteric enzymes- control flux in metabolic pathways, have quaternary structure, respond to environmental signals, and are cooperative
  • Allosteric effectors- regulatory molecules that inhibit or stimulate allosteric enzymes
• ATCase


  • Inhibitor- CTP
  • Activator- ATP
• Homotropic and heterotropic effects

  • Homotropic- disruption of T=R equilibrium by substrates
  • Heterotropic- disruption of T=R equilibrium by regulators, not substrates
• Temperature and pH effects on enzyme activity

  • Temperature enhances rate
  • Most enzymes have an optimal pH
• Reversible and irreversible inhibitors

  • Reversible- bind non-covalently and are later released
  • Irreversible- bind covalently very tightly and are not released
• Inhibition types


  • Competitive- inhibitor binds active site
  • Noncompetitive- inhibitor binds enzyme or ES complex
  • Uncompetitive- inhibitor binds only ES complex
• Irreversible inhibitors


  • Substrate analogs, transition analogs, suicide inhibitors
  • Bind covalently to modify active site residues
• Catalytic mechanism of chymotrypsin


  • Serine 195 and histidine 57 are critical
  • Serine hydroxyl is the nucleophile that attacks the substrate
  • Water is the nucleophile that attacks the acyl-enzyme intermediate
• Glycolysis


  Common to virtually all cells, first stage of glucose metabolism
• DIPF


  Modifies serine 195, a residue in chymotrypsin, and inhibits the enzyme
• DIPF verifies that the residue is at the active site
• Catalysis by chymotrypsin


  Occurs in a rapid step (pre-steady state) and a slower step (steady state)