PREPARATION FOR EXAM ONE
October 1, 2003
BASICS:
Know the meaning of basic thermodynamic terms such as free energy, enthalpy, entropy. Know how
observed free energy varies with the equilibrium position and how standard free energy relates to the
equilibrium constant. Know the difference between standard free energy and observed free energy. Know
the basis of chemical bonding, covalent bonds, electrostatic bonds, hydrophobic bonds. Know the
properties of water, dielectric constant, ionization. Know terms such as pH, pOH, pK. Be able to tell if a
molecule is a conjugate acid or conjugate base by identifying its ionizable groups.
BUFFERS
Be able to use the Henderson-Hasselbach equation. Know the meaning of pK as applied to buffers,
measurements of pH given acid/base concentrations, calculations of pH changes based on addition of small
amounts of acid or base to a buffer, the meaning of buffering region
AMINO ACIDS
Know the R-group structure of all amino acids, the difference between D and L, the various functional
groups that give rise to basic, acidic, polar non-charged, and hydrophobic amino acids, the pKs for the R
groups or aspartate, glutamate, histidine, tyrosine, lysine and arginine, the alpha -COOH and -NH3+. Know
the titration curves for simple amino acids and amino acids with charged R groups. Know how to calculate
isoelectric point of any amino acid. Be able to draw the structures of amino acids in the categories: sulfurcontaining, hydroxy, basic, acidic, aromatic.
PEPTIDES
Know how amino acids link together to from peptides, the double bond character, the atoms in a plane, the
phi and psi torsion angles, the meaning of stereo hindrance, the C and N termini. Know what a
Ramachandran Plot is used for, what it means. Know how to titrate a peptide and determine its isoelectric
point. Know how to determine the amino acids in a peptide and their sequence when given information
such as reaction with trypsin, chymotrypsin, CNBr, UV light, titration curves, N and C terminal reagents,
ninhydrin, Edman's reagent.
PROTEIN STRUCTURE
Know the basics of protein purification. Ways to remove water, salt ions, and other proteins. The basics of
ion exchange, exclusion chromatography, the application of electrophoresis. Know ways to determine the
molecular weight of a protein, the difference between relative and true molecular weight. Know how a
protein behaves in the presence of trichloroacetic acid, boiling 6 N HCl, Edman's reagent, reducing agents
such as glutathione, mercaptoethanol. Know the meaning of primary, secondary, tertiary and quaternary
structure. Know the basics of helix structure, the alpha helix, the 3-10 helix. Know what a beta sheet is
and how it contributes to the structure of a globular protein or a fibrous protein. Know what is meant by
pitch, antiparallel chains, residues per turn. Know the basics of forces that hold a protein together
including hydrogen bonds, hydrophobic bonds, salt or electrostatic bonds, and disulfide bonds. Know the
difference between globular proteins and fibrous proteins. Know the structure of alpha keratin, silk fibroin,
collagen, elastin. Know the structural order of a protein from helix, beta sheet, beta turns to random coil.
Know why a protein denatures, what bonds are broken. Know what is meant by quaternary structure, why
proteins have multiple subunits, ways to tell is a protein has subunits, the functional significance of
subunits.
MYOGLOBIN, HEMOGLOBIN AND OTHER PROTEINS
Know the binding curve that describe oxygen reacting with myoglobin. Know the meaning of fractional
saturation, P50 as it applies to myoglobin. Know the chemistry behind the binding of oxygen to
myoglobin, the role of the heme group, ferrous iron. Know the binding curve for oxygen reacting with
hemoglobin, the meaning of sigmoid plot, the P50, the region of cooperative binding. Know the meaning
of Hill plots, the Hill coefficient, the information one obtains about positive, negative, or no cooperativity.
Know the theory behind T and R states of hemoglobin, how oxygen binding creates an R state, the role of
acid and base, CO2, BPG, in assisting or retarding release of oxygen from hemoglobin. Know the
biochemistry behind sickle cell anemia. Know the basis of antibody structure.