MIDTERM EXAM NOTES FOR WEEKS 1-3
April 21, 2009
Paul A. Price
The midterm exam will cover the material presented in the first 5 weeks of lecture and in problem sets 1
The midterm exam notes below give you a specific description of the major areas that will be
covered in this exam from the first 3 weeks of lecture and from problem sets 1 to 3.
Another “midterm exam
notes” will be handed out later that covers the material from lectures in weeks 4 and 5 and from problem sets 4
A thorough understanding of the material in these two handouts should prepare you for the exam.
Copies of the exams from past years can be obtained at the course website.
examination question will
deal with information presented in the text but not in lecture, midterm exam notes, or a problem set.
Any problem in problem sets #1-3, or slight variations on these problems, may be on the exam.
Be able to identify each of the 20 common amino acids if you are given the correctly drawn structure.
the three and one letter abbreviations for each amino acid.
Know the definitions of the 4 levels of protein structure (eg, primary, secondary,
tertiary, and quaternary).
Know which amino acids have non-polar side chains, which have uncharged polar
side chains, and which have charged polar side chains.
Know that the
helix is a right handed coil in which
all N-H groups hydrogen bond with C =O groups 4 residues apart in the sequence, and that all R groups project
outward from the
helix core and define the character of the helix surface.
Know the difference between
parallel and antiparallel pleated sheet structures, and know that all N-H groups and C =O groups in an interior
strand form hydrogen bonds with one or the other adjacent
Know that R groups alternately project
above and below the
sheet plane and so define the character of the surfaces of the sheet.
Know that pure
helices are found in some fibrous structures (hair) while pure
sheets are found in other fibrous structures (eg,
silk) and that, in a typical globular protein, helices are
15 residues long and
10 residues long.
Know that, in typical globular
proteins, all amino acids with hydrophobic side chains are found on the
interior of the molecule, where they associate to escape contact with water, and that amino acids with polar and
charged side chains are found on the protein surface.
Know that the tendency of oil and water to separate into
phases is the same driving force that causes the hydrophobic amino acid side chains to associate on the protein
interior to escape contact with water, and that this hydrophobic association drives the formation of the 3D
structure of a protein.
Know that all interior peptide bonds are involved in N-H to O =C hydrogen bonds, and
that the structure will be de-stabilized by 15 to 30 kJ/mole for each H bond that isn’t formed.
Know that the
protein interior is solidly packed, with a density equal to that of an organic crystal, and that there is no water in