MIDTERM EXAM NOTES
Paul A. Price
The midterm exam will cover the material presented in the first 10 lectures and problem sets 1 through 5.
Please use the required reading in the text to better understand the material covered in lecture and to obtain the
necessary background information for the solution of problems.
No examination question will deal with
information presented in the text but not in lecture, notes to exam, or a problem set.
The following list gives
you a specific description of the major areas that will be covered in this exam and the types of problems to
expect, and a thorough understanding of this material should prepare you for the exam.
Copies of the exams
from 2004 can be obtained at soft reserves starting the 5
week of the quarter.
Any problem in problem sets #1-5, 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 (i.e., 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 (eg, hair) while pure
sheets are found in other fibrous structures
(eg, silk) and that, in a typical globular protein,
helices are only 10-15 residues long and typical
only 3-10 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-stablized by 15 to 30kJ/mole for each H bond that isn’t
Know that the protein interior is solidly packed, with a density equal to that of an organic crystal, and