MIDTERM EXAM NOTES 2006
Paul A. Price
The midterm exam will cover the material presented in the first 10 lectures and problem sets 1 through 5.
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 exam from 2005
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,
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
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
hydrogen bonds with one or the other adjacent
Know that R groups alternately project above and
sheet plane and so define the character of the surfaces of the sheet.
Know that pure
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
15 residues long and typical
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
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 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 the