FCH 530 Homework 4
1. Define the following and give an example of each as it relates to biochemistry:
Hydrophobic interaction-The presence of water forces nonpolar groups into ordered
arrangements to avoid water
Hydrogen bonds-Occur between a hydrogen atom bonded to an electronegative atom and
second electronegative atom. Seen with interations between H on H2O and and O from –
OH group. Also between peptide bonds.
Disulfide bonds-Disulfide bridge (-S-S-) that covalently links peptides between two –SH
groups from Cysteine amino acids. Can be reduced by DTT or beta mercaptoethanol to
convert –S-S- back to two –SH groups in the side chain.
Van der Waals forces-occur between molecules with temporary dipoles induced by
fluctuating electrons. May occur between any two atoms in close proximity.
2. The pitch (p) of a helix is defined as p = dn, In which n is the number of repeating
units per turn and d is the distance along the helix axis per repeating unit. Therefore, the
pitch is a measure of the distance from any point on the helix to the corresponding point
on the helix to the corresponding point on the next turn of the helix.
a. What is the pitch of an -helix and the distance per residue? p=dn therefore for alpha
helix, p=5.4 Å =d(3.6), d=5.4 Å/3.6 aa per turn=1.5 Å
b. How long would myoglobin be if it were one continuous -helix?
Myoglobin is 153 amino acids. If it were entirely alpha helix and d=p/n, then, the total
length would be 1.5 Å/aa * 153 aa = 229.5 Å
c. How long would myoglobin be if it were one continuous -sheet?
If we look at Figure 8-17 there is an axial distance of 3.5 Å between adjacent residues
which gives the beta sheet a 7 Å pitch. This is far more extended compared to only 1.5 Å
between adjacent residues observed for alpha helices. Thus for a hypothetical continuous
beta sheet, the distance must be 3.5 Å/aa * 153 aa = 535.5Å
d. How long would myoglobin be if it were fully extended (distance/residue = 0.36 nm)?
0.36 nm/aa *153 aa = 55.08 nm ~ 550.8 Å.
3.
Make tables highlighting the following:
a. Differences between the -helix and a 310 helix.
310 helix.
-helix
3 aa/turn
aa/turn
6.0 Å Pitch
Å pitch
Most common with nearly optimum
Rare. Occur for very short segments,
hydrogen bonding
single-turn transition between one end of
an alpha helix and the adjoining portion of
a polypeptide chain
b. Differences between antiparallel and parallel -sheets?
Antiparallel
Parallel
Sheets in which neighboring hydrogen
Hydrogen bonded chains extend in the
bonded polypeptides run in the opposite
same direction.
direction.
More stable
Less stable due to non optimal H bonding
c. Differences between fibrous proteins and globular proteins?
Fibrous proteins
Globular proteins
Highly elongated molecules whose
Diverse group of proteins tahat exist as
secondary structures are the dominant
compact spherical molecules
structural motifs
Rarely crystallize but can form fibers
Most structural info from X-ray and NMR
Skin, tendon, bone-protective, connective
or supportive roles
Enzymes, transport, and receptor proteins
d. The main advantages and disadvantages for solving protein structures with X-ray
diffraction and NMR?
X-ray diffraction
NMR
Directly images molecules
Used for relatively small proteins (<40 kD)
Requires synchrotron to generate X-rays
Can be used to measure protein dynamics
Make electron density map
Requires crystal of protein able to diffract
X-rays
Less than atomic resolution most times due
to high water content (40-60% water).
Static structure
Measure interatomic distances between
protons that are 5Å apart
Often shown as a sample of structures due
to movement
Can be done in solution
Can be done for proteins that fail to
crystallize
4. Examine figure 8-39 in your book (Myoglobin structure page 244)
a. What is the predominant secondary structure of myoglobin? Alpha helix
b. How many obvious -helices are present? 8. How many  -sheets? 0. How
many collagen-like helices? 0
c. What fraction of the molecule (rough estimate) appears to have ordered structure?
80%
d. What amino acid residues might you expect at points where helices are broken
or change direction? The two most common would be Gly and Pro.
5. The possible structures of a polypeptide are limited by the geometry of the peptide
bond and amino acid side chains. The six atoms of a peptide bond (amide) bond all lie in
the same plane (see figure). With C as a
reference point, amide plane 1 (top) can
rotate only around the C-C axis. Verify for
yourself, using models if necessary, that
because of the tetrahedral orientation of the
bonds to Cthe new two planes can be
coplanar only when both are perpendicular to
a third plane defined by H1 and the C-R1
bond (reference orientation). The angles 
and are defined as the degree of clockwise
rotation of planes one and two respectively,
away from the reference orientation. When
defined for each pair of adjacent residues, the
values of  and completely determine the
conformation of the polypeptide. Some 
and angles are favorable because there is
no crowding of atoms, and some are
unfavorable because they bring atoms too
close together. For example, at  = 180° and
°, the two carbonyl oxygen atoms are
crowded into an energetically unfavorable
configuration.

When a polypeptide assumes a repeating structure, for example an helix, every
peptide bond in the chain will have the same  and angles. As a consequence, any
repeating structure may be defined by  and angles. These angles are presented in the
Ramachandran diagram (Figure 8-7 from your book).
a. What are the Ramachandran angles for a collagen helix? 
b. How does an  helix differ from a collagen helix in terms of Ramachandran
angles? for an alpha helix. The main difference is in  which
differs by ~200 degrees.
c. How does an antiparallel  sheet differ from a collagen helix? ? The main
difference is in  which differs by ~80 degrees.
d. What are the Ramachandran angles for an antiparallel  sheet.
for an antiparallel beta sheet.
e. What will be the conformation of a random coil in terms of  andWhat
limitations are imposed? The -160to -80 degrees and will be between -80
to -30 and 30 to 180 degrees
f. All the common favorable secondary structures fall within the range of  = 20° (160) to  =140 (-80)°. What advantage does this range have for every amino acid
except Gly? In this angle, the carbonyl group of the peptide bond is rotated away
from the side chain of the alpha carbon.