Practice_Exam_1

Biophysics BCHS
4304 Robert O. Fox
September 11,
2014

1. a. A crystal has a unit cell of a=25, b=50, c=100, 90.

b. What are the values for a*, b*, and c*?
c. What is the d-spacing of the (124) reflection? (hkl) = (124)
d. What is the d-spacing of the (248) reflection?
e. Which (h00) reflection would be near to a 2.00 d-spacing?

2. a. Draw vectors from point A on the diagram that indicate which of the diffracted beams of X-
rays will be produced from a crystal oriented as it is in the diagram below?

b. What are
the (hkl)
values all of
the
diffracted
beams from
a crystal
oriented as it
is in the
diagram
below?
3. There are 230 space groups, but proteins isolated from cells can occur in only 65 of them?
Why?

4. What symmetry operators are not present in protein crystals?

a. glide planes
b. center of inversion
c. 5-fold axes
d. 6-fold axes
e. 63 screw axes

5. Draw the unit cell, all symmetry operators within the unit cell, and identify the plane group for the
following drawings:
6. A 2D lattice has unit cell dimensions a=10, b=20, =115. Draw and label the real space and
reciprocal space lattices.

7. You have a 3-carbon atom structure (Assume the scattering factor is 6e for this reflection). For
a particular hkl, atom 1 has a phase angle () of 45, atom 2 has =0 and atom 3 has = -45.
Construct an Argand diagram and plot. What is the final phase angle and amplitude for that
structure factor?

8. What is the phase problem and how is it solved?

9. That is the angle of incidence and reflection that will give first-order diffraction of 1.54
wavelength X-rays striking a series of planes with a d-spacing of 10?
 10. Match:

____ Braggs Law 1 F(hkl) F(-h,-k,-l)

____ Structure Factor Equation 2 [(ha*)2+(kb*)2+(lc*)2]1/2

____ Electron Density Equation 3 aS=h; bS=k; cS=l

____ |S| 4 ha*+kb*+lc*

____ S 5 n = 2d sin

____ Laue Equations 6 F(hkl) = F(-h,-k,-l)

____ Used to solve the phase problem 7

____ Friedels Law 8

11. What is the phase angle for a reflection h=3 for a 1D structure with a single carbon at a
fractional coordinate of 0.2?
CHAPTER 1 BIOLOGICAL MACROMOLECULES

12. Which of the matrices below would result in an all D-amino acid protein configuration (x,
y, z) when applied all the coordinates of an L-amino acid protein?

A B

D None of the above

E Both A and B
13. Characterize the conformations of the following drawings using eclipsed/staggered,
gauche/anti nomenclature.

1 2

What is the approximate torsion angle of the Cl-C-C-Cl bonds in the two structures?

1:

2:
14. Give the name of the amino acid at right using the three letter code.
Indicate whether it is D or L and R or S.

In order for an amino acid to be R, what property must the side have?

Do any of the twenty naturally occurring amino acids have this

property? If so, which?
15. For each pair of molecules indicate whether the figure represents a change in
configuration or conformation.
16. Indicate the type of structure (primary, secondary, tertiary, quaternary) present in the
following molecules.

1 2 3
4
17. Here are three drawings of amino acids. Name them using the three letter code and
determine whether they are D or L. Write your answer in the blanks below the structure.
Example: L-Tyr.

18. Pick the interaction that has the shortest range of

interaction:

A. charge-charge

B. dipole-dipole

C. covalent bonding

D. hydrogen bonding

E. dispersion forces

19. The amino acids His31 and Asp70 are separated by ~0.35 nm in T4 lysozyme. If we
consider that denatured T4 lysozyme is in an extended chain with 0.36 nm per residue, what is
the ratio of the electrostatic potential in the native state over the unfolded state?
20. Match the equations for the bonded potential energy terms with figures.

1 2 3
4

a. V13=V13 +k13 (rro)2

b. Vbond=Vbond0 +kbond(rr0) 2

c. V=V0 +Vncos ( + n ) n=2

d. V=V0 +Vncos ( + n ) n=3

e. quantum mechanical