Name:
Chem 464
Biochemistry
Multiple choice (4 points apiece):
1. The pH of a solution of 1 M HCl is:
A)
0.1
B)
1
C)
10
D)
-1
E)
0
2. The Henderson-Hasselbalch equation:
A)
relates the pH of a solution to the pKa and the concentrations of acid and conjugate
base.
B)
allows the graphic determination of the molecular weight of a weak acid from its
pH alone.
C)
does not explain the behavior of di- or tri-basic weak acids
D)
employs the same value for pKa for all weak acids.
E)
is equally useful with solutions of acetic acid and of hydrochloric acid.
3. Which of the following statements about aromatic amino acids is correct?
A)
All are strongly hydrophilic.
B)
On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
C)
Histidine's ring structure results in its being categorized as aromatic or basic,
depending on pH.
D)
E)
The major contribution to the characteristic absorption of light at 280 nm by
proteins is the phenylalanine R group.
The presence of a ring structure in its R group determines whether or not an amino
acid is aromatic.
4. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the
population of amino acids in solution will have:
A)
a net positive charge.
B)
a net negative charge.
C)
no charged groups.
D)
no net charge.
E)
positive and negative charges in equal concentration.
5. All of the following are considered "weak" interactions in proteins, except:
A)
van der Waals forces.
B)
hydrogen bonds.
C)
hydrophobic interactions.
D)
ionic bonds.
E)
peptide bonds.
2
6. A D-amino acid would interrupt an helix made of L-amino acids. Another naturally occurring
hindrance to the formation of an á-helix is the presence of:
A)
a nonpolar residue near the carboxyl terminus.
B)
a positively charged Lys residue.
C)
a Pro residue.
D)
two Ala residues side by side.
E)
a negatively charged Asp residue
7. Proteins are classified within families or superfamilies based on similarities in:
A)
evolutionary origin.
B)
physico-chemical properties.
C)
subcellular location.
D)
subunit structure.
E)
structure and/or function.
Longer questions (70 points total)
7. (20 points) Fill in the following table:
Name
Valine
Arginine
Cysteine
3 letter
abbreviation
Val
Arg
Cys
1 letter
abbreviation
V
R
C
Structure
side chain pKa
(if ionizable)
General
classification
(nonpolar,
polar, etc)
12.48
Non-polar
Positively Charged or
Basic
8.18
Polar
3
8 Draw the structure of the peptide W-A-D-E at pH 7 including the appropriate charges. What is
the charge on this peptide at pH 1?
at pH 1 Charge = +1
9. I have a circular peptide of 4 residues so it has no N-terminal and no C-terminal. If the peptide
has a glutamic acid and an aspartic acid and pI of 7.39, what other residues must it contain. Why?
So far the peptide has a -2 charge, to have a pI around 7 you will have to add 2 + charges.
Specifically to have a pI of 7.39 , 7.39=(4.25+X)/2 so X=10.53 and one residue has to be Lysine,
and the other residue has to have a pKa >10.53, and that would be Arginine.
A few people mentioned that to get a circular peptide with only 4 residues you would need to have
a gly or a pro to get such a tight turn, and I gave partial credit for this answer.
10. Tell me about the structure of the á-helix, the â-sheet, and the â-turn.
Helix - main points right handed helix, 3.6 residues/turn. 5.4Å rise per turn, main chains on
inside with side chains pointed away from center, peptide dipole point to stabilize - charge at
amino terminus and + charge at C terminus, Proline and glycine and multiple adjacent like charges
tend to break up helix Other points -described by Pauling in 1948, found in á keratin in hoof hair
and nails
SheetMain points - Peptide fully extended, may be parallel or antiparallel, Main chain H bonds
from one strand to nextacross sheet, side chains above and below sheet, sheet are not flat but have
a twist, other points described by Pauling 1951, found in silk fiberoinin which is rich in A and G,
natural souce is silk. Very strong
â turns -180 degree change of peptide path in 4 residues. 6 types, Often have proline or Glycine
4
11. What is meant by (You may skip 1)
A super-secondary structure
A recognizable folding pattern built with two or more connected secondary structural elements.
A domain
A part of a polypepide chain that could fold into an independently stable unit or that could move as
a single entity within a protein.
A Ramachandran plot
If Phi describes the rotation of the peptide bond on the amino side of a Cá residue, and phi
describes the rotation of the peptide bond and the CO side of the Cá , a Ramachandarm plot plots
conformationally allowed the phi values along the X axis and the allowed psi angle along the y
axis.
A super-family (In protein structure)
A set of two or more protein structural families that have little sequence similarity but have the
same structural motif or function in a similar manner.
A protofibril
In the structure of á ketain, 2 helices first wind around each other to make a 2 chain coiled
coil. A number of these coiled coils wind around each other to form a protofibril, and then several
protofibrils wind around each other to form a protofibril. The protofibrils are then assembled to
create the actual hair structure.
12. The á-helix and the â-sheet structures are seen in both fibrous and globular proteins. Explain
why you probably won’t see the triple helix of collagen in a globular protein.
With my luck a globular protein containing a collagen-like triple helix will probably be discovered
in a globular protein next week. As a result I tried to be generous with this and give credit if you
had any kind of logic that seemed to make sense and demonstrated a basic understanding of protein
structure. One logic that I saw several times was that a fiber, with a long, skinny structure is not
compatible with a globular protein where the chain has to turn back on itself. Another theme that I
likes was that globular proteins do not contain knots or close contact between chains. Both of
these happen in the collagen where the three strands wind around each other and have a close
contact in the central core. Finally I was hoping that somebody would mention that to have a triple
helix, with all three strands running in the same direction, the peptide chain at the far end of the
globular protein would have to turn around and get back to the start three times without getting
tangled. I think this would be very hard to fold.