Proteins

1)Draw one aminoacid belonging to each of the following categories :

-polar acid
-polar basic
-non polar
-aromatic
-polar neutral

2)Draw a dipeptide

3-5
When egg white is heated, the proteins in it denature and the egg white
hardens. The denaturation is irreversible, but hard-boiled egg white can be
dissolved by heating it in a solution containing a strong detergent (such as
sodium dodecil sulfate) together whit a reducing agent like 2-mercaptoethanol.
Neither the reagent alone has effetc.
A. Why does boiling an egg white cause it to harden?
B. Why does it require both a detergent and a reducing agent to dissolve the
hard-boiled egg white?
3-13
Like -helices, -sheets often have on side facing the surface of the protein and
one side facing the interior, giving rise to an anphipathic sheet with one
hydrophobic surface and one hydrophilic surface. From the sequences listed
below pick the one that could form a strand in an amphipatic -sheet.(See
inside back cover for one-letter aminoacid code).
a. ALSCDVETYWLI
b. DKLVTSIAREFM
c. DSETKNAVFLIL
d. TLNISFQMELDV
e. VLEFMDIASVLD
3-20
Comparison of a homeodomain protein from yeast and Drosophila shows that
only 17 of the 60 amino acids are identical. How is it possible for a protein to
change over 70% of its amino acids and still fold in the same way?

1. The interactions of ligands with proteins:

A. Are relatively non-specific.
B. Are usually irreversible.
C. Are usually transient.
D. Usually result in the inactivation of the proteins.
E. Are relatively rare in biological systems.
2. Which of the following best characterizes the relationship between a ligand
and its binding site on a protein?
A. Non-specific.
B. Identical in chemical properties.
C. Complementary in chemical properties.
D. Covalent linkage.
E. Symmetric.
3. Which of the following statements about protein-ligand binding is correct?
A. The larger the Ka (association constant) the lower the affinity.
B. The larger the Ka the faster is the binding.
C. The larger the Ka the smaller the Kd (dissociation constant).
D. The Ka is equal to the concentration of ligand when half of the binding
sites are occupied.
E. The Ka is independent of conditions such as salt concentration and pH.
4. Myoglobin and the subunits of hemoglobin have:
A. Very similar primary and tertiary structures.
B. Very similar primary structures, but different tertiary structures.
C. Very similar tertiary structures, but different primary structures.
D. Very different primary and tertiary structures.
E. No obvious structural relationship.
5. An allosteric interaction between a ligand and a protein is one in which:
A. Two different ligands can bind to the same binding site.
B. The binding of the ligand to the protein is covalent.
C. Multiple molecules of the same ligand can bind to the same binding site.
D. The binding of a molecule to a binding site affects the binding of an
additional molecule to the same site.
E. The binding of a molecule to a binding site affects the binding properties
of another site on the protein.
7. Amino acids are ampholytes because they can function as either a(an):
A. Polar or nonpolar molecule.
B. Acid or a base.
C. Neutral molecule or an ion.
D. Transparent or a light-absorbing compound.
E. Standard or a nonstandard monomer in proteins.
8. Which of the following is correct with respect to the amino acid composition
of proteins?
A. Proteins with the same molecular weight have the same amino acid
composition.

B. Proteins contain at least one each of the twenty different standard amino
acids.
C. Larger proteins have a more uniform distribution of amino acids than
smaller proteins.
D. Proteins with different functions usually differ significantly in their amino
acid composition.
E. The average molecular weight of an amino acid in a protein increases
with the size of the protein.
9. What are the structural characteristics common to all amino acids found in
naturally occuring proteins?
11. aspartate is very soluble in water; phenylalanine is much less soluble in
water. In two or three sentences, explain this difference in solubility.
12. What amino acid characteristics can be used to detect proteins by the
absorbance of ultraviolet light?
13. In an aqueous solution, protein conformation is determined by two major
factors. One is the formation of the maximum number of hydrogen bonds. The
other is the:
A. Formation of the maximum number of hydrophilic interactions.
B. Maximization of ionic interactions.
C. Minimization of entropy by the formation of a water solvent shell around
the protein.
D. Placement of polar amino acid residues around the exterior of the
protein.
E. Placement of hydrophobic amino acid residues within the interior of the
protein.
14. In the helix the hydrogen bonds:
A. Are perpendicular to the axis of the helix.
B. Occur mainly between electronegative atoms of the R groups.
C. Occur mainly between electronegative atoms of the backbone.
D. Occur only between some of the amino acids of the helix.
E. Occur only near the amino and carboxyl termini of the helix.
15. In the helix, the R groups on the amino acids residues:
A. Are found on the outside of the helix spiral.
B. Generate the hydrogen bonds that form the helix.
C. Stack within the interior of the helix.
D. Cause only right-handed helices to form.
E. Alternate between the outside and inside of the helix.