Short Answer Questions

Chapter 2
1. Weak interactions in aqueous systems
Page: 47–55
Name and briefly define four types of non-covalent interactions that occur
between biological molecules.

2. Weak interactions in aqueous systems

Page: 53
Explain with an appropriate diagram why amphipathic molecules tend to form
micelles in water. What force drives micelle formation?
It results from the system’s achieving greatest thermodynamic stability by minimizing
number of ordered water molecules required to surround hydrophobic portions of the
solute molecules.
3. Weak interactions in aqueous systems
Page: 57
(a) Briefly define “isotonic,” “hypotonic,” and “hypertonic” solutions. (b)
Describe what happens when a cell is placed in each of these types of solutions.
isotonic : no net water movement.
hypertonic: water moves out and cell shrinks.
Hypotonic: water moves in, creating outward pressure; cell swells, may eventually
burst.
Chapter 3
1. Amino acids
Page: 76
What are the structural characteristics common to all amino acids found in
naturally occurring proteins?

2. Amino acids
Page: 81
Why do amino acids, when dissolved in water, become zwitterions?

3. Amino acids
Page: 83
In the amino acid glycine, what effect does the positively charged —NH3+ group
have on the pKa of an amino acid’s —COOH group?

Repulsion between the amino group and the departing proton lowers the pKa for the
carboxyl group, and oppositely charged groups lower the pKa by stabilizing the
zwitterion.

4. Amino acids
Page: 84
What is the pI, and how is it determined for amino acids that have non-ionizable
R groups?

The characteristic pH at which the net electric charge is zero is called the isoelectric
point or isoelectric pH, designated pI.
5. Amino acids
How to estimate a protein’s concentration?

6. Amino acids
Page: 85
What is the uniquely important acid-base characteristic of the histidine R
group?

histidine has an R group (pKa = 6.0) providing significant buffering power near the
neutral pH usually found in the intracellular and extra cellular fluids of most animals
and bacteria

7. Peptides and proteins

Page: 86
Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide
bonds quite stable?

Hydrolysis of a peptide bond is an exergonic reaction, it occurs slowly because of its

high activation energy. As a result, the peptide bonds in proteins are quite stable, with
an average half-life (t1/2) of about 7 years under most intracellular conditions.

8. Peptides and proteins

Page: 87
If the average molecular weight of the 20 standard amino acids is 138, why do
biochemists divide a protein’s molecular weight by 110 to estimate its number of
amino acid residues?

If we take into account the proportions in which the various amino acids = occur in
proteins, the average molecular weight of protein amino acids is nearer to 128
Because a molecule of water (Mr 18) is removed to create each peptide bond, the
average molecular weight of an amino acid residue in a protein is about 128 - 18 =
110
9. Peptides and proteins
What is “amino acid analysis”? What does “prosthetic group” mean?

some proteins contain permanently associated chemical components in addition to

amino acids; these are called conjugated proteins.

10. Peptides and proteins

Page: 88
Define the primary structure of a protein.

A description of all covalent bonds (mainly peptide bonds and disulfide bonds)
linking amino acid residues in a polypeptide chain is its primary structure.

11. Working with proteins

What kind of methods can be used to separate and purify a protein from crude
extract? What are the principles?

fractionation
utilize differences in protein solubility, which is a complex function of pH,
temperature, salt concentration, and other factors.
dialysis
separates proteins from solvents by taking advantage
of the proteins’ larger size.

12. Working with proteins

Pages: 90-91
Why do smaller molecules elute after large molecules when a mixture of proteins
is passed through a size-exclusion (gel filtration) column?

Large proteins cannot enter the cavities, and so take a short (and rapid) path through
the column, around the beads. Small proteins enter the cavities, and migrate through
the column more slowly as a result.
13. Working with proteins
Pages: 90-91
For each of these methods of separating proteins, describe the principle of the
method, and tell what property of proteins allows their separation by this
technique.
(a) ion-exchange chromatography
exploits differences in the sign and magnitude of the net electric charges of proteins
at a given pH.

(b) size-exclusion (gel filtration) chromatography

separates proteins according to size. The column matrix is a cross-linked polymer
with pores of selected size. Larger proteins migrate faster than smaller ones

(c) affinity chromatography

separates proteins by their binding specificities. The proteins retained on the column are
those that bind specifically to a ligand cross-linked to the bead

14. Working with proteins

What is the function of SDS (Sodium Dodecyl Sulfate) in SDS gel
electrophoresis?

The bound SDS contributes a large net negative charge, give a similar charge-to-mass
ratio; Native conformation of a protein is altered when SDS is bound, and most
proteins assume a similar shape.

15. Working with proteins

Pages: 93-95
How can isoelectric focusing be used in conjunction with SDS gel
electrophoresis?
16. Working with proteins
Pages: 94-95
As a protein is purified, both the amount of total protein and the activity of the
purified protein decrease. Why, then, does the specific activity of the purified
protein increase?

17. The covalent structure of proteins

How to determine a protein’s amino acid sequence?

An enormous number of protein sequences can now be derived indirectly from the DNA sequences

Short polypeptides are sequenced by Edman degradation carried out on a machine.

called a sequenator.

Large Proteins Must Be Sequenced in Smaller Segments.

Breaking Disulfide Bonds
Cleaving the Polypeptide Chain
Sequencing of Peptides
Ordering Peptide Fragments
Locating Disulfide Bonds
mass spectrometry
18. The covalent structure of proteins
Pages: 97-100
In one or two sentences, describe the usefulness of each of the following reagents
or reactions in the analysis of protein structure:
(a) Edman reagent (phenylisothiocyanate)

labels and removes only the amino-terminal residue from a peptide, leaving all other
peptide bonds intact. The peptide is reacted with phenylisothiocyanate under mildly
alkaline conditions
(b) Sanger reagent (1-fluoro-2,4-dinitrobenzene, FDNB)

to label and identify the amino-terminal amino acid residue

hydrolysis stage destroys the polypeptide, this procedure cannot be used to sequence a
polypeptide beyond its amino-terminal residue.
(c) trypsin
the digestive enzyme trypsin catalyzes the hydrolysis of only those peptide bonds in which the
carbonyl group is contributed by either a Lys or an Arg residue,

19. Protein sequences and evolution

Page: 107
Distinguish between homologs, paralogs, and orthologs as classes of related
proteins.
Homologs: The members of protein families
paralogs : two homologs are present in the same species
orthologs: Homologs from different species
20. Protein sequences and evolution
Page: 109
How are “signature sequences” useful in analyzing groups of functionally related
proteins?
Because certain segments of a protein sequence may be found in the organisms of one
taxonomic group but not in other groups.