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BioC 3021 First Midterm

Tuesday, September 27, 2011


1. A buffer solution is made from a weak acid, HA (pKa 6.0) and its conjugate base A-.
What is the ratio of the base A- to the acid HA at pH 5.0?
a)
b)
c)
d)
e)

1/100
1/10
1
10/1
100/1

2. Which of these elements is the least common in organic compounds within living cells?
a)
b)
c)
d)
e)

carbon
hydrogen
nitrogen
sulfur
fluoride

3. If the hydrogen ion concentration of the blood increases ten-fold, how much does the pH
change?
a)
b)
c)
d)
e)

It is lower by ten pH units


It is lower by one pH unit
It does not change
It higher by one pH unit
It higher by one pH unit

4. If the pH changes from 7.0 to 6.0 which amino acid R-group is the most affected?
(Hint: The most affected R-group is the one with a pK the closest to pH 7.0)
a)
b)
c)
d)
e)

arginine
glutamate
lysine
aspartate
histidine

5. Which type of bond involves shared electrons and serves as the basic linkage in organic
compounds?
a)
b)
c)
d)
e)

ionic
hydrogen
hydrophobic
covalent
van der Waals forces

6. Which amino acid is essentially incompatible with alpha helix and beta sheet formation?
a)
b)
c)
d)
e)

histidine
tryptophan
alanine
proline
cysteine

7. Which type of interaction is NOT stabilized by hydrogen bonds:


a)
b)
c)
d)
e)

between water and a polar R-group


between water and a nonpolar R-group
between two polar R-groups
between two water molecules
between hydrogen atoms and carbonyl oxygen atoms within an alpha helix

8. In proteins the R-groups of the polar but uncharged amino acids, serine and glutamine
generally can form _______ bonds with each other.
a)
b)
c)
d)
e)

Hydrogen
Hydrophobic
Ionic
Peptide
Disulfide

9. The side chains of valine and isoleucine can form _______ bonds with each other.
a)
b)
c)
d)
e)

Hydrogen
Hydrophobic
Ionic
Peptide
Disulfide

10. Which amino acid changes the charge on its R-group as a function of pH?
a)
b)
c)
d)
e)

Lysine
Leucine
Isoleucine
Valine
Methionine

11. Primary protein structure refers to:


a)
b)
c)
d)
e)

units of -helix within a protein subunit


units of -sheet within a protein subunit
a series of amino acids linked by peptide bonds
the total three dimensional structure of a single protein subunit
noncovalent interactions between two subunits

12. Organic carboxyl groups generally function as:


a)
b)
c)
d)
e)

weak acids
weak bases
strong acids
strong bases
none of the above

13. Which of the following does NOT contain a type of amide bond?
a.
b.
c.
d.
e.

The R-group of glutamine


The R-group of asparagine
The peptide bond
The R-group of alanine
The reaction product of an amine and a carboxylic acid.

14. A purification method which depend on highly selective interactions between a proteins
binding site and a specific ligand ________.
a)
b)
c)
d)
e)

ion exchange chromatography


gel filtration chromatography.
SDS polyacrylamide gel electrophoresis.
affinity chromatography
mass spectrometry

15. NMR analysis is often used to determine:


a)
b)
c)
d)
e)

the molecular weight of a molecule


interactions between hydrogen atoms within a molecule
the charge on a small molecule
the rate of an enzyme reaction
the total three dimensional form of a molecule

16. What type of protein would stick very tightly to a positively charged DEAE-cellulose ion
exchange column?
a)
b)
c)
d)
e)

a protein that was highly negatively charged


a protein that was highly positively charged
a protein that carried no net charge
a protein that was highly hydrophobic
a protein with many lysine, histidine and arginine residues

17. The migration of protein subunits in an SDS-polyacrylamide gel electrophoresis system


depends mostly on
a)
b)
c)
d)
e)

the charge on the native protein


the hydrophobicity of the native protein
the size of the native protein subunits
a combination of charge and size of the native protein
the number of polar groups in the native protein

18. A technique that is used to determine the three dimensional form of a protein is:
a)
b)
c)
d)
e)

NMR
Gel filtration
Mass Spectrometry
Ion exchange chromatography
X-ray Diffraction

19. What is NOT true about a peptide bond?


a)
b)
c)
d)
e)

It has a planar structure because of partial double bonding.


It can pick up a proton to carry a net positive charge
It is a type of amide bond
It has a carbonyl group linked to a nitrogen atom
It resonates between single and double bonds (exists as a hybrid)

20. Enzymes can:


a)
b)
c)
d)
e)

Change the equilibrium constant of a reaction


Change the free energy of a reaction.
Change the rate of a reaction
Change the amount of product at equilibrium
The net balance of substrate and product at equilibrium

21. What is the primary reagent used to sequence proteins during the Edman degradation?
a)
b)
c)
d)
e)

ninhydrin
trypsin.
pepsin
phenylisothiocyanate
chymotrypsin

22. What reagent is used to prevent reoxidation of sulfhydryl groups during the reduction of
protein disulfides:
a)
b)
c)
d)
e)

hydrochloric acid
iodoacetate
succinate
cyanogen bromide
cesium chloride

23. The phi and psi bonds that flank peptide bonds in proteins:
a)
b)
c)
d)
e)

rotate freely and can assume almost any combination of bond angles
are able to rotate but generally assume certain combinations of bond angles
do not rotate at all because they are planar
only rotate in a few selective locations in the protein
are compatible with alpha helix but not with beta sheet sturctures

24. The overall free energy change for a chemical reaction is positive if the reaction:
a)
b)
c)
d)
e)

releases a lot of energy


favors product formation
does not favor product formation
has a low energy of activation
exhibits very fast kinetics

25. Which factor is NOT a component of tertiary protein structure?


a)
b)
c)
d)
e)

Hydrogen bonding between R-groups


Hydrophobic interactions between R-groups
Interactions between R-groups and water
Ionic interactions between R-groups
Interactions between two separate protein chains

26. Vitamins are:


a)
b)
c)
d)
e)

Nutritionally required inorganic ions


Organic molecules that catalyze reactions
Enzyme cofactors or components of enzyme cofactors
Molecules that inhibit enzymes
Molecules which humans can synthesize

27. Biochemists use a modified form of the standard free energy because:
a)
b)
c)
d)
e)

Enzyme reactions are faster than uncatalyzed reactions


Enzyme reactions are more sensitive to heat than chemical reactions
Enzyme reactions use a different pathway than chemical reactions
Enzyme reactions usually take place around pH 7.0
Enzyme reactions are reversible

28. The factor which measures the number of molecules of substrate reacted per enzyme
active site and which does not change as an enzyme is purified:
a)
b)
c)
d)
e)

Vmax
Km
Turnover number
Specific activity
Keq

29. Which of the following is NOT true about the ATP cofactor:
a)
b)
c)
d)
e)

It carries a net negative charge


Is often hydrolyzed to ADP to promote enzyme reactions
Is often hydrolyzed to Adenosine to promote enzyme reactions
It contains three phosphate groups
It releases energy upon hydrolysis

30. Which of the following is NOT true about oxidation-reduction reactions?


a)
b)
c)
d)
e)

Often involve inorganic cofactors


Often involve organic cofactors
Often involve the exchange of electrons
Often involve the oxidation of NADH or FADH2
Often involve the oxidation of ATP

31. Chemical reactions and enzyme reactions:


a)
b)
c)
d)
e)

vary in rate but ultimately can produce the same level of product
have the same energy of activation
have the same reaction pathway
have different standard free energy values
have different equilibrium constants

32. Which of the following is NOT true about the 20 common amino acids:
a)
b)
c)
d)
e)

all contain C,H, O and N atoms


with one exception are all of the L-form when found in proteins
can be positive, negative or neutral depending on the pH
can occur at any place in a protein sequence
all have R-groups which can hydrogen bond with water

33. What are the four levels of protein structure and what kinds of bonds contribute to and
stabilize each level of structure?
.

34. Outline the various ways in which enzyme reactions differ from analogous chemical
reactions.

35. How and why are protein molecules affected by the pH of the environment? How can the
Henderson-Hasselbalch equation be used to tell us about the response of protein
molecules to changes in pH?

36. Describe the use of affinity chromatography and explain why it is such a powerful
technique for purifying proteins. Why is it more powerful than most other methods?