Biochemistry Revision Questions

1.      Which of the following compounds has the lowest side-chain pKa
        value?

        a.) valine
        b.) tyrosine
        c.) cysteine
        d.) lysine
        e.) arginine

2.      Osteocalcin is an important protein which binds calcium ions
        in hard tissues such as bone and teeth.  However, the binding 
        of calcium ions is a very pH-dependent process.  If a
        histidine residue in the amino acid sequence of osteocalcin
        had a pKa value of 6.0 for its side chain and the pH value of
        the environment was 5.5, what percentage of that side chain
        would be protonated?

        a.) 24%
        b.) 32%
        c.) 58%
        d.) 76%
        e.) Need more information to solve
        

3.      You are in charge of a laboratory which is currently measuring
        lactic acid levels in individuals going through a series of
        exercises.  Your lab assistant prepares a standard solution of
        lactic acid: one liter of 25 mM lactic acid (having a pKa value
        of 3.73).  Unfortunately, the assistant made up the solution
        at the wrong pH: 4.21.  You tell the assistant to add l ml of
        a l.0 M solution of potassium hydroxide.  What is the new pH
        value?

        a.) 4.31
        b.) 4.51
        c.) 5.62
        d.) 6.11
        e.) 7.40

4.      A sample of  L-valine hydrochloride (i.e., the totally
        protonated form of L-valine) is dissolved into a one liter
        solution having a concentration of 50 mM.  To this solution is
        added 90 ml of 0.8 M NaOH.  What is the final pH value? 
        (Assume L-valine has the following pKa values:  2.29 and 9.74) 

        a.) 2.40
        b.) 6.02
        c.) 9.38
        d.) 9.64
        e.) 9.85
        

5.      Which of the following is a "branched-chain" amino acid?

        a.) arginine
        b.) valine
        c.) serine
        d.) tryptophan
        e.) methionine
      

7.      What is the isoelectric point (i.e., the pI value) of
        arginylcysteinylglutamyltyrosine?  Assume that the pKa values
        of this compound are identical with the appropriate pKa values
        of the individual amino acids.

        arginine 1.82, 8.99, 12.48
        cysteine 1.92, 8.35, 10.46      
        glutamic acid 2.10, 4.07, 9.47
        tyrosine 2.20, 9.11, 10.13

        a.) 3.14 
        b.) 6.21
        c.) 7.70
        d.) 8.28
        e.) 9.24
        

8.      Which of the following reagents will generate a blue color in
        the presence of an amino acid?

        a.) ninhydrin
        b.) o-phthalaldehyde    
        c.) dicyclohexylcarbodiimide (DCCD)
        d.) benzyl chlorocarbonate
        e.) two of the above

9.      Which of the following compounds would be most retarded (i.e.,
        bind the tightest) to a cation exchange column at pH 6.23?

        a.) glutamylglutaminylasparagine
        b.) methionylhistidylleucine
        c.) valylarginyllysine
        d.) arginylglutamylleucine
        e.) serylvalylalanine
        
10.     Which of the following amino acids has four distinct
        stereoisomers?

        a.) lysine
        b.) cystine
        c.) valine
        d.) isoleucine
        e.) methionine
        
11.     An investigator wishes to synthesize a particular dipeptide. 
        Prior to the procedure which results in the formation of the
        peptide bond, the researcher blocks the amino group on one
        amino acid and the carboxyl group on another amino acid. 
        Which of the following refers to the step in which the
        carboxyl group is blocked?

        a.) reaction with an acyl chloride
        b.) reaction with dicyclohexylcarbodiimide (DCCD)
        c.) acid hydrolysis
        d.) decarboxylation
        e.) esterification

12.     In a random polypeptide chain, rotation is severely restricted
        about the following bonds:

        a. Bond from backbone alpha-carbon to alpaha-amino or to
           alpha-carboxyl groups.
        b. Peptide bond.
        c. Backbone alpha-carbon to the side-chain carbons.
        d. Terminal alpha-amino to alpha-carbon.
        e. None of the above.
        
13.     Which statement is not true about protein structure?

        a. No two atoms should approach one another more closely than
           is allowed by their van der Waals radii
        b. The polypeptide backbone freely rotates about the peptide
           bonds.
        c. Non-covalent bonding stabilizes regular folding of
           proteins.
        d. Rotations within an amino acid residue can occur about the
           bonds to the alpha-carbon.
        e. None of the above.

14.     How many amino acid residues are there per turn in an
        alpha-helix?

        a. 2.0
        b. 3.0
        c. 3.6
        d. 4.4
        e. 5.0
        
15.     Theoretically, an alpha-helix can have the following
        structural characteristic:

        a. Forms a right-handed helix only.
        b. Forms a left-handed helix only.
        c. Can form either a right-handed or a left-handed helix.
        d. Can form neither a right-handed nor a left-handed helix.
        e. None of the above.
        
16.     A beta-sheet structure can be formed from the following
        primary structure elements:

        a. Two -helices 
        b. Polypeptide segments within the same polypeptide chain.
        c. Polypeptide segments of different polypeptide chains.
        d. All of the above.
        e. Only b and c.
        
17.     Which secondary structure element(s) is(are) held together by
        hydrogen bonding?

        a. alpha-helices
        b. beta-sheets
        c. beta-turns
        d. All of the above.
        e. Just a. and b.

18.     The protofibrils of keratin are composed of the following:

        a. beta-sheets and beta-turns.
        b. alpha-helices and beta-turns.
        c. alpha-helices, beta-sheets, and beta-turns.
        d. coiled coil of two alpha-helices.
        e. Both c. and d.

19.     The tertiary structure of globular proteins have the following
        characteristics:

        a. All globular proteins have a defined inside
          (containing mostly hydrophobic amino acid residues) and
           outside (containing mostly hydrophilic residues).
        b. beta-sheets are twisted or wrapped into barrel structures.
        c. The primary structure of the polypeptide chain clearly
           predicts the final tertiary structure of globular proteins.
        d. All of the above.
        e. Both a. and b., but not c.

20.     An important factor(s) in the thermodynamics of protein
        folding is(are) the following:

        a. The conformational entropy change in going from the random
           polypeptide chain to the folded protein favors the final
           tertiary structure.
        b. The collapse of the clathrate structure of water around
           hydrophobic amino acid residues in the polypeptide chain
           favors the final folded tertiary structure.
        c. Internal hydrogen-bond formation favors the final folded
           tertiary structure.
        d. All of the above.
        e. Both b. and c., but not a.

21.     The secondary structure of myoglobin and the structure of
        individual subunits of hemoglobin consist of the following.

        a. A single polypeptide chain, folded around a heme group,
           with 4 alpha-helices.
        b. A single polypeptide chain, folded around a heme group,
           with 6 alpha-helices.
        c. A single polypeptide chain, folded around a heme group,
           with 8 alpha -helices.
        d. A single polypeptide chain, folded around a heme group,
           with 10 alpha-helices.
        e. None of the above.

22.     Hemoglobin (Hb) has the following quaternary structure
        characteristics:

        a. Hb is a tetramer of four identical myoglobin subunits.
        b. Hb is a tetramer of four identical myoglobin-like subunits.
        c. Hb is a tetramer composed of two identical subunits, each
           with a myoglobin-like structure.
        d. Hb is a tetramer of four different myoglobin-like subunits.
        e. None of the above.

23.     Upon O2 binding in hemoglobin, the following occurs:

        a. The O2 binds to the Fe in heme group.
        b. The heme group is no longer planar.
        c. Steric interactions between the heme group and amino acid
           residues of the polypeptide side chain cause tertiary
           structural changes in hemoglobin.
        d. All of the above.
        e. Both a. and c., but not b.

24.     Deoxyhemoglobin and oxyhemoglobin, have the following
        quaternary structural characteristics:

        a. Oxyhemoglobin has a more compact structure than
           deoxyhemoglobin.
        b. Deoxyhemoglobin has a larger central cavity than
           oxyhemoglobin.
        c. Subunits reorient in the transition from deoxyhemoglobin to
           oxyhemoglobin and the reverse.
        d. All of the above.
        e. None of the above.
        

25.     The allosteric effector, 2,3-bisphosphoglycerate (BPG),
        changes the way O2 is used in the following manner.

        a. BPG acts to enhance the O2 binding affinity of hemoglobin.
        b. BPG acts to lower the O2 binding affinity of hemoglobin.
        c. BPD binds in the central cavity of hemoglobin through
           electrostatic interactions.
        d. Both a. and c., but not b.
        e. Both b. and c., but not a.

26.     The O2 binding affinity of hemoglobin decreases with:

        a. increase in pH
        b. decrease in 2,3-bisphosphoglycerate concentration.
        c. decrease in CO2 concentration.
        d. increase in CO2 concentration.
        e. Both a. and c.
        
27.     The allosteric behavior of O2 binding in hemoglobin results in
        the following:

        a. Oxygen binds to all four heme groups of hemoglobin with the
           same binding affinity as the single heme group in
           myoglobin.
        b. Hemoglobin binds O2 with decreasing affinity as the number
           of heme groups in hemoglobin binding O2 increases.
        c. Hemoglobin binds O2 with increasing affinity as the number
           of heme groups in hemoglobin binding O2 increases.
        d. Hemoglobin binds O2 in lungs and tissue with the same
           affinity.
        e. Both c. and d.

28.     Muscle fibers are complex arrangements of supramolecular (i.e.
        beyond the molecular scale) structures.  In the contractile
        muscle system, the filaments of the sacromere have the
        following characteristic. 

        a. The thin filaments are composed of helical polymers of
           actin monomer subunits.
        b. The thick filaments are composed of myosin subunits.
        c. The thin filaments are composed of a coiled-coil of only
           alpha-helices.
        d. All of the above.
        e. Both a. and b., but not c.

29.     Which of the following describes the action of an enzyme?

        a.) an enzyme lowers the G value for a reaction, making it
            more favorable
        b.) an enzyme alters the entropy associated with a reaction by
            increasing the degree of "disorder" in the products
        c.) an enzyme lowers the energy of activation for a reaction
        d.) an enzyme alters the equilibrium constant for the overall
            reaction
        e.)  two of the above are true

30.     In the derivation of the Michaelis-Menten equation, the
        steady-state assumption refers to the condition that: (best
        answer)

        a.)  The rate of increase of product concentration with time
             is steady. 
        b.)  The reaction conditions (pH, ionic strength, temperature,
             etc.)are steady over the time course of the experiment.
        c.)  The total concentration of the enzyme is steady over the
             time course of the experiment (e.g., the enzyme is not
             becoming inactivated by denaturation).
        d.)  The values for G0,  H0, and  S0 are steady over the time
             course of the reaction.                    
        e.)  The concentration of any particular enzyme form (e.g.,
             EX)remains constant and steady over the time course of
             the experiment.

31.     An enzyme has been isolated from the blood plasma of an
        individual and found to obey Michealis-Menten kinetics.  At a
        substrate concentration of 0.028 M, the velocity of the
        enzyme-catalyzed reaction was found to be 10.6  moles/min. 
        The Vmax value was reported to be 38.0 moles/min.  What is the
        Km value for the substrate?

        a.)  0.028 M 
        b.)  0.063 M
        c.)  0.072 M
        d.)  0.100 M
        e.)  0.121 M
      
        
33.     Which of the following is the best means for determining the
        most efficient substrate for a particular enzyme?   

        a.)  a high Vmax value
        b.)  a high Km value
        c.)  a low Km value
        d.)  a low Vmax/Km value
        e.)  a high Vmax/Km value
        
34.     Which of the following is true of an uncompetitive inhibitor?

        a.)  The inhibitor binds to the free enzyme 
        b.)  Saturating levels of substrate completely remove all
             signs of inhibition
        c.)  In a standard double-reciprocal plot, the slope of the
             line does not change in the presence of the inhibitor
        d.)  The inhibitor binds to the same site as the substrate
        e.)  Two of the above are true.

36.     An investigator has synthesized a pharmaceutical which
        inhibits a certain enzyme-catalyzed reaction.  If one did a
        kinetic study of the enzyme in the presence of the inhibitor,
        it would appear that the substrate actually bound tighter to
        the enzyme's active site. (compared to the situation in which
        the inhibitor was absent).  Most likely, the inhibitor

        a.)  is a competitive inhibitor
        b.)  is a partial inhibitor, allowing the reaction to proceed
             even when the inhibitor is bound
        c.)  binds twice to the enzyme (i.e., an E-I-I complex can
             form)
        d.)  is an uncompetitive inhibitor
        e.)  none of the above

37.     An inactive precursor of an enzyme is often referred to as: 

        a.)  a repressed enzyme
        b.)  a zymogen
        c.)  an inducer
        d.)  an isozyme
        e.)  a prezyme

       
38.     Which of the following is never true of isozymes?
 
        a.)  Isozymes, since they catalyze the same reaction, have
             identical primary structures
        b.)  Isozymes can have different Km values
        c.)  Isozymes can have the same Vmax ratios
        d.)  Isozymes can have different Vmax/Km ratios
        e.)  Isozymes can be feedback inhibited by different compounds
        
39.     Cooperativity is a form of enzyme regulation.  One of the
        explanations for cooperativity is allosterism.  There are at
        least two models for allosterism.  In the
        Monod-Wyman-Changeaux model (the MWC model)

        a.)  when the substrate binds to the enzyme, it induces a
             conformation change in the tertiary structure of the
             protein 
        b.)  in the absence of the substrate, there are two different
             conformational forms of the enzyme in equilibrium with
             each other
        c.)  there is a slow, or lag, step prior to the binding of the
             substrate
        d.)  the substrate can only bind after another molecule (not
             the substrate) has already bound
        e.)  all of the above are false

40.     Which of the following coenzymes participates in amino
        transfer reactions?

        a.)  coenzyme A
        b.)  thiamin pyrophosphate
        c.)  flavinadenine dinucleotide (FAD)
        d.)  pyridoxal phosphate
        e.)  biotin
        
41.     The Wernicke-Korsakoff Syndrome (having characteristics of
        mental confusion, unsteady gait, and loss of eye coordination)
        is directly associated with a dietary deficiency of:

        a.)  folic acid 
        b.)  riboflavin
        c.)  ascorbic acid
        d.)  vitamin B12
        e.)  thiamin
        
42.     NAD+ is biosynthesized from the vitamin niacin as well as from:

        a.)  riboflavin
        b.)  trypotophan        
        c.)  glyceraldehyde     
        d.)  leucine
        e.)  tyrosine

43.     Which of the following vitamins is associated with
        "one-carbon" chemistry?

        a.)  thiamin 
        b.)  pantothenate
        c.)  folic acid
        d.)  lipoic acid
        e.)  riboflavin
        
44.     Which of the following is a major storage pool for energy in
        muscle?

        a.)  MgADP
        b.)  phosphoarginine
        c.)  carnitine
        d.)  phosphocreatine
        e.)  glucose
        
45.     Which of the following is true concerning ATP? 

        a.)  The hydrolysis of ATP has a more negative G value at a
             lower pH.

        b.)  At physiological levels of magnesium ions, Mg2+ tends to
             make the value less negative for the hydrolysis of ATP.
        c.)  The resonance seen in the purine (i.e., adenine) ring of
             ATP makes the G value for hydrolysis more negative.   
        d.)  There are additional degrees of hydration of the
             reactants (in the hydrolysis of ATP) than there are in
             the products.
        e.)  None of the above are true.

46.     Which of the following conditions is most likely to be true
        for a biochemical pathway proceeding in a forward direction?

        a.)  G0 > 0   and   H < 0
        b.)  H < 0   and   S < 0 
        c.)  G0 > 0   and   G < 0
        d.)  H > 0   and   H0 < 0
        e.)  G > 0   and   G0 < 0
        

47.     Which of the following compounds is an epimer of D-glucose?

        a.)  D-fructose
        b.)  L-glucose
        c.)  D-galactose
        d.)  D-lactose
        e.)  none of the above
        
48.     Which of the following forms a hemiketal?

        a.)  fructose
        b.)  glucose
        c.)  maltose
        d.)  glyceraldehyde
        e.)  cellobiose
        
49.     Which of the following compounds has a alpha-(l4)linkage?

        a.)  sucrose
        b.)  maltose
        c.)  cellobiose
        d.)  gentiobiose
        e.)  none of the above

50.     Which of the following contains galactose as one of the sugar
        subunits?

        a.)  sucrose   
        b.)  ribose
        c.)  mannose
        d.)  lactose
        e.)  none of the above