Biology 403: Homework Assignments

Assignment due 1700 hours, Friday 30 January 2004:

  1. Name three extensive and three intensive properties that relate to thermodynamic quantities. What is the basic difference between these two types of properties?
  2. Why can we equate internal energy and enthalpy for most biochemical reactions?
  3. Transfer of a hydrophobic molecule (e.g. a hydrophobic amino acid and side chain) from an aqueous to a nonaqueous environment is entropically favorable. Explain.
  4. The hydrolysis of lactose (D-galactosyl-β-(1,4) D-glucose) to D-galactose and D-glucose occurs with a ΔGo' of -4.0 kcal/mole.

Assignment due 1700 hours, Friday 6 February 2004:

  1. A buffer was prepared by dissolving 3.71 g of citric acid and 2.91 g of KOH in water and diluting to a final volume of 250 mL. What is the pH of this buffer? What is the [H+]? Use 3.14, 4.77, and .39 for the pKa's of citric acid.
  2. Which of the naturally occurring amino acid side changes are charged at pH 2? pH 7? pH 12? (Consider only those amino acids whose side chains have > 10 percent charge at the pH examined.)
  3. From a rare fungus you have isolated an octapeptide that prevents baldness, and you wish to determine the peptide sequence. The amino acid composition is Lys(2), Asp, Tyr, Phe, Gly, Ser, Ala. Reaction of the intact peptide with FDNB yields DNP-alanine plus two moles of ε-DNP-lysine on acid hydrolysis. Cleavage with trypsin yields peptides the compositions of which are (Lys,Ala,Ser) and (Gly,Phe,Lys) plus a dipeptide. Reaction with chymotrypsin releases free aspartic acid, a tetrapeptide with the composition (Lys,Ser,Phe,Ala) and a tripeptide the composition of which, following acid hydrolysis, is (Gly,Lys,Tyr). What is the sequence?
  4. If we compare two proteins and find that they differ by the replacement of one amino acid with another at a specific position on the protein, we describe that as a substitution. A substitution that has little effect on the structure or function of the protein is said to be a conservative substitution. Suppose we replace a serine residue in a protein with either an aspartic acid residue or an asparagine residue. Which of these is a more conservative substitution, particularly at neutral pH? Why?
  5. What are some consequences of changing a hydrophilic residue to a hydrophobic residue on the surface of a globular protein? What are the consequences of changing an interior hydrophobic residue to a hydrophilic residue in the protein?
  6. Consider the peptide
    (Met-Ala-(Leu-Phe-Ala)3-(Leu-Met-Phe)3-Pro-Asn- Gly-Met-Leu-Phe)
    This peptide would probably form a long helix, broken where the proline residue occurs. It would be facile at inserting itself into a membrane because the first twenty helical residues would tend to lie along the membrane, with the hydrophobic residues facing toward the membrane. Suppose we changed every other Leu residue in the peptide to an Asp. Would this necessarily alter the secondary structure? Explain whether insertion into the membrane would be affected by these changes.
  7. Many proteins (e.g., important metabolic enzymes) are insoluble in water and are found "attached" to membranes within cells. What amino acid residues do you expect to find on the "side" of the protein that "attaches" to the membrane. Why?
  8. Suppose a dimeric protein is made up of monomers that resemble the triose phosphate isomerase barrel structure (fig. 4.25(a) in Horton's book, or at http://agni.phys.iit.edu/~howard/biol403/1I45x500.jpg. Suppose further that one of the helices in one monomer loops out and becomes part of the neighboring monomer's barrel. Is this likely to increase or decrease the stability of the quaternary structure of the protein? Why?

Assignment due 1700 hours, Monday 16 February 2004:

  1. (a)Suppose we wish to determine the structure of a 56-residue protein. Would NMR or X-ray crystallography be likely to be more successful and informative? Why?
    (b) Same as above, but this time it's a 75 kDa protein.
  2. Assume the following results from an enzyme inhibition study. The initial enzyme concentration is 1 * 10-8 M.
    [S], mM v0, Ms-1 [S], mM v0, Ms-1
    0.200 1.92*10-7 0.250 2.24*10-7
    0.333 2.70*10-7 0.500 3.33*10-7
    1.000 4.44*10-7 2.000 5.26*10-7
    Compute Km, Vmax, and the specificity constant for this enzyme.
  3. In characterizing protein structures, biochemists commonly use ____ to denote the torsion angle about the bond between the main-chain nitrogen and the alpha carbon, and ___ to denote the angle between the alpha carbon and the carbonyl carbon. The third main-chain torsion, about the peptide bond, is essentially fixed at 180° owing to the partial __________ character of that bond. As a result of this fixed value of 180°, the six main-chain atoms in the peptide all lie in a _____.
  4. Suppose an aqueous cellular protein has a "patch" of mostly hydrophobic residues on one portion of its surface. What simple strategy might the cell adopt to prevent these hydrophobic residues from being exposed to the solvent? Assuming that changing the conformation of the protein monomer is energetically disallowed.

Assignment due 1700 hours, Friday 27 February 2004:

  1. At least two formulations besides the Lineweaver-Burk plot exist for simple computations of Km and Vmax in enzyme kinetics calculations. One is the Eadie-Hofstee plot and the other is the Hanes plot. In the Eadie-Hofstee plot, the independent variable is v/[S] and the dependent variable is v. In the Hanes plot the independent variable is [S] and the dependent variable is [S]/v.
    (a) For the Eadie-Hofstee plot, show that the slope is -Km and the Y-intercept is Vmax.
    (b) For the Hanes plot, show that the slope is 1/Vmax, the Y intercept is Km/Vmax, and the X intercept is -Km.
    (c) If an enzyme is inhibited competitively, how will the Eadie-Hofstee plot change?
    (d) If an enzyme is inhibited noncompetitively, how will the Hanes plot change?

  2. Chemical reactions obey a relationship between reaction rate k and activation energy ΔG‡ that can be written k = Qexp(-ΔG‡/RT) where Q is a constant characteristic of the reaction and R is the gas constant, 0.001986 kcal/(mol-deg). The activation energy ΔG‡ for a particular uncatalyzed reaction is 15 kcal/mol and the overall difference in energy between reactants and products ΔG0 is 0.
    (a) By what factor will the reaction rate change if we increase the temperature from 300K to 360K?
    (b) An enzyme catalyzes the reaction so that the enzymatic reaction has a ΔG‡ = 5 kcal/mol. By what factor will the reaction rate increase at 300K if we compare the catalyzed reaction to the uncatalyzed reaction?

  3. Activate a web browser and point it at www.prenhall.com/horton. In the main body of the page, find the selection list labeled "Select a Topic." Click on "6: Mechanisms of Enzymes" and click the "Begin" button. You should have arrived at the portion of the textbook's website devoted to chapter six. Then go to the menu on the lefthand side of the page and click on "Practice Exercises I". Take the ten-question quiz located there and arrange to send the results to me as e-mail.

Assignment due 1700 hours, Friday 12 March 2004:

Note that although this is due after the exam, you may find it useful to complete the assignment prior to the exam so you can use it as a study aid.

  1. Suppose you characterize a biochemical reaction involving the transfer of a methylene group between one metabolite and another. Of the coenzymes we studied in chapter 7, which one would you expect would be involved in an enzymatic reaction mechanism that catalyzes this transfer? Why?

  2. Below is the structure of naphthoquinone.

    What coenzymes and vitamins does it resemble? What kind of reactions might it participate in? Draw the results of adding one electron to this compound, and the results of adding two electrons plus two protons to this compound.

  3. Bearning in mind the results shown in table 9.1, suppose you formulate a product to be sold as a margarine substitute that contains 20% sodium oleate and 80% sodium palmitate, plus trace amounts of colorants and odorants. How would the properties of this formulation change if you were to increase the percentage of unsaturated fatty acid to 40%?

  4. (a) Why are transmembrane helices all of a characteristic length in integral membrane proteins? Note that the helices tend to align with their axes almost perpendicular to the plane of the membrane itself in these proteins.

    (b) Typical integral membrane protein monomers have seven transmembrane helices. Suppose there is an ordinary globular domain attached to the N-terminal end of a seven-helical integral membrane protein domain and another ordinary globular domain attached to the C-terminal end of the helical domain. Sketch this arrangement.

    (c) If the N-terminal globular domain of the protein in (b) is found on the cytoplasmic side of a cell membrane, on which side with the C-terminal globular domain be? Why?

  5. Activate a web browser and point it at www.prenhall.com/horton. In the main body of the page, find the selection list labeled "Select a Topic." Click on "8: Carbohydrates" and click the "Begin" button. Then go to the menu on the lefthand side of the page and click on "Practice Exercises II". Take the ten-question quiz located there and arrange to send the results to me as e-mail.

  6. Activate a web browser and point it at www.prenhall.com/horton. In the main body of the page, find the selection list labeled "Select a Topic." Click on "10: Introduction to Metabolism" and click the "Begin" button. Then go to the menu on the lefthand side of the page and click on "Practice Exercises II". Take the ten-question quiz located there and arrange to send the results to me as e-mail. Note that the answers to two of the questions depend on knowing that the equilibrium in the hydrolysis of ATP is actually driven to the right by an increase in pH, in spite of the fact that H+ is a product of the reaction, presumably owing to the greater repulsion of the phosphate groups in ATP from one another at higher pH. See the website for a biophysics course at our neighboring university, UIUC, for more information.