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Part I:  [69 pts]:  For multiple choice, choose the one BEST answer.  Circle its letter. Read each question and
all 5 choices carefully because more than one answer might seem correct at first glance. 1.5 pt each

1.  A peptide is rigid and planar because
     a.  the peptide bond [C-N] has a partial double bond character, and therefore is not free to rotate
     b.  the amino acid sequence specifies the conformation of the protein
     c.  the two R groups are usually trans to one another
     d.  a and b
     e.  all of the above

2.  Which of the following explains the significance of water’s cohesive properties?
     a.  water greatly weakens electrostatic forces and hydrogen bonds between surrounding molecules by
          competing for their attractions, making it a good solvent
     b.  the positively charged portion of the water molecule is attracted to the negatively charged region of
          neighboring H2O molecules, therefore water molecules tend to stick to one another easily
     c.  since water is not a linear molecule, and since oxygen is more electronegative than hydrogen,
          electron density is shifted toward the O, making water a polar molecule
     d.  because of its polar nature, water can cling to many surfaces, such as glass.
     e.  water’s cohesiveness prevents water molecules from interfering with electrostatic forces or H-
          bonding between other polar molecules

3.  Which of the following is the Henderson-Hasselbalch equation
     a.  pH = pKa + log ([A-]/[HA])
     b.  pH = 14 - pOH
     c.  pH = -log[H+]
     d. [H+] x [OH-]= 10-14
     e.  none of the above

4. Protein tertiary structure is stabilized by
     a.  H-bonds
     b.  Van der Waals forces
     c.  covalent bonds
     d.  a and b
     e.  all of the above

5. A peptide bond is
     a.  a planar linkage between the  -carboxyl groups of one amino acid and the  -amino group of an
          adjacent amino acid
     b.  a flexible covalent linkage between the  -carbons of two adjacent amino acids
     c.  formed between two amino acids by addition of a water molecule (hydration synthesis)
     d.  a cross-linkage formed by oxidation of the sulfhydryl groups of two cysteines
     e.  the only type of bond found in protein

6. Which chromatography uses specific binding between the substrate and the target molecule?
     a.  ion-exchange
     b.  affinity
     c.  solubility
     d.  charge
     e.  gel-filtration

7. Which of the following is NOT true of water?
     a.  it is a polar molecule in which oxygen tends to draw electrons away from hydrogens
     b.  it is adhesive due to the ability of water molecules to bond strongly to each other
     c.  it  is an important part of biological system because it comprises a large part of the intracellular
          environment
     d.  it is an important part of biological system because it comprises a large part of the extracellular
          environment
     e.  all of the above ARE true of water

8.  Which of the following is NOT true of pH?
     a.  the pH at which an base is 50% dissociated is that base’s pK
     b.  the ability to resist pH change is characteristic of a good buffer
     c.  at pH 11 the amino terminus of any amino acid will be ionized
     d.  pH is a measure of hydrogen ion concentration in aqueous solution
     e.  pH + pOH =14

9.  The middle point in the plateau of a titration curve for an base BOH represents the pH where
     a.  [BOH] = [B+]
     b.  [OH-] =  [B+]
     c.  pOH = pH
     d.  pKb = pH
     e.  none of the above

10.  Which of the following would be the most likely result of treating a protein with glutathione?
     a.  inactivation when the S-S bonds are disrupted
     b.  activation or inactivation (depending on the protein) when prolines are hydroxylated
     c.  insertion into the membrane with the addition of this hydrophobic modification
     d.  stabilization of tertiary structure and maintenance of function
     e.  inactivation when the C-N bonds are disrupted

11.  Chemical reactions in biological systems are usually
     a.  catalyzed by proteins called enzymes
     b.  catalyzed by enzymes called proteins
     c.  endothermic, so the reactions are spontaneous
     d.  exothermic, so the reactions are spontaneous
     e.  catalyzed by a variety of inorganic materials

12.  Of the following, which is the strongest bond ?
     a.  hydrogen
     b. Van der Waals
     c.  hydrophobic
     d.  covalent
     e.  ionic

13.  Water is
     a.  polar
     b.  adhesive
     c.  cohesive
     d.  a and b
     e.  all of the above

14. The Henderson-Hasselbalch equation is useful because
     a.  knowing the pH of a solution, pK can be calculated
     b.  knowing the pK of a solution, pH can be calculated
     c.  knowing the pK of a solution and [A] and [HA], pH can be calculated
     d.  a and b
     e.  all of the above

15.   The bond between the carboxyl carbon and the N in a peptide is
     a.  a double bond
     b.  free to rotate
     c.  longer than expected
     d.  a single bond
     e.  none of the above

16.  Amino acids at neutral pH are usually
     a.  ionized
     b.  non-ionized
     c.  buffers
     d.  acidic or basic
     e. other : explain:  insert answer:

17.  Insulin is synthesized
     a.  in its final active state, so it is secreted very quickly to avoid affecting the cells which produce it
     b.  in an inactive state; it is activated by dehydroxylation of serine to alanine
     c.  as two chains which are dimerized by covalent S-S linkage
     d.  as a single chain with an intrachain S-S linkage; activation requires removal of a piece from the
          middle of the chain, resulting in a two chain final product
     e.  insulin is a hormone, not a protein; it is synthesized in the SER

18.  pH is a measure of
     a. [H+]
     b. [OH-]
     c.  pK
     d.  a and b
     e.  all of the above

19.  An amino acid may include all of the following groups EXCEPT
     a. carboxyl
     b. a nitrogenous base
     c. a carbon atom
     d. a side group (R group)
     e. a hydrogen atom

20.The bond between the  -carbon and the N in a peptide is
     a.  a double bond
     b.  free to rotate
     c.  longer than expected
     d.  a  partial  double, or  not quite single   bond
     e.  none of the above

21.  Protein functions include
     a.  transport and storage
     b.  control of growth
     c.  immune protection
     c.  recognition
     d.  cell structure
     e.  all of the above

22.  In which of the following is the side chain (R-group) bonded to both the main chain N and the  -carbon?
     a.  tryptophan
     b.  tyrosine
     c.  methionine
     d.  proline
     e.  cysteine

23.  Which of the following is the best buffer?
     a.  weak acid
     b.  weak base
     c.  weak acid-base conjugate pair
     d.  strong acid
     e.  strong base

24.  What kind of bond is usually formed between the unattached ends of these two molecules:
     R         CH2-COO-       and        H3+N-CH2        R
     a.  covalent bond
     b.  Van der Waals bond
     c.  hydrogen bond
     d.  electrostatic bond
     e.   London dispersion force

25.  Which of the following has the highest energy content (kcal/mol)?
     a. ATP
     b. H-bond
     c. glucose
     d. C-C bond
     e. this question can not be answered - energy can only be measured when bonds are broken

26.  Which of the following is FALSE?
     a.  a polypeptide is a functional unit of protein
     b.  changing the 1o structure of a polypeptide may alter a protein’s conformation but not its function
     c.  changing the 1o structure of a polypeptide may alter a protein’s  function but not its conformation
     d.  some proteins have disulfide bonds linking two cysteines
     e.  none of the above are false

                                27.  Name two reducing agents

                and oxidizing agent

             28.  List the following in size order from smallest to largest:
a. glucose molecule -   b. ribosome -   c. hemoglobin molecule -   d.  oxygen molecule -   e.  red blood cell

          For # 29-34, do not use the same answer more than once.

            29. The amino acid with the simplest structure is

            30. Name an acidic amino acid

            31. Name a polar amino acid

            32. Name a basic amino acid

            33. Name an aromatic amino acid

            34. Name a non-polar amino acid

35. A base is a proton donor / acceptor

36. Adding an acid to water causes pH to increase / decrease / remain the same

     For each of the following molecules, choose the best description  from the following list:
          a.  very hydrophobic
          b.  more hydrophobic than hydrophilic
          c.  more hydrophilic than hydrophobic
          d.  very hydrophilic
          e.  other - or - need more information:  if you choose this response, you MUST explain

            37.  lipid

            38.  glucose

            39.  water

            40.  amino acid

            41. 1   =           m

42-43.   Draw a titration curve for lysine.
     Its pKs are 2.2;  9.3; 10.8

     Show which ionized/non-ionized form(s)
     are found under each condition.
 
 

44-46.  Indicate whether each of the following is typical of eukaryotes (E), prokaryotes (P), both (B) or neither
(N).

     a.  RNA as the hereditary material      b. nuclear envelope

     c.  multicellular organisms             d. ribosomes

     e.  no membranous organelles            f.  uses l-amino acids in protein

      g. > 2 µm diameter                h. plasma membrane

       j.  uses l-amino acids in protein

Part II.  [32 pts]  Short answer.  Choose 4.  8 points each

1.  Name four distinct post-translational modifications of amino acids.  For each , state what would be the
expected effect on protein structure, and the expected effect on function (if any).  Briefly explain the basis for
your expectation.
a.
 
 

b.
 
 

c.
 
 

d.
 
 
 

2.  Explain the expected buffering capacity of histidine under physiological conditions.   Be sure to include in
your explanation a description of  what a buffer is,  how one works,  why is a weak acid or base a better buffer
than a strong acid or base.
 
 
 
 
 
 
 
 
 
 
 
 
 
 

3.   a.  Name (identify) two amino acids which you would expect to find commonly in  -helices.  Explain
the characteristic(s) which are important for a helix-building amino acid.
 
 
 
 
 

     b. Name (identify) two amino acids which you would expect to find commonly in  -sheets.  Explain the
characteristic(s) which are important for amino acids in  -sheets.
 
 
 
 
 

     c. Name (identify) two amino acids which you would expect to find rarely if ever in  -helices.  Explain
the characteristic(s) which are important for a helix-breaking amino acid. 4.  Define or explain the terms primary,  secondary, tertiary, and quaternary structure (1o, 2o, 3o, and 4o) of
protein.  What determines each of these?
 
 
 
 
 
 
 
 
 
 
 
 

5.   a. Draw a dipeptide, demonstrating the formation of the peptide bond.
 
 
 
 
 

     b. Draw a disulfide linkage between two peptide chains.  Why are disulfide bridges so important in
protein function?  How are they regulated?
 
 
 
 
 

     c.  Would you expect phosphorylation of ser to cause the activity of a protein to change?  Would
phosphorylation be more likely to increase or decrease the activity of the protein?  EXPLAIN your answer
(credit depends more on the explanation than the initial yes/no part of the answer).
 
 
 
 
 
 
 
 
 
 

EXTRA CREDIT: Write you own question and answer it.  HINT: this is you opportunity to show what you
know.  Do not ask yourself a question if you aren't sure of the answer.  Ask the question you were sure would
be on the exam, so you studied the material, and then somehow it was left off!  Your score will depend on the
quality of the question as well as the answer - up to a possible maximum of 5 pts.