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. Which of the following best describes a "hydrophobic attraction"
a. water adheres to a surface that has a net positive charge
b. non-attracting non-polar molecules are driven together because of the cohesiveness of water
c. two hydrophobic molecules are attracted to each other with high affinity
d. water interacts with nonpolar molecules
e. water weakens ionic bonds and forms hydration shells around each ion

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. Characteristics of amino acids include:
a. the tetrahedral arrangement of bonding around the a-carbon makes all amino acids optically inactive
b. (a) is true, except for glycine which is optically active
c. the tetrahedral arrangement of bonding around the a-carbon makes all amino acids optically active
d. (c) is true, except for glycine which is optically inactive
e. all amino acids found in proteins are L-amino acids

4. Aromatic amino acids
a. are all very hydrophobic
b. have cyclic R-groups which are non-polar and non-reactive
c. a and b are generally true, except that tyrosine has a reactive and polar -OH group
d. include cystine, because of its sulfhydryl bond
e. none of the above

5. A peptide bond is
a. a planar linkage between the a-carboxyl groups of one amino acid and the a-amino group of an adjacent amino acid
b. a flexible covalent linkage between the a-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. A peptide is rigid and planar because
a. the amino acid sequence specifies the conformation of the protein
b. the C-N bond has a partial double bond character, and therefore is not free to rotate
c. the two R groups are usually trans to one another
d. a and b
e. all of the above

7. The phosphorylation of tyr in a polypeptide is an example of
a. phosphorylation of a protein, conferring upon it new capabilities
b. protein regulation
c. peptide bond cleavage
d. a and b
e. all of the above

8. Which of the following is NOT true of pH?
a. the pH at which an acid is 50% dissociated is that acid’s pK_a
b. the ability to resist pH change is characteristic of a good buffer
c. at pH 2 the carboxyl 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 acid HA represents the pH where
a. [HA] = [A^-]
b. [H+] = [A^-]
c. pOH = pH
d. pK_a = pH
e. none of the above

10. Which of the following is true of myoglobin?
a. it is a tetrameric protein
b. it is found in red blood cells
c. it is an example of a protein function including transport and storage
d. it has little affinity for oxygen
e. hemoglobin and myoglobin are identical except for the number of subunits in the functional form

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 weakest non-covalent bond ?
a. hydrogen
b. Van der Waals
c. hydrophobic
d. electrostatic
e. ionic

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

14. Non-polar molecules tend to be driven together because
a. the non-polar molecules have high affinity to each other
b. non-polar molecules bond each other
c. polar molecules hydrogen bond with non-polar molecules in specific sites
d. attraction between polar molecules drive non-polar molecules together
e. attraction between non-polar molecules drive polar molecules together

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

16. 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

17. 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

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

19. 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

20. On a titration curve, the pK is
a. the slope below the plateau
b. the slope of the plateau
c. the slope above the plateau
d. the pH at the inflection point of the plateau
e. it does not show on such a graph

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 a-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. Which of the following binds O₂ well?
a. ferrihemoglobin
b. ferrohemoglobin
c. methemoglobin
d. a and b
e. all of the above

25. Enzymes
a. increase the rate of reaction by decreasing the activation energy
b. increase the rate of reaction by increasing the activation energy
c. decrease the rate of reaction by decreasing the activation energy
d. decrease the rate of reaction by increasing the activation energy
e. none of the above; they actually insert answer:

26. Which of the following is FALSE?
a. a protein is a functional unit of polypeptide
b. changing the 1^o structure of a polypeptide may alter a protein’s conformation but not its function
c. changing the 1^o 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. Both hemoglobin and myoglobin are important because
a. they increase the oxygen content of cells
b. aerobic life would not be possible without them
c. they facilitate the movement and storage of oxygen in cells
d. they help overcome the problem of low oxygen solubility on water
e. all of the above

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

29. The amino acid with the simplest structure is

30. Name an aromatic amino acid

31. Name an acidic amino acid

32. Name a basic amino acid

33. Name a polar amino acid

34. Name a non-polar amino acid

35. An acid is a proton donor / acceptor

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

37. The main oxygen carrier protein found in muscle is named

38. The main oxygen carrier protein found in muscle has subunits

40. The main oxygen carrier protein found in muscle is

41. The main oxygen carrier protein found in red blood cells has subunits

42. The prosthetic group used in oxygen carrier proteins is called

43. 1 A = m

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

a. DNA as the hereditary material b. nuclear envelope

c. multicellular organisms d. ribosomes

e. membranous organelles f. cell wall

g. <0.2mm diameter h. plasma membrane

j. uses d-amino acids in protein

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

1. Which of the following statements are true? Explain, in English (and/or with diagrams) what each statement means.

Which of the following is the Henderson-Hasselbalch equation?
a. pH = pK_a + log ([A^-]/[HA])
b. pH = 14 - pOH
c. pH = -log[H⁺]
d. [H⁺] x [OH^-]= 10^-14

2. a. What are enzymes for? Could reactions occur under physiological conditions without enzymes? Explain why or why not (or why some could and some could not).

b. What does the term "activation energy of a reaction" mean? Using this concept, explain why enzymes are so important in living systems. (these may be answered together or separately)

3. a. Draw a titration curve for histidine. Its pKs are 1.8; 6.0; 9.3. Be sure to show which ionized/non-ionized form are found under each condition.

b. Explain the expected buffering capacity of histidine under physiological condiditions. [What is a buffer? How does one work? Why is a weak acid or base a better buffer than a strong acid or base?]

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

c. Name (identify) two amino acids which you would expect to find rarely if ever in a-helices. Explain the characteristic(s) which are important for a helix-breaking amino acid.

5. Define or explain the terms primary, secondary, tertiary, and quarternary structure (1^o, 2^o, 3^o, and 4^o) of protein.

What determines each of these?

6. 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. Explain the expected result of a mutation of the codon for the proximal histidine in myoglobin so that some other amino acid is inserted instead.

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.