University of Houston BCHS 3304

Exam I. Instructor: Dr. wang, Feb. 13, 2020 Printed Name_____

Answer all questions; 100 maximum points; 40 questions; 2.5 pts each question.
Multiple choice – Circle the single letter (i.e. a., b., c., d., or e.) of the most correct answer on the EXAM, then
mark it on the Scantron sheet with a #2 pencil. Mark BOTH the exam AND the Scantron sheet

1-10. True or False questions.

1) The total energy in the universe is conserved, which means it cannot be generated or
destroyed.
A). TRUE
B). FALSE

2) The most abundant chemical element in the human body dry weight is carbon.
A). TRUE
B). FALSE

3) A distance of 22.1 µm is 0.0221 mm.

A). TRUE
B). FALSE

4) If the enthalpy change of a process is positive and the entropy change is also positive, the
reaction is Spontaneous at any temperature.
A). TRUE
B). FALSE

5) Weak acids are insoluble in water.

A). TRUE
B). FALSE

6) Kw, the ionization constant of water, is 10–14 at 25°C.

A). TRUE
B). FALSE

7) The amino acid ILE has a hydrophobic side chain.

A). TRUE
B). FALSE

8) The 3-dimentional structure of a water molecule (H-O-H) is nonlinear because the oxygen
atom takes “sp3” hybrid orbitals.
A). TRUE
B). FALSE

9) When transport hemoglobin proteins in pure water, the blood cell will shrink due to
hypotonic condition.
A). TRUE
B). FALSE
10) A crude enzyme extract exhibits an activity of 3,750,000 nkat per 50,000 mg extract; and
after a DEAE-cellulose column, the enzyme exhibits 10,000,000 nkat activity per 5,000 mg.
The fold of purification is (10,000,000/5,000)*( 3,750,000 /50,000).

A). TRUE
B). FALSE

11-40. These questions have only one correct choice. If more than one answer is correct,
looking for the option of “more than one answer” or equivalent. If no answer is correct,
looking for the option of “none is correct” or equivalent.

11) What does it mean when q and w are positive?

A). It means the system gained heat from the surrounding, and it did work to the
surrounding.
B). It means the system gave heat to the surrounding, and it did work to the surrounding.
C). It means the system gave heat to the surrounding, and surrounding did work to the
system.
D). It means the system gained heat from the surrounding, and surrounding did work to the
system.
E). none is correct.
Answer: a. q positive means heat flowed into the system, i.e. the surrounding transferred heat
into the system. W positive means the system has done work to the surrounding.
O B
NH 2
O

O P O N

A H
O
H
O
H H
OH OH NH2
O P O
N
C
N
O
N
N

H
O
H
D
H H
OH O
E
O P O

12) Which arrow points at an amide bond?

A). A
B). B
C). C
D). D
E). E
13) The two molecules in the following figure from left to right are

A). L-Valine and L-Leucine, respectively

B). L-Leucine and L-Isoleucine, respectively
C). D-Valine and L-leucine, respectively
D). L-Valine and D-leucine, respectively
E). No correct answer

They are (2S, 3R)-Threonine and (2S, 3S) isoleucine.

14) Identify the Cahn-Ingold-Prelog stereochemistry of the following molecule, which is

drawn in a Fischer projection.

A). L
B). R
C). S
D). D
E). +

15) Which of the following are a pair of acid and conjugate base:
A). HCl and NaOH
B). HA and H+
C). HAc and Ac-
D). Lys1+ and Lys
E). more than one answer
Both C and D

16) What can be used to test for pregnancy, HIV and a patient’s cholesterol level?
A). DEAE column
B). ELISA
C). Beer’s law
D). more than one answer
E). none of above
17) Hydrogen bonds are approximately ____% of the bond strength of covalent C-C or C-H
bonds?
A). 1%
B). 5%
C). 20%
D). 50%
 E). 95%

18) What conformation of the following amino acids cannot exist in any pH? You do not
need to know the side chain pKs for this question.

+
H
H3N C COOH

(CH2)4

NH3+
A). B). C).
H
H2N C COO-

(CH2)4

NH3+
D). E). more than one answer

answer B: pKa(Asp)=3.9; N-terminus=9.9; C-terminus=2.0. The amino groups cannot be

deprotonated before the side chain carboxyl groups. C is complete protonated form. D
deprotonated N- and C-terminals, which is fine. B cannot exist because side chain should
deprotonate before N-terminal.

19) What is the identity of the following organic functional group?

A). Ester
B). Carboxyl
C). ketone
D). Carbonyl
E). none is correct

It is Aldehyde.
20). Which molecular structure below is the predominant form of arginine at pH 7.5 (pKa =
1.82;8.99;12.48).

Answer : C. only cooH loses its proton.

21) What will the pH change when 0.5M of NaAc is added into water solution at pH 7?
A). pH will decrease because Na+ embraces some OH-
B). pH will increase because Na+ embraces some OH-
C). pH will increase because Ac- embraces some H+
D). pH decrease because Ac- embraces some H+
E). remain neutral because NaAc is neither acid nor base

22) Calculate the pI of the amino acid Lys. The Pkas are 2.2; 9.06; 10.54.
A). 9.06
B). 2.2
C). 7.72
D). 9.8
E). 5.8

pI=0.5*(10.54+9.06) = 9.8

23) What is the value of DG° for the reaction A + B D C + D at 25°C when the equilibrium
conditions are : [A] = 1 µM; [B] = 5 µM; [C] = 10 µM; [D] = 2 µM?

A). –3.43 kJ/mol

B). –1.49 kJ/mol
C). -1.49 J/mol
D). –3.43 J/mol
E). 3.43 kJ/mol

Answer: d. Use the equation: DG° = –RT ln Keq = –RT ln([C][D]/[A][B]).

DG° = –RT ln(2x10/1x5) = –RT ln(4) = –RT (1.39)
DG° = –8.3145 J/mol-K(298K)(1.39)/1000 J/kJ = – 3.44 kJ/mol

24). What is the chemical energy for the reaction at 298K

ATP => ADP + Pi

if: ATP = 10 M, ADP = 0.8 M, and Pi = 4M,

10
A). DG = DG 0' + RT ln
4 * 0.8
10 * 4
B). DG = DG 0' + RT ln
0.8
C). DG = DG 0' + RT ln(4 * 0.8) *10
D). more than one correct answer
4 * 0.8
E). DG = DG 0' + RT ln
10

25). Calculate the pH of a mixing solution containing 100mL of 3M acetic acid and 200mL of
2M sodium acetate? The pKa of acetic acid is 4.76.
A). 4.88
B). 5.11
C). 4.64
D). 2.51
E). 6.10
Acetic acid: (0.10L)(3M) = 0.30Mole
Acetate: (0.20L)(2M)) = 0.40Mole

pH = pKa + log([acetate]/[acetic acid]) = 4.76 + log(0.40/0.30) = 4.76 + (0.12) = 4.88

26) If you add NaOH to water to a final concentration of 0.01M, the pH of the solution
becomes:
A). 1
B). 0.01
C). 12
D). 2
E). none of the above

poH = -log(oH-) = -log(0.01) = 2, ph = poh-ph =12

27) Into 0.1 M HAc (pK= 4.76) solution of 100 ml, 20 ml of 0.2M of NaOH was added.
What is the final pH (assuming the final volume is 120 ml).
A). 5.43
B). 4.94
C). 1x10-5
D). no correct answer
E). 4.58
 Answer: mole of HAc: 0.1*0.1=0.01mole; mole of NaOH: 0.02*0.2 = 0.004mole. It will
generate 0.004 mole of NaAc- left 0.06mole of HAc. So pH = pKa +log(ac/HAC) =
4.7+log(0.004/0.006) = 4.52

28) What percentage of a hypothetical amino acid’s side chain group (A) is protonated at pH
6.5? (pKa is 7.0)
A). 6.47%
B). 67%
C). 24.0%
D). 76%
E). No correct answer
answer: b. pH = pK + log (A-/HA)
6.5 = 7 + log (A-/HA)
log (A-/HA) = -0.5
A-/HA = 0.316
HA/(HA+A-) =1/(1+0.316) = 76%

29). Identify the sequence of the following peptide.

A). KFDLYT
B). DFMKFS
C). DHCVFS
D). DHMKYT
E). TYKMHD

30). Calculate the PI of the above peptide.

A). (3.9+2.2)/2
B). (2.2+9.4)/2
C). (9.4+10.54)/2
D). (6.04+9.4)/2
E). no correct answer

31). HAc n H+ + Ac- The pKa is 4.7, which graph describes this reaction?
 D). No correct answer.
E). depending on concentration, it could be either A or B.

Answer B

32). The ribosomal protein L27 contains total number of (Asp + Glu): 20; and total number of
(Arg + Lys): 43. To retain this protein on an ion-exchange column at pH 7, which type of
column should be used:
A). DEAE-cellulose
B). CM-cellulose
C). His-tag affinity column
D). size exclusive column
E). more than one answer

The PI is basic because more Arg+Lys. So at pH 7, the protein is positively charged. CM-
cellulose column should be used.

33). Indicate the predominate ionic species of phosphoric acid at pH 8.

A). H3PO4
B). H2PO4-
C). HPO42-
D). PO43-
E). all of them are in similar concentration because it is a buffer
answer: c
H3PO4 ó H2PO4- + H+ pK= 2.15 (1)

H2PO4-ó HPO42- + H+ pK = 6.82 (2)

HPO42-ó PO43- + H+ pK= 12.38 (3)

At pH 8, reaction 1 is completely to the left because the pH >> pK; reaction3 is completely to
the left because pH << pK. Reaction (2) is the one that needs to consider.
H2PO4- ó HPO42- + H+ pK = 6.82 (2)
pH = pK+ log(HPO42-/ H2PO4-)
8 = 6.82 + log(HPO42-/ H2PO4-)
log(HPO42-/ H2PO4-) = 8-6.82 = 1.18
HPO42-/ H2PO4- = 101.18 = 15
34). The ribosomal protein XX’s PI is 7.0, MW 15 KDa. I want to purify this protein with an
ion exchange column in a buffer solution. Which of the following combination is good
combination of buffer and column:

A). H2PO4- for a buffer of pH 7.0, then use a DEAE column

B). acetic acid for a buffer of pH 5.0, then use a CM column
C). acetic acid /for a buffer of 8.0, then use a DEAE column
D). boric acid for a buffer of pH 9, then use a DEAE column
E). more than one answer
Both B and D should do. Acetic acid for pH 8 is not good because buffer ability is pka +-1 .

35). After I collect the column fractions, I want to identify the purity of protein XX (above)
on a SDS-PAGE gel (A Gel is shown). Which band should I
look at?
A). A
B). B
C). C
D). D
E). E

36). Which of the following molecule will be integrated into the

palmitic acid micelles (not inside or outside, but integrated)?
A). +H3N-CH2-COO-
B). +H3N-CH2CH2-COO-
C). H3C-(CH2)11-COO-
D). amino acids with hydrophobic side chains
E). none of above

palmitic acid

Answer: C. The structure of palmitic acid is shown above. It is amphiphilic. It forms

micelles in water due to the hydrophobic interaction. C is amphiphilic molecules to be
incorporated in the micelles.

37). Which peptide has greater absorbance at 280nm?

A). VKPLCKWW
B). VKPLCKFT
C). VKPLCKFW
D). VKPLCKFF
E). VKPLCKYYY

answer: a. Tryptophan has the highest absorbance at 280 nm. It is 10 times higher than
tyrosine . So, the more tryptophan in the peptide the greater the absorbance.

38). The enthalpy change (DH) for a reaction is –5.5 kJ/mol and the entropy change (DS) is
–5.5 cal/(mol K), what is the free energy (DG) for the reaction in kJ/mol at 310K? Please
note that 1 cal = 4.18 J.
 A). ~ –3.80 kJ/mol
B). ~ 1.63 kJ/mol
C). ~ –12.63 kJ/mol
D). ~ 7128 kJ/mol
E). ~ 3.80 kJ/mol

DG = DH – TDS = –5.5 kJ/mol – 310K(–5.5 cal/mol/K*4.184 kJ/kcal / (1000 J/kJ)) = 1.63

kJ/mol

39). In the following reaction: 4NH3(g) ® 2N2(g) + 6H2 (g), the A). product is a solid
B). entropy decreases
C). entropy increases
D). free energy increases
E). free energy decreases

40). The order of amino acids (Lys, Asp, ILE) eluted from an anion-exchange column at pH 7
should be
A). KDI
B). DIK
C) DKI
D) DKA
E) no correct answer
The order should be KID
Thermodynamic: 1;3;4;11;23;24;38
Water: 2;8;9;12;17;19;36;39
Acid: 5;6;15;21;25;26;27;29,33
Amino acid: 7;13;14;18;20;22;30;31;37
Protein purification: 10;16;28;32;34;35;40
R = 8.3145 J/mol-K
1 cal = 4.18 J
pH = pKa + log {(A-)/(HA)}
when pH > pKa, deprotonate proton leaves
when pH < pKa, protonate, proton stays
when pH > pI, - protein
when pH < pI, + protein