University of Houston BCHS 3304

Exam I. Instructor: Dr. Briggs, Feb. 9, 2006 Printed Name_____ANSWER KEY________

Answer all questions; show all work. Multiple choice Circle the single letter (i.e. a., b., c., d., or e.) of the most correct answer, then mark it on the Scantron sheet with a #2 pencil. Mark BOTH the exam AND the Scantron sheet.

1). What is a Brnsted acid? (2 pts) a. A molecule that can accept a proton b. A molecule that can form a hydrogen-bond c. A molecule that has a net charge d. A molecule that can donate a proton e. A molecule that cannot form a hydrogen-bond 2). How many nm are there in 32.1 m? (2 pts) a. 32.1x10-9 nm b. 3.21x10-9 nm c. 0.321x10-9 nm d. 32.1x109 nm e. 3.21x109 nm 1 nm = 1x10-9 m; conversion factor = 1nm/1x10-9 m 1nm 1nm 1= ; x32.1m = 32.1x109 nm 9 1x10 m 1x10 9 m 32.1 m = 32.1x109 nm

3). How many picoseconds are there in 23.1 ms? (2 pts) a. 2.31x10-15 ps b. 2.31x10-9 ps c. 2.31x109 ps d. 23.1x109 ps e. 2.31x1015 ps 1 ps (picosecond) = 1x10-12 s; 1 ms (millisecond) = 1x10-3 s 23.1ms 1x103 s 1 ps x x = 23.1x109 ps 1x1012 s ms 4). How many kJ/mol are there in 2.31 kcal/mol? (2 pts) a. 9.67 kJ/mol b. 9.67 kcal/mol c. 0.1034 kJ/mol d. 0.1034 kcal/mol e. 2.31 kJ/mol 1 kcal/mol = 4.184 kJ/mol 2.31 kcal / mol 4.184 kJ / mol = 9.67 kJ / mol x 1 kcal / mol

5). If the enthalpy change of a process is negative and the entropy change is positive, the free energy change is: (2 pts) a. spontaneous b. non-spontaneous c. zero d. temperature independent e. catalyzed by an enzyme See Table 1-3 in the book G = H TS = () T(+) = 6). What is the pH of a 0.05 M HCl solution? (Hydrochloric acid completely dissociates in H2O) (2 pts) a. 7.05 b. 3.0 c. 0.30 d. 1.3 e. 0.5 pH = log[H+], [H+]=0.05M, pH=1.3 7). What is the pH of a 0.005 M NaOH solution? (Sodium hydroxide completely dissociates in H2O) (2 pts) a. 7.0 b. 11.7 c. 1.27 d. 1.3 e. 12.7 pH = log[H+], Kw=[H+][HO-]=1.0x10-14=[H+](0.005); [H+]=2x10-12 pH=-log(2x10-12), pH=11.7 8). The enthalpy change (H) for a reaction is 3.5 kJ/mol and the entropy change (S) is 2.5 cal/mol/K, what is the free energy (G) for the reaction in kJ/mol at 298K? (2 pts) a. 6.62 kJ/mol b. 6.62 kJ/mol c. 0.38 kJ/mol d. 3.12 kJ/mol e. Is not spontaneous
G = H TS = 3.5 kJ/mol 298K(2.5 cal/mol/K*4.184 kJ/kcal / (1000 J/kJ)) = 6.62 kJ/mol

9). What is the pH of a 1L solution that has 600mL of 1M NaOH? (2 pts) a. 13.8 b. 14.3 c. 7.0 d. 0.6 e. neutral pH = log [H+] [HO-] = (0.6L)(1M)/1L = 0.6M; [H+] = 1x10-14/[HO-] = 1x10-14M2/0.6M = 1.67x10-14M pH = log [H+] = log (1.67x10-14) = 13.8 10). Calculate the pH of a 1L solution containing 100mL of 3M acetic acid and 150mL of 1M sodium acetate? The pKa of acetic acid is 4.76. (2 pts) a. 7.00 b. 4.24 c. 4.46 d. 4.06 e. 3.94 Acetic acid: (0.10L)(3M)/1L = 0.30M Acetate: (0.15L)(1M)/1L) = 0.15M pH = pKa + log([acetate]/[acetic acid]) = 4.76 + log(0.15/0.30) = 4.76 + (0.30) = 4.46 11). If the [H+] is less than 1x10-7, the solution is (2 pts) a. acidic b. basic c. a solid d. gaseous e. neutral 12). What Greek letter is used to identify the CH2 group in the Met amino acid side chain that is just before the S? (2 pts) a. alpha b. beta c. gamma d. delta e. epsilon

NH3+ -OOC

13). What is the pKa of the side chain of Lys? (2 pts) a. 10.54 b. 12.48 c. 9.4 d. 2.2 e. 6.04

14). What is the pKa of the C-terminus of an amino acid? (2 pts) a. 10.54 b. 12.48 c. 9.4 d. 2.2 e. 6.04 15). Given the amino acid sequence DAHGHFMKAGKT, what reagent would cleave the last residue, T, from the peptide? That is, one of the products after treatment will be the free amino acid: T. (2 pts) a. Trypsin cleaves to the right of Arg and Lys b. Phenyl isothiocyanate Cleaves disulfide bonds c. Cyanogen bromide Cleaves to the right of Met d. Chymotrypsin cleaves to the right of Phe, Trp, and Tyr e. Iodoacetate Reacts with Cys sidechains 16). What is the one letter code for the amino acid: Phe? (2 pts) a. P b. T c. F d. R e. E 17). What is the three letter code for the amino acid: R? (2 pts) a. Trp b. His c. Lys d. Arg e. Asn 18). What amino acid sequence will be cleaved by cyanogen bromide (CNBr)? (2 pts) a. CAMEHERE CNBr cleaves AFTER Met (M) residues b. CAPEFEAR c. CAPEDAVENGER d. SINEWAVE e. SITDWNE

19). What form of this amino acid cannot exist in the pH range 2-14? (2 pts)
H H2N C COOCH2 H H2N C COOH CH2 H NH3+ C COOCH2

a.

COO-

b.

COOH

c.

COO-

H NH3+ C COOCH2

NH3+

H C COOH CH2 COOH

d.

COOH

e.

20). What is the identity of the following organic functional group? (2 pts) O
O Carbonyl Carboxyl Ether Ester Amide

a. b. c. d. e.

21). What is the identity of the following organic functional group? (2 pts) a. b. c. d. e.
O Carbonyl Carboxyl Ether Ester Amide

22). Calculate the pI of the amino acid Lysine. (2 pts) a. 9.4 b. 2.2 c. 9.97 pI=0.5*(10.54+9.4) d. 5.8 e. None, it is always positively charged. 23). In how many hydrogen-bonds can a water molecule participate? (2 pts) a. 0 b. 1 c. 2 d. 3 e. 4 Four - two as an acceptor (oxygen) and two as a donor (hydrogens) 24). How many ngstroms () are there in 0.54 nm? (2 pts) 1x10 9 m 1Angstrom a. 5.4 0.54nm = 5.4 A 1nm 1x10 10 m b. 54 c. 0.054 d. 0.00054

e. 540 25). Which one of the following conditions will lead to an unconditionally spontaneous process? (2 pts) a. H < 0; TS > 0 G = H TS (G < 0, spontaneous) NOTE that I said UNCONDITIONALLY spontaneous! b. H < 0; TS < 0 c. H > 0; TS > 0 d. H > 0; TS < 0 e. None of the above 26). What reagent can be used to cleave a disulfide bond? (2 pts) a. Dansyl chloride b. Performic acid c. Cyanogen bromide d. Water e. Naphthalene 27). What is the relationship between two identical right-handed gloves? (2 pts) a. Enantioners b. Diastereomers c. Chiral d. Superimposable e. No relationship 28). In the following reaction: N2 + 3H2 2NH3, the (2 pts) a. entropy decreases b. product is a solid c. entropy increases d. free energy increases e. free energy decreases

29). Given a free energy change for a reaction of 2.5 kcal/mol, what is the equilibrium constant (Keq) at 20 oC? (R = 8.3145 J/mol-K) (2 pts) a. 16.6 b. 73 c. 293.15 d. 8.3145 e. It cant be computed from the given information.

G = -RTlnKeq, (-2.5 kcal/mol)(4.184kJ/kcal) = -(8.3145 J/mol-K)(/1000J/KJ)(293K)lnKeq, -10.46 = -2.44 lnKeq ; Keq = 72.97
30). What is the value of Kw (i.e. the equilibrium constant for the dissociation of water)? (2 pts) a. 14 b. 7 c. 1x10-7 d. 1x10-14 e. 4 31). For a chiral molecule with two chiral centers, how many possible stereoisomers exist. (2 pts) a. 1 b. 3 c. 4, 22 d. 6 e. 8 32). What is the primary structure of a protein? (2 pts) a. alpha helix b. beta sheet c. amino acid sequence d. amino acid composition e. disulfide bonds 33). What is the one amino acid that is not chiral? (2 pts) a. Ala b. Gly c. Glu d. Gln e. None of the above. 34). Which amino acid has an imidazole side chain? (2 pts) a. D b. H c. V d. A e. L

35). Entropy is a measure of (2 pts) a. the spontaneity of a process b. the order of a system c. the disorder of a system d. the non-spontaneity of a process e. the exothermicity of a process 36). A polypeptide was subjected to the following degradative techniques resulting in polypeptide fragments with the indicated amino acid sequences. What is the amino acid sequence of the entire polypeptide? (2 pts) I. Cyanogen bromide treatment 1. Asp-Ile-Lys-Gln-Met 2. Lys 3. Lys-Phe-Ala-Met 4. Tyr-Arg-Gly-Met II. Trypsin hydrolysis 5. Gln-Met-Lys 6. Gly-Met-Asp-Ile-Lys 7. Phe-Ala-Met-Lys 8. Tyr-Arg a). QMKFAMKYRGMDIK b). YRGMDIKQMKFAMK CNBr cleaves after Met, Trypsin cleaves after Arg and Lys. Tyr-Arg-Gly-Met-Asp-Ile-Lys-Gln-Met-Lys-Phe-Ala-Met-Lys Y - R- G- M- D- I- K- Q- M- K- F- A- M- K 37). When two amino acids form a peptide bond what molecule is eliminated? (2 pts) a. oxygen b. hydrogen c. water d. nitrogen e. none of the above

38). Which molecular structure below is the predominant form of Aspartic acid at pH 1. (2 pts) a). b. c. COOCOOCOONH3+ COOH

H2N

COO-

NH3+

COO-

d.
COOH NH3+ COO-

e.
COOH NH3+ COOH

39). What is the stereochemistry of the following chiral molecule (R or S)? (2 pts) a. R b. S c. Molecule is not chiral

F HO

H
3

SH

Use Cahn-Ingold-Prelog rules rank order is based on atomic mass. Remember also that the lowest ranked group is supposed to be pointing away from you it is facing you here 40). Identify the following amino acid. (2 pts)

NH3+

COO-

a. E b. I c. V d. L e. R

41). Identify the following amino acid. (2 pts)

O O

NH3+

COO-

a. E b. I c. V d. L e. R 42). Identify the following amino acid. (2 pts)

H2N NH2+ HN (CH2)3 NH3+
COO-

a. E b. I c. V d. L e. R 43). Identify the sequence of the following peptide. (2 pts)

NH3+ OH N H H N O COOO N H H N O O N H COO-

NH3+
CH3

CH3

a. MSIDML b. ATLDAK c. KADLTA d. LMDISM e. NCCNCC

44). Calculate the pI of the following tripeptide. (2 pts)

NH OH
H N H O H O N H O H O

NH3+

a. b. c. d. e.

7.72 pI=0.5*(6.04+9.4) 9.4 2.2 5.8 None, it is always positively charged.

45). What percentage of the histidine imidazole is protonated at pH 7.0? (2 pts) a. 100.0% b. 14.45% c. 9.88% d. 9.12% e. 0.0%
Henderson-Hasselbalch pH = pKa + log [ApH - pKa = log [A-]/[HA] [A-]/[HA] = 10(pH-pKa) = 10(7.0-6.04) = 9.12 %HA = 100 x [HA] ([HA] + [A-]) %HA = 100 x [HA]/[HA] ([HA]/[HA] + [A-]/[HA]) %HA = 100 x 1 = 9.88% (1 + 9.12)

46). How many grams of sodium succinate (mol wt=140 g/mol) must be added to 1L of water containing disodium succinate (mol wt=162 g/mol) to produce a solution with pH=6.5 and a total solute concentration of 70 mM? Note that the pKa of sodium succinate=5.64. (2 pts) a. 2.1g b. 1.2g c. 9.96g d. 5.7g e. 6.5g pH =pKa + log([A-]/[HA]) [A-] + [HA] = 0.07 M; [A-] = 0.07 M [HA] 6.5 5.64 = log([A-]/[HA]); [A-]/[HA] = 7.24 0.07 M [HA] = 7.24[HA]; 0.07 M = 8.24[HA]; [HA] = 0.0085 M [A-] = 0.07 M [HA] = 0.0615 M Grams sodium succinate = 0.0085 moles 140 g x x 1 liter = 1.2 g liter mol Grams of disodium succinate = 0.0615 moles 162 g x x 1 liter = 9.96 g liter mol

47). Identify the following molecule which is drawn in a Fischer Projection. (2 pts) COONH3+ H H OH CH3

a. L-Threonine b. L-Glyceraldehyde c. D-Glyceraldehyde d. L-Serine e. D-Serine

48). Identify the Cahn-Ingold-Prelog stereochemistry of the following molecule which is drawn in a Fischer Projection. (2 pts)

a. L b. S c. D d. R e. + 49). An amphiphile is a (2 pts) a). alligator b). compound that is hydrophobic c). compound that is hydrophilic d). neutral compound e). both b and c 50). Treatment of a polypeptide with 2-mercaptoethanol yields two polypeptides: (2 pts) 1. Ala-Val-Cys(a)-Arg-Thr-Gly-Cys(b)-Lys-Asn-Phe-Leu 2. Tyr-Lys-Cys(c)-Phe-Arg-His-Thr-Lys-Cys(d)-Ser Treatment of the intact polypeptide with trypsin yields fragments with the following amino acid compositions: 3. (Ala, Arg2, Cys2, Phe, Val) 4. (Cys2, Gly, Lys, Ser, Thr) 5. (Asn, Leu, Phe) 6. (His, Lys, Thr) 7. (Lys, Tyr) What disulfide bonds exist in the intact polepeptide? a. Cys(a)- Cys(b) and Cys(c)- Cys(d) b. Cys(a)- Cys(d) and Cys(b)- Cys(c) c. Cys(a)- Cys(c) and Cys(b)- Cys(d) d. None See Chapter 5, Problem 9 solution, first possible solution (web page)