1. There are four molecules whose structures are indicated below.

Which bond is usually used to provide energy in order to change the conformation of a protein?
O PH O O O P O HO O N N N N N N O O P HO O HO O O P O O O

O O P O P O O

O O

N NH2 O
O

N NH2 O

A.

B.
O P O O P O

O P OH O O
O

O P O

P O

O P O O N N N O

O P O

O O P O O HO

O O P OH O O

O O O N N N

HO O N N N

N NH2

N NH2

N NH2

C.

D.

E.

B is ATP molecule 5-phosphate. C, E are the same. This is why the question says there are four molecules.
2. Which statement of the following about a reaction is TRUE? A. A reaction is said to be spontaneous when it can proceed in either the forward or reverse direction. B. A spontaneous process always happens very quickly C. A nonspontaneous reaction will proceed spontaneously in the reverse direction D. A spontaneous process can occur with a large decrease in entropy E. Increase of reaction temperature will make a nonspontaneous reaction spontaneous. 3. Which one of the following structures occurs most often in a protein?
O O R1 R1 N H2
+

R2 R2 N R3 O

R1 R2 R1 R2 O

A.

R2

B.

C.

R1

D.

N H

E.

Peptide bond. Amide bond.

4. Which one of the following is least soluble in H2O? A. H3C-CH2-CH3 B. H3C-CH2-O-CH3 C. H3C-CO-NH2 E. CH3-CH2-CHO D. H2N-CO-NH2

A: no polarity.

5. How many H-bonds can the following molecule form?

N HN

A. 0

B. 1

C. 2

D. 3

E. 4

Receptor. The donor N can not accept H.

6. The following detergents can be used to solubilize a membrane protein. Which one can not be used if we want to determine the ATP hydrolysis activity by the membrane protein? A. Octyl--D-glucoside B. Decyl--D-maltoside C. Dodecyl--D-maltoside D. Octyl--D-maltoside E. Sodium dodecylsulfate

Strong ionic detergent will denature proteins.

7. To make a 1M NaH2PO4 solution pH at 7.0, 120g NaH2PO4 will be first dissolved in 800ml H2O. Then use 10M sodium hydroxide solution to adjust the pH slowly. With the increase of pH: A. [PO43-] increases B. [H2PO4-] decreases C. [OH-] increases D. [Na+] increases E. All above 8. What is the approximate pI value of glutathione? (1 mark) A. 2.22 B. 3.21 C. 5.36 D. 6.22 E. 8.92

Glu-Cys-Gly. The reduced or oxidized form does not matter.

9. How many net charge does a glutathione molecule carry at pH 7.0? A. +2 B. +1 C. 0 D. -1 E. -2

10. The following figure represents a titration curve of phosphoric acid. What is the approximate pKa for the reaction H2PO4- = H+ + HPO42-? A. 2.0 B. 4.0 C. 7.0 D. 9.0 E. 12.0

11. What is the pH of a 1L H2O after a drop (100 microL) of 0.002M HCl solution is added? (1 mark) A. 6.00 B. 6.55 C. 6.62 D. 6.79 E. 7.00 0.002 M 0.0001 L = 2 10-7 mol H2O = H+ + OHx x -7 +2 10 x (x + 2 10-7) = 10-14 x = 2.414 10-7

pH = -log(2.414 10-7) = 6.62

12. Given a weak acid buffer, when the pH is 2 units larger than the pKa, the ratio of conjugate base to weak acid is. A. 100 B. 10 C. 1 D. 0.1 E. 0.01 pH = pKa + log [base]/[acid] 13. Which of the following amino acid derivates is directly from arginine?
HO

HO O

NH+ 3

H N
+

H3 N N

A.
I OH

B.

C.

NH+ 3

O I I

NH+ 3

D.

E. None of the above

A. is from Glutamic Acid. Arginine is not aromatic amino acid. 14. Which of the following amino acid does NOT likely occurs in lipid bilayer when it is on the surface of a protein? A. Ala B. Asp C. Gly D. Lys E. None of the above Asp is small charged amino acid. 15. Which of the following amino acid does NOT likely occurs in the surface of a soluble protein? A. Glu B. Thr C. Lys D. Asp E. Ile Lys can somehow because of the long CH2-CH2-CH2-CH2-NH3+ side chain.

16. Which statement of the following about Arg is NOT correct? A. It is a big amino acid B. It is a polar amino acid C. It is always charged inside cells D. It is always located on the surface of a protein E. The side chain can form hydrogen bond Arg can be located in the interior part and forms ionic interaction with other groups. 17. Which statement of the following about amino acids is correct? A. Sulphur containing amino acids can form disulfide bonds B. Ribosome only recruits L-amino acids for the synthesis of polypeptide chains C. The side chain of an aromatic acid is highly hydrophobic D. A protein is optically active because all amino acids are optically active E. The side chain of an Ala in a protein involved in signaling pathway can be phosphorylated. 18. Five patients are suspected to have abnormal hemoglobin function and their hemogloving sequences are determined. The following alignment shows segments of hemoglobin sequences from patients A to E. Which patient is most likely to have a hemoglobin associated disease? (1 Mark) Normal: A. B. C. D. E. LeuValValTyrProTrpThrGlnArgPhe LeuValValTyrProTrpSerGlnArgPhe normal because Thr, Ser are similar LeuValValTyrProTrpThrGlnArgPhe exactly the same sequence IleValValTyrProTrpThrGlnArgPhe normal. Ile is similar to Leu. LeuArgValTyrProTrpThrGlnArgPhe x hydrophobic changed to charged. LeuValValTyrProTrpThrGlnLysPhe probably normal. Positively charged.

19. A peptide has the following amino acids: AspGluAlaLysPheGlyAsnGlyGluAla. To determine the relative amount of each amino acid in the peptide, the peptide is hydrolyzed using 6M HCl, neutralized and then labeled with PITC. How many peaks in the chromatography profile do you expect to determine the PTC-amino acids? (1 mark) A. 5 B. 6 C. 7 D. 8 E. 10 7 different amino acids. But Asp and Asn will act as one. 20. The molecular mass of a protein is about 100,000 Da. It is very abundant in the cells. Without knowing other information, which method of the following cab be tried to purify the protein from cell lysate? A. Salting out B. Gel filtration C. Anion exchanger D. Cation exchanger E. All the above All can be tried. Some proteins with pI < 7.0 can bind cation exchanger column because of local positive charge. 5

21. The molecular mass of a protein is about 100,000 Da. The pI of the protein is 4.73. Without knowing other information, which method of the following should be tried first to purify the protein from cell lysate? A. Salting out B. Anion exchanger C. Cation exchanger D. Affinity chromatography E. Salting out The protein is negatively charged under physiological pH. Anion exchanger should be tried first though cation exchanger may work. Gel-filtrated usually last step of purification. 22. A protein shows a molecular mass of 50kDa by SDS-PAGE with -mercaptoethanol. However, the protein shows a molecular mass of 60kDA by gel filtration. Which of the following is most likely true? A. B. C. D. The protein forms a dimmer with a disulfide bond linking the two subunits. The protein is partially degraded during the process of SDS-PAGE. The protein exists as a monomer but it is not globular. During the gel filtration process, the protein interacts with the charged group of the matrix in the column and delays the protein elution. E. The concentration of -mercaptoethanol used in SDS-PAGE is too low. 23. The matrix in a chromatography column is linked to the following group: O-CH2-CHOH-CH2-OCHOH-CH2-SO3-. The column can be most likely used to bind proteins with the following property: A. pI = 5.10 B. pI = 8.73 E. C-terminus contains a FLAG tag. C. Molecular mass = 200kDA D. Hydrophobic

Used to bind positively charged molecules. 24. For each cycle of Edman degradation, what is the compound analyzed in the last step to determine the N-terminal amino acid. A. PTH-amino acid B. PITC-amino acid C. PTC-amino acid D. PMT-amino acid E. PIT-amino acid 25. Trypsin digestion of a protein is usually very fast. But by limiting the amount of trypsin or shortening the digestion time, a protein or peptide can be partially digested, that is to say, for some peptides not all cleavage sites will be cut. How many peptides will exist in the digestion mixture if the following peptide undergoes a partial digestion by trypsin? Ala-Arg-Val-Val-LysGly-Lys-Trp-Tyr (1 mark) A.4 B. 6 C. 8 D. 10 E. 12

Ala-Arg- -Val-Val-Lys- -Gly-Lys- -Trp-Tyr 6