UNIVERSITY OF THE FREE STATE 9. Which amino acids are most often found at reverse turns in proteins?

A. Glu, Pro B. Gly, Pro C. Gly, Phe D. Gln, Pro

MAIN CAMPUS E. Glu, Phe F. Gly, Arg G. Gln, Phe H. Glu, Phe
BOCB2616
Use the following information to answer questions 13 to 16. You have 500 ml of a sodium
DEPARTMENT OF MICROBIAL, BIOCHEMICAL & FOOD BIOTECHNOLOGY formate/formic acid buffer containing 0,75 moles sodium formate and 0,75 moles formic acid.
The Ka of formic acid is 1,78 x 10-4 M:
Semester Test 1: 4 March 2020
ASSESSOR: Prof. M.S. Smit 10. What is the concentration of this sodium formate/formic acid buffer?
MODERATOR: Prof. H.G. O’Neill A. 0,24 M B. 0,66 M C. 1,00 M D. 1,50 M E. 3,0 M

TIME: 1 hour MARKS: 50 11. What is the pH of this sodium formate/formic acid buffer?
A. 3,00 B. 3,75 C. 3,93 D. 10,25 E. 4,42
Section 1 [20]
Multiple choice questions 12. How many moles of NaOH should one add to change the pH of this solution to pH 5.75?
ANSWER ALL QUESTIONS IN THIS SECTION ON THE PINK OPTICAL FORM A. 1,48 mol B. 735 mmol C. 73,5 mmol D. 7,3 mmol E. 1 mmol
REMEMBER TO ENTER YOUR STUDENT NUMBER AND NAME!! F. HCl and not NaOH should be added
1. Which compounds were present on the early earth?
A. H2O & O2 B. NH3 & O2 C. O2 & CO D. CO2 & H2O Study the following peptide structure to answer questions 13 to 20.
2. pKa is defined as (Ka is dissociation constant of acid)
A. log of Ka
B. negative log of Ka
C. negative antilog of Ka
D. antilog of Ka

3. A dipole is when...
A. covalent bonding doesn't work
B. opposite ends of a bond have opposite partial charges
C. electrons are shared equally
D. opposite ends of a linear molecule have the same charge
E. two oppositely charged functional groups form a bond

4. Alanine has pK1 2,4 and pK2 9,2. At which pH will the buffering capacity of an alanine
buffer be optimal? 13. How many amino acid residues in this peptide?
A. 11 B. 2,4 C. 5,8 D. 7 A. 6 B. 7 C. 8 D. 9
5. The pH of a 1 µM NaOH solution is 14. The amino acid sequence of this peptide in one letter code is:
A. 8 B. 3 C. 6 D. 11 A. CFKMDVN B. MFRCEVQ C. MFKCDVN D. MFKCDIN
E. CFKMDIN F. MFRCDVN G. MFKCDVQ H. MFRCDIN
6. Which is the most electronegative atom?
A. O B. N C. H D. C 15. Three amino acids in this peptide with hydrophobic side chains are:
A. Cys, Phe, Val l B. Met, Phe, Val C. Gln, Val, Met D. Met, Phe, Ile
7. What is the name of the reaction of two amino acids forming a peptide bond
A. hydrolysis B. condensation C. oxidation D. reduction Questions 16 to 20: Match the functional groups marked on the peptide structure given above
to the following terms by marking the relevant letter on the optical form:
8. Which level of structure of a protein is characterized by alpha-helices and/or beta-pleated 16. Peptide bond
sheets? 17. Carboxylate group
A. primary B. secondary C. tertiary D. quaternary 18. Sulfhydryl (thiol) group
19. Side chain amide group
20. Phenyl group
SECTION 2 [30]
ANSWER ALL QUESTIONS IN THIS SECTION ON TEST PAPERS. REMEMBER TO
ENTER YOUR STUDENT NUMBER!!

Question 1 [5]
Give the terms used to describe the following:
(a) a water soluble protein folded into an approximate spherical shape
(b) a measure of the force of an atom’s attraction for electrons it shares in a chemical bond
with another atom
(c) an organelle with its own DNA which is the site of energy-yielding oxidation reactions
(d) the three dimensional shape in which a protein has biological activity
(e) a fibrous protein found in connective tissue of animals that consists of three polypeptide
chains wrapped around each other

Question 2 [5]
Briefly describe the following: ……:
(a) Hydrogen bonding in ice. (2)
(b) Hydrogen bonding in an α-helix. (2)
(c) Hydrogen bonding in the tertiary structure of proteins. (1)

Question 3 [10]
The pKa values of lysine are pK1 (α-COOH) = 2,2; pK2 (α-NH3+) = 9,0; pKR (RH) =10,5.
(a) Calculate the isoelectric point of lysine. Show your calculation. (2)
(b) Draw the structure of lysine at its isoelectric point. Show all atoms. Remember to
indicate all charges. (3)
(c) What will be the charge on lysine at pH 12? (1)
(d) Give the one and three letter codes for lysine. (1)
(e) Use the Henderson-Hasselbalch equation to explain why half the lysine molecules will
be in the zwitterion form in a solution in water at pH 9,0. What will be the charge on the
other half of the lysine molecules? (3)

Question 4 [10]
a. Draw the tripeptide Ile-Asn-Tyr. Show all atoms. Indicate charges as they would be at
pH 7. Encircle the polar side-chain(s) in this tripeptide. Assume the pKa values to be
pK1 (α-COOH) ≈ 2,3 and the pK2 (α-NH3+) ≈ 9,6. (6)
b. Give the names and one letter abbreviations of each amino acid in this tripeptide. (3)
c. Give the name and three letter abbreviation of the amino acid that forms disulfide
bonds. (1)