BICH 410 FINAL A
A December 16, 2002
_______________________
Name
BUFFERS, AMINO ACIDS, PEPTIDES and PROTEIN. Put down a number that matches the question asked
ONLY NUMBERS (Questions 1-45, 2 PTS each)
____1. The pH of a neutral solution
____2. The [H+] concentration of a neutral solution
____3. The [OH-] concentration of a neutral solution
____4. The ion product (Kw) or water
____5. The pH of a 10-3 M HCl solution
____6. The pH of a 10-3 M solution of acetic acid (pKa =4.7) that is 10% ionized.
____7. The number of equivalents of base required to reach the pK point of fully protonated acetic acidic.
____8. The approximate pKa of an -COOH group of an amino acid.
____9. The approximate pKa of an -NH2 group of an amino acid.
___10. The approximate pH when glycine exist entirely as a zwitterion
___11. The pKa of the imidazole group of histidine
___12. The number of equivalents of base that are required to titrate all the protons in fully protonated aspartate
___13. The minimum number of (lysine + arginine) residues in a peptide cleaved into 4 fragments by trypsin
___14. The highest pKa value for an R group on an amino acid
___15. The number of peptide bonds in a tripeptide
___16. The number of iron atoms in a molecule of myoglobin
___17. The number of porphyrin ring structures in a molecule of hemoglobin
___18. The approximate number of residues in one turn of an alpha helix
___19. The number of N-terminals in a tetrameric protein
___20. A number that would signify no cooperativity in a Hill plot.
CARBOHYDRATES, FATTY ACIDS and NUCLEIC ACIDS
___21. The number of carbons atoms in glucose
___22. The number of carbon atoms in lactose
___23. The number of carbon atoms in oleic acid
___24. The number of carbon atoms in ATP
___25. The number of fatty acids attached to a diacylglycerol
___26. The number of phosphate groups in a molecule of lecithin
___27. The number of cis double bonds in arachidonic acid.
___28. The ratio of C/N (carbon to nitrogen) in the base adenine.
___29. The number of hydrogen bonds that join cytosine to guanine in DNA
___30. The S value for the small subunit of a mammalian ribosome
ENZYMES, ENERGY and MEMBRANES
___31. The number of micromoles of substrate changed per unit time when 3 units of enzyme activity are observed
___32. The ratio of [ES] to [E]total when [S] equals the numerical value for Km
___33. The value for G when a reaction is at equilibrium
___34. The charge on a molecule of cholesterol oleate at pH 7
___35. The molecules of S converted per minute per molecule of enzyme whose turnover number is 60 sec-1
Questions 36-45 (Write in the letter (s) that match the description). All must be correct to earn one point.
A. Sucrose
B. Glycerol
C. Hemoglobin
D. Cholesterol
E. CO2
F. Sphingomyelin
36. Arranged A-F by increasing molecular weight: ____ < ____ < ____ < ____ < ____ < ____
37. 3 are associated with molecules classified as lipids: ____ and ____ and ____
LETTERS
ONLY
38. One is a protein: ____
39. One can be hydrolyzed to two components by mild acid: ____
40. One assists in the release of oxygen from hemoglobin: ____
41. One has phosphate in its structure: ____
42. 2 have nitrogen atoms in their structure: ____ and ____
43. 2 are found in the cell membrane bilayer: ____ and ____
44. One is a carbohydrate: ____
45. One is a gas: ____
ANSWER QUESTIONS 1-15 on the scantron 2 PTS for a correct response. ONLY ONE ANSWER IS CORRECT
In this course we stressed the STRUCTURE-FUNCTION principle to rationalize why certain molecules are chosen to
perform the functions of living cells. See if you have grasped this principle.
1.
Proteins owe their strength to covalent bonds that:
a) have double-bond character and join amino acids together
b) have the same bond strength as amide bonds
c) are electrostatic and depend on the pH of the solution to unite (+) and (-) charges
d) are hydrophobic bonds that hold groups together by van der Waals forces
e) all of the above are examples of covalent bonds found in proteins
2.
A friend asks your advice as to whether lettuce will contribute to tooth decay. You reply.
a) Yes, because lettuce is composed of cellulose which is broken down to glucose by -amylases in saliva
b) Yes, because -amylases in saliva are able to digest the cellulose in the lettuce
c) No, because our amylase enzymes are unable to digest cellulose
d) Yes, because our enzymes break down all polysaccharides and release glucose that could cause tooth decay
e) No, because cellulose is a fiber that is digested in the intestine, not the mouth
3.
Which of the following does not have D-ribose as part of its structure:
a) ATP
b) RNA
c) NAD+
d) DNA
e) c and d
4.
Spot the molecule whose solubility property is different from the others:
a) L-fructose
b) L-tryptophan
c) D-glycerol
d) -D-glucose
e) oleic acid
Spot the molecule that is NOT a building block of a larger molecule:
a) L-isoleucine
b) D-galactose
c) L-ascorbate d) guanine
e) stearic acid
5.
6.
Spot the molecule that would have the most difficulty penetrating the cell membrane:
a) hemoglobin
b) LDL
c) D-glucose
d) cholesterol
e) L-tyrosine
7.
Other than serine, which amino acid residue is apt to be at the active site of a serine protease?
a) glycine
b) glucose
c) sialic acid
d) glutathione
e) histidine
8.
Which enzyme below uses NAD+ as a substrate
a) alcohol dehydrogenase
c) diphtheria toxin A
b) DNA ligase
d) lactate dehydrogenase
e) a, b, c, d
9.
What do the factors Rho and RF-3 have in common?
a) both are subunits of RNA polymerase
b) both are involved in a termination reaction
c) both are proteins that bind to the ribosome
d) both bind GTP and function in RNA synthesis
e) both bind GTP and function in translation
10. What do 5’-3 exonuclease, topoisomerase, 3’-5’ exonuclease, and EcoR1 have in common?
a) all are enzymes that hydrolyze phosphodiester bonds
d) all are enzymes that hydrolyze DNA and RNA
b) all are enzyme involved in DNA synthesis
e) all take part in protein biosynthesis
c) all are enzymes that repair DNA
11. What is EF-Tu?
a) a specific protein designed to remove GDP from the structure of another protein
b) a specific protein that translocates the mRNA-peptidyl-tRNA complex
c) a specific protein that adds GTP to another protein
d) a specific protein designed to assist in the binding of aminoacyl-tRNA to the ribosome
e) a lunatic asylum in Austin Texas
12. If for some reason IF-3 failed to function, then:
a) a 70S ribosome would remain intact and not dissociate into 50S and 30S subunits
b) a 30S ribosome would not be present to bind the mRNA
c) f-met-tRNA would not be able to initiate protein biosynthesis
d) a ribosome would remain attached to the polysome
e) a, b, c
13. A friend asks why f-met-tRNA and not met-tRNA is the first amino acid added to the ribosome. You reply.
a) because f-met-tRNA has an AUG codon
b) because only f-met-tRNA can bind to the A site on the ribosome
c) because the amino group must be blocked to prevent N-group attachment of the next amino acid
d) because f-met-tRNA is the initiating tRNA species
e) because that is what my textbook says
14. We learned in class that diphtheria toxin targets
a) IF-3
b) eEF-2
c) EF-G
d) DNA synthesis
e) RNA polymerase
15. How would you (or an enzymologist) classify the action of puromycin as an antibiotic?
a) an inactivator
c) a non-competitive inhibitor
e) a weapon of mass destruction
b) a competitive inhibitor
d) a ribosomal disrupter
SHORT ANSWER PROBLEMS
5 PTS 1. Based on your understanding of protein biosynthesis, what prevents f-met tRNA from binding to an internal AUG
codon. (HINT: the answer lies in the mechanism of initiation verses elongation).
5 PTS 2. You are waiting for a 100 car train to clear before you can cross over to the West campus. If the train is traveling at
a rate of 0.5 cars per second, how many molecules of glucose from your morning breakfast have been digested before
the train clears. Consider that you have 550 molecules of the digestive enzyme with a turnover number of 468 min -1.
(SHOW ALL WORK)
10 PTS
3. Below is a double strand of DNA. Arrow indicates direction of replicating fork
5’ - A A T G T G C A A T T G A G T A
T T A C A C G T T A A C T C C T
a)
A strand
B strand
Would a repair enzyme be required to fix this DNA? Explain
b) Is there a potential restriction nuclease site in this DNA? Explain
c)
Which strand (A or B) would represent the leading strand? Explain
d)
Assuming RNA polymerase II moves in the direction of the replicating fork, write the structure of the mRNA
segment that would be formed.
d) How many amino acids would be coded by this segment of mRNA? (Hint: recall initiating and stop codons)
Put scantron inside exam before turning in. Grades will be available Wednesday P.M.