Download 103 Rev Ex2 key Win06

Key to Review Worksheet for Exam 2
Chem 103, Winter 2006
1. Draw the Fischer projection and the wedge and dash structure for the zwitterions
form of L-Cysteine.
CO2
CO2
H 3N
H
H 3N
CH2 SH
CH2 SH
H
2. Draw the structure of lysine at the following pH’s:
a) pH = 7
H 3N
NH3
H
C
b) pH = 9.7
CO2
H 2N
NH3
H
C
CO2
c) pH = 14
H 2N
H
C
CO2
NH2
3. Why do amino acids typically have very high melting points?
Amino acids typically have high melting points because they exist as zwitterions, which
act like salts. They have very strong intermolecular forces because of their dipolar
nature.
4. What is electrophoresis and how could it be used to separate a mixture of alanine
and aspartic acid?
Electrophoresis is a technique used to separate charged species using an electric field.
To separate alanine and aspartic acid you could use a buffer with a pH of 6. At this pH,
the alanine is neutral and will not move, while the aspartic acid is negatively charged
and will move towards the positive terminal (anode). Or, you could use a buffer with a
pH between 2 and 6. In this pH range, the alanine is positively charged and will move
towards the negative electrode (cathode), while the aspartic acid will be neutral and
will not move.
5. Draw the structure of Ser-Phe-Gly. Label the C-terminus and the N-terminus.
O
H 3N
N-term.
H
C
CH2
C
O
N
H
H
C
C
O
N
H
C
H2
C
O
C-term.
CH2
OH
6. Di-peptides are more stable to acid hydrolysis than disaccharides. What makes the
peptide bond so particularly stable and strong? Use drawings to illustrate your answer.
Di-peptides contain amide bonds, while disaccharides contain ether bonds (they are
acetals). The lone-pair of electrons on the amide nitrogen is delocalized through the
carbonyl pi system, while the lone-pairs of electrons on the ether oxygen are localized
on that oxygen. This is because nitrogen is less electronegative than oxygen, and so can
better stabilize a positive charge. More electron delocalization = more stable.
O
O
NH2
NH2
7. What do each of the following structural levels in proteins represent?
a) primary
The primary structure represents the amino acid sequence of the protein.
b) quaternary
The quaternary structure represents the joining of more than one polypeptide subunit
to form a functional protein.
8. How is a polypeptide held together in an -helix?
An -helix is held together by hydrogen bonding between the backbone amide
hydrogen in one loop and the backbone carbonyl oxygen on an adjacent loop.
9. What amino acids are most prevalent in -pleated sheets?
Amino acids with small side-chains, like glycine, alanine and serine are most prevalent
in -pleated sheets.
10. What type of cross-linking mainly holds the helices together in -keratins?
The helices in the fibrils of -keratins are mainly held together by disulfide bonds
between cysteines, which are abundant in these fibrous proteins.
11. What are salt-bridges?
A salt-bridge is an ionic bond between ionized side-chains of acidic and basic amino
acids. Salt-bridges are involved in cross-linking in tertiary and quaternary structure.
12. How does isopropyl alcohol (rubbing alcohol) act as a disinfectant?
The alcohol forms hydrogen bonds with the amino acids of proteins, disrupting their
secondary, tertiary and quaternary structures. Isopropyl alcohol disinfects by passing
through the cell walls of bacteria, where it denatures their proteins.
13. How does a catalyst speed up a chemical reaction?
A catalyst speeds up a chemical reaction by providing an alternate pathway for the
reaction that has a lower activation energy than the uncatalyzed reaction.
14. Assign a name for an enzyme that would catalyze each of the following reactions:
a) oxidizes serine
b) hydrolyzes lactose
Serine oxidase
Lactase
15. How does the induced-fit model explain how hexokinase can recognize both
glucose and fructose?
According to the induced-fit model, as the substrate binds the enzyme, they each adjust
their structure to better fit each other. The substrate takes on a conformation that is
similar to the transition state. So, the enzyme may recognize more than one substrate if
the transition states for the substrates are similar.
16. What are isoenzymes, and how are they used to diagnose specific tissue damage?
Isoenzymes are different forms of an enzyme that catalyze the same reaction, but in
different parts of the organism. They are quaternary proteins with different
combinations of subunits. Levels of isoenzymes from specific tissues can be measured
in the blood to determine if that tissue has been damaged. (When the cells die, their
contents, including enzymes, are released.)
17. If an enzyme has a maximum activity at 40C, would the activity be most reduced
at 30C or at 50C? Explain.
At lower temperatures, reaction rates are slowed because there is not enough energy
available to surpass the activation energy. At higher temperatures, the enzyme is
denatured and completely loses activity. Thus, activity falls off more quickly above the
ideal temperature than below it. The activity would be more reduced at 50C.
18. Draw a plot of reaction rate versus substrate concentration for a typical enzyme
catalyzed reaction. Explain the shape of the curve of your plot.
Reaction
Rate
Substrate Concentration
The rate of reaction increases with increasing substrate concentration until all the
enzymes are saturated, then the rate becomes constant.
19. Why does increasing the substrate concentration reverse the inhibition by a
competitive inhibitor?
A competitive inhibitor works by binding to the active site of the enzyme, so that the
substrate can’t bind. However, the inhibitor comes on and off the enzyme, and when
it’s off, the substrate can bind. So, if the substrate concentration is high relative to the
inhibitor concentration, then substrate can out-compete the inhibitor for binding.
20. What is an irreversible inhibitor, and why are they so toxic?
An irreversible inhibitor is one that doesn’t come off the enzyme once it binds. It
usually forms a covalent bond with an amino acid side-chain in the active site. They are
so toxic because they completely destroy enzyme function, making it impossible to
compensate by an increase in substrate concentration.
21. Antibiotics are irreversible inhibitors. Why are they so toxic to bacteria and not to
us?
Antibiotics are toxic to bacteria and not to us because they are specific inhibitors for
bacterial enzymes, and are not recognized by our own enzymes.
22. Make a drawing to show how a noncompetitive inhibitor works.
23. What are zymogens, and how are they useful in digestion?
Zymogens are enzymes that are not produced in their active form. They are activated
by removal of small peptide sections. They are useful in digestion because they can be
stored in an inactive form, so they don’t injure surrounding tissue, and then be released
and activated rapidly when needed.
24. How does feedback control work? Make a drawing to illustrate your answer.
Feedback control is a mechanism by which the production of a product is regulated by
its local concentration. The product is a noncompetitive inhibitor for the first enzyme in
a series of enzymes for a reaction. So, when lots of product is around, its production is
reduced.
25. Is a coenzyme the same thing as a cofactor? Explain.
A coenzyme is a type of cofactor. A cofactor is a small molecule or metal ion that is
required for an enzyme to be active. A coenzyme is a small organic molecule cofactor,
such as a vitamin.
26. What are two common functions of metal ions as cofactors?
Metal ions often are involved in electron transfer (redox) reactions in the active site.
They also can activate the substrate by interacting with electron-rich atoms on the
amino acid side-chains. They stabilize the transition state, and so lower the activation
energy for the catalyzed reaction.
27. What is a vitamin?
A vitamin is an organic molecule that is essential, but cannot be biosynthesized, so must
be consumed in the diet. Most water-soluble vitamins are used to make coenzymes.
28. Which vitamin is not present in plants?
Vitamin B12 is not present in plants.
29. Which vitamin is involved in cholesterol synthesis?
Pantothenic acid (vitamin B5) is involved in cholesterol synthesis.
30. Why does a deficiency of vitamin C lead to weakened connective tissue?
Vitamin C (ascorbic acid) is essential for the synthesis of hydroxyproline and
hydroxylysine, which are used in collagen synthesis. Without the hydroxyproline and
hydroxylysine, the collagen has reduced hydrogen bonding between the polypeptides
in the triple helices, so the helices can unravel. Collagen is the main component of
connective tissue.
31. Is beta-carotene the same thing as vitamin A? Explain.
One beta-carotene molecule can be cleaved by oxidation of the central double bond to
form two molecules of vitamin A. Thus, beta-carotene is not vitamin A, but is an
excellent source of vitamin A.
32. Why is vitamin D not technically a vitamin?
Vitamin D is not technically a vitamin because we can biosynthesize it from 7dehydrocholesterol in the presence of direct sunlight.
33. Why can a deficiency of vitamin K be dangerous going into surgery?
A deficiency of vitamin K can be dangerous going into surgery because vitamin K is
required for synthesis of the zymogens used for blood clotting. This reduced clotting
ability could produce excessive bleeding during surgery.