Key to Final Review Worksheet
Chem 103, Winter 2006
1. Draw an example of each of the following:
a) an aldopentose
b) a ketotriose
O
H
HO
H
H
OH
CH2 OH
H
OH
O
CH2 OH
CH2 OH
2. Consider the monosaccharide galactose.
a) Draw the Fischer projection for L-galactose.
O
HO
H
H
H
OH
H
OH
HO
H
CH2 OH
b) What is the stereochemical relationship between L-galactose and D-galactose?
They are enantiomers.
c) What is the stereochemical relationship between D-galactose and D-glucose?
They are diastereomers.
d) What must happen to D-galactose before it can enter glycolysis?
D-galactose must be converted to D-glucose (actually to glucose-6-phosphate).
e) Draw the Haworth structure for -L-galactose
H
O OH
CH2 OH
OH
H
H
OH
H
OH
H
3. What is mutorotation?
Mutorotation is the process by which alpha and beta anomers are interconverted, going
through the open chain form between anomers.
4. Suppose that you have two sugar solutions, one is sucrose and the other is maltose.
Unfortunately, you forgot to label them and have now got them mixed up. What
experiments could you do (besides measuring optical rotation) to determine which
solution is which, and how would you tell?
You could perform Tollens’ and/or Benedict’s tests on a small amount of each solution.
Since sucrose is not a reducing sugar, it should test negative (no reaction). Maltose is a
reducing sugar, so should test positive (silver coating on glass for Tollens’ and red
precipitate/disappearance of blue for Benedict’s).
5. How would you synthesize D-glucitol (D-sorbitol)? Write out the reaction, including
structures and reagents.
O
H
CH2 OH
H
H
OH
H
H2
H
OH
Pt
H
OH
HO
OH
HO
H
H
OH
H
OH
CH2 OH
CH2 OH
D-Glucitol (D-Sorbitol)
D-Glucose
6. Draw the structure for the product you would get by reacting D-glucose with
methanol and an acid catalyst.
CH2 OH
H
O
H
OH
H
H
OH
OCH3
H
OH
7. Maltose is a disaccharide obtained from starch.
a) Draw the structure of -maltose.
CH2 OH
CH2 OH
H
O
H
OH
H
H
OH
OH
H
H
O
O
H
OH
H
H
OH
OCH3
H
-1,4 glycosidic bond
b) What type of glycosidic bond does maltose have?
c) Maltose is used for brewing malt beverages (like beer). Explain how maltose is
converted to ethanol. Include all reaction steps.
Yeast contains enzymes that carry out the following processes. First the maltose is
hydrolyzed to glucose. The glucose is then converted to pyruvate by glycolysis. The
pyruvate is decarboxylated to form acetaldehyde, which is then reduced to ethanol
along with the oxidation of NADH to NAD+.
d) Is maltose a reducing sugar? Why or why not?
Yes, maltose is a reducing sugar. One of the glucoses is a hemiacetal and can undergo
mutorotation. Because it can open up to the chain form, the aldehyde can be oxidized.
8. Suppose that you are attempting to hydrolyze lactose.
a) What reagents could you use for the hydrolysis?
H3O+ and heat, or lactase.
b) How could you test the reaction solution to see if the hydrolysis worked?
You could test the reaction with optical rotation to see if it worked.
9. What is the difference between amylose and amylopectin?
Amylose is unbranched and forms a helix, while amylopectin is branched and does not
form a helix.
10. Iodine forms a dark blue complex with amylose, but not with cellulose. Explain
why.
Iodine stacks inside the coils of amylose, forming a strong, dark blue complex.
Cellulose has beta-1,4 glycosidic bonds, giving it a more rigid structure that does not
form coils, so the iodine does not complex strongly with cellulose.
11. What is a lipid?
A lipid is a biomolecule that is soluble in nonpolar solvents.
12. Which types of lipids do not contain fatty acid chains?
Prostaglandins and steroids.
13. Would you expect trans-fatty acids to be liquids or solids at room temperature?
Explain why or why not.
Trans-fatty acids are usually solids at room temperature. The trans double bonds give
the fatty acid chains a fairly linear structure, so that they stack well together, giving
them stronger intermolecular forces than cis-fatty acids. Stronger intermolecular forces
lead to a higher melting point.
14. How does an NSAID, such as ibuprofen, reduce pain and swelling from an injury?
NSAIDS generally reduce pain and swelling by inhibiting prostaglandin synthesis.
They work by inhibiting the enzymes that convert arachidonic acid to prostaglandins.
15. How is a wax related to a fatty acid?
Waxes are esters of saturated fatty acids.
16. What is the main function of triacylglycerides?
Energy storage.
17. Why are fats generally solid at room temperature, while oils are generally liquids at
room temperature?
Fats have a higher content of saturated fatty acids than oils. The saturated fatty acids
are flexible straight chains, and can stack well together, giving them stronger
intermolecular forces (dispersion forces) than unsaturated fatty acids. The cis double
bonds in unsaturated fatty acids give them a kinked structure that doesn’t stack well.
18. Trans fats are formed during traditional methods for the hydrogenation of
unsaturated oils.
Write the reaction for the hydrogenation of cis-oleic acid,
CH3(CH2)7CH=CH(CH2)7CH3, and show how trans-oleic acid could form during the
reaction.
H
H
O
H2/Ni
OH
H
H
Ni
Ni
O
OH
Ni Cataly st
Isomerization
H
OH
Addition of H 2
H
O
O
OH
19. Show the products for the oxidation of oleic acid, CH3(CH2)7CH=CH(CH2)7CH3.
OH
O
O
+
O
HO
OH
20. What is saponification? Show an example of a saponification reaction.
Saponification is the process of making soap and glycerol from hydrolysis of fats or oils
with strong base.
O
H 2C
O
C
O
(CH2)14CH3
H 2C
OH
O
NaOH
HC
O
C
O
(CH2)14CH3
HC
OH
H 2C
O
C
(CH2)14CH3
H 2C
OH
+ 3 Na
O
C
(CH2)14CH3
(Soap)
21. What are the main functions of glycerophospholipids, and how does their structure
make them suited for those roles?
Glycerophospholipids have polar heads and nonpolar tails that make them able to form
the lipid bilayers of cell membranes, and the lipid layer on the surface of lipoproteins.
The polar heads interface with the aqueous environments inside and outside of the cell,
while the nonpolar tails face each other in the lipid bilayers and face nonpolar lipids in
the lipoproteins.
22. Draw a diagram of the general structure of a glycosphingolipid. What are the main
functions of glycosphingolipids?
Glycosphingolipids have saccharides components that hang off of the cell surface and
are involved in cell recognition and immunity and act as receptors for hormones,
viruses and other substances.
23. Draw the steroid nucleus.
C
A
D
B
24. Too much cholesterol is bad. However, cholesterol is essential for our cells.
a) What are the main functions of cholesterol?
Cholesterol has many functions, including being part of cell membranes and nerve
tissue, and being a precursor for bile salts, vitamin D and steroid hormones.
b) How do vegetarians get cholesterol?
Cholesterol can be made in the liver.
25. What are HDL and LDL, and what are their functions?
HDL and LDL are lipoproteins that transport nonpolar lipids, such as cholesterol,
through the bloodstream. HDL carries cholesterol from the tissues to the liver, where is
can be converted to bile salts. LDL carries cholesterol from the liver to the tissues. If
there is too much cholesterol in the tissues, the LDL deposits excess cholesterol on the
arterial walls.
26. Where, and from what, are bile salts synthesized and what are their main functions?
Bile salts are synthesized from cholesterol in the liver, stored in the gall bladder, and
released into the small intestines to help digest fats and oils. They act in a similar
manner to soaps, breaking apart the globs of fat into smaller clumps of molecules that
can be hydrolyzed by enzymes.
27. Where are steroid hormones synthesized and what is their general function?
Steroid hormones are synthesized in various glands.
messengers between different parts of the organism.
They function as chemical
28. What are the roles of each of the following in cell membranes?
a) cholesterol
Makes the membrane stronger and more rigid.
b) glycoproteins
Involved in cell signaling and cell recognition.
c) integral proteins
Act as channels for transport of substances across the membrane.
29. What is the difference between simple and facilitated transport?
In simple transport the substance just crosses the membrane, in the direction of the
chemical gradient. In facilitated transport the substance moves through a channel
(integral protein). Neither process uses ATP energy.
30. Which of the nonpolar amino acids can participate in H-bonding?
Tryptophan
31. The pI for serine is 5.7. Draw the structure of serine at the following pH’s:
a) 5.7
b) 9.0
HO
c) 3.0
HO
HO
O
H 3N
O
OH
H 2N
O
H 3N
O
O
32. Draw the Fischer projection for D-leucine.
CO 2H
H
NH2
33. Suppose that you have a mixture of amino acids from a protein that you are
analyzing. How could you use electrophoresis to determine which amino acids are
present in the mixture?
You could run the mixture with buffers of different pH’s, and make matching control
runs with known amino acids. Then, match the amino acids in the mixture to the
known amino acids.
34. Peptides are resistant to hydrolysis than triacylglycerols. Explain what gives
peptides their special stability. Use drawings to illustrate your answer.
Di-peptides contain amide bonds, while triacylglycerols contain ester bonds. The lonepair of electrons on the amide nitrogen is delocalized through the carbonyl pi system,
while the lone-pairs of electrons on the ester 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
O
Vs.
NH2
O
NH2
35. Draw the structure for Cys-Tyr-Ile
O
H 3N
H
C
C
O
N
H
H
C
C
O
N
H
H
C
O
HS
OH
36. What type of secondary structure predominates in -keratin? What type in keratin?
Alpha-keratin is made up of braided alpha-helices and beta-keratin is made up
primarily of beta-pleated sheets.
37. What is the primary type of cross-linking in secondary structure?
H-bonding
38. Describe the structure of collagen and explain what makes it so strong.
Collagen is made up of polypeptide chains braided into triple helix structures. The
collagen polypeptides are rich in smaller amino acids, like glycine, alanine and proline.
They also contain the modified amino acids hydroxyproline and hydroxylysine, which
are involved in hydrogen bonding between the polypeptides in the triple helices,
making them stronger. The helices also wrap around each other to form fibrils, giving
them additional strength.
39. What is a salt bridge? Show an example.
A salt bridge is an ionic bond formed between oppositely charged side-chains on acidic
and basic amino acids.
O
NH3
O
40. Are enzymes typically globular or fibrous proteins?
Globular
41. How do heavy metal ions denature proteins?
Heavy metal ions form ionic bonds with the sulfur atoms of cysteine atoms, disrupting
disulfide bonds.
42. What is a catalyst?
A catalyst speeds up a reaction, but is not used up in the reaction. A catalyst usually
speeds the reaction up by stabilizing the transition state, and so lowering the activation
energy.
43. What are the two main overall purposes of enzymes in our cells?
Enzymes are needed to speed up cellular reactions (metabolism) that would otherwise
be too slow. Enzymes also provide specificity so that products are only made where
and when they are needed, improving cellular efficiency.
44. Give the substrate and the type of reaction catalyzed for each of the following
enzymes:
a) maltase
maltose, hydrolysis
b) pyruvate carboxylase
pyruvate, carboxylation (adding a carboxyl group)
c) lipase
lipids, hydrolysis
45. Explain the induced-fit model of enzyme action.
The induced-fit model allows for the broader specificity seen in some enzymes. It says
that the active site and the substrate adjust their shapes to fit each other upon binding.
Once the fit is achieved, the substrate is properly lined up for catalysis (its shape may
also closely resemble the transition state for the reaction). After the reaction occurs, the
fit is no longer favorable, and the product leaves.
46. Why does an enzyme lose its activity when the pH not optimum?
Changes in pH that go too far from the optimum pH for an enzyme cause disruption of
salt bridges and hydrogen bonding. The changes in tertiary structure alter the active
site, and can destroy activity.
47. Draw a graph of reaction rate vs. time for an enzyme catalyzed reaction where the
substrate concentration is not held constant, but instead the substrate gets used up
during the experiment.
Reaction
Rate
Time
48.
Explain why increasing the substrate concentration reverses the activity of a
competitive inhibitor. Use a drawing to illustrate your answer.
Because the competitive inhibitor comes on and off the enzyme, and is competing with
the substrate for the active site, increasing the substrate concentration decreases the
amount of time that inhibitor is bound to the enzyme.
49. Explain how zymogens are important in digestion.
Since zymogens are not produced in their active state, they can be stored and then
activated under the proper conditions. Digestive zymogens are only activated when
needed, preventing digestion of the pancreas, stomach and intestines between use.
50. What is an allosteric enzyme and how are they involved in feedback control?
An allosteric enzyme has a binding site other than the active site, called the allosteric
site. No catalysis takes place at the allosteric site, but binding of regulators causes
changes in the active site. Positive regulators alter the active site to be more favorable
for substrate binding and negative regulators alter the active site to be less favorable for
substrate binding. In feedback control, the product of a series of enzymatic reactions
acts as a negative regulator when it binds to an allosteric site on the first enzyme of the
series.
51. What are the main functions of metal ions as cofactors?
Metal ions often undergo redox reactions as part of enzyme catalysis. They also
frequently participate in catalysis by activating the substrate, or stabilizing the
transition state, in the active site.
52. Is the statement “water-soluble vitamins are coenzymes” valid? Explain.
No, only a few water-soluble vitamins act as coenzymes directly, most make up part of
a coenzyme.
53. Which vitamin is used to make each of the following coenzymes?
a) FAD
b) NAD+
c) CoA
B2 (riboflavin)
B3 (niacin)
B5 (pantothenic acid)
54. Vitamin A is a fat-soluble vitamin.
a) What are the three forms of vitamin A?
Retinol, retinal and retinoic acid are the three forms of vitamin A.
b) What are some dietary sources of vitamin A?
Dietary sources include: carrots, broccoli, bell peppers, apricots, peaches and papyas.
c) Do plants actually contain vitamin A? Explain.
Plants do not contain vitamin A, they contain beta-carotenes, which are cleaved in the
liver to produce vitamin A.
d) What are the main functions of vitamin A?
Vitamin A is involved in vision, particularly night vision, and is also involved in the
synthesis of RNA and glycoproteins.
55. What are the three main structural components of nucleic acids?
Nucleic acids consist of a nitrogen base, a pentose sugar and a phosphate group.
56. Is Thymine a purine or a pyrimidine?
57. Write out the full name for GDP.
Pyrimidine
Guanosine 5’-diphosphate
58. Consider the following DNA sequence:
AATCGC
a) Label the 5’ and 3’ ends.5’-AATCGC-3’
b) Write the complementary DNA sequence.
TTAGCG
c) Write the mRNA sequence that would be transcribed from the DNA sequence.
UUAGCG
d) Write the amino acid sequence that would be translated from the mRNA sequence.
Leu-Ala
59. What is a replication fork?
A section of DNA where the strands are unwound, and DNA replication can begin.
60. What is an Okazaki fragment?
Short strands of newly synthesized DNA from the lagging strand that are joined
together to make a single strand.
61. What are the three main types of RNA and what are their basic functions?
Ribosomal RNA is the main component of ribosomes, where proteins are synthesized.
Messenger RNA brings the code from DNA in the nucleus to ribosomes in the
cytoplasm, to be translated into proteins. Transfer RNA carries amino acids to the
ribosomes for synthesis of proteins.
62. Where does processing of mRNA take place? Describe the process. Use drawings
to illustrate your answer.
Messenger RNA is processed in the nucleus before going to the ribosomes in the
cytosol. The original mRNA consists of exons and introns. The introns are cut out, and
the exons are spliced together, so that the final mRNA contains only the parts needed to
make the protein.
63. Describe how the lactose operon works.
The lactose operon, which is present in some prokaryotes, contains a control site for the
genes that code for enzymes that hydrolyze lactose. When lactose is not present in the
cell, a repressor protein binds to the control site and blocks transcription of the genes.
When lactose is present, the lactose acts as an inducer by binding to the repressor so
that it can’t bind to the control site, and transcription is allowed to occur.
64. Draw a schematic of the structure of tRNA, showing the binding sites for the amino
acid and for the mRNA.
Amino acid binds here
mRNA binds here
65. Why is a frame-shift mutation more likely to destroy protein function than a
substitution mutation?
A substitution mutation only changes one base pair. Even if the base is in a functional
part of the DNA, the mutation may or may not alter the amino acid sequence. And,
even if it does alter the amino acid sequence, it may or may not alter the protein
function. In addition, a single base change is usually repairable. However, a frameshift mutation causes the entire sequence, beginning with the mutation, to shift. This
usually causes drastic changes in the amino acid sequence, leading to complete loss of
protein function.
66. What is a genetic disease?
A genetic disease is a disease caused by a defective enzyme that results from a
mutation, or mutations, in the gene coding for that enzyme.
67. What is a plasmid?
A plasmid is a small circular piece of prokaryotic DNA that is capable of replication.
68. What is recombinant DNA?
Recombinant DNA contains a fragment of DNA from another organism.
69. Where do restriction enzymes come from, and what do they do?
Restriction enzymes come from bacteria. They cut DNA at specific sequences.
70. How could DNA fingerprinting be used to determine parenthood?
DNA from both the child and the suspected parent could be analyzed by DNA
fingerprinting. The DNA is cut up by restriction enzymes and analyzed by gel
electrophoresis. Since about half of the child’s DNA comes from each parent, the DNA
passed on from a parent should match in both sets of DNA. The genes won’t
necessarily match exactly, because there is some mixing during reproduction (too
complicated to discuss here), but the matching should be complete enough to determine
parenthood.
71. Describe how a viral infection occurs.
First, a virus attaches to a host cell and injects its DNA (or RNA). The host cell’s
enzymes and amino acids are then used to replicate the viral DNA and to synthesize
viral RNA and proteins. The viruses are then assembled, and when there are enough of
them, the cell bursts, releasing more virus particles that can infect more cells.
72. Nucleoside analogs, like AZT, which are used to treat HIV, have nasty side effects.
Give a possible explanation for why.
Nucleoside analogs treat HIV by being incorporated into the viral DNA, preventing
viral replication. However, they can also be incorporated into cellular DNA, preventing
cellular replication. This can cause bad side effects.
73. At what location does each of the following processes occur?
a) glycolysis
b) reduction of pyruvate
Cytosol
Cytosol
c) oxidative phosphorylation
Inner membrane of mitochondria
74. Where in the cell are ribosomes located?
In the cytosol and on rough endoplasmic reticulum.
75. Draw a diagram of a mitochondrion. Label the matrix, the intermembrane space,
the outer membrane and the inner membrane.
76. Why is ATP considered a high-energy molecule?
ATP is a high-energy molecule because it has three phosphate groups that can be
hydrolyzed. Each hydrolysis releases 7.3 kcal (31 kJ)/mol of energy.
77. The coenzyme NAD+ is involved in many cellular reactions.
a) What are the three main structural components of NAD+?
NAD+ consists of nicotinamide, ribose and adenosine diphosphate.
b) Which of the three components is reduced during conversion to NADH?
The nicotinamide is reduced when NAD+ is converted to NADH.
c) In what type of reactions does NAD+ generally take part?
NAD+ is usually involved in reactions that involve formation of a carbonyl bond.
78. Describe what happens to starch in the mouth, before it is swallowed.
First, chewing physically breaks down the starch into smaller pieces. Then, amylase, an
enzyme in the saliva, breaks down amylose and amylopectin into smaller pieces called
dextrins, maltose and a small amount of glucose.
79. Where in the body are fructose and galactose converted to glucose?
The liver.
80. Write the overall net reaction of glycolysis.
Glucose + 2ADP + 2Pi + 2NAD+
 2Pyruvate + 2ATP + 2NADH + 4H+
81. How is ATP involved in regulation of glycolysis?
High levels of ATP inhibit steps 3 and 10 of glycolysis.
82. What are the three pathways for pyruvate, and under what conditions do they
occur?
Pyruvate can be converted to acetyl CoA by aerobic organisms in the presence of
oxygen. Pyruvate can be converted to lactate by aerobic, and some anaerobic,
organisms in the absence of oxygen. Some anaerobic organisms can convert pyruvate
to ethanol in the absence of oxygen.
83. What is the role of UDP in glycogenesis?
UDP activates glucose, and is released when the glucose attaches to the glycogen chain,
providing the energy for that reaction.
84. Which compounds activate glycogenolysis?
Glucagon and Epiniphrine
85. Write the overall reaction for gluconeogenesis.
2 pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 6H2O
 glucose + 4ADP + 2GDP + 6Pi + 2NAD+
86. What is the Cori cycle, and why is it important? Make a diagram showing the Cori
cycle.
The Cori cycle is the connection between glycolysis, lactate production and glucose
synthesis. During exercise, pyruvate is converted to lactate in muscle tissue, this
process produces NAD+, allowing glycolysis to continue to produce ATP. The lactate is
transported to the liver, where it is converted to pyruvate and then to glucose through
gluconeogenesis. The glucose is returned to the muscles for glycolysis and glycogen
synthesis.
87. Write the overall reaction for the citric acid cycle.
Acetyl CoA + 3NAD+ + FAD + GDP + Pi + 2H2O
 2CO2 + 3NADH + 2H+ + FADH2 + HS-CoA + GTP
88. Why is the citric acid cycle called a cycle?
It’s a cycle because the citrate that is formed in the first step is reformed in the last step
from the last intermediate and a new acetyl CoA.
89. State whether each of the following activates or inhibits the citric acid cycle:
a) ATP
b) ADP
c) NADH
Inhibits
Activates
Inhibits
90. What are the four main types of electron carriers in the electron transport chain?
Flavins, iron-sulfur clusters, coenzyme Q and cytochromes.
91. Draw a diagram of an iron-sulfur cluster in its oxidized state. What happens to it
when it accepts an electron?
The iron ion in the oxidized state is Fe3+. When it accepts an electron it’s oxidized to
form Fe2+.
92. In which complex of the electron transport chain is FADH2 oxidized to FAD?
FADH2 is oxidized to FAD in complex II.
93. In which complex of the electron transport chain is NADH oxidized to NAD+?
NADH is oxidized to NAD+ in complex I.
94. Draw a diagram of ATP synthase, showing the two subunits, F0 an F1. Show where
the protein crosses the intermitochondrial membrane and label the intermembrane
space and the matrix. Show where the protons enter, where they leave and where the
ATP is synthesized.
95. Write the overall net reaction for the complete oxidation of glucose.
C6H12O6 + 6O2 + 36ADP + 36Pi  6CO2 + 6H2O + 36ATP
96. How are regulation of glucose levels and regulation of ATP levels related? Discuss
in terms of the various cycles involved in glucose metabolism.
ATP levels are regulated through control of glucose metabolism. When ATP levels in
the cell are low (and ADP levels are high), glycolysis, glycogenolysis and the citric acid
cycle are activated, so that more ATP is produced. When cellular ATP levels are high,
these processes are inhibited and glucose is stored as glycogen or fat.