Key to Final Review Worksheet
Chem 103, Winter 2006
1. Draw an example of each of the following:
a) an aldopentoseb) a ketotriose
2. Consider the monosaccharide galactose.
a) Draw the Fischer projection for L-galactose.
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
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.
6. Draw the structure for the product you would get by reacting D-glucose with methanol and an acid catalyst.
7. Maltose is a disaccharide obtained from starch.
a) Draw the structure of -maltose.
b) What type of glycosidic bond does maltose have?-1,4 glycosidic bond
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.
19. Show the products for the oxidation of oleic acid, CH3(CH2)7CH=CH(CH2)7CH3.
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.
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.
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. They function as chemical messengers between different parts of the organism.
28. What are the roles of each of the following in cell membranes?
a) cholesterolMakes the membrane stronger and more rigid.
b) glycoproteinsInvolved 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) 5.7b) 9.0c) 3.0
32. Draw the Fischer projection for D-leucine.
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 lone-pair 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.
35. Draw the structure for Cys-Tyr-Ile
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.
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) maltasemaltose, hydrolysis
b) pyruvate carboxylasepyruvate, carboxylation (adding a carboxyl group)
c) lipaselipids, 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.
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) FADb) 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?Pyrimidine
57. Write out the full name for GDP.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.
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 frame-shift 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.