# Chemistry A Molecular Approach

## Educators

Problem 1

What is biochemistry? What significant advances in biochemistry have helped diabetics?

Alexander F.

Problem 2

What is a lipid? What roles do lipids play in living organisms?

Kristopher K.

Problem 3

What is a fatty acid? Draw the general structure of a fatty acid.

Alexander F.

Problem 4

What effect do double bonds have within the hydrocarbon chain of a fatty acid?

Kristopher K.

Problem 5

What are triglycerides? Draw a general structure of a triglyceride.

Alexander F.

Problem 6

Explain the difference, both in terms of structure and in terms of properties, between a saturated fat and an unsaturated fat.

Kristopher K.

Problem 7

Describe the basic structure of phospholipids and glycolipids. What functions do these lipids have in living organisms?

Alexander F.

Problem 8

What is a steroid? List some functions of steroids.

Kristopher K.

Problem 9

What are carbohydrates? What role do they play in living organisms?

Alexander F.

Problem 10

How do monosaccharides and disaccharides differ? Aldoses and ketoses?

Kristopher K.

Problem 11

How do simple and complex carbohydrates differ?

Alexander F.

Problem 12

How do cellulose, starch, and glycogen differ? Describe the function of each.

Kristopher K.

Problem 13

What roles do proteins play in living organisms? List specific examples.

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Problem 14

Describe the basic structure of an amino acid. How are amino acids linked together to form proteins?

Kristopher K.

Problem 15

How do the properties of the R groups in amino acids relate to the properties of proteins?

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Problem 16

Why are amino acids chiral?

Kristopher K.

Problem 17

Draw the structure of a neutral amino acid and its dipolar ion.

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Problem 18

Draw the structure of any two amino acids, showing how they link together to form a dipeptide.

Kristopher K.

Problem 19

Why is protein structure important?

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Problem 20

How do fibrous proteins and globular proteins differ?

Kristopher K.

Problem 21

Describe the various levels of protein structure (primary, secondary, tertiary, and quaternary).

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Problem 22

What types of interactions or bonds maintain each of the structures listed in the previous problem?

Kristopher K.

Problem 23

Describe the secondary structures known as $\alpha$ -helix and $\beta$ -pleated sheet.

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Problem 24

What is the function of nucleic acids in living organisms?

Kristopher K.

Problem 25

What is the general structure of a nucleic acid?

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Problem 26

The bases in nucleic acids are complementary. What does this mean?

Kristopher K.

Problem 27

What is a codon? A gene? A chromosome?

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Problem 28

Do most cells contain complete copies of an organism's DNA? Do most cells express all of the genes contained in their DNA?

Kristopher K.

Problem 29

Explain the mechanism by which DNA is replicated.

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Problem 30

Explain the mechanism by which proteins are synthesized from the information contained within DNA.

Kristopher K.

Problem 31

Determine whether or not each molecule is a lipid. If the molecule is a lipid, indicate the kind of lipid. If it is a fatty acid or a triglyceride, classify it as saturated or unsaturated.

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Problem 32

Determine whether or not each molecule is a lipid. If the molecule is a lipid, state the kind of lipid. If it is a fatty acid or a triglyceride, classify it as saturated or unsaturated.

Kristopher K.

Problem 33

Determine whether or not each molecule is a fatty acid. If it is a fatty acid, classify it as saturated, monounsaturated, or polyunsaturated.

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Problem 34

Which fatty acid is most likely to be a solid at room temperature?

Kristopher K.

Problem 35

Draw structures showing the reaction of glycerol with linoleic acid to form the triglyceride trilinolean. Would you expect this triglyceride to be a fat or an oil?

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Problem 36

Draw structures showing the reaction of glycerol with myristic acid to form the triglyceride trimyristin. Would you expect this triglyceride to be a fat or an oil?

Kristopher K.

Problem 37

Determine whether or not each structure is a carbohydrate. If the molecule is a carbohydrate, classify it as a monosaccharide, disaccharide, or trisaccharide.

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Problem 38

Determine whether or not each structure is a carbohydrate. If the molecule is a carbohydrate, classify it as a monosaccharide, disaccharide, or trisaccharide.

Kristopher K.

Problem 39

Classify each saccharide as an aldose or a ketose. Also classify each as a triose, tetrose, pentose, and so on.

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Problem 40

Classify each saccharide as an aldose or a ketose. Also classify each as a triose, tetrose, pentose, and so on.

Kristopher K.

Problem 41

How many chiral carbon atoms are in each of the structures in Problem 39$?$

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Problem 42

How many chiral carbon atoms are in each of the structures in Problem 40$?$

Kristopher K.

Problem 43

Draw structures for the straight-chain and ring forms of glucose.

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Problem 44

Draw structures for the straight-chain and ring forms of fructose.

Kristopher K.

Problem 45

Draw the products that result from the hydrolysis of the carbohydrate pictured on the right.

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Problem 46

Draw the products that result from the hydrolysis of the carbohydrate pictured on the right.

Kristopher K.

Problem 47

Draw the structure of sucrose. Label the glucose and fructose rings in this disaccharide.

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Problem 48

Lactose is a disaccharide of glucose and galactose. Draw the structure of lactose.

Kristopher K.

Problem 49

Draw each amino acid in its dipolar ion form.
$$\text {a. Thr} \quad \text {b. Ala} \quad \text {c. Leu } \quad \text {d. Lys}$$

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Problem 50

Draw each amino acid in its dipolar ion form.
$$\text {a. Val} \quad \text {b. Phe} \quad \text {c. Tyr } \quad \text {d. Cys}$$

Kristopher K.

Problem 51

Draw the structures of the two enantiomers of alanine.

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Problem 52

Draw the structures of the two enantiomers of cysteine.

Kristopher K.

Problem 53

How many different tripeptides can form from serine, glycine, and cysteine? List the amino acid sequence of each one.

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Problem 54

How many dipeptides can form from leucine and serine? List the amino acid sequence for each one.

Kristopher K.

Problem 55

Draw the reaction by which serine and tyrosine form a peptide bond.

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Problem 56

Draw the reaction by which valine and asparagine form a peptide bond.

Kristopher K.

Problem 57

Draw a structure for each tripeptide.
$$\text {a. Gln-Met-Cys} \quad \text {b. Ser-Leu-Cys} \quad \text {c. Cys-Leu-Ser}$$

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Problem 58

Draw a structure for each tripeptide.
$$\text {a. Ser-Ala-Leu-Cys} \quad \text {b. Gln-Met-Cys-Gly} \quad \text {c. Gly-Cys-Met-Gln}$$

Kristopher K.

Problem 59

A phenylalanine amino acid on a protein strand undergoes hydrophobic interactions with another phenylalanine amino acid that is 26 amino acid units away. The resulting fold in the protein is an example of which kind of structure? (primary, secondary, tertiary, or quaternary)

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Problem 60

An amino acid on a protein strand forms a hydrogen bond to another amino acid that is four amino acid units away. The next amino acid on the chain does the same, hydrogen-bonding to an amino acid that is four amino acids away from it. This pattern repeats itself over a significant part of the protein chain. The resulting pattern in the protein is an example of which kind of structure? (primary, secondary, tertiary, or quaternary)

Kristopher K.

Problem 61

The amino acid sequence in one section of a protein is shown here. It represents which kind of structure? (primary, secondary, tertiary, or quaternary)
$$\text {-Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-}$$

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Problem 62

A dimeric protein is composed of two individual chains of amino acids. The way these two chains fit together is an example of which kind of structure? (primary, secondary, tertiary, or quaternary)

Kristopher K.

Problem 63

Determine whether or not each structure is a nucleotide. For each nucleotide, identify the base as $\mathrm{A}, \mathrm{T}, \mathrm{C},$ or $\mathrm{G}$ .

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Problem 64

Determine whether or not each structure is a nucleotide. For each nucleotide, identify the base as $\mathrm{A}, \mathrm{T}, \mathrm{C},$ or $\mathrm{G}$ .

Kristopher K.

Problem 65

Draw the structures of the two purine bases in nucleic acids.

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Problem 66

Draw the structures of the three pyrimidine bases in nucleic acids.

Kristopher K.

Problem 67

Draw the DNA strand that is complementary to the DNA strand shown here.

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Problem 68

Draw the DNA strand that is complementary to the DNA strand shown here.

Kristopher K.

Problem 69

A monomeric protein contain 154 amino acids. How many codons code for these amino acids? How many nucleotides?

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Problem 70

A dimeric protein contains 142 amino acids in one strand and 148 in the other. How many codons code for these amino acids? How many nucleotides?

Kristopher K.

Problem 71

Determine the class of biochemical compound that contains
$\begin{array}{ll}{\text { a. peptide bonds }} & {\text { b. glycosidic linkage }} \\ {\text { c. ester linkage }}\end{array}$

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Problem 72

Name the type of polymer associated with each monomer.
$\begin{array}{ll}{\text { a. nucleotide }} & {\text { b. amino acid }} \\ {\text { c. saccharide }}\end{array}$

Kristopher K.

Problem 73

What is the difference between a codon and a nucleotide? A codon and a gene?

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Problem 74

What is the difference between a fatty acid and a triglyceride? A triglyceride and a phospholipid?

Kristopher K.

Problem 75

The amino acid alanine has the condensed structural formula shown here:
$$\mathrm{NH}_{2} \mathrm{CH}\left(\mathrm{CH}_{3}\right) \mathrm{COOH}$$
Determine the VSEPR geometry about each internal atom and make a three-dimensional sketch of the molecule.

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Problem 76

The amino acid serine has the condensed structural formula shown here:
$$\mathrm{NH}_{2} \mathrm{CH}\left(\mathrm{CH}_{2} \mathrm{OH}\right) \mathrm{COOH}$$
Determine the VSEPR geometry about each internal atom and make a three-dimensional sketch of the molecule.

Kristopher K.

Problem 77

Which amino acids in Table 22.3 are most likely to be involved in hydrophobic interactions?

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Problem 78

Sickle-cell anemia is caused by a genetic defect that substitutes valine for glutamic acid at one position in two of the four chains of the hemoglobin protein. The result is a decrease in the water solubility of hemoglobin. Examine the structures of valine and glutamic acid and explain why this occurs.

Kristopher K.

Problem 79

Determining the amino acid sequence in a protein usually involves treating the protein with various reagents that break up the protein into smaller fragments that can be individually sequenced. Treating a particular $11-$ a-can be individually with one reagent produced the fragments:
$$\text {Ala-Leu-Phe-Gly-Asn-Lys Trp-Glu-Cys Gly-Arg}$$
Treating the same polypeptide with a different reagent produced the fragments:
$$\text {Glu-Cys Gly-Asn-lys-Trp Gly-Arg-Ala-Leu-Phe}$$
What is the amino acid sequence of the polypeptide?

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Problem 80

Treating a particular polypeptide with one reagent (as described in the previous problem) produced the fragments:
$$\text {Gly-Glu-Ser-Lys Trp-Arg Leu.Thr-Ala-Trp}$$
Treating the same polypeptide with a different reagent produced the fragments:
$$\text {Gly-Glu Thr-Ala-Trp Ser-Lys-Trp-Arg-Leu}$$
What is the amino acid sequence of the polypeptide?

Kristopher K.

Problem 81

Naturally occurring D-glucose is one of a pair of enantiomers. Its mirror image is L-glucose. Draw the two cyclic six-membered isomers of L-glucose that differ in the configuration around Cl and indicate which is $\alpha$ and which is $\beta$ .

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Problem 82

Calculate the mass percent of phosphorus in a strand of DNA that consists of equal amounts of each of the four N-bases.

Kristopher K.

Problem 83

The double helical structure of DNA disrupts on heating but reforms on cooling. Use thermodynamic reasoning to account for these observations.

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Problem 84

From the structural formula of cholesterol shown on page $1034,$ determine (a) the composition, and (b) the number of chiral centers.

Kristopher K.

Problem 85

One way to fight viral infections is to prevent a virus from replicating its DNA. Without DNA replication, the virus cannot multiply. Some viral drug therapies cause the introduction of fake nucleotides into cells. When the virus uses one of these fake nucleotides in an attempt to replicate its DNA, the fake nucleotide doesn't work and viral DNA replication is halted. For example, azidothymidine (AZT), a drug used to fight the human immunodeficiency virus (HIV) that causes AIDS, results in the introduction of the following fake thymine-containing nucleotide into cells. Examine the structures of the real nucleotide and the AZT fake nucleotide. Propose a mechanism for how this fake nucleotide might halt DNA replication.

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Problem 86

Draw each molecule and identify the chiral centers within them.
a. ribose
b. galactose
c. 5 -deoxyribose (Hint: The 5 indicates that the oxygen is removed from the 5 th carbon.)

Kristopher K.

Problem 87

Glucose transport across the red blood cell membranes (erythrocyte membrane) is a well-studied system. One laboratory project obtained the data shown here for glucose transport. The kinetics of glucose transport through the membrane follows the Michaelis-Menten equation:
$$V_{0}=\frac{V_{\max }[\text { glucose }]}{K_{t}+[\text { glucose }]}$$
$$V_{0}= \text {rate of glucose entry}$$
\begin{aligned} V_{\max }=& \text { maximum rate (the point at which addition of } \\ & \text { glucose has no effect on the rate) } \end{aligned}
$$K_{t}= \text {transport constant}$$
The Michaelis-Menten equation can be rearranged so that a plot 1$/ V_{0}$ versus 1$/[$ glucose] produces a straight line. Rearrange the equation and plot the data in order to determine $K_{t}$ and $V_{\text { max }}$ for glucose transport across the erythrocyte membrane.

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Problem 88

Eukaryotic DNA is equipped with special ends called telomers. Telomers are made up of hexanucleotide sequences that repeat at the ends of the DNA. For example, human DNA features repeating AGGGTT sequences. Functionally, telomers protect the ends of chromosomes from being treated as a broken piece of DNA in need of repair. Interestingly, telomers are cut off each time the DNA is replicated, indicating a possible cellular clock that allows only a certain number of cellular replications. Telomerase is the enzyme that catalyzes the synthesis of telomers. Telomerase is present in limited quantities within certain cells such as fetal tissue, adult male germ cells, and stem cells. It is also found in over 85$\%$ of tumor cells. Researchers speculate that the telomerase activity may be linked to cancer. Propose an explanation for why telomerase activity could be associated with cancer and speculate on ways in which cancer treatments in the future may capitalize on research on this enzyme.

Kristopher K.

Problem 89

Write the major equilibrium that is established in a solution of glycine at $\mathrm{pH}=2$ and at $\mathrm{pH}=10 .$ The $\mathrm{pK}_{\mathrm{a}}$ of the COOH group is 2.3 and the $\mathrm{pK}_{\mathrm{a}}$ of the $\mathrm{NH}_{3}^{+}$ group is $9.6 .$ Determine the relative concentrations of each member of the relevant conjugate acid-base pair at $\mathrm{pH}=2$ and $\mathrm{pH}=10 .$ Calculate the pH at which glycine is neutral.

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Problem 90

How many different tetrapeptides can form from four different amino acids?

Kristopher K.

Problem 91

Could the genetic code have been based on just three bases and three-base codons? Explain why or why not. (Assume that the code must accommodate 20 different amino acids.)

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Problem 92

The genetic code is random, which means that a particular codon could have coded for a different amino acid. The genetic code is also nearly universal, meaning that it is the same code in nearly all organisms (and in the few where it differs, it does so only slightly. If scientists ever find life on another planet, they will be curious to know its genetic code. What would a completely different genetic code indicate about the origin of the life forms? What would a genetic code identical to terrestrial life indicate?

Kristopher K.

Problem 93

Compare and contrast cornstarch with cotton balls, which are made of almost pure cellulose. Include at least three ways in which they are similar and three ways in which they are different. Mention aspects you have observed in daily life and aspects on the molecular scale.

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Problem 94

With group members acting as atoms, molecules, or molecular fragments, act out the formation of a peptide bond.

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Problem 95

Describe how a common object or toy (e.g., a train, building blocks, or beads on a string) could represent a protein. Describe how amino acids and peptide bonds are represented in your analogy. Also describe the representation of primary, secondary, tertiary, and quaternary structure in your analogy.

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Problem 96

Use the tabulated key to decipher the mRNA encoded message. Group members may split up the message and decode separate parts, but each part must be decoded by at least two group members (to prevent errors). Describe how the process your group uses to decode the message is significant for biochemistry.

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Problem 97

Working individually, draw an accurate structure for one of the following (don't tell other group members which one you choose): a monosaccharide, a disaccharide, a polysaccharide, a fatty acid, a triglyceride, a steroid, an amino acid, or a dipeptide. After each group member has completed drawing a structure, take turns showing your structure to the group. How many group members can correctly identify the structure you drew? How many of your group members' structures can you correctly identify?

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Problem 98

Lactose is a disaccharide sugar present in milk. Lactose is composed of two monosaccharides, galactose and glucose, that are joined together by a $\beta$ -glycosidic bond. The $\beta$ -glycosidic bond forms between the hydroxyl group on $C-1$ of galactose and C-4 of glucose. When lactose is digested, the glycosidic bond between galactose and glucose is hydrolyzed. The enzyme responsible for hydrolyzing lactose is lactase, which is found in the small intestine. Millions of people lack sufficient levels of lactase, and as a result, they experience lactose intolerance. If lactose is not hydrolyzed, it remains in the intestines. Bacteria in the gut ferment the lactose, causing many unpleasant symptoms such as indigestion, cramping, and gas. Fortunately, commercial preparations can enable lactoseintolerant individuals to consume and digest milk products without discomfort. Use the information provided to answer the following questions: a. Draw the structure of lactose. (The structures of galactose and glucose are shown on page 1037 with their carbon numbering scheme.) b. Lactase enzyme activity, like most enzymes, is sensitive to pH. Figure a $\Delta$ illustrates how lactase activity is affected by the pH of a solution. Based on the data in Figure a, what can you conclude about the $\mathrm{pH}$ of the small intestine? c. A glutamic acid in the active site of lactase is suspected to be involved in the catalytic mechanism. Draw the structure of the glutamicacid side chain in the ionization state that likely exists when lactase is most catalytically active.

Kristopher K.