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Chapter 5
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Biol 1002 - Spring 2013

Chapter 5

Resources

Chapter 5 Due: 9:00am on Monday, February 18, 2013 Note: You will receive no credit for late submissions. To learn more, read your instructor's Grading Policy

Chemistry Review - Organic Molecules: Polymers

Review the Polymers tutorial. Then answer the questions.

Part A
Which statement is true of polymers? ANSWER: They are always made of monomers. Their synthesis generally consumes water. They are always made by condensation reactions. They are often made by a hydrolysis process. None of the above.

Correct
Correct! A polymer is a chain of monomers.

Part B
The organic molecule called DNA is an example of .... ANSWER: a polymer made of amino acids. a monomer. a protein. a polymer made of nucleotides. a polymer made of nucleotes.

Correct
Good choice! DNA is a nucleic acid, a polymer made of nucleotide monomers.

Chemistry Review - Carbohydrates: Disaccharides

Review the Disaccharides tutorial. Then answer the questions.

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Part A
Which statement is true of sucrose? ANSWER: (a) It's a disaccharide. (b) It contains glucose. (c) It's table sugar. Both (a) and (c). (a), (b), and (c).

Correct
Good work! We use sucrose as our table sugar because plants make plenty of it. They use it as their main circulating fuel, and sugar beets and sugar cane store a lot of it. It's a disaccharide made of glucose and fructose.

Part B
Which statement is true of the molecule shown here?

ANSWER: It differs from sucrose in that an O atom links the sugars. Inability to digest it causes some adults to be unable to tolerate milk. It's a polysaccharide. It's made by breaking down starch, during beer production. It's called maltose.

Correct
Right! It's lactose, or milk sugar. Nearly all children can digest it, but many adults lose the enzyme needed to separate the sugars.

Chemistry Review - Carbohydrates: Functions of Carbohydrates

Review the Functions of Carbohydrates tutorial. Then answer the question.

Part A
Polymers that contain sugars ...

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ANSWER: (a) may store hereditary information. (b) may store energy. (c) may protect cells. Both (b) and (c). (a), (b), and (c).

Chapter 5

Correct
Good choice! Polymers that contain sugars do all the named functions and more. For example, they also lubricate the path of roots through soil and they glue plant cells together.

Chemistry Review - Carbohydrates: Monosaccharides

Review the Monosaccharides tutorial. Then answer the questions.

Part A
Unmodified sugars (those with the formula C n H2 n O n ) can have ... ANSWER: (a) H covalently bound to the C of a C=O group. (b) a C atom that is covalently bound to three H atoms. (c) the formula C3H6O3. Both (a) and (c). Both (b) and (c).

Correct
The best choice! Glucose is one of many sugars that have H bound to C=O; they're called aldoses. The simplest sugar has the formula C3H6O3.

Part B
A molecule has the formula C n H2 n O n . What else does it need to be an unmodified monosaccharide? ANSWER: (a) Nothing. (b) A carboxyl group. (c) O bound to every C. (d) At least 5 carbon atoms. Both (b) and (c).

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Correct
Great! If a monosaccharide has C without O attached, its been modified.

Part C
What is the LEAST that two molecules can differ, and still be called different kinds of sugars? ANSWER: One is a ring, the other is linear. The orientation of an OH group differs. The location of the carbonyl group differs. The number of C atoms differs. None of the above.

Correct
Right! In the open-chain form, two sugars may differ in the orientation (right or left) of just one OH group.

Part D
The alpha and beta forms of glucose, found in starch and cellulose, differ in ... ANSWER: how one of the -OH groups is oriented. whether the molecule is a ring or an open chain. whether the first C atom is bound to one or two O atoms. whether the ring contains five or six C atoms. None of the above.

Correct
Correct! One particular -OH group points to one side of the ring in alpha glucose; the other side in beta glucose.

Part E
What happens when glucose forms a ring? ANSWER: (a) The molecule loses its carbonyl group. (b) The molecule loses one O atom. (c) The sixth C atom binds to the first C atom. Both (b) and (c). Both (a) and (c).

Correct
Yes! The C=O group becomes -O-C-OH.

Part F
Which number indicates the sugar that is the principal circulating fuel molecule in the human body?

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ANSWER: 5 1 4 2 3

Correct
Good! This is glucose, often called blood sugar. It has many other functions too.

Part G
This molecule is one member of a large family of related molecules. Members of this family can be found in ...

ANSWER: (a) ATP. (b) DNA. (c) starch. Both (a) and (c). Phos(a), (b), and (c). phate group

Correct
Correct! Sugars provide both structure and energy, and are important in the molecules of heredity.

Part H
A sugar can have ... ANSWER: (a) H covalently bound to the C of a C=O group. (b) a C atom that is covalently bound to three H atoms. (c) the formula C5H8O5. Both (a) and (c). Both (b) and (c).

Correct
True. This occurs in linear aldoses such as glucose.

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Chemistry Review - Proteins: Functions of Proteins

Review the Functions of Proteins tutorial. Then answer the question.

Part A
Which biological activity does NOT directly involve proteins? ANSWER: Defending cells against viruses. Breaking food polymers into smaller molecules. Changing the shape of a cell. Sensing light. None of the above; proteins are involved in all of them.

Correct
Right! Proteins have all the listed functions and many more.

Chemistry Review - Proteins: Levels of Structure

Review the Levels of Structure tutorial. Then answer the questions.

Part A
The protein shown here has ...

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ANSWER: tertiary structure. secondary structure. primary structure. All of the above. All of the above, plus quaternary structure.

Correct
Correct! All proteins have primary structure; the compact overall folding is tertiary, and the corkscrews and parallel strands are secondary.

Part B
This ribbon diagram represents a protein in water. Even without showing the side chains, it's clear that the protein's quaternary structure ...

ANSWER: is stabilized by forces between backbone groups. is stabilized by hydrogen bonds. consists of helices. is weaker than that of entirely helical proteins. None of the above. There's no quaternary structure.

Correct
Right! Quaternary structure requires at least two polypeptide chains. There's only one chain here.

Chemistry Review - Proteins: Models of Proteins

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Review the Models of Proteins tutorial. Then answer the question.

Chapter 5

Part A
A major limitation of the ribbon model of a protein is: ANSWER: (a) It's hard to see how the backbone folds. (b) It can't show the orientation of key side chains. (c) It gives a false sense of open space in the protein. Both (a) and (c). (a), (b), and (c).

Correct
Good choice! Only the space filling model gives a true sense of how tightly packed the space inside the folded protein really is.

Chemistry Review - Proteins: Primary Structure

Review the Primary Structure tutorial. Then answer the questions.

Part A
The human myoglobin protein contains 153 amino acids. If you take one guess at the amino acid sequence, what is your chance of being right? ANSWER: One chance in 15320. One chance in 20x153. One chance in 20153. One chance in 18153. One chance in 153.

Correct
Yes! That number is gigantic. For comparison, there are only about 1081 electrons in the entire universe. With all those possibilities, organisms have only built a tiny fraction of the possible proteins in the entire history of life.

Part B
A biochemist modified a protein so the amino acid lysine occurred where the amino acid aspartic acid previously occurred. This change could ... ANSWER:

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(a) alter the protein's secondary structure without affecting the primary structure. (b) alter the protein's tertiary structure. (c) affect the protein's backbone. Both (b) and (c). (a), (b), and (c).

Correct
Good thinking! A change in primary structure can alter the forces that determine tertiary structure.

Part C
Identify the empirical formula of a free amino acid whose side chain is just H. ANSWER: CH6O2N C2H5O2N C2H4O2N C2H5ON None of the above.

Correct
Right! Did you draw the structure to check it out? If you didn't, give it a try.

Part D
An amino acid residue in a protein differs from a free amino acid in having ... ANSWER: (a) one less H. (b) one less OH. (c) one less H and one less OH. Either (a) or (b). Could be any of the above.

Correct
Good work! A residue at one end of a protein may lack either H or OH, while a residue in the middle of a protein lacks both.

Part E
Amino acids are called "acids" because they ... ANSWER: contain amino groups in the backbone part. contain carboxyl groups in the side chain part. contain amino groups in the side chain part. act as acids when they are bound to proteins. contain carboxyl groups in the backbone part.

Correct
Right! Carboxyl groups act as acids, releasing H+ to water.

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Part F
In a protein, peptide bonds connect ... ANSWER: C-R to N-H. C=O to N-H. N-H to C-H. C=O to C-R. All the above.

Correct
Right! It's the link between two amino acid residues.

Part G
Which statement is true of the side chains that occur in proteins? ANSWER: (a) Some of them contain only C and H. (b) Some of them contain carboxyl groups. (c) None of them join the backbone at more than one point. Both (a) and (b). All the above.

Correct
Right! Side chains with just C and H are nonpolar, while those with carboxyl are acidic. Proline's side chain joins the backbone at two points.

Part H
A certain amino acid side chain ionizes at low pH but not at very high pH. What else is true of this side chain? ANSWER: It is one of 7 kinds of amino acids that share this property. It contains an amino group. It donates H+ to water at low pH. It is acidic. It contains a carboxyl group.

Correct
Excellent! All the basic side chains contain N, which tends to take H+ from water-especially when H+ abounds, at low pH.

Part I
In this diagram a biological polymer is being broken down; the fuzzy yellow lines represent a chemical reaction that is removing a subunit. Which statement is true?

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ANSWER: (a) The reaction is removing a nucleotide from a DNA molecule. (b) R represents an atom that could belong to one of 20 chemical elements. (c) The arrow is pointing at a peptide bond. (d) The reaction is a decomposition. Both (b) and (d).

Correct
Right! It's the bond that links two amino acids in a protein.

Chemistry Review - Proteins: Secondary Structure

Review the Secondary Structure tutorial. Then answer the questions.

Part A
The helical foldings of proteins are stabilized mainly by bonds between ... ANSWER: water molecules. CO and NH. side chains. ionic groups. S and S.

Correct
Right! Hydrogen bonds between these groups keep the helix coiled.

Part B
Which of the following is true of pleated sheet foldings within a polypeptide? ANSWER:

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The side chains are parallel to the plane of the sheet. They depend on regular occurrence of CO and NH. Its loops are held in place mainly by disulfide bridges. They are part of the polypeptide's quaternary structure. All the above.

Chapter 5

Correct
Yes! Occurring at regular intervals along the backbone, these groups stabilize the sheet by forming many hydrogen bonds between neighboring segments of the polypeptide.

Part C
What will probably be the effect on a protein if you replace the amino acid proline with the amino acid glycine (side chain -H) at several points? ANSWER: There will be less rotation around backbone bonds than before. The altered protein will have shorter helices than before. The altered protein will have longer helices than before. The altered protein will have fewer hydrogen bonds than before. The primary structure of the altered protein will be shorter than before.

Correct
Great! Helical segments come to an end when they meet a proline residue, because proline grips the backbone in two places. Remove proline, and the helix can continue.

Part D
The helical foldings in proteins ... ANSWER: are kept folded by hydrogen bonds. are kept folded by base-pairing. are part of the protein's primary structure. are kept folded by forces between side chains on adjacent turns of the helix. None of the above.

Correct
Yes! The hydrogen bonds form between C=O and N-H groups of the backbone.

Activity: Making and Breaking Polymers

Click here to complete this activity.

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Then answer the questions.

Chapter 5

Part A
What name is given to the process seen in this animation? To view the animation, click here. Then click on the image to start the animation. ANSWER: dehydration synthesis catabolism hydrolysis water formation monomerization

Correct
The linking of the monomers involves the removal of water.

Levels of Structure in Proteins

Protein structure is conceptually divided into four levels, from most basic to higher order: Primary structure describes the order of amino acids in the peptide chain. Secondary structure describes the basic three-dimensional structures, -helices and -sheets. Tertiary structure describes how the secondary structures come together to form an individual globular protein. Quaternary structure results from individual proteins coming together to form multi-subunit protein complexes.

Part A
Complete the following vocabulary exercise relating to the level of structure in proteins. Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.

Hint 1. Select the level of structure described in the folding of chains

At what level of protein structure do -sheets of amino acids and -helices, located at a distance from each other along the length of a

polypeptide chain, come together to form a globular protein? ANSWER: primary structure secondary structure tertiary structure quaternary structure

Hint 2. Select the level of structure described in the sequence of amino acids
What level of protein structure describes an amino acid sequence such as Ala-Gly-Ser-Val-Glu-Glu-Glu-Ala-His...? ANSWER: primary structure secondary structure tertiary structure quaternary structure

Hint 3. Select the level of structure described in the coming together of protein subunits
At what level of protein structure do the ANSWER: and protein subunits come together to catalyze the hydrolysis reaction?

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primary structure secondary structure tertiary structure quaternary structure

Chapter 5

Hint 4. Select the correct level of structure described by local folding

At what level of protein structure do the chains of amino acids fold into an ANSWER: primary structure secondary structure tertiary structure quaternary structure -helical structure?

ANSWER:

Correct

Part B
Sort the images according to the level of structure in the proteins shown. Sort the items into the appropriate bin.

Hint 1. How to approach the problem

Each image shows a certain level of protein structure. In general, higher levels of structure involve interactions between more atoms than lower levels. If you look at the relative complexity of the structure with this in mind, you should be able to sort the images correctly. ANSWER:

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Correct
The tertiary and quaternary structures of proteinshow they fold into their overall three-dimensional shapes, and how different protein subunits come together to interactboth ultimately depend on the primary structure, the sequence of amino acids in the proteins. A different sequence of amino acids will lead to different secondary structures and a different shape of the overall protein.

Activity: Structure of RNA and DNA

Click here to view this animation. Then answer the questions.

Part A
Which structure is not a component of a nucleotide?

Hint 1.
Review the structure of a nucleotide. ANSWER:

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Phosphate group Pentose Sulfhydryl Oxygen group Nitrogen-containing base

Chapter 5

Correct
A nucleotide does not contain an sulfhydryloxygen group.

Part B
Which of the following statements about nucleotide structure is false?

Hint 1.
How are the components of a nucleotide bonded together? ANSWER: The nitrogenous base is bonded to the sugar. The sugar is bonded to the phosphate group. The phosphate group is bonded to the nitrogenous base. The sugar can be either ribose or deoxyribose.

Correct
The phosphate group is bonded to the sugar, not to the nitrogenous base.

Part C
True or false? Guanine and uracil are examples of nitrogenous bases.

Hint 1.
What are nitrogenous bases? ANSWER: True False

Correct
Guanine and uracil are indeed examples of nitrogenous bases; adenine, thymine, and cytosine are the others.

Part D
Which linkage forms the backbone of a nucleic acid?

Hint 1.
Remember that nucleotides are linked together by phosphodiester bonds. ANSWER:

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A base-phosphate linkage A sugar-base-phosphate linkage A sugar-phosphate linkage A sugar-base linkage

Chapter 5

Correct
Nucleic acids have a sugar-phosphate backbone.

Part E
Which of the following statements about DNA structure is true?

Hint 1.
Think about how nucleic acids are formed. ANSWER: The nucleic acid strands in a DNA molecule are oriented antiparallel to each other. The arrangement of the sugar-phosphate groups determines the genetic code. Phosphodiester bonds form between the phosphate group of one nucleotide and the 5 carbon of the adjacent nucleotide. DNA is always synthesized in the 3 to 5 direction.

Correct
The 5 end of one strand in a DNA molecule is oriented opposite the 3 end of the other strand, making the strands antiparallel.

Part F
What is the complementary DNA sequence to 5 ATGCATGTCA 3?

Hint 1.
Remember to write the complementary base sequence in the correct orientation. ANSWER: 5 TGACATGCAT 3 5 ATGCATGTCA 3 5 ACTGTACGTA 3 5 TACGTACAGT 3

Correct
This sequence is complementary and in the correct orientation.

Activity: Nucleic Acid Structure

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Chapter 5

Click here to complete this activity. Then answer the questions.

Part A
If a strand of DNA has the nitrogen base sequence 5'-ATTTGC-3', what will be the sequence of the matching strand? ANSWER: 3'-TUUUCG-5' 3'-TAAACG-5' 3'-ATTTGC-5' 3'-GCAAAT-5' 3'-UAAACG-5'

Correct
Adenine pairs with thymine and guanine pairs with cytosine.

Part B
If a DNA double helix is 100 nucleotide pairs long and contains 25 adenine bases, how many guanine bases does it contain? ANSWER: 150 200 50 75 25

Correct
100 nucleotide pairs are a total of 200 nucleotides. Because of base pairing, if there are 25 adenine there must also be 25 thymine. This leaves 20050 = 150 nucleotides to be divided evenly between guanine and cytosine.

Part C
The two strands of a DNA double helix are held together by _____ that form between pairs of nitrogenous bases. ANSWER: hydrophilic interactions hydrogen bonds ionic bonds covalent bonds SS bonds

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Correct
Nitrogenous base pairs are joined by hydrogen bonds.

Part D
A nucleotide is composed of a(n) _____. ANSWER: amino group, a nitrogen-containing base, and a five-carbon sugar phosphate group, a nitrogen-containing base, and a hydrocarbon sulfhydryl group, a nitrogen-containing base, and a five-carbon sugar phosphate group, a nitrogen-containing base, and a five-carbon sugar glycerol, a nitrogen-containing base, and a five-carbon sugar

Correct
These are the components of a nucleotide.

Nucleic Acid Building Blocks

The nucleic acids DNA and RNA are made from chains of nucleotides. Nucleotides consist of three components: a five-carbon sugar (either ribose or deoxyribose), a nitrogenous base attached to the sugars 1'-carbon, and a phosphate group attached to the sugars 5'-carbon.

Part A - Components of nucleotides

Sort these nucleotide building blocks by their name or classification.

Hint 1. Can you identify ribose?

Which of the following molecules is ribose? ANSWER:

Hint 2. Can you identify phosphate?

Which of the following molecules is phosphate? ANSWER:

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Hint 3. Can you identify a purine base?

Which of the following is a nitrogenous base known as a purine? ANSWER:

ANSWER:

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Correct
All of the genetic material in all living organisms is made from these basic building blocks of nucleotides.

Part B - Comparing RNA and DNA

Sort the parts of a nucleic acid according to whether each occurs exclusively in DNA, exclusively in RNA, or in both types of nucleic acid.

Hint 1. Which sugar is found in deoxyribonucleotides?

Which of the following sugars is the sugar found in deoxyribonucleotides? ANSWER:

glucose sucrose ribose galactose deoxyribose

Hint 2. Which base is found exclusively in RNA?

Which of the following nitrogenous bases is found in RNA but is not found in DNA sequences? ANSWER:

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ANSWER:

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Correct
DNA is used for storage of genetic information. The presence of deoxyribose as the sugar in DNA makes the molecule more stable and less susceptible to hydrolysis. The 2'-oxygen on the ribose found in RNA makes RNA much more susceptible to breakdown. It is important that mRNA be easily broken down, to ensure that the correct levels of protein are maintained in the cell.

Part C - Identifying a DNA nucleotide

Identify three possible components of a DNA nucleotide.

Hint 1. How to approach the problem

Recall that a nucleotide consists of a pentose (five-carbon) sugar, a nitrogenous base, and a phosphate group. Determine which sugar is present in DNA and then identify the four possible nitrogenous bases found in DNA.

Hint 2. What is the sugar in DNA?

Enter the name of the pentose sugar found in DNA. ANSWER: deoxyribose

Hint 3. What are the bases in DNA?

Name the four nitrogenous bases that occur in DNA. List the full names of the bases in alphabetical order separated by commas. ANSWER: adenine,cytosine,guanine,thymine

ANSWER: cytosine, phosphate group, ribose deoxyribose, phosphate group, thymine deoxyribose, phosphate group, uracil guanine, phosphate group, ribose cytidine, phosphate group, ribose adenine, phosphate group, ribose

Correct
DNA and RNA have similar structures: a pentose sugar with a nitrogenous base and a phosphate group. DNA and RNA differ in the type of pentose sugar each possesses (DNA has deoxyribose; RNA has ribose) and in one base (DNA has thymine; RNA has uracil).

Misconception Question 21

Part A
Which feature of large biological molecules explains their great diversity? ANSWER:

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The many classes of large biological molecules

Chapter 5

The many ways that monomers of each class of biological molecule can be combined into polymers The diversity of elements found in large biological molecules

Correct
Biological molecules belong to four main classes, and are constructed from only 40 to 50 common monomers (and a few rare ones) made of only a few of the 92 naturally occurring elements. The diversity of biological molecules is due to differences in the arrangements of the monomers in each molecule.

Misconception Question 22

Part A
What structural difference accounts for the functional differences between starch and cellulose? ANSWER: Starch can be digested by animal enzymes, whereas cellulose cannot. Starch and cellulose differ in the glycosidic linkages between their glucose monomers. Starch is a polymer of glucose, whereas cellulose is a polymer of fructose.

Correct
Both starch and cellulose are glucose polymers, but the glycosidic linkages in these two polymers differ. Glucose can have two slightly different ring structures. When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below (alpha) or above (beta) the plane of the ring. In starch, all the glucose monomers are in the alpha configuration. In cellulose, all the glucose monomers are in the beta configuration. As a result, every other glucose monomer is upside down with respect to its neighbors. The differing glycosidic linkages in starch and cellulose give the two molecules distinct three-dimensional shapes, leading to key functional differences.

Misconception Question 25

Part A
Which molecule is a nucleotide? ANSWER: Deoxyribose ATP The amino acid glycine

Correct
A nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and one or more phosphate groups. ATP consists of a nitrogenous base (adenine), a pentose sugar, and three phosphate groups. Score Summary: Your score on this assignment is 82.8%. You received 14.08 out of a possible total of 17 points.

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