Mastering biololgy-Chapter 16 PDF

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Mastering Biology Ch.16...

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12/12/2020

Chapter 16

Chapter 16 Due: 11:59pm on Monday, December 14, 2020 You will receive no credit for items you complete after the assignment is due. Grading Policy

DNA Replication (1 of 2): DNA Structure and Replication Machinery (BioFlix tutorial) DNA is composed of two strands that are bound together, resembling a rope ladder with rigid rungs. This DNA ladder is twisted, forming what is called the double helix. The structure of the DNA double helix depends on the complementary pairing of bases between the two strands. Replication of DNA requires that the two strands of the helix separate, as shown in the image below. New daughter molecules are constructed by the sequential addition of nucleotides and the formation of base pairs between the new strand and the parent (template) strand. The replication of the double helix results in two daughter molecules, each composed of one parent strand and one new strand. The enzymes that accomplish the replication of DNA are called DNA polymerases.

Before beginning this tutorial, watch the DNA Replication animation. Pay particular attention to the structure of the DNA, how the double helix is unwound to form a replication bubble, a how nucleotides are added to the new strands in the replication bubble.

Part A - The chemical structure of DNA and its nucleotides The DNA double helix is composed of two strands of DNA; each strand is a polymer of DNA nucleotides. Each nucleotide consists of a sugar, a phosphate group, and one of four nitrogenous bases. The structure and orientation of the two strands are important to understanding DNA replication. Drag the labels to their appropriate locations on the diagram below. Targets of Group 1 can be used more than once.

Hint 1. Distinguishing the 3' and 5' ends of a DNA strand A strand of DNA consists of a linear polymer of DNA nucleotides. The "backbone" of the DNA strand consists of a repeating pattern of sugar and phosphate groups in which the phosphate of one nucleotide is covalently attached to the sugar of the next nucleotide. This sugar-phosphate-sugar arrangement is called a phosphodiester linkage.The two ends of a DNA strand are distinct from each other. The 5' end has a phosphate group, which is attached to the 5' carbon of a deoxyribose sugar. At the 3' end, there is a hydroxyl (-OH) group attached to the 3' carbon of a deoxyribose sugar.

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Hint 2. What are the components of a DNA strand? A strand of DNA consists of a sequence of covalently linked DNA nucleotides. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ANSWER:

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1. DNA possesses many negative charges because of the presence of phosphate groups , which also help form the backbone of each DNA strand. 2. DNA contains deoxyribose sugars , which distinguish DNA from RNA and help form the backbone of each DNA strand. 3. Adenine and thymine are examples of nitrogenous bases , which pair with each other in the double helix. 4. The complementary DNA strands of a double helix are held together by hydrogen bonds between their nitrogenous bases.

ANSWER:

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5' end

hydrogen bond

deoxyribose sugar

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3' end

nitrogenous base

phosphate group 3' end

5' end

3' end 5' end

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Correct The DNA double helix is constructed from two strands of DNA, each with a sugar-phosphate backbone and nitrogenous bases that form hydrogen bonds, holding the two strands together. Each DNA strand has two unique ends. The 3' end has a hydroxyl (-OH) group on the deoxyribose sugar, whereas the 5' end has a phosphate group. In the double helix, the two strands are antiparallel, that is, they run in opposite directions such that the 3' end of one strand is adjacent to the 5' end of the other strand.

Part B - The role of DNA polymerase III In DNA replication in bacteria, the enzyme DNA polymerase III (abbreviated DNA pol III) adds nucleotides to a template strand of DNA. But DNA pol III cannot start a new strand from scratch. Instead, a primer must pair with the template strand, and DNA pol III then adds nucleotides to the primer, complementary to the template strand. Each of the four images below shows a strand of template DNA (dark blue) with an RNA primer (red) to which DNA pol III will add nucleotides. In which image will adenine (A) be the next nucleotide to be added to the primer?

Hint 1. Watch DNA polymerase III add nucleotides to a new DNA strand

In bacteria, a new strand of DNA is synthesized by the enzyme DNA pol III, using one of the two parental DNA strands as a template. Watch how DNA pol III adds new nucleotides to one end of the growing strand. Hint 2. Which bases form pairs in DNA? In a DNA double helix, the two complementary strands of DNA are held together by hydrogen bonds between pairs of nitrogenous bases on each strand. This pairing of bases between the two strands is the basis of many of DNA’s unique properties. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ANSWER:

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1. During DNA replication, if the next base on the template strand is A (adenine), the next nucleotide G (guanine) U (uracil)

added to the new strand will contain T (thymine)

as a base.

2. In the DNA double helix, the base G (guanine) forms a hydrogen bond with C (cytosine) .

A (adenine)

Hint 3. To which end of a primer does DNA polymerase add new nucleotides? In bacteria, DNA polymerase III is the enzyme that adds new nucleotides to a primer or growing strand of DNA. Which of the following statements correctly describes the formation of the bond between a new nucleotide and the primer? ANSWER: The newly added nucleotide forms a bond with the phosphate group on the 5' end of the primer. The newly added nucleotide forms a bond with the phosphate group on the 3' end of the primer. The newly added nucleotide forms a bond with the hydroxyl (-OH) group on the 5' end of the primer. The newly added nucleotide forms a bond with the hydroxyl (-OH) group on the 3' end of the primer.

ANSWER:

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Correct In the example above, DNA pol III would add an adenine nucleotide to the 3' end of the primer, where the template strand has thymine as the next available base. You can tell which end is the 3' end by the presence of a hydroxyl (-OH) group. The structure of DNA polymerase III is such that it can only add new nucleotides to the 3' end of a primer or growing DNA strand (as shown here). This is because the phosphate group at the 5' end of the new strand and the 3' -OH group on the nucleoside triphosphate will not both fit in the active site of the polymerase.

Part C - The replication bubble and antiparallel elongation DNA replication always begins at an origin of replication. In bacteria, there is a single origin of replication on the circular chromosome, as shown in the image here. Beginning at the origin of replication, the two parental strands (dark blue) separate, forming a replication bubble. At each end of the replication bubble is a replication fork where the parental strands are unwound and new daughter strands (light blue) are synthesized. Movement of the replication forks away from the origin expands the replication bubble until two identical chromosomes are ultimately produced.

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In this activity, you will demonstrate your understanding of antiparallel elongation at the replication forks. Keep in mind that the two strands in a double helix are oriented in opposite directions, that is, they are antiparallel. Drag the arrows onto the diagram below to indicate the direction that DNA polymerase III moves along the parental (template) DNA strands at each of the two replicati forks. Arrows can be used once, more than once, or not at all.

Hint 1. Watch the two DNA polymerases at a replication fork

This short clip shows two DNA polymerases synthesizing two new DNA strands at a replication fork. Note the direction that DNA pol III moves on each parental strand. In the animation, the lower strand is shown forming a loop after the replication fork. It may help you to visualize that loop extended straight out from the replication fork, like the upper strand. Does the polymerase on the lower strand move in the same direction or in the opposite direction as the polymerase on the upper strand?

Hint 2. What will be the directionality of the two new DNA strands? This image shows a replication bubble in a bacterial chromosome. The region enclosed by the box includes the two parental DNA strands (dark blue) and the two newly synthesized strands (light blue). Each of the images below shows the same four segments of DNA. Which of the following correctly represents the directionality of the two new DNA strands (light blue) compared to the two parental strands?

ANSWER:

ANSWER:

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Correct DNA polymerase III can only add nucleotides to the 3' end of a new DNA strand. Because the two parental DNA strands of a double helix are antiparallel (go from 3' to 5' in opposite directions), the direction that DNA pol III moves on each strand emerging from a single replication fork must also be opposite. For example, in the replication fork on the left, the new strand on top is being synthesized from 5' to 3', and therefore DNA pol III moves away from the replication fork. Similarly, the new strand on the bottom of that same replication fork is being synthesized from 5' to 3'. But because the bottom parental strand is running in the opposite direction of the top parental strand, DNA pol III moves toward the replication fork. In summary, at a single replication fork, one strand is synthesized away from the replication fork, and one strand is synthesized toward the replication fork. When you look at both replication forks, note that a single new strand is built in the same direction on both sides of the replication bubble.

Part D - Unwinding the DNA As DNA replication continues and the replication bubble expands, the parental double helix is unwound and separated into its two component strands. This unwinding and separatin of the DNA requires three different types of proteins: helicase, topoisomerase, and single-strand binding proteins. Sort the phrases into the appropriate bins depending on which protein they describe.

Hint 1. Watch helicase unwind DNA

As the replication bubble expands, the two strands of parental DNA must be separated from each other, a process often referred to as “unwinding” the DNA. This is accomplished by an enzyme called helicase. Watch helicase (the green protein) unwind the DNA at the replication fork.

Hint 2. How does topoisomerase work? Topoisomerase is an enzyme that relieves the strain (tighter twisting) caused by the unwinding of parental DNA by the helicase at the replication fork. Which of the following statements correctly describes how topoisomerase functions? ANSWER:

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Chapter 16 Topoisomerase breaks a covalent bond in the backbone of one parental strand. Topoisomerase breaks a covalent bond between a deoxyribose sugar and a nitrogenous base in one parental strand. Topoisomerase breaks hydrogen bonds between the two parental strands. Topoisomerase breaks covalent bonds in the backbones of both parental strands.

Hint 3. What is the function of single-strand binding proteins? Which of the following statements correctly describes the role of single-strand binding proteins in DNA replication? ANSWER:

Single-strand binding proteins bind to the newly synthesized strand of DNA immediately after the DNA polymerase. Single-strand binding proteins bind to parental DNA immediately after the helicase, preventing the two single strands from joining and re-forming a double helix. Single-strand binding proteins bind to double-stranded DNA, causing the two strands to separate into single strands. Single-strand binding proteins bind to double-stranded DNA ahead of the replication fork, relieving the strain caused by helicase.

Hint 4. The role of hydrogen bonds in DNA structure In a DNA double helix, the two strands of DNA are held together by hydrogen bonds between complementary base pairs. When two single complementary strands of DNA are near each other, hydrogen bonding between the bases usually causes the two strands to join and form a double helix.

ANSWER:

Reset

binds at the replication fork

binds ahead of the replication fork

binds after the replication fork

breaks H-bonds between bases

breaks covalent bonds in DNA backbone

prevents H-bonds between bases

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Correct At each replication fork, helicase moves along the parental DNA, separating the two strands by breaking the hydrogen bonds between the base pairs. (This makes the two parental DNA strands available to the DNA polymerases for replication.) As soon as the base pairs separate at the replication fork, single-strand binding proteins attach to the separated strands and prevent the parental strands from rejoining. As helicase separates the two parental strands, the parental DNA ahead of the replication fork becomes more tightly coiled. To relieve strain ahead of the replication fork, topoisomerase breaks a covalent bond in the sugar-phosphate backbone of one of the two parental strands. Breaking this bond allows the DNA to swivel around the corresponding bond in the other strand and relieves the strain caused by the unwinding of the DNA at the helicase.

Video Tutor Session Quiz: DNA Structure Watch the Video Tutor Session to your right. You can also download the video or view the text of the tutor session to read while you are watching. After you have watched the tutor session, answer the questions. Estimated time: 15 minutes

Part A

ANSWER:

green yellow white black blue

Correct In this model, the deoxyribose sugar is the blue five-sided structure at the center.

Part B

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ANSWER: base sugar deoxyribose phosphate polyphosphate

Correct A polynucleotide contains a sugar/phosphate backbone, where the sugar of one nucleotide binds to the phosphate of the next, and so on.

Part C

ANSWER: 3'-ATCG-5' 3'-GCAC-5' If one strand is 5'-GCAC-3', the complementary strand must be

3'-GTGC-5' 3'-CGTG-5' 3'-CACG-5'

Correct According to the base pairing rules, A goes with T, and G goes with C. And complementary strands are antiparallel. Therefore, the sequence 5'-GCAC-3' matches with the sequence 3'-CGTG-5'.

Part D

Note: For this question, consider only DNA nucleotides. ANSWER:

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2 3 16 8 4

Correct There are four kinds of DNA nucleotides, abbreviated A, T, C, and G.

Part E

ANSWER: base only sugar, phosphate, and base sugar only sugar and phosphate only phosphate only

Correct The sugar and phosphate groups are the same for all DNA nucleotides. The base is the one part that changes.

Campbell Figure Walkthrough: Addition of a Nucleotide to a DNA Strand Watch this video and then answer the questions.

Part A What is the role of DNA polymerase during DNA synthesis? ANSWER:

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DNA polymerase removes inorganic phosphate from the template strand of DNA to catalyze the polymerization reaction. DNA polymerase provides the free energy to catalyze the endergonic addition of a nucleotide onto the 3’ end of a growing DNA strand. DNA polymerase is the enzyme that catalyzes the addition of a nucleotide onto the 3’ end of a growing DNA strand. DNA polymerase catalyzes the synthesis of the template strand of DNA.

Correct DNA polymerase is the enzyme complex responsible for synthesizing a new strand of DNA, using an existing strand as a template.

Part B A hydroxyl is present at the 3’ end of the growing DNA strand. What is at the 5’ end? ANSWER: a nitrogenous base a deoxyribose a ribose a phosphate group

Correct The 5' phosphate is an important player in the reaction that joins the next deoxyribonucleotide onto the growing strand.

Part C Addition of a nucleotide onto a DNA strand is an endergonic reaction. What provides the energy to drive the reaction? ANSWER: Binding of the pre-existing new strand, the template strand, and the incoming nucleotide to the active site of the DNA polymerase Release of pyrophosphate from the incoming nucleotide, and then hydrolysis of the pyrophosphate to inorganic phosphate Complementary bases on the template and the incoming nucleotide are attracted to each other, releasing free energy. The dehydration reaction between the 5’-phosphate of the incoming nucleotide and the 3’-OH of the growing strand of DNA

Correct Each deoxyribonucleotide enters the reaction as a triphosphate, and hydrolysis of the phosphates releases the free energy needed for the nucleotide to bind to the growing strand.

Part D Given a template strand of 3’-ATGCTTGGACA-5’ and a partially-made complementary strand containing only 5’-TAC-3’, what would be the sequence of the new strand of DNA (including the 5’-TAC-3’) if the only additional nucleotides available to DNA polymerase were those containing the bases G, A, and C? ANSWER:

3’-TACGAACCTGT-5’ 5’-GAACC-3’ 5’-TACGAACC-3’ 5’-TAC-3’; All four nucleotides are required for DNA polymerase to function.

Correct DNA polymerase will continue to add nucleotides onto the growing strand as long as it has nucleotides with the bases required to complement the template strand. If it is missing one kind of base, it will stop at that point on the strand.

Part E What materials does DNA polymerase require in order to synthesize a complete strand of DNA? Select all that apply. ANSWER:

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Single-stranded DNA template ATP 3'-OH end of the new DNA strand Inorganic phosphate All four deoxyribonucleotides triphosphates (containing A, C, T, or G)

Correct In order for DNA polymerase to synthesize a complete new strand of DNA, it...