Mastering Biology Chapter 16 HW

topoisomerase

- breaks covalent bonds in DNA backbone - binds ahead of the replication fork

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?

5'-TACGAACC-3'

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?

B *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.

Duplication of chromosomes occurs during S phase of the cell cycle. Duplication requires the separation of complementary DNA strands to allow for DNA replication. Which of the following statements best explains how weak hydrogen bonds function better in this situation than stronger bonds would?

Complementary DNA strands are separated or "unzipped" for the replication process. Weak hydrogen bonds between complementary strands are easily disrupted during DNA replication because they are not high-energy chemical bonds.

DNA is a double-stranded molecule made up of complementary, antiparallel strands. Based on what you know about complementary base pairing, fill in the rest of the details in the figure.

*The nucleotide pairs in double-stranded DNA follow the base-pairing rules: A with T, and G with C. The complementary strands are antiparallel, with one strand running 5' to 3', and its complement running 3' to 5'. The 3' end of a DNA strand has an exposed -OH group, and the 5' end has a phosphate group.

Which of the following diagrams most clearly shows the overall 3D shape and atomic composition of DNA?

*The space-filling model shows each atom making up the two strands, and reveals the helical shape and the double-stranded structure of the DNA molecule.

helicase

- binds at the replication fork - breaks H-bonds between bases

Nucleic acids are assembled in the _____ direction.

5' to 3' *New nucleotides are added to the 3' end of a growing polynucleotide.

A nitrogenous base is indicated by the letter _____.

C

Which of these is(are) pyrimidines?

C, D, and E *Pyrimidines are single-ring structures

Which of these is a difference between a DNA and an RNA molecule?

DNA is usually double-stranded, whereas RNA is usually single-stranded.

What is the role of DNA polymerase during DNA synthesis?

DNA polymerase is the enzyme that catalyzes the addition of a nucleotide onto the 3' end of a growing DNA strand.

True or False: The -OH group on the 3' carbon of the sugar unit is the attachment site for the nitrogenous base.

False

True or False: Complementary base pairing relies on the number of hydrogen bonds that each base can make.

True

True or False: In a single nucleotide, the phosphate group is attached to the 5' carbon of the sugar unit.

True

True or False: The phosphate attached to the 5' carbon of a given nucleotide links to the 3' -OH of the adjacent nucleotide.

True

A hydroxyl is present at the 3' end of the growing DNA strand. What is at the 5' end?

a phosphate group

The bonds or interactions that hold together complementary bases from opposite strands of DNA are __________.

hydrogen bonds

You can tell that this is an image of a DNA nucleotide and not an RNA nucleotide because you see a _____.

sugar with two, and not three, oxygen atoms *DNA nucleotides are composed of deoxyribose sugars, whereas RNA nucleotides are composed of ribose sugars.

both strands

synthesized 5' to 3'

Which of these nitrogenous bases is found in DNA but not in RNA?

thymine

Rank the primers in the order they were produced. If two primers were produced at the same time, overlap them.

Earliest A&H together B&G together C&F together D&E together Latest * As soon as the replication bubble opens and the replication machinery is assembled at the two replication forks, the two primers for the leading strands (primers a and h) are produced. The production of the first primers on the lagging strands (those closest to the origin of replication, b and g) is delayed slightly because the replication forks must open up further to expose the template DNA for the lagging strands. After completion of the first segments of the lagging strands, additional template DNA must be exposed before the second primers (c and f) can be produced. And after completion of the second segments, additional template DNA must be exposed before the third primers (d and e) can be produced. In summary, because of the way the replication bubble expands, the lagging strand primers near the origin of replication were produced before the primers near the replication forks.

A DNA molecule consists of two antiparallel strands of polynucleotides. Each strand is composed of nucleotides bound to each other along the sugar-phosphate backbone. True or False: The antiparallel arrangement of double-stranded DNA is due to the phosphate group being bonded to the 3' carbon on one strand and the 5' carbon on the complementary strand.

False

Addition of a nucleotide onto a DNA strand is an endergonic reaction. What provides the energy to drive the reaction?

Release of pyrophosphate from the incoming nucleotide, and then hydrolysis of the pyrophosphate to inorganic phosphate

The bonds or interactions that hold together adjacent nucleotides in the sugar-phosphate backbone of DNA are ___________.

covalent bonds

This is an image of a(n) _____.

nucleotide

The letter A indicates a _____.

phosphate group

In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand.

thymine ... cytosine

The bonds or interactions between stacked nucleotide units that help hold the DNA molecule together are __________.

van der Waals interactions

In the accompanying image, a nucleotide is indicated by the letter _____.

B

leading strand

- made continuously - only one primer needed - daughter strand elongates toward replication fork

In a nucleotide, the nitrogenous base is attached to the sugar's _____ carbon and the phosphate group is attached to the sugar's _____ carbon.

1' ... 5' *The nitrogenous base is attached to the sugar's 1' carbon and the phosphate group is attached to the sugar's 5' carbon.

lagging strand

- multiple primers needed - daughter strand elongates away from replication fork - made in segments

single strand binding proteins

- prevents H-bonds between bases - binds after the replication fork

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 replication forks. Arrows can be used once, more than once, or not at all.

* 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.

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.

* 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.

Which of the following diagrams most clearly shows the details of the bonds between nitrogenous bases of complementary nucleotide pairs?

*only the structural diagram shows the molecular details--the specific number and location of hydrogen bonds that form between complementary base pairs.

What materials does DNA polymerase require in order to synthesize a complete strand of DNA?

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

Drag the labels to their appropriate locations in the flowchart below, indicating the sequence of events in the production of fragment B. (Note that pol I stands for DNA polymerase I, and pol III stands for DNA polymerase III.)

Step 1: A new fragment begins with DNA polymerase III binding to the 3' end of the most recently produced RNA primer, primer B in this case, which is closest to the replication fork. DNA pol III then adds DNA nucleotides in the 5' to 3' direction until it encounters the previous RNA primer, primer A. Step 2: DNA pol III falls off and is replaced by DNA pol I. Starting at the 5' end of primer A, DNA pol I removes each RNA nucleotide and replaces it with the corresponding DNA nucleotide. (DNA pol I adds the nucleotides to the 3' end of fragment B.) When it encounters the 5' end of fragment A, DNA pol I falls off, leaving a gap in the sugar-phosphate backbone between fragments A and B. Step 3: DNA ligase closes the gap between fragments A and B. These steps will be repeated as the replication fork opens up. Try to visualize primer C being produced to the right (closest to the replication fork). Fragment C would be synthesized and joined to fragment B following the steps described here.