Exam 5 review - chapter 16 homework

earliest - latest

(a,h) , (b,g) , (c,f) , (d,e,)

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.

...

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.

Nucleic acids are assembled in the _____ direction.

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

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'-TAC-3'; All four nucleotides are required for DNA polymerase to function. 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.

The diagram below shows a replication bubble with synthesis of the leading and lagging strands on both sides of the bubble. The parental DNA is shown in dark blue, the newly synthesized DNA is light blue, and the RNA primers associated with each strand are red. The origin of replication is indicated by the black dots on the parental 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.

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

All four deoxyribonucleotides triphosphates (containing A, C, T, or G), Single-stranded DNA template, 3'-OH end of the new DNA strand. In order for DNA polymerase to synthesize a complete new strand of DNA, it requires a template to determine the order of bases on the new strand, a 3'-OH end to add more nucleotides onto, and the full set of four kinds of nucleotides (A,C,T,G) if they are needed to complement the template strand.

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 separating of the DNA requires three different types of proteins: helicase, topoisomerase, and single-strand binding proteins.

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.

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

B.

As the two parental (template) DNA strands separate at a replication fork, each of the strands is separately copied by a DNA polymerase III (orange), producing two new daughter strands (light blue), each complementary to its respective parental strand. Because the two parental strands are antiparallel, the two new strands (the leading and lagging strands) cannot be synthesized in the same way.

Because DNA polymerase III can only add nucleotides to the 3' end of a new DNA strand and because the two parental DNA strands are antiparallel, synthesis of the leading strand differs from synthesis of the lagging strand. * The leading strand is made continuously from a single RNA primer located at the origin of replication. DNA pol III adds nucleotides to the 3' end of the leading strand so that it elongates toward the replication fork. *In contrast, the lagging strand is made in segments, each with its own RNA primer. DNA pol III adds nucleotides to the 3' end of the lagging strand so that it elongates away from the replication fork. In the image below, you can see that on one side of the origin of replication, a new strand is synthesized as the leading strand, and on the other side of the origin of replication, that same new strand is synthesized as the lagging strand. The leading and lagging strands built on the same template strand will eventually be joined, forming a continuous daughter strand.

A nitrogenous base is indicated by the letter _____.

C

Which of these is(are) pyrimidines?

C, D, E. Pyrimidines are single-ring structures.

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. Hydrogen bonds connect complementary bases from opposite strands of the DNA molecule. Hydrogen bonds are relatively weak, low-energy interactions that allow complementary DNA strands to "unzip" during S phase replication.

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

DNA is usually double-stranded, whereas RNA is usually single-stranded. With some exceptions, DNA is a double-stranded molecule and RNA is a single-stranded molecule.

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.

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.

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

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

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

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 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.

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. 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.

Various types of chemical bonds or interactions maintain the three-dimensional (3D) structure of large biological molecules like DNA. Not all types of bonds or interactions are shown in all diagrams. The types of bonds or interactions shown depend on the emphasis of the particular diagram. Which of the following diagrams most clearly shows the overall 3D shape and atomic composition of DNA?

Space-filling model. 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.

In contrast to the leading strand, the lagging strand is synthesized as a series of segments called Okazaki fragments. The diagram below illustrates a lagging strand with the replication fork off-screen to the right. Fragment A is the most recently synthesized Okazaki fragment. Fragment B will be synthesized next in the space between primers A and B.

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.

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

Structural diagram. While the complementary nature of the interactions between the base pairs is demonstrated in all four diagrams, only the structural diagram shows the molecular details--the specific number and location of hydrogen bonds that form between complementary base pairs.

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.

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.

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.

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

True

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

single-strand binding protein

binds after the replication fork prevents H-bonds between bases

helicase

binds at the replication fork breaks H-bonds between bases

topoisomerase

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

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

covalent bonds

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

hydrogen bonds

leading strand

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

lagging strand

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

This is an image of a(n) _____.

nucleotide. nucleotides are composed of a pentose sugar, a nitrogenous base, and a phosphate group.

The letter A indicates a _____.

phosphate group. Phosphate groups contain phosphorus..

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

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. This is referred to as specific base pairing.

Complementary base pairing relies on the number of hydrogen bonds that each base can make.

true

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

van der Waals interactions