E.C Chapter 16 DNA Structure and Replication

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. Sort the phrases into the appropriate bins depending on which protein they describe.

- Helicase > Binds at the replication fork > breaks H-bonds between bases - Topoisomerase > binds ahead of the replication fork > breaks covalent bonds in DNA backbone - Single-strained binding protein > binds after the replication fork > prevents H-bonds between bases

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'

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. Drag "True" or "False" to the end of each statement.

1. 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 2. The phosphate attached to the 5' carbon of a given nucleotide links to the 3' -OH of the adjacent nucleotide. TRUE 3. Complementary base pairing relies on the number of hydrogen bonds that each base can make. TRUE 4. The -OH group on the 3' carbon of the sugar unit is the attachment site for the nitrogenous base. FALSE 5. In a single nucleotide, the phosphate group is attached to the 5' carbon of the sugar unit. TRUE

Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

1. The bonds or interactions that hold together adjacent nucleotides in the sugar-phosphate backbone of DNA are covalent bonds. 2. The bonds or interactions that hold together complementary bases from opposite strands of DNA are hydrogen bonds. 3. The bonds or interactions between stacked nucleotide units that help hold the DNA molecule together are van der Waals interactions.

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

3'-CGTG-5'

How many kinds of DNA nucleotides are there

4

Nucleic acids are assembled in the _____ direction.

5' to 3'

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 analyzing the number of different bases in a DNA sample, which result would be consistent with the base-pairing rules?

A + G = C + T

Where would RNA polymerase attach?

A - RNA polymerase attaches to DNA

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

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

You can use Chargaff's rules to predict the percentage of one or more bases in the DNA of a species if at least one value is known. Data from several papers by Chargaff: for example, E. Chargaff et al., Compositionof the desoxypentose nucleic acids of four genera of sea-urchin, Journal of BiologicalChemistry 195: 155-160 (1952). What is the %T in wheat DNA?

Approximately 28%

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

B

The synthesis of a new strand begins with the synthesis of a(n) _____.

RNA primer complementary to a preexisting DNA strand

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

Tables like the one shown here are useful for organizing sets of data representing a common set of values (in this case, percentages of A, G, C, and T) for a number of different samples (in this case, species). Data from several papers by Chargaff: for example, E. Chargaff et al., Compositionof the desoxypentose nucleic acids of four genera of sea-urchin, Journal of BiologicalChemistry 195: 155-160 (1952). Does the distribution of bases in sea urchin DNA and salmon DNA follow Chargaff's rules?

Yes, because the %A approximately equals the %T and the %G approximately equals the %C in both species.

If Chargaff's equivalence rule is valid, then hypothetically we could extrapolate this to the combined genomes of all species on Earth (as if there were one huge Earth genome). In other words, the total amount of A in every genome on Earth should equal the total amount of T in every genome on Earth. Likewise, the total amount of G in every genome on Earth should equal the total amount of C in every genome on Earth. Calculate the average percentage for each base in your completed table. Do Chargaff's equivalence rules still hold true when you consider those six species together?

Yes, the average for A approximately equals the average for T, and the average for G approximately equals the average for C.

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

a phosphate group

Many enzymes are named for the substrate on which they work, either to build or disassemble molecules. Also, enzyme names often end in "-ase." For example, lactase is the enzyme that breaks down lactose. With a name like "telomerase," we can deduce that telomerase is probably:

an enzyme that regulates the assembly of DNA at the ends of chromosomes

During mitosis, centromeres separate and chromatids become individual chromosomes during which phase?

anaphase

What color is the deoxyribose sugar with the five-sided structure?

blue

The elongation of the leading strand during DNA synthesis

depends on the action of DNA polymerase.

After DNA replication is completed, _____.

each new DNA double helix consists of one old DNA strand and one new DNA strand

The first step in the replication of DNA is catalyzed by _____.

helicase

The letter C indicates _____.

histones

The two strands of a DNA double helix are held together by _____ that form between pairs of nitrogenous bases.

hydrogen bonds

During _____, the cell grows and replicates both its organelles and its chromosomes.

interphase

As a result of its involvement in a chemical reaction, an enzyme

is unchanged by the reactants or products.

Short segments of newly synthesized DNA are joined into a continuous strand by _____.

ligase

15c

look in photo

5a

look in photo

7c

look in photo

9f

look in photo

What is this an image of?

loops

This is an image of a(n) _____.

nucleotide

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

phosphate

The letter A indicates a _____.

phosphate group

What are telomeres?

regions of DNA at the end of chromosomes which do not code for making proteins

The action of helicase creates _____.

replication forks and replication bubbles

In his work with pneumonia-causing bacteria and mice, Griffith found that

some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic.

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

What groups are the same for all DNA nucleotides. The base is the one part that changes?

sugar and phosphate only

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

What is this an image of?

supercoils

An old DNA strand is used as a _____ for the assembly of a new DNA strand.

template

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

What are chromosomes made of?

DNA and proteins

The letter A indicates _____.

DNA double helix

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

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

Why is the new DNA strand complementary to the 3' to 5' strands assembled in short segments?

DNA polymerase can assemble DNA only in the 5' to 3' direction

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

DNA polymerase can join new nucleotides only to the 3 end of a pre-existing strand, and the strands are antiparallel.

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 replication is said to be semiconservative. What does this mean?

Each new double helix consists of one old and one new strand.

Which of the following has the greatest potential as a cancer treatment?

Find a way to turn off the gene for making telomerase in cancer cells, since the cells would stop dividing when the telomeres were gone.

Which of the following is true of DNA during interphase?

It exists as chromatin and is less condensed than mitotic chromosomes.

What is the function of helicase in DNA replication?

It untwists the double helix and separates the two DNA strands.

Which of the following problems during DNA replication is being illustrated with the kids in the video?

Nucleotides at the ends of the DNA strands are lost when DNA replicates.

DNA is a self-replicating molecule. What accounts for this important property of DNA?

The nitrogenous bases of the double helix are paired in specific combinations: A with T and G with C.

Griffith's experiments with S. pneumoniae were significant because they showed that traits could be transferred from one organism to another. What else did he find that was significant?

The transferred traits were heritable.

Which of the following is NOT true about naked mole rats?

Their cells do not produce telomerase.

During DNA replication, the leading strand is synthesized continuously, whereas the lagging strand is synthesized as Okazaki fragments. Why is this so?

DNA synthesis can take place only in the 5' to 3' direction.

A nitrogenous base is indicated by the letter _____.

C

Which of these is(are) pyrimidines?

C, D, and E

How is the aging process linked to telomeres?

Cells with short telomeres can no longer divide, so damaged tissues cannot be repaired.

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.

Which of these is responsible for catalyzing the formation of an RNA primer?

D - primase catalyzes

Which cells are most likely to have the gene for making telomerase switched on?

The cells in a developing embryo.