Deck 2: The Structure of DNA

Question 1

Which figure (I or II) shows the correct structure for a nucleic acid chain?

A) I
B) II

Answer 1

I

Question 2

The phosphodiester linkage between adjacent nucleotides to form a DNA or RNA chain occurs by a _______________ reaction involving the removal of _____________ and pyrophosphate.

A) hydrolysis, H₂O
B) hydrolysis, CO₂
C) condensation, H₂O
D) condensation, CO₂

Answer 2

condensation, H₂O

Question 3

Edwin Chargaff found that the base composition of DNA, defined as the "percent G+C,"

A) differs among species
B) is constant in all cells of an organism within a species
C) is the same among species
D) both A and B

Answer 3

both A and B

Question 4

The abbreviation dNTP stands for

A) nucleoside 5 '-triphosphate.
B) nucleoside 3 '-triphosphate.
C) deoxynucleoside 5 '-triphosphate.
D) deoxynucleoside 3 '-triphosphate.

Question 5

In practice, the unit of length used for DNA is the kilobase pair, which corresponds to

A) 10 base pairs
B) 100 base pairs
C) 1000 base pairs
D) 1,000,000 base pairs

Question 6

In the two common Watson-Crick base pairs of DNA

A) Adenine (A) is joined to thymine (T) by three hydrogen bonds, while guanine (G) is joined to cytosine (C) by two hydrogen bonds.
B) Adenine (A) is joined to thymine (T) by two hydrogen bonds, while guanine (G) is joined to cytosine (C) by three hydrogen bonds.
C) Adenine (A) is joined to cytosine (C) by three hydrogen bonds, while guanine (G) is joined to thymine (T) by two hydrogen bonds.
D) Adenine (A) is joined to cytosine (C) by two hydrogen bonds, while guanine (G) is joined to thymine (T) by three hydrogen bonds.

Question 7

One DNA molecule varies from another by the

A) composition of the sugar-phosphate backbone
B) spacing of the major and minor grooves
C) way in which the bases are attached to the sugars
D) sequence of nitrogenous bases

Question 8

The __________________ carries a message (the base sequence of DNA) in a form that can be read by DNA-binding proteins; the bases form __________________ with the side chains of amino acids of proteins.

A) major groove, hydrogen bonds
B) minor groove, hydrogen bonds
C) major groove, peptide bonds
D) minor groove, peptide bonds

Question 9

The predominant form of DNA in vivo is

A) A-DNA
B) Z-DNA
C) B-DNA
D) C-DNA

Question 10

Which statement about B-DNA is not true?

A) B-DNA occurs under conditions of relatively low humidity and relatively low salt.
B) B-DNA forms a right-handed helix.
C) B-DNA has 10.5 bases per turn of the helix.
D) B-DNA has a wide major groove of moderate depth.

Question 11

Which statement is not true about Z-DNA?

A) Z-DNA forms a left-handed helix
B) Z-DNA is not present in cells
C) Z-DNA may play a role in regulating gene expression
D) At a B-Z junction, one base pair is extruded from the DNA helix

Question 12

Watson and Crick noted that DNA's structure is interesting because it suggested a possible copying mechanism. What about DNA's structure facilitates copying?

A) It has the same number of purines and pyrimidines.
B) The nitrogenous bases are located on the inside of the double helix.
C) The strands of the double helix are complementary.
D) DNA always goes from 5' to 3'.

Question 13

As DNA denatures its absorption of UV light increases, a phenomenon known as:

A) melting
B) reannealing
C) thermal agitation
D) hyperchromicity

Question 14

The melting temperature (T_m) of DNA is:

A) the temperature at which half the bases in a double-stranded DNA sample have denatured.
B) the temperature at which half the bases in a single-stranded DNA sample have renatured.
C) the temperature at which half the phosphodiester bonds in a double-stranded DNA sample have broken.
D) the temperature at which all the bases in a double-stranded DNA sample have denatured.

Question 15

When two strands of DNA from different sources are hybridized in the lab, what provides the chemical stability for holding the two strands of DNA in a double helix structure?

A) hydrophobic interactions (base-stacking) interactions and hydrogen bonds
B) covalent bonds
C) phosphodiester bonds
D) hydrogen bonds only

Question 16

Lowering the salt concentration of a DNA solution

A) promotes renaturation.
B) promotes denaturation.
C) promotes formation of hydrogen bonds.
D) removes cations that shield the positive charges on the two strands from each other.

Question 17

You determine that a sequence of DNA contains numerous tandem repeats. What unusual DNA secondary structure would this sequence be most likely to form?

A) cruciform
B) triple helix
C) slipped structure
D) tandem helix

Question 18

Friedreich's ataxia is a rare inherited neurological disease caused by a

A) trinucleotide repeat expansion in the first intron of the Friedrich's ataxia gene
B) formation of triple helix DNA in the Friedrich's ataxia gene
C) cruciform structures in the frataxin protein
D) both A and B

Question 19

A Hoogsteen base pair differs from a Watson-Crick base pair by

A) an altered pattern of hydrogen bonding in the Hoogsteen AT pair
B) the Hoogsteen GC pair only forms two hydrogen bonds
C) Hoogsteen GC pairs are not stable at neutral pH
D) all of the above

Question 20

Consider a linear DNA molecule of 20 complete turns (or twists, T=20) with 10.5 base pairs (bp) per turn in solution. If the double helix is underwound by one full turn to the left and then the ends are sealed together, the result is a strained circle with 11.67 bp per turn, where L (linking number) =19 and T=19. If one negative supercoil is spontaneously introduced, the DNA circle will have the following characteristics:

A) L=19, T=20, 11.6 bp/turn
B) L=19, T=20, 10.5 bp/turn
C) L=20, T=20, 10.5 bp/turn
D) L=20, T=20, 11.6 bp/turn

Question 21

Topoisomerases are enzymes that

A) relax supercoiled DNA
B) denature double-stranded DNA
C) synthesize a new strand of DNA from a single-stranded DNA template
D) synthesize a strand of DNA from an RNA template

Question 22

Which statement is not true about DNA supercoiling?

A) Negative supercoiling puts energy into DNA.
B) In bacteriophages, negative supercoiling is associated with decreased activity in replication and transcription.
C) Positive supercoiling occurs ahead of replication forks and transcription complexes.
D) Most DNA within both prokaryotic and eukaryotic cells exists in the negative supercoiled state.

Question 23

As genome complexity increases, the time required for reannealing

A) doesn't change
B) increases
C) decreases
D) either B or C depending on the genome

Question 24

Supercoiling is a form of DNA

A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure

Question 25

Most sequence-specific DNA binding proteins interact with

A) the minor groove of Z-DNA
B) the major groove of B-DNA
C) the backbone of A-DNA
D) locally unwound DNA

Question 26

DNA loop domains

A) are stabilized by proteins at loop junctions
B) join B-DNA and Z-DNA segments
C) are also known as DNA cruciforms
D) form spontaneously

Question 27

The polarity of doubled-stranded DNA arises from

A) negative charges on the backbone phosphates
B) the presence of 5' phosphates on one end and 3' hydroxyls on the other
C) base pairing
D) the sequence of bases, which is strand-specific

Question 28

DNA-mediated heredity derives from which part of its nucleotide building blocks?

A) the sugars
B) the phosphates
C) the nitrogenous bases
D) none of the above

Question 29

Distinguish between the terms "nucleoside" and "nucleotide."

Question 30

Starting with the dNTP shown below, draw a clearly labeled diagram showing where the linking bond is between two nucleotides in the same DNA chain. Name the bond. Label the 5′ and 3′ ends of the DNA chain.
‪

Question 31

You have isolated a DNA molecule that is 12,200 base pairs in length. How many kilobase pairs is the DNA molecule?

Question 32

Briefly describe the two main types of interactions that provide chemical stability to the DNA double helix.

Question 33

Which DNA purine forms three H bonds with its partner in the other DNA strand? Which forms two H bonds?

Question 34

Which DNA pyrimidine forms three H bonds with its partner in the other DNA strand? Which forms two H bonds?

Question 35

Explain what is meant by the following descriptions of the DNA double helix: "polarity in each strand," and "the two strands are antiparallel."

Question 36

Which form of DNA is predominant in cells - A, B, or Z DNA? Do other forms ever occur under special circumstances? Explain your answers.

Question 37

Use a drawing to illustrate the principles of denaturation, renaturation, and nucleic acid hybridization.

Question 38

Draw a typical DNA denaturation curve. Label the axes and point out the melting temperature (T_m). Indicate at what points all of the DNA is double-stranded and all of the DNA is single-stranded.

Question 39

Use a graph to illustrate the effect of lowering the salt concentration of a solution on the melting temperature (T_m) of a DNA sample. What is the explanation for this relationship?

Question 40

Explain to a patient with Friedreich's ataxia the underlying cause of his disease.

Question 41

Discuss the significance of DNA supercoiling in vivo.

Question 42

The DNA duplexes below are denatured and then allowed to reanneal. Which of the two molecules would have the highest T_m? Which of the two is least likely to re-form the original structure? Why?
(a) 5′-ATATCATATGATATGTA-3′
3′-TATAGTATACTATACAT-5′
(b) 5′-CGGTACTCGTGCAGGT-3′
3′-GCCATGAGCACGTCCA-5′

Question 43

When the base composition of DNA from a grasshopper was determined, 29% of the bases were found to be adenine.
(a) What is the percentage of cytosine?
(b) What is the % composition of each of the four nucleotides in the DNA sequence?
(c) What is the [G] + [C] content?

Question 44

Explain why positively supercoiling of genomic DNA might be advantageous for themophilic organisms.

Question 45

Explain how "hydrophobic bonding" stabilizes double-stranded DNA in aqueous solution.