Deck 11: Structure of Nucleic Acids

Question 1

Which of the following enzymes introduces negative supercoils into DNA?

A) DNA polymerase
B) DNA gyrase
C) DNA ligase
D) primase
E) DNA photolyase

Answer 1

B

Question 2

The function of DNA topoisomerases is:

A) packaging DNA into nucleosomes.
B) forming cruciform DNA.
C) unwinding G:C rich areas in DNA.
D) breaking one or more strands of DNA, winding them tighter or looser, and rejoining the ends.
E) promoting DNA hybridization.

Answer 2

D

Question 3

How is a fluorescent tag that is unique for each nucleotide incorporated into the newly synthesized DNA using the chain termination protocol for DNA sequencing?

A) Each of the ddNTPs is labeled with a specific fluorophore
B) The primer strand is labeled with a specific fluorophore
C) The template strand is labeled prior to the experiment with complimentary fluorophores
D) The 5'-end is labeled with a fluorophore.
E) All dNTPs are labeled with a fluorophore

Answer 3

A

Question 4

DNA intercalating agents include all of the following EXCEPT:

A) ethidium bromide.
B) actinomycin D.
C) acridine orange.
D) streptomycin.
E) all are true.

Question 5

The hyperchromic shift that occurs when dsDNA is ____ is a(n) ____ in absorption at ____ nm.

A) methylated; increase; 220
B) methylated; decrease; 260
C) denatured; decrease; 260
D) denatured; increase; 260
E) melted; decrease; 280

Question 6

What is the nucleotide sequence of the DNA strand that is complementary to 5'-ATCGCAACTGTCACTA-3'?

A) 5'-TAGCGTTGACAGTGAT-3'
B) 5'-UAGUGACAGUUGCGAU-3'
C) 5'-TAGCGTTGACAGTGAT-3'
D) 5'-TAGTGACAGTTGCGAT-3'
E) 5'-ATCACTGTCAACGCTA-3'

Question 7

DNA double helix structure is stabilized by all of the following EXCEPT:

A) the sugar-phosphate backbones are oriented in opposite directions.
B) the glycosidic bonds holding paired bases are directly across the helix from one another.
C) cations such as Mg²⁺ bind to the anionic phosphates.
D) bases stack together through hydrophobic interactions and van der Waals forces.
E) appropriate base pairing builds a polymer whose external dimensions are uniform.

Question 8

DNA ____ is analogous to twisting or untwisting a two stranded rope so that it is torsionally stressed.

A) buoyant density
B) hairpin turn
C) cloverleaf
D) supercoiling
E) all of the above

Question 9

Which of the following explains why it is often easier to sequence a gene rather than sequence the corresponding protein?

A) DNA sequencing can be performed on picogram quantities of DNA
B) DNA is composed of only 4 different monomers while proteins are composed of 20 different monomers
C) restriction endonucleases can be used to cut DNA at specific sequences to generate DNA fragments that can easily be sequenced
D) all of the above
E) both B and C are correct

Question 10

All are true for linking number EXCEPT:

A) It is a basic parameter characterizing supercoiled DNA.
B) L = T + W.
C) It is the number of times that two strands are intertwined providing both strands remain covalently intact.
D) L = 40 in a relaxed circular DNA duplex of 400 bp.
E) All are true.

Question 11

All are true for DNA polymerase EXCEPT:

A) requires a primer with a free 5'-OH end, but the 3'-end may be phosphorylated.
B) copies the sequence of nucleotides of one strand to form a new second strand.
C) copies the sequence of nucleotides of one strand in a complementary fashion.
D) generates dsDNA from ssDNA
E) synthesizes new strands by adding successive nucleotides in the 5'→3' direction.

Question 12

Urea and formamide are agents that denature dsDNA by

A) intercalating between base pairs and disrupting van der Waals interactions.
B) forming ionic bonds with the backbone phosphates.
C) competing effectively with the H-bonding between the base pairs.
D) changing the pH to cause hydrolysis.
E) none are true

Question 13

ssDNA will renature requiring ____ of the DNA strands into a dsDNA and this is called ____ which occurs best if the temperature is ____ T_m but warm enough to promote diffusion of the DNA molecules.

A) hydrolysis; reannealing; below
B) reassociation; reannealing; below
C) reassociation; melting; above
D) complementing; solidifying; below
E) none are true

Question 14

Nucleic acid hybridization is a commonly employed procedure in molecular biology to investigate all EXCEPT:

A) evolutionary relationships.
B) specific genes against a vast background.
C) specific probe based isolation of genes.
D) quantify gene expression.
E) all are true.

Question 15

Naturally occurring, self-replicating, extra-chromosomal DNA molecules found in bacteria that carry genes specifying novel metabolic capacity advantageous to the bacterium are called:

A) probes.
B) cruciform.
C) toroidal DNA.
D) plasmids.
E) all of the above.

Question 16

The higher the ____ content of a DNA, the ____ the melting temperature, and the ____ the ionic strength, the ____ the melting temperature.

A) G:C; higher; higher; lower
B) G:C; lower; higher; lower
C) G:C; higher; lower; lower
D) A:T; higher; higher; lower
E) A:T; lower; lower; higher

Question 17

Double helical DNA:RNA hybrids and double-stranded regions of RNA chains often assume an:

A) A-like conformation.
B) B-like conformation.
C) Z-like conformation.
D) all of the above.
E) none of the above.

Question 18

B-DNA is characterized by which of the following?

A) 12 base pairs per helix turn
B) helix axis runs through the minor groove
C) a wide major groove an narrow minor groove
D) right-handed helix
E) both C and D are correct

Question 19

Which of the following statements correctly describes the process of DNA sequencing by chain termination?

A) the enzyme DNA polymerase is used to form a primer that binds to the template DNA
B) in order to effectively sequence the DNA, the dideoxynucleotides must be present at a higher concentration than the deoxynucleotides
C) the use of 4 unique fluorescent labels attached to the dideoxynucleotides allows for a single reaction to be run
D) the dideoxynucleotides lack a 5'-OH and therefore can not serve as acceptors in nucleotide addition
E) both B and C are correct

Question 20

All of the following are characteristics for in vitro DNA synthesis EXCEPT:

A) DNA polymerase adds nucleotides in a 5'→3' direction.
B) The primer strand of DNA determines the nucleotides added.
C) Correct hydrogen bonding is the primary check of the newly synthesized DNA.
D) A primer strand must contain a free 3'-OH.
E) DNA polymerase copies the complementary strand of DNA.

Question 21

DNA sequences that are inverted repeats, or ____, have the potential to form a ____ structure known as a ____ if the normal ____ base pairing is replaced by ____ pairing.

A) probes; secondary; cruciform; interstrand; intrastrand
B) palindromes; tertiary; cruciform; interstrand; intrastrand
C) cruciforms; secondary; palindrome; intrastrand; interstrand
D) palindromes; tertiary; cruciform; intrastrand; interstrand
E) none are true.

Question 22

Histones are rich in the amino acids ____, and interact with DNA via ____.

A) alanine and glycine; covalent bonds
B) glutamic acid and aspartic acid; hydrogen bonds
C) glutamic acid and aspartic acid; ionic bonds
D) lysine and arginine; hydrogen bonds
E) lysine and arginine; ionic bonds

Question 23

Which of the following histone proteins has only one copy per nucleosome?

A) H1
B) H2A
C) H2B
D) H3
E) H4

Question 24

Discuss the changes in UV absorbance when DNA is denatured in certain temperature conditions.​

Question 25

The dimethoxytrityl (DMTr) group protects which functional group during synthetic DNA synthesis?

A) the primary amine group of adenine and guanine
B) the primary amine group of cytosine
C) the 3' hydroxyl of the deoxyribose
D) the 5' hydroxyl of the deoxyribose
E) both A and B are correct

Question 26

All are secondary structure components of tRNA EXCEPT:

A) acceptor stem.
B) D loop.
C) Anticodon loop.
D) TΨC loop.
E) All are true.

Question 27

Discuss riboswitches.​

Question 28

All are properties of nucleosomes EXCEPT:

A) protein spools neatly wrapped with DNA.
B) fundamental structural unit in chromatin.
C) protein spools made up of pairs of histones H2A, H2B, H3 and H4 octameric aggregates.
D) DNA binds histones by ionic bonds of positively charged amino acids and the negative charged phosphate groups.
E) all are true.

Question 29

Discuss SMC proteins.​

Question 30

Phylogenetic comparisons of secondary structures of rRNAs from a variety of species reveals ____ structures and ____ nucleotide sequences of the rRNAs themselves.

A) strikingly similar; high degree of similarity
B) strikingly similar; low degree of similarity
C) dissimilar; high degree of similarity
D) dissimilar; low degree of similarity
E) none of the above

Question 31

Individual amino acids are attached to their corresponding tRNAs:

A) through an ester linkage to the 3'-OH in the acceptor stem.
B) through an amide linkage to the anticodon loop.
C) through an amide linkage to the adenine ring at the 3'end of the tRNA.
D) through a phosphoester linkage to the 5' end of the tRNA.
E) None of the above.

Question 32

All are characteristics of DNA gyrase in E.coli EXCEPT:

A) It hydrolyzes ATP during its reaction mechanism.
B) It cuts both strands of a dsDNA.
C) It works to induce negative supercoiling in DNA.
D) It is classified as a topoisomerase.
E) All are true.

Question 33

Explain how electrostatic interactions stabilize the DNA double helix.​

Question 34

rRNA strands exhibit which of the following:

A) instrastrand sequence complementarity
B) highly folded patterns including many stem-loop structures
C) an anticodon loop
D) both a and b
E) a, b and c

Question 35

Discuss the chain termination protocol in Sanger's chain termination method to find the sequence of an unknown DNA fragment.​