Question 1

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

Accepted Answer

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 
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 D

Question 2

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

Accepted Answer

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

Question 3

Urea and formamide are agents that denature dsDNA by

Accepted Answer

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 
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 C

Question 4

Explain how electrostatic interactions stabilize the DNA double helix.​

Accepted Answer

A prominent feature of the backbone of a

Question 5

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.

Accepted Answer

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. 
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 6

All are true for linking number EXCEPT:

Accepted Answer

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. 
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 7

All are true for DNA polymerase EXCEPT:

Accepted Answer

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. 
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 8

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

Accepted Answer

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 
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 9

Discuss riboswitches.​

Accepted Answer

Riboswitches are a naturally occurring c

Question 10

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

Accepted Answer

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. 
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 11

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

Accepted Answer

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

Question 12

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

Accepted Answer

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

Question 13

Which of the following enzymes introduces negative supercoils into DNA?

Accepted Answer

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

Question 14

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

Accepted Answer

When duplex DNA molecules are subjected

Question 15

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

Accepted Answer

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 
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 16

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

Accepted Answer

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

Question 17

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

Accepted Answer

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 
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 18

Individual amino acids are attached to their corresponding tRNAs:

Accepted Answer

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. 
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 19

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

Accepted Answer

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

Question 20

All are secondary structure components of tRNA EXCEPT:

Accepted Answer

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

Exam 11: Structure of Nucleic Acids

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

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

Urea and formamide are agents that denature dsDNA by

Explain how electrostatic interactions stabilize the DNA double helix.​

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.

All are true for linking number EXCEPT:

All are true for DNA polymerase EXCEPT:

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

Discuss riboswitches.​

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

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

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

Which of the following enzymes introduces negative supercoils into DNA?

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

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

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

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

Individual amino acids are attached to their corresponding tRNAs:

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

All are secondary structure components of tRNA EXCEPT:

The Facts of Life: Chemistry Is the Logic of Biological Phenomena

Water: the Medium of Life

Thermodynamics of Biological Systems

Amino Acids and the Peptide Bond

Proteins: Their Primary Structure and Biological Functions

Proteins: Secondary, Tertiary, and Quaternary Structure

Carbohydrates and the Glycoconjugates of Cell Surfaces

Lipids

Membranes and Membrane Transport

Nucleotides and Nucleic Acids

Recombinant Dna, Cloning, Chimeric Genes, and Synthetic Biology

Enzymeskinetics and Specificity

Mechanisms of Enzyme Action

Enzyme Regulation

Molecular Motors

Metabolism: an Overview

Glycolysis

The Tricarboxylic Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Fatty Acid Catabolism

Lipid Biosynthesis

Nitrogen Acquisition and Amino Acid Metabolism

Synthesis and Degradation of Nucleotides

Metabolic Integration and Organ Specialization

Dna Metabolism: Replication, Recombination, and Repair

Transcription and the Regulation of Gene Expression

Protein Synthesis

Completing the Protein Life Cycle: Folding, Processing, and Degradation

The Reception and Transmission of Extracellular Information

Filters

Explain how electrostatic interactions stabilize the DNA double helix.

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.

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

Discuss riboswitches.

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

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

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

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.