Question 1

Which statement is TRUE of the pentoses found in nucleic acids?

Accepted Answer

A)  C-5 and C-1 of the pentose are joined to phosphate groups. 
B)  The pentoses are in a planar configuration. 
C)  The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond. 
D)  The pentoses are always in the $\beta$-furanose forms. 
E)  The straight-chain and ring forms undergo constant interconversion. 
A)  C-5 and C-1 of the pentose are joined to phosphate groups. 
B)  The pentoses are in a planar configuration. 
C)  The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond. 
D)  The pentoses are always in the $\beta$-furanose forms. 
E)  The straight-chain and ring forms undergo constant interconversion.

Question 2

In the Watson-Crick model of DNA structure:

Accepted Answer

A)  both strands run in the same direction, 3' $\rightarrow$ 5'; they are parallel. 
B)  phosphate groups project toward the middle of the helix, where they are protected from interaction with water. 
C)  T can form three hydrogen bonds with either G or C in the opposite strand. 
D)  the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines. 
E)  the distance between two adjacent bases in one strand is about 3.4 Å. 
A)  both strands run in the same direction, 3' $\rightarrow$ 5'; they are parallel. 
B)  phosphate groups project toward the middle of the helix, where they are protected from interaction with water. 
C)  T can form three hydrogen bonds with either G or C in the opposite strand. 
D)  the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines. 
E)  the distance between two adjacent bases in one strand is about 3.4 Å.

Question 3

A tetraplex of DNA is MOST likely to form with which residue?

Accepted Answer

A)  Adenosine 
B)  Thymidine 
C)  Guanosine 
D)  Cytidine 
E)  A tetraplex is equally likely with all bases. 
A)  Adenosine 
B)  Thymidine 
C)  Guanosine 
D)  Cytidine 
E)  A tetraplex is equally likely with all bases.

Question 4

The image below shows a DNA sequencing gel using the Sanger method. The top of the gel is the anode and the bottom is the cathode. What is the sequence of the template DNA?

Accepted Answer

A)  5' ACTAGTGACCGT 3' 
B)  5'TGCCAGTGATCA 3' 
C)  5' ACGGTCACTAGT 3' 
D)  5' TGATCACTGGCA 3' 
E)  It cannot be determined from this information. 
A)  5' ACTAGTGACCGT 3' 
B)  5'TGCCAGTGATCA 3' 
C)  5' ACGGTCACTAGT 3' 
D)  5' TGATCACTGGCA 3' 
E)  It cannot be determined from this information.

Question 5

The MOST striking difference between A-, B-, and Z-form DNA is that:

Accepted Answer

A)  A -orm does not contain a major and minor groove. 
B)  B-form has the smallest helical diameter. 
C)  Z-form is left handed. 
D)  B-form has the greatest number of base pairs per helical turn. 
E)  A-form maximizes base stacking interactions. 
A)  A -orm does not contain a major and minor groove. 
B)  B-form has the smallest helical diameter. 
C)  Z-form is left handed. 
D)  B-form has the greatest number of base pairs per helical turn. 
E)  A-form maximizes base stacking interactions.

Question 6

Which sequence is palindromic?

Accepted Answer

A)  AGGTCC
TCCAGG 
B)  CCTTCC
GCAAGG 
C)  GAATCC
CTTAGG 
D)  GGATCC
CCTAGG 
E)  GTATCC
CATAGG 
A)  AGGTCC
TCCAGG 
B)  CCTTCC
GCAAGG 
C)  GAATCC
CTTAGG 
D)  GGATCC
CCTAGG 
E)  GTATCC
CATAGG

Question 7

In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is:

Accepted Answer

A)  DNA-DNA > DNA-RNA > RNA-RNA. 
B)  DNA-DNA > RNA-RNA > DNA-RNA. 
C)  RNA-DNA > RNA-RNA > DNA-DNA. 
D)  RNA-RNA > DNA-DNA > DNA-RNA. 
E)  RNA-RNA > DNA-RNA > DNA-DNA. 
A)  DNA-DNA > DNA-RNA > RNA-RNA. 
B)  DNA-DNA > RNA-RNA > DNA-RNA. 
C)  RNA-DNA > RNA-RNA > DNA-DNA. 
D)  RNA-RNA > DNA-DNA > DNA-RNA. 
E)  RNA-RNA > DNA-RNA > DNA-DNA.

Question 8

In DNA sequencing by the Sanger (dideoxy) method:

Accepted Answer

A)  radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic synthesis of complementary strands. 
B)  specific enzymes are used to cut the newly synthesized DNA into small pieces, which are then separated by electrophoresis. 
C)  the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence. 
D)  the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs occur in the template strands. 
E)  the template DNA strand is radioactive. 
A)  radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic synthesis of complementary strands. 
B)  specific enzymes are used to cut the newly synthesized DNA into small pieces, which are then separated by electrophoresis. 
C)  the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence. 
D)  the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs occur in the template strands. 
E)  the template DNA strand is radioactive.

Question 9

The scientists who used x-ray crystallography to shed light on the three-dimensional structure of DNA were:

Accepted Answer

A)  Erwin Chargaff and colleagues. 
B)  Alfred D. Hershey and Martha Chase. 
C)  James Watson and Francis Crick. 
D)  Rosalind Franklin and Maurice Wilkins. 
E)  Oswald T. Avery, Colin MacLeod, and Maclyn McCarty. 
A)  Erwin Chargaff and colleagues. 
B)  Alfred D. Hershey and Martha Chase. 
C)  James Watson and Francis Crick. 
D)  Rosalind Franklin and Maurice Wilkins. 
E)  Oswald T. Avery, Colin MacLeod, and Maclyn McCarty.

Question 10

In nucleotides and nucleic acids, syn and anti conformations relate to:

Accepted Answer

A)  base stereoisomers. 
B)  rotation around the phosphodiester bond. 
C)  rotation around the sugar-base bond. 
D)  sugar pucker. 
E)  sugar stereoisomers. 
A)  base stereoisomers. 
B)  rotation around the phosphodiester bond. 
C)  rotation around the sugar-base bond. 
D)  sugar pucker. 
E)  sugar stereoisomers.

Question 11

A) Explain the similarities and differences between monocistronic and polycistronic mRNAs.
B) State the domains (Bacteria, Archaea, Eukaryota) in which these types of mRNAs may be found.

Accepted Answer

Monocistronic and polycistronic mRNAs ar

Question 12

Write a double-stranded DNA sequence containing a six-nucleotide palindrome.

Accepted Answer

5'- ATCGAT

Question 13

A pyrimidine is joined covalently to the pentose sugar through the:

Accepted Answer

A)  N-1 of the base to the 1' carbon of the pentose. 
B)  N-9 of the base to the 1' carbon of the pentose. 
C)  N-1 of the base to the 5' carbon of the pentose. 
D)  N-9 of the base to the 5' carbon of the pentose. 
E)  None of the answers is correct. 
A)  N-1 of the base to the 1' carbon of the pentose. 
B)  N-9 of the base to the 1' carbon of the pentose. 
C)  N-1 of the base to the 5' carbon of the pentose. 
D)  N-9 of the base to the 5' carbon of the pentose. 
E)  None of the answers is correct.

Question 14

Which base compositions for single-stranded RNA are possible? %A
%G
%C
%T
%U

Accepted Answer

A)  5
45
45
0
5 
B)  25
25
25
0
25 
C)  35
10
30
0
25 
D)  All of the answers are correct. 
E)  None of the answers is correct. 
A)  5
45
45
0
5 
B)  25
25
25
0
25 
C)  35
10
30
0
25 
D)  All of the answers are correct. 
E)  None of the answers is correct.

Question 15

The chemical difference between a nucleotide and a nucleoside is that:

Accepted Answer

A)  a different nitrogenous base is added to each. 
B)  nucleotides do not contain phosphate groups. 
C)  nucleosides do not contain phosphate groups. 
D)  nucleotides do not contain pentose sugars 
E)  nucleosides do not contain pentose sugars. 
A)  a different nitrogenous base is added to each. 
B)  nucleotides do not contain phosphate groups. 
C)  nucleosides do not contain phosphate groups. 
D)  nucleotides do not contain pentose sugars 
E)  nucleosides do not contain pentose sugars.

Question 16

Which of the following would have the HIGHEST melting temperature?

Accepted Answer

A)  20-mer double-stranded DNA-DNA duplex 
B)  20-mer double-stranded RNA-RNA duplex 
C)  40-mer double-stranded DNA-DNA duplex 
D)  40-mer double-stranded DNA-RNA duplex 
E)  40-mer double-stranded RNA-RNA duplex 
A)  20-mer double-stranded DNA-DNA duplex 
B)  20-mer double-stranded RNA-RNA duplex 
C)  40-mer double-stranded DNA-DNA duplex 
D)  40-mer double-stranded DNA-RNA duplex 
E)  40-mer double-stranded RNA-RNA duplex

Question 17

Describe qualitatively how the tm for a double-stranded DNA depends on its nucleotide composition.

Accepted Answer

The t for a double-stranded DNA depends

Question 18

Match the type of bond with the role below:
Bond type
Role
(a) phosphodiester
___ links base to pentose in nucleotide
(b) N-glycosidic
___ joins adjacent nucleotides in one strand
(c) phosphate ester
___ joins complementary nucleotides in two strands
(d) hydrogen
___ difference between a nucleoside and a nucleotide

Accepted Answer

The correct match between the type of bo

Question 19

The covalent backbone of DNA and RNA consists of:

Accepted Answer

A)  alternating phosphate groups and nitrogenous bases. 
B)  alternating phosphate groups and pentose residues. 
C)  alternating pentose residues and nitrogenous bases. 
D)  alternating pentose residues and cyclic nucleosides. 
E)  None of the answers is correct. 
A)  alternating phosphate groups and nitrogenous bases. 
B)  alternating phosphate groups and pentose residues. 
C)  alternating pentose residues and nitrogenous bases. 
D)  alternating pentose residues and cyclic nucleosides. 
E)  None of the answers is correct.

Question 20

What would happen if blocking tags were NOT used in reversible terminator sequencing, a next-generation method of DNA sequencing?

Accepted Answer

A)  The DNA fragments to sequence/read would be too large. 
B)  More than one dNTP could be incorporated to the same growing nucleotide chain during a single cycle. 
C)  The flow cell could not immobilize DNA fragments. 
D)  Multiple fluorescent colors could be observed across the flow cell at the same time. 
E)  Luciferase would not react in the presence of ATP. 
A)  The DNA fragments to sequence/read would be too large. 
B)  More than one dNTP could be incorporated to the same growing nucleotide chain during a single cycle. 
C)  The flow cell could not immobilize DNA fragments. 
D)  Multiple fluorescent colors could be observed across the flow cell at the same time. 
E)  Luciferase would not react in the presence of ATP.

Exam 8: Nucleotides and Nucleic Acids

Which statement is TRUE of the pentoses found in nucleic acids?

In the Watson-Crick model of DNA structure:

A tetraplex of DNA is MOST likely to form with which residue?

The image below shows a DNA sequencing gel using the Sanger method. The top of the gel is the anode and the bottom is the cathode. What is the sequence of the template DNA?

The MOST striking difference between A-, B-, and Z-form DNA is that:

Which sequence is palindromic?

In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is:

In DNA sequencing by the Sanger (dideoxy) method:

The scientists who used x-ray crystallography to shed light on the three-dimensional structure of DNA were:

In nucleotides and nucleic acids, syn and anti conformations relate to:

A) Explain the similarities and differences between monocistronic and polycistronic mRNAs. B) State the domains (Bacteria, Archaea, Eukaryota) in which these types of mRNAs may be found.

Write a double-stranded DNA sequence containing a six-nucleotide palindrome.

A pyrimidine is joined covalently to the pentose sugar through the:

Which base compositions for single-stranded RNA are possible? %A %G %C %T %U

The chemical difference between a nucleotide and a nucleoside is that:

Which of the following would have the HIGHEST melting temperature?

Describe qualitatively how the tm for a double-stranded DNA depends on its nucleotide composition.

The covalent backbone of DNA and RNA consists of:

What would happen if blocking tags were NOT used in reversible terminator sequencing, a next-generation method of DNA sequencing?

The Foundations of Biochemistry

Water

Amino Acids, Peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

DNA-Based Information Technologies

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

DNA Metabolism

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

Describe qualitatively how the t_m for a double-stranded DNA depends on its nucleotide composition.