Question 1

If negatively supercoiled plasmid DNA is mixed with human topoisomerase I and ATP, which effect would be observed?

Accepted Answer

A)  Rapid ATP hydrolysis would occur. 
B)  The linking number for the plasmid would increase. 
C)  The writhe on the plasmid would increase. 
D)  The superhelical density would become more negative. 
E)  None of these effects would be observed. 
A)  Rapid ATP hydrolysis would occur. 
B)  The linking number for the plasmid would increase. 
C)  The writhe on the plasmid would increase. 
D)  The superhelical density would become more negative. 
E)  None of these effects would be observed. C

Question 2

The DNA of virtually every cell is underwound (i.e., negatively supercoiled) relative to B-form DNA. In bacteria, an enzyme called (a) _____ introduces negative supertwists into DNA using (b) _____ as a source of energy. This enzyme is classified as a type (c) _____, which affects the linking number in steps of (d) _____. The usual substrate for this enzyme within an E. coli cell is the bacterial chromosome. This circular DNA molecule of 4,700,000 base pairs has a linking number of approximately (e) _____ when it is closed and relaxed. This enzyme would (f) _____ (decrease/increase/not change) this linking number when acting upon this DNA molecule in the presence of the above energy source.

Accepted Answer

A: The DNA of virtually every cell is underwound (i.e., negatively supercoiled) relative to B-form DNA. In bacteria, an enzyme called (a) DNA gyrase (or topoisomerase II) introduces negative supertwists into DNA using (b) ATP as a source of energy. This enzyme is classified as a type (c) II topoisomerase, which affects the linking number in steps of (d) 2. The usual substrate for this enzyme within an E. coli cell is the bacterial chromosome. This circular DNA molecule of 4,700,000 base pairs has a linking number of approximately (e) 4,700,000/10.5 ≈ 447,619 when it is closed and relaxed (assuming about 10.5 base pairs per turn of the DNA helix). This enzyme would (f) decrease this linking number when acting upon this DNA molecule in the presence of the above energy source.

Question 3

The fundamental repeating unit of organization in a eukaryotic chromosome is the:

Accepted Answer

A)  centrosome. 
B)  lysosome. 
C)  microsome. 
D)  nucleosome. 
E)  polysome. 
A)  centrosome. 
B)  lysosome. 
C)  microsome. 
D)  nucleosome. 
E)  polysome. D

Question 4

The DNA in a bacterial (prokaryotic) chromosome is BEST described as:

Accepted Answer

A)  a single circular double-helical molecule. 
B)  a single linear double-helical molecule. 
C)  a single linear single-stranded molecule. 
D)  multiple linear double-helical molecules. 
E)  multiple linear single-stranded molecules. 
A)  a single circular double-helical molecule. 
B)  a single linear double-helical molecule. 
C)  a single linear single-stranded molecule. 
D)  multiple linear double-helical molecules. 
E)  multiple linear single-stranded molecules.

Question 5

The chromosomal region that is the point of attachment of the mitotic spindle is the:

Accepted Answer

A)  centromere. 
B)  endomere. 
C)  exon. 
D)  intron. 
E)  telomere. 
A)  centromere. 
B)  endomere. 
C)  exon. 
D)  intron. 
E)  telomere.

Question 6

Heterochromatin is NOT associated with:

Accepted Answer

A)  histone H1. 
B)  "beads on a string" conformation. 
C)  lower transcriptional rates than euchromatin is. 
D)  higher-order nucleosome-nucleosome interactions. 
E)  highly compact chromatin structures. 
A)  histone H1. 
B)  "beads on a string" conformation. 
C)  lower transcriptional rates than euchromatin is. 
D)  higher-order nucleosome-nucleosome interactions. 
E)  highly compact chromatin structures.

Question 7

B-DNA has 10.5 base pairs per turn, while Z-DNA has 12 base pairs per turn. What will be the effect on a plasmid where 24 base pairs switch from the B to the Z form?

Accepted Answer

A)  The linking number will decrease by 2. 
B)  The writhe will decrease by approximately 2. 
C)  The twist will increase by approximately 4. 
D)  The writhe will increase by approximately 4. 
E)  The writhe will decrease by approximately 2, and the twist will increase by approximately 4. 
A)  The linking number will decrease by 2. 
B)  The writhe will decrease by approximately 2. 
C)  The twist will increase by approximately 4. 
D)  The writhe will increase by approximately 4. 
E)  The writhe will decrease by approximately 2, and the twist will increase by approximately 4.

Question 8

Which statement does NOT apply to the topoisomerase IA mechanism?

Accepted Answer

A)  A covalent bond is formed from the protein to the 3' phosphate of a nucleotide. 
B)  Two strands of the nucleic acid remains intact. 
C)  The action of the enzyme changes the linking number by single increments. 
D)  The action of the enzyme will decrease the magnitude of the superhelical density. 
E)  Energy for the process comes from the supercoiling strain in the nucleic acid. 
A)  A covalent bond is formed from the protein to the 3' phosphate of a nucleotide. 
B)  Two strands of the nucleic acid remains intact. 
C)  The action of the enzyme changes the linking number by single increments. 
D)  The action of the enzyme will decrease the magnitude of the superhelical density. 
E)  Energy for the process comes from the supercoiling strain in the nucleic acid.

Question 9

Which statement is FALSE?

Accepted Answer

A)  Histones are very conserved at the primary sequence level in eukaryotes. 
B)  Histones H2A, H2B, and H1 all contain the histone fold domain (HF
D) . 
C)  CENPA is most closely related to histone H3. 
D)  The amino terminal tail of histone H3 is the location of most of its covalent modifications. 
E)  Amino terminal ends of core histones are involved in internucleosome interactions. 
A)  Histones are very conserved at the primary sequence level in eukaryotes. 
B)  Histones H2A, H2B, and H1 all contain the histone fold domain (HF
D) . 
C)  CENPA is most closely related to histone H3. 
D)  The amino terminal tail of histone H3 is the location of most of its covalent modifications. 
E)  Amino terminal ends of core histones are involved in internucleosome interactions.

Question 10

If a plasmid has 11,025 base pairs and a superhelical density of -0.06, what is the linking number? Assume the structure is B-DNA (10.5 bases/turn).

Accepted Answer

A)  389 
B)  661 
C)  987 
D)  1,050 
E)  1,113 
A)  389 
B)  661 
C)  987 
D)  1,050 
E)  1,113

Question 11

When plasmid DNA is purified from E. coli and then subsequently analyzed by electrophoresis in the presence of ethidium bromide (EtBr), three separate bands are typically observed. What would you predict to be the difference in each band, and how would you predict they would migrate relative to each other (i.e., slowest to fastest)?

Accepted Answer

When plasmid DNA is purified from E. col

Question 12

Which statement does NOT contradict the one gene-one enzyme hypothesis?

Accepted Answer

A)  Some genes code for subunits in a quaternary structure. 
B)  Some genes codes for structural RNA products. 
C)  Some genes codes for RNA catalysts. 
D)  Regulatory sequences provide signals outside coding regions of DNA. 
E)  None of these statements contradicts the one gene-one enzyme hypothesis. 
A)  Some genes code for subunits in a quaternary structure. 
B)  Some genes codes for structural RNA products. 
C)  Some genes codes for RNA catalysts. 
D)  Regulatory sequences provide signals outside coding regions of DNA. 
E)  None of these statements contradicts the one gene-one enzyme hypothesis.

Question 13

In which cell-cycle step does condensin dissociate from chromatids?

Accepted Answer

A)  G1/S 
B)  S/G2 
C)  during prophase 
D)  during anaphase 
E)  during telophase 
A)  G1/S 
B)  S/G2 
C)  during prophase 
D)  during anaphase 
E)  during telophase

Question 14

Describe the composition and structure of a nucleosome.

Accepted Answer

A nucleosome is the basic unit of DNA pa

Question 15

Nucleosomes:

Accepted Answer

A)  are important features of chromosome organization in eukaryotes and bacteria. 
B)  are composed of proteins rich in acidic amino acids, such as Asp and Glu. 
C)  are composed of protein and RNA. 
D)  bind DNA and alter its supercoiling. 
E)  occur in chromatin at irregular intervals along the DNA molecule. 
A)  are important features of chromosome organization in eukaryotes and bacteria. 
B)  are composed of proteins rich in acidic amino acids, such as Asp and Glu. 
C)  are composed of protein and RNA. 
D)  bind DNA and alter its supercoiling. 
E)  occur in chromatin at irregular intervals along the DNA molecule.

Question 16

The genome of the bacterium E. coli is 4,639,675 bp long and consists of 4435 genes; the human genome is 3,070,128,600 bp long and consists of roughly 29,000 genes. Calculate the average gene size in each organism and provide an explanation for the difference.

Accepted Answer

The average gene size in E. coli can be

Question 17

Which list ranks the organisms in order of INCREASING number of genes?

Accepted Answer

A)  S. cerevisiae < humans < rice 
B)  S. cerevisiae < rice < humans 
C)  rice < humans < S. cerevisiae 
D)  rice < S. cerevisiae < humans 
E)  humans < S. cerevisiae < rice 
A)  S. cerevisiae < humans < rice 
B)  S. cerevisiae < rice < humans 
C)  rice < humans < S. cerevisiae 
D)  rice < S. cerevisiae < humans 
E)  humans < S. cerevisiae < rice

Question 18

Indicate whether the following statements are true (T) or false (F).
___ The linking number (Lk) of a closed-circular DNA molecule can be changed only by breaking one or both strands.
___ DNA of all organisms is overwound (i.e., positively supercoiled).
___ Topoisomerase I relaxes DNA that is highly negatively supercoiled.

Accepted Answer

The linking number (Lk) of a closed-circ

Question 19

If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference ($\sigma$) is -0.05, the number of:

Accepted Answer

A)  bases is decreased by 5%. 
B)  bases is increased by 5%. 
C)  helical turns is decreased by 5%. 
D)  helical turns is increased by 5%. 
E)  helical turns is unchanged. 
A)  bases is decreased by 5%. 
B)  bases is increased by 5%. 
C)  helical turns is decreased by 5%. 
D)  helical turns is increased by 5%. 
E)  helical turns is unchanged.

Question 20

If relaxed plasmid DNA is treated with E. coli DNA gyrase and ATP, which effect would NOT be observed?

Accepted Answer

A)  ATP hydrolysis would occur. 
B)  The linking number for the plasmid would decrease. 
C)  The writhe on the plasmid would increase. 
D)  The superhelical density would become more negative. 
E)  All of these effects would be observed. 
A)  ATP hydrolysis would occur. 
B)  The linking number for the plasmid would decrease. 
C)  The writhe on the plasmid would increase. 
D)  The superhelical density would become more negative. 
E)  All of these effects would be observed.

Exam 24: Genes and Chromosomes

If negatively supercoiled plasmid DNA is mixed with human topoisomerase I and ATP, which effect would be observed?

The fundamental repeating unit of organization in a eukaryotic chromosome is the:

The DNA in a bacterial (prokaryotic) chromosome is BEST described as:

The chromosomal region that is the point of attachment of the mitotic spindle is the:

Heterochromatin is NOT associated with:

B-DNA has 10.5 base pairs per turn, while Z-DNA has 12 base pairs per turn. What will be the effect on a plasmid where 24 base pairs switch from the B to the Z form?

Which statement does NOT apply to the topoisomerase IA mechanism?

Which statement is FALSE?

If a plasmid has 11,025 base pairs and a superhelical density of -0.06, what is the linking number? Assume the structure is B-DNA (10.5 bases/turn).

Which statement does NOT contradict the one gene-one enzyme hypothesis?

In which cell-cycle step does condensin dissociate from chromatids?

Describe the composition and structure of a nucleosome.

Nucleosomes:

The genome of the bacterium E. coli is 4,639,675 bp long and consists of 4435 genes; the human genome is 3,070,128,600 bp long and consists of roughly 29,000 genes. Calculate the average gene size in each organism and provide an explanation for the difference.

Which list ranks the organisms in order of INCREASING number of genes?

If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference ( σ\sigmaσ ) is -0.05, the number of:

If relaxed plasmid DNA is treated with E. coli DNA gyrase and ATP, which effect would NOT be observed?

The Foundations of Biochemistry

Water

Amino Acids, Peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

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

DNA Metabolism

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

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If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference ( $\sigma$ ) is -0.05, the number of: