Question 1

S. cerevisiae chromosome XI is 666,448 base pairs long. Calculate the length of this molecule, assuming it takes the form of B DNA.

Accepted Answer

To calculate the length of the Saccharom

Question 2

Describe a current hypothesis to explain the presence of functional DNA in mitochondria and chloroplasts.

Accepted Answer

One current hypothesis to explain the pr

Question 3

The gene for the hemoglobin $\beta$ subunit is 1,420 bp long and contains two introns that are 131 bp and 851 bp long. How long is the $\beta$-subunit polypeptide?

Accepted Answer

A)  146 amino acids long 
B)  327 amino acids long 
C)  438 amino acids long 
D)  473 amino acids long 
E)  2,140 amino acids long 
A)  146 amino acids long 
B)  327 amino acids long 
C)  438 amino acids long 
D)  473 amino acids long 
E)  2,140 amino acids long

Question 4

Which protein does NOT contribute to the octameric histone core?

Accepted Answer

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

Question 5

Which statement does NOT accurately describe a difference between histone H1 and the other histone proteins?

Accepted Answer

A)  Histone H1 is larger than the other histone proteins. 
B)  Histone H1 is not part of the nucleosome core. 
C)  Histone H1 has a lower percentage of basic amino acids than the other histones. 
D)  Histone H1 proteins occur at a lower frequency than other histones in 30-nm fibers. 
E)  Histone H1 associates with linker DNA, while the other histones do not. 
A)  Histone H1 is larger than the other histone proteins. 
B)  Histone H1 is not part of the nucleosome core. 
C)  Histone H1 has a lower percentage of basic amino acids than the other histones. 
D)  Histone H1 proteins occur at a lower frequency than other histones in 30-nm fibers. 
E)  Histone H1 associates with linker DNA, while the other histones do not.

Question 6

It is correct to say that DNA supercoiling CANNOT:

Accepted Answer

A)  be induced by strand separation. 
B)  be induced by underwinding of the double helix. 
C)  form if there is Z-DNA structure present. 
D)  occur if a closed circular double-stranded DNA molecule has a nick. 
E)  result in compaction of the DNA structure. 
A)  be induced by strand separation. 
B)  be induced by underwinding of the double helix. 
C)  form if there is Z-DNA structure present. 
D)  occur if a closed circular double-stranded DNA molecule has a nick. 
E)  result in compaction of the DNA structure.

Question 7

Which DNA structures are NOT generally circular?

Accepted Answer

A)  plasmids 
B)  yeast chromosomes 
C)  bacterial chromosomes 
D)  mitochondrial DNA 
E)  chloroplast DNA 
A)  plasmids 
B)  yeast chromosomes 
C)  bacterial chromosomes 
D)  mitochondrial DNA 
E)  chloroplast DNA

Question 8

Intercalating agents like ethidium bromide (EtBr) will tend to reduce the twist for DNA where it binds. What other changes would accompany EtBr binding to purified plasmid DNA?

Accepted Answer

A)  The linking number for the plasmid would increase. 
B)  The linking number for the plasmid would decrease. 
C)  Supercoils would become more positive (less negative). 
D)  Supercoiling would become more negative (less positive). 
E)  None of these changes would occur. 
A)  The linking number for the plasmid would increase. 
B)  The linking number for the plasmid would decrease. 
C)  Supercoils would become more positive (less negative). 
D)  Supercoiling would become more negative (less positive). 
E)  None of these changes would occur.

Question 9

Of the side-chain modifications listed, which ones will decrease the positive charge on a histone?

Accepted Answer

A)  lysine acetylation only 
B)  serine phosphorylation only 
C)  lysine methylation only 
D)  both lysine methylation and acetylation 
E)  both lysine acetylation and serine phosphorylation 
A)  lysine acetylation only 
B)  serine phosphorylation only 
C)  lysine methylation only 
D)  both lysine methylation and acetylation 
E)  both lysine acetylation and serine phosphorylation

Question 10

Calculate values for the following topological properties of a closed-circular DNA molecule containing 2000 base pairs (for simplicity, assume there are 10 base pairs per turn in the relaxed DNA).
(a) The linking number when the DNA is relaxed
(b) The linking number when the DNA has been underwound by 10 enzymatic turnovers of DNA gyrase (+ATP)
(c) The linking number when the DNA has been underwound by binding five nucleosomes followed by complete relaxation by a eukaryotic topoisomerase
(d) The superhelical density of the DNA molecule in (b)
(e) The superhelical density of the DNA molecule in (c)

Accepted Answer

(a) The linking number when the DNA is r

Question 11

Which factor distinguishes Type I from Type II topoisomerases?

Accepted Answer

A)  covalent attachment of the nucleic acid to a tyrosine 
B)  the presence of arginine and lysine residues in DNA binding sites 
C)  the use of phosphoanhydride bonds to provide energy 
D)  a mixture of covalent and noncovalent forces in binding of substrate 
E)  cleavage of the sugar-phosphate backbone in the nucleic acid substrate 
A)  covalent attachment of the nucleic acid to a tyrosine 
B)  the presence of arginine and lysine residues in DNA binding sites 
C)  the use of phosphoanhydride bonds to provide energy 
D)  a mixture of covalent and noncovalent forces in binding of substrate 
E)  cleavage of the sugar-phosphate backbone in the nucleic acid substrate

Question 12

A plasmid containing 16,700 base pairs has a superhelical density of -0.015 (superhelical density = writhe/twist). Assuming the duplex is all B-DNA, calculate the number of rounds of a Type II topoisomerase that would be required to relax this DNA (as close as possible to completely relaxed).

Accepted Answer

To calculate the number of rounds of a T

Question 13

The linking number (Lk) of a closed-circular, double-stranded DNA molecule is changed by:

Accepted Answer

A)  breaking a strand, then rejoining it. 
B)  breaking a strand, unwinding or rewinding the DNA, then rejoining it. 
C)  breaking all hydrogen bonds in the DNA. 
D)  supercoiling without the breaking of any phosphodiester bonds. 
E)  underwinding without the breaking of any phosphodiester bonds. 
A)  breaking a strand, then rejoining it. 
B)  breaking a strand, unwinding or rewinding the DNA, then rejoining it. 
C)  breaking all hydrogen bonds in the DNA. 
D)  supercoiling without the breaking of any phosphodiester bonds. 
E)  underwinding without the breaking of any phosphodiester bonds.

Question 14

Functional DNA is NOT found in:

Accepted Answer

A)  bacterial nucleoids. 
B)  chloroplasts. 
C)  lysosomes. 
D)  mitochondria. 
E)  nuclei. 
A)  bacterial nucleoids. 
B)  chloroplasts. 
C)  lysosomes. 
D)  mitochondria. 
E)  nuclei.

Question 15

Which description is NOT accurate regarding telomeres?

Accepted Answer

A)  sequences that are found at the ends of linear DNA chromosomes 
B)  portions of DNA that contain stretches of small, repetitive DNA sequences 
C)  sequences that are involved in DNA replication 
D)  sequences that are involved in the initiation of replication in eukaryotes 
E)  sequences that do not correspond to genes 
A)  sequences that are found at the ends of linear DNA chromosomes 
B)  portions of DNA that contain stretches of small, repetitive DNA sequences 
C)  sequences that are involved in DNA replication 
D)  sequences that are involved in the initiation of replication in eukaryotes 
E)  sequences that do not correspond to genes

Question 16

The DNA in a eukaryotic 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 17

How long is the linker DNA between nucleosomes in the 30-nm fiber?

Accepted Answer

A)  approximately 20 base pairs 
B)  approximately 50 base pairs 
C)  approximately 100 base pairs 
D)  approximately 150 base pairs 
E)  approximately 200 base pairs 
A)  approximately 20 base pairs 
B)  approximately 50 base pairs 
C)  approximately 100 base pairs 
D)  approximately 150 base pairs 
E)  approximately 200 base pairs

Question 18

When plasmids are mixed with histones, they will bind fewer histones than the equivalent length of linear DNA. Upon addition of a topoisomerase, more histones will be bound. Explain this observation.

Accepted Answer

The observation that plasmids bind fewer

Question 19

What are histones and what is their principal role in chromatin structure?

Accepted Answer

Histones are a type of protein found in

Question 20

What is satellite DNA?

Accepted Answer

Satellite DNA refers to repetitive and n

Exam 24: Genes and Chromosomes

S. cerevisiae chromosome XI is 666,448 base pairs long. Calculate the length of this molecule, assuming it takes the form of B DNA.

Describe a current hypothesis to explain the presence of functional DNA in mitochondria and chloroplasts.

The gene for the hemoglobin β\betaβ subunit is 1,420 bp long and contains two introns that are 131 bp and 851 bp long. How long is the β\betaβ -subunit polypeptide?

Which protein does NOT contribute to the octameric histone core?

Which statement does NOT accurately describe a difference between histone H1 and the other histone proteins?

It is correct to say that DNA supercoiling CANNOT:

Which DNA structures are NOT generally circular?

Intercalating agents like ethidium bromide (EtBr) will tend to reduce the twist for DNA where it binds. What other changes would accompany EtBr binding to purified plasmid DNA?

Of the side-chain modifications listed, which ones will decrease the positive charge on a histone?

Which factor distinguishes Type I from Type II topoisomerases?

A plasmid containing 16,700 base pairs has a superhelical density of -0.015 (superhelical density = writhe/twist). Assuming the duplex is all B-DNA, calculate the number of rounds of a Type II topoisomerase that would be required to relax this DNA (as close as possible to completely relaxed).

The linking number (Lk) of a closed-circular, double-stranded DNA molecule is changed by:

Functional DNA is NOT found in:

Which description is NOT accurate regarding telomeres?

The DNA in a eukaryotic chromosome is BEST described as:

How long is the linker DNA between nucleosomes in the 30-nm fiber?

When plasmids are mixed with histones, they will bind fewer histones than the equivalent length of linear DNA. Upon addition of a topoisomerase, more histones will be bound. Explain this observation.

What are histones and what is their principal role in chromatin structure?

What is satellite DNA?

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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The gene for the hemoglobin $\beta$ subunit is 1,420 bp long and contains two introns that are 131 bp and 851 bp long. How long is the $\beta$ -subunit polypeptide?