Question 1

What is satellite DNA?

Accepted Answer

Satellite DNA (also known as highly repetitive or simple-sequence DNA)consists of regions of the eukaryotic genome that are different enough in base composition from the bulk of the chromosomal DNA that they can be separated from it by density gradient centrifugation.Satellite DNA is often associated with centromeres and telomeres and consists of short sequences (5 to 10 base pairs)that are repeated millions of times per cell.

Question 2

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)200; 
(b)180; 
(c)195 
(d)-0.1; 
(e)-0.025

Question 3

Define topoisomerase,and explain the difference between type I and type II topoisomerases.

Accepted Answer

Topoisomerases are enzymes that change the linking number in a closed-circular,double-stranded DNA molecule by breaking one or two strands,adding or removing twists,and rejoining the strand(s).Type 1 topoisomerases break and rejoin only one strand,changing the linking number in increments of 1.Type 2 topoisomerases break and rejoin both strands,changing the linking number in increments of 2.

Question 4

Describe the structure and function of a typical bacterial plasmid.

Accepted Answer

Bacterial plasmids are generally closed-

Question 5

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)E.coli topoisomerase II or

Question 6

Which of the following contributes to the structure of nucleosomes?

Accepted Answer

A) Plectonemic supercoiled DNA 
B) Relaxed closed-circular DNA 
C) Solenoidal supercoiled DNA 
D) Spacer DNA 
E) Z (left-handed)DNA 
A) Plectonemic supercoiled DNA 
B) Relaxed closed-circular DNA 
C) Solenoidal supercoiled DNA 
D) Spacer DNA 
E) Z (left-handed)DNA

Question 7

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 8

A commonality between type I and type II topoisomerases is that they both:

Accepted Answer

A) change the linking number in increments of 1 or 2. 
B) require ATP. 
C) go through a mechanism using a covalent enzyme-substrate intermediate. 
D) are inhibited by quinoline antibiotics. 
E) All of the above 
A) change the linking number in increments of 1 or 2. 
B) require ATP. 
C) go through a mechanism using a covalent enzyme-substrate intermediate. 
D) are inhibited by quinoline antibiotics. 
E) All of the above

Question 9

Describe two functions of DNA supercoiling.

Accepted Answer

Supercoiling allows for the extreme comp

Question 10

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 E.coli gene is 1046 bp long;

Question 11

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 12

DNA in a closed-circular,double-stranded molecule with no net bending of the DNA axis on itself is:

Accepted Answer

A) a left-handed helix. 
B) a mixed right- and left-handed helix. 
C) relaxed. 
D) supercoiled. 
E) underwound. 
A) a left-handed helix. 
B) a mixed right- and left-handed helix. 
C) relaxed. 
D) supercoiled. 
E) underwound.

Question 13

Bacterial chromosomes:

Accepted Answer

A) are highly compacted into structures called nucleoids. 
B) are seen in electron microscopy as "beads on a string." 
C) are surrounded by a nuclear membrane. 
D) contain large numbers of nucleosomes. 
E) when fully extended are as long as the bacterial cell. 
A) are highly compacted into structures called nucleoids. 
B) are seen in electron microscopy as "beads on a string." 
C) are surrounded by a nuclear membrane. 
D) contain large numbers of nucleosomes. 
E) when fully extended are as long as the bacterial cell.

Question 14

What are introns?

Accepted Answer

Introns are regions of genes (primarily

Question 15

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

Accepted Answer

Histones are small basic proteins that b

Question 16

SMC proteins facilitate the structural maintenance of chromosomes;describe the roles of the two main classes.

Accepted Answer

The cohesins help link sister chromatids

Question 17

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 18

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

Accepted Answer

These organelles are thought to have ori

Question 19

Define,in the context of DNA structure,"topological bonds."

Accepted Answer

Topological bonds are links be

Question 20

Introns:

Accepted Answer

A) are frequently present in prokaryotic genes but are rare in eukaryotic genes. 
B) are spliced out before transcription. 
C) are translated but not transcribed. 
D) can occur many times within a single gene. 
E) encode unusual amino acids in proteins. 
A) are frequently present in prokaryotic genes but are rare in eukaryotic genes. 
B) are spliced out before transcription. 
C) are translated but not transcribed. 
D) can occur many times within a single gene. 
E) encode unusual amino acids in proteins.

Exam 24: Genes and Chromosomes

What is satellite DNA?

Define topoisomerase,and explain the difference between type I and type II topoisomerases.

Describe the structure and function of a typical bacterial plasmid.

Which of the following contributes to the structure of nucleosomes?

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

A commonality between type I and type II topoisomerases is that they both:

Describe two functions of DNA supercoiling.

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.

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

DNA in a closed-circular,double-stranded molecule with no net bending of the DNA axis on itself is:

Bacterial chromosomes:

What are introns?

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

SMC proteins facilitate the structural maintenance of chromosomes;describe the roles of the two main classes.

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:

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

Define,in the context of DNA structure,"topological bonds."

Introns:

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

Recombinant Dna Technology

Lipids

Biological Membranes and Transport

Biosignaling

Principles of Bioenergetics

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

Integration and Hormonal Regulation of Mammalian Metabolism

Dna Metabolism

Rna Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

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: