Deck 24: Genes and Chromosomes

Question 1

Topoisomerases can:

A)change the linking number (Lk)of a DNA molecule.
B)change the number of base pairs in a DNA molecule.
C)change the number of nucleotides in a DNA molecule.
D)convert D isomers of nucleotides to L isomers.
E)interconvert DNA and RNA.

Answer 1

change the linking number (Lk)of a DNA molecule.

Question 2

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

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.

Answer 2

a single circular double-helical molecule.

Question 3

The DNA in a eukaryotic chromosome is best described as:

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.

Answer 3

a single linear double-helical molecule.

Question 4

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

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 5

Plectonemic supercoils in a negatively supercoiled DNA molecule:

A)are always left-handed.
B)are always right-handed.
C)are balanced by solenoidal supercoils
D)can be either right- or left-handed.
E)never occur.

Question 6

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

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

Question 7

It is correct to say that DNA supercoiling cannot:

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 8

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

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

Question 9

Topoisomerases:

A)can change the linking number in increments of 1 or 2.
B)can act on single-stranded DNA circles.
C)change the degree of supercoiling of a DNA molecule but not its linking number of DNA.
D)occur in bacteria,but not in eukaryotes.
E)always require energy from ATP.

Question 10

Which of the following does not contribute to the octameric histone core?

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

Question 11

Which of these statements about nucleic acids is false?

A)Mitochondria and chloroplasts contain DNA.
B)Plasmids are genes that encode plasma proteins in mammals.
C)The chromosome of E.coli is a closed-circular,double-helical DNA.
D)The DNA of viruses is usually much longer than the viral particle itself.
E)The genome of many plant viruses is RNA.

Question 12

Histones are _______ that are usually associated with _________.

A)acidic proteins;DNA
B)acidic proteins;RNA
C)basic proteins;DNA
D)basic proteins;RNA
E)coenzymes derived from histidine;enzymes

Question 13

Functional DNA is not found in:

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

Question 14

Introns:

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.

Question 15

The most precise modern definition of a gene is a segment of genetic material that:

A)codes for one polypeptide.
B)codes for one polypeptide or RNA product.
C)determines one phenotype.
D)determines one trait.
E)that codes for one protein.

Question 16

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:

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 17

Approximately what fraction of the human genome is tranaposable elements?

A)1)5%
B)5%
C)10%
D)45%
E)80%

Question 18

Bacterial plasmids:

A)are always covalently joined to the bacterial chromosome.
B)are composed of RNA.
C)are never circular.
D)cannot replicate when cells divide.
E)often encode proteins not normally essential to the bacterium's survival.

Question 19

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

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 20

For a closed-circular DNA molecule of 10,000 base pairs in the fully relaxed form,the linking number (Lk)is about:

A)10,000.
B)950.
C)100.
D)9)5.
E)2)

Question 21

Bacterial chromosomes:

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 22

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.

Question 23

Which of the following contributes to the structure of nucleosomes?

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

Question 24

Define "specific linking difference" ( $\sigma$ ),also called superhelical density.

Question 25

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

Question 26

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

Question 27

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)

Question 28

What are introns?

Question 29

What is satellite DNA?

Question 30

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

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

Question 31

Explain how inhibitors of topoisomerase would inhibit the growth of tumors.Would these drugs be expected to inhibit the growth of normal cells as well?

Question 32

The SMC proteins (for structural maintenance of chromosomes)include cohesins and condensins,and are known to have all of the following properties except:

A)a complete ATP binding site.
B)a hinge region.
C)topoisomerase activity to produce positive supercoils.
D)the ability to condense DNA.
E)two coiled-coil domains.

Question 33

Define,in the context of DNA structure,"topoisomers."

Question 34

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

Question 35

Describe the structure and function of a typical bacterial plasmid.

Question 36

Nucleosomes:

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 37

A condensed eukaryotic chromosome is known to be associated with all of the following proteins,except for:

A)core histones H2A,H2B,H3,and H4.
B)histone H1.
C)SMC proteins.
D)topoisomerase I.
E)topoisomerase II.

Question 38

Describe two functions of DNA supercoiling.

Question 39

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.

Question 40

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.

Question 41

Explain the difference between plectonemic and solenoidal supercoiling of DNA;use diagrams to help in your explanation.

Question 42

The overall compaction of a eukaryotic chromosome is greater than ____________ -fold.The first level is nucleosome formation,which compacts about _________ -fold.Next is the 30 nm fiber,which compacts about ________ -fold overall.Higher order folding involves association of the DNA with a nuclear ______________________,which contains large amounts of ________________ and ___________________.

Question 43

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

Question 44

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

Question 45

Describe the composition and structure of a nucleosome.

Question 46

Briefly describe the changes in eukaryotic chromosome structure during the cell cycle.