Deck 24: Genes and Chromosomes

Question 1

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.

Answer 1

B

Question 2

Functional DNA is NOT found in:

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

Answer 2

C

Question 3

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 3

A

Question 4

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.

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

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 7

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 8

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 9

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 answers are correct.

Question 10

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 11

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.

Question 12

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 13

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 14

C)

Question 15

Which protein does NOT contribute to the octameric histone core?

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

Question 16

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 17

Approximately what fraction of the human genome is tranaposable elements?

A) 1.5%
B) 5%
C) 10%
D) 45%
E) 80%

Question 18

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 19

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

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

Question 20

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 21

Which statement 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 22

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?

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 23

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

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 24

Which description is NOT accurate regarding telomeres?

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 25

The genome of organism A is 4.6 million base pairs long, while that of organism B is 12.1 million base pairs long. Given this information, what can be stated regarding these two organisms?

A) Organism B will contain approximately three times the number of genes as organism A.
B) Organism B will contain approximately 7.5 million more base pairs in introns compared with organism A.
C) Organism B will contain three times as many chromosomes as organism A.
D) All of the statements are valid.
E) None of the statements is valid.

Question 26

Which factor 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 27

With which protein(s) is a condensed eukaryotic chromosome NOT known to be associated?

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

Question 28

Unwinding a portion of the duplex to carry out transcription on a plasmid will:

A) decrease the overall linking number.
B) decrease the overall twist.
C) make the writhe more negative.
D) increase the overall twist.
E) increase the overall linking number.

Question 29

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 30

Which statement is FALSE regarding supercoils in nucleic acids?

A) Supercoils allow DNA to become more compact.
B) Most naturally occuring DNA has a linking number that is greater than the twist.
C) Supercoiling requires DNA that is either circular or has constrained ends.
D) Positive solenoidal supercoils have the opposite handedness to positive plectonemic supercoils.
E) The twist for Z-DNA will have a negative value.

Question 31

The formation of cruciforms in relaxed, circular DNA will be associated with what other effect?

A) a change in linking number
B) a change in superhelical density
C) the formation of negative supercoils
D) All of these effects would occur.
E) None of these effects would occur.

Question 32

Which statement does NOT contradict 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 33

What kind of supercoils are formed around nucleosomes?

A) positive plectonemic supercoils
B) negative plectonemic supercoils
C) positive solenoidal supercoils
D) negative solenoidal supercoils
E) a mixture of solenoidal and plectonemic supercoils

Question 34

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 35

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?

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 36

The SMC proteins (for structural maintenance of chromosomes) include cohesins and condensins and are NOT known to have:

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 37

Which elements are NOT necessary to make a stable yeast artificial chromosome (YAC)?

A) centromeres
B) replication origins
C) satellite DNA sequences
D) telomeres
E) All of these are required to make a stable YAC.

Question 38

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?

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 39

Which statement is FALSE concerning human mitochondrial DNA (mtDNA)?

A) Human mtDNA is circular.
B) Human mtDNA is smaller than the E. coli genome.
C) Human mtDNA encodes the majority of mitochondrial protein genes.
D) Human mtDNA is typically found as multiple copies in mitochondria.
E) Human mtDNA encodes both polypeptide and tRNA genes.

Question 40

Partially denaturing a stretch of duplex in closed, circular plasmid DNA will have what effect?

A) It will decrease linking number and increase writhe.
B) It will decrease twist and linking number.
C) It will increase writhe and decrease twist.
D) It will decrease both writhe and twist.
E) It will increase linking number and reduce writhe.

Question 41

Which DNA structures are NOT generally circular?

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

Question 42

Under what conditions will the linking number for a plasmid change?

A) cruciform formation
B) addition of an intercalating agent
C) denaturation
D) addition of histones
E) None of these conditions will change the linking number.

Question 43

Which factor distinguishes Type I from Type II topoisomerases?

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 44

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).

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

Question 45

How many nucleosomes would you expect to find in a 1,000 bp piece of linear DNA?

A) zero to one
B) two to three
C) four to five
D) six to seven
E) eight to nine

Question 46

Starting with a 5,000 bp plasmid containing one positive supercoil, after one round of E. coli DNA gyrase action, what would be the supercoiling state of the plasmid?

A) three positive supercoils
B) two positive supercoils
C) no supercoils
D) one negative supercoil
E) two negative supercoils

Question 47

Which statement is FALSE regarding the formation of nucleosomes?

A) Histone core proteins occur as pairs in the nucleosome.
B) The coiling of DNA around the nucleosome is plectonemic.
C) The coiling of DNA around the nucleosome is left-handed.
D) Electrostatic interactions between histones and DNA are critical in nucleosome formation.
E) The sequence affects the ability of DNA to adopt the curvature in a nucleosome.

Question 48

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

Question 49

Which factor distinguishes bacterial topoisomerase III from topoisomerase IB?

A) consumption of ATP
B) cleavage of one or two strands
C) relaxing or increasing the amount of supercoiling
D) the mechanism of action
E) amino acid involved in covalent attachment to nucleic acid

Question 50

If negatively supercoiled plasmid DNA is mixed with human topoisomerase I and ATP, which effect 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.

Question 51

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

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 52

Which statement is TRUE for histones?

A) They vary in size from 200 to 400 amino acids in length.
B) They form covalent complexes with DNA.
C) They form both protein:DNA and protein:protein interactions.
D) They contain large amounts of Asp residues.
E) DNA wraps around them in a right-handed helical structure.

Question 53

Which statement does NOT apply to the topoisomerase IA mechanism?

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 54

Which statement is FALSE regarding DNA-binding proteins?

A) DNA-binding proteins always contain zinc finger domains.
B) DNA-binding proteins are important in DNA compaction.
C) DNA-binding proteins typically interact with DNA via electrostatic interactions.
D) DNA binding protein binding to DNA is influenced by the sequence of the nucleic acid.
E) DNA-binding proteins often contain Arg and Lys residues.

Question 55

Which protein binds to the linker DNA between nucleosomes?

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

Question 56

What is the twist on a piece of relaxed Z-DNA that is 9,600 base pairs long?

A) -960
B) -800
C) 800
D) 914
E) 960

Question 57

Which statement is FALSE regarding histones?

A) Overall, histones are positively charged proteins.
B) Lys and Arg residues are abundant in histones relative to other proteins.
C) Histone H1 is found in the nucleosome core.
D) The nucleosome core contains eight histone proteins.
E) None of these statements is false.

Question 58

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

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 59

Which protein is NOT important in the compaction of eukaryotic DNA?

A) histone H1
B) cohesins
C) condensins
D) topoisomerases
E) HU proteins

Question 60

Which statement is FALSE for euchromatin?

A) Euchromatin is a form of chromatin.
B) Euchromatin has less H1 associated with it than heterochromatin.
C) Euchromatin is being more actively transcribed than heterochromatin.
D) Euchromatin is more densely packed than heterochromatin.
E) None of these statements is false.

Question 61

What kind of posttranslational modifications occur in histones?

A) methylation only
B) acetylation only
C) phosphorylation only
D) methylation and acetylation
E) methylation, acetylation and phosphorylation

Question 62

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

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 63

Nucleosome formation condenses DNA by approximately sevenfold and 30-nm fiber formation condenses DNA by a further 100-fold. How long will a 450,000 bp segment of linear DNA be after compaction to a 30-nm fiber?

A) ~2 nm
B) ~20 nm
C) ~200 nm
D) ~2,000 nm
E) ~20,000 nm

Question 64

Which aspect does NOT distinguish bacterial SMC proteins from eukaryotic SMC proteins?

A)formation of coiled-coil structures
B)binding and hydrolysis of ATP
C)formation of "hinge" domains
D)formation of "head" domains
E)formation of homodimers versus heterodimers

Question 65

An average base pair in DNA is 650 Da. Histone masses are shown in the table. What is the approximate mass of a nucleosome core in kiloDaltons (kDa)? Histone
Mass (Daltons)
Histone H1
21,130
Histone H2A
13,960
Histone H2B
13,774
Histone H3
15,273
Histone H4
11,236

A) ~55 kDa
B) ~75 kDa
C) ~170 kDa
D) ~205 kDa
E) ~230 kDa

Question 66

Which histone is replaced in nucleosomes found in the vicinity of centromeres?

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

Question 67

The eukaryotic SMC protein condensin contains which SMC subunits?

A) SMC1 and SMC2
B) SMC1 and SMC3
C) SMC2 and SMC3
D) SMC2 and SMC4
E) SMC3 and SMC4

Question 68

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

Question 69

What is satellite DNA?

Question 70

In which phase of the cell cycle is DNA MOST condensed?

A) G1 phase
B) S phase
C) G2 phase
D) prophase
E) metaphase

Question 71

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 72

Describe the structure and function of a typical bacterial plasmid.

Question 73

What are introns?

Question 74

In which cell-cycle step does condensin become associated with chromatids?

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

Question 75

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

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

Question 76

Describe two functions of DNA supercoiling.

Question 77

Which protein carries out ATP hydrolysis?

A) histone H2A
B) histone H1
C) E. coli topoisomerase I
D) condensin
E) E. coli topoisomerase III

Question 78

Acetylation of lysine residues in histones has what effect?

A) It increases the positive charge on the protein and increases compaction.
B) It increases the positive charge on the protein and decreases compaction.
C) It decreases the positive charge on the protein and increases compaction.
D) It decreases the positive charge on the protein and decreases compaction.
E) None of the answers is correct.

Question 79

Which protein(s) is/are NOT associated with bacterial DNA compaction?

A)SMC
B)HU
C)Type I topoisomerases
D)Type II topoisomerases
E)condensin

Question 80

Heterochromatin is NOT associated with:

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.