Deck 7: Genomes and Chromosomes

Question 1

DNA and RNA polymerases can only synthesize in the ________ direction.

A) forward
B) 3'-to-5'
C) 5'-to-3'
D) reverse
E) 5'-to-3' or 3'-to-5'

Answer 1

C

Question 2

A nucleoid gently released from Escherichia coli appears as 30-100 tightly wound loops, each defined by anchoring

A) histones.
B) histone-like proteins.
C) transcription factors.
D) rho factors.
E) sigma factors.

Answer 2

B

Question 3

Supercoiling in bacteria is typically introduced by enzymes called

A) gyrases.
B) helicases.
C) ligases.
D) polymerases.
E) endonucleases.

Answer 3

A

Question 4

The genome of the bacterium ________, the agent of Lyme disease, is not contained in a circular DNA molecule but rather in a linear chromosome and more than twenty plasmids.

A) Escherichia albertii
B) Staphylococcus aureus
C) Legionella pneumophila
D) Borrelia burgdorferi
E) Burkholderia cepacia

Question 5

The nucleoids of bacteria and most archaea, as well as the nuclear DNA of eukaryotes, are kept ________ supercoiled.

A) positively
B) neutrally
C) negatively
D) loosely
E) extra

Question 6

The thermal stability of the helix is predominantly due to the ________ of the hydrophobic base pairs.

A) attraction
B) binding
C) repulsion and van der Waals forces
D) stacking
E) redox potential

Question 7

The backbone of the DNA double helix allows the formation of major and minor ________ through which DNA-binding proteins interact with the bases without separating the strands.

A) cohesive ends
B) grooves
C) nicks
D) attractions
E) repulsions

Question 8

Gene transfer from parent to progeny is called

A) expression.
B) horizontal gene transfer.
C) vertical gene transfer.
D) transformation.
E) recombination.

Question 9

The entire genetic complement of DNA in a cell of a particular organism is called

A) genome.
B) transcriptome.
C) proteome.
D) metabolome.
E) lipidome.

Question 10

During replication, the lagging strand is synthesized ________, while the leading strand can be synthesized ________.

A) continuously; discontinuously
B) discontinuously; continuously
C) 5'-to-3'; 3'-to-5'
D) 3'-to-5'; 5'-to-3'
E) quickly; slowly

Question 11

Hyperthermophilic archaea possess an unusual gyrase called ________, which introduces positive supercoils into the chromosome in order to protect the DNA from ________.

A) reverse DNA gyrase; thermal denaturation
B) DNA helicase; thermal denaturation
C) topoisomerase I; gene overexpression
D) DNA ligase; thermal denaturation
E) reverse transcriptase; gene overexpression

Question 12

Some of the smallest cellular genomes identified thus far are those of

A) Escherichia coli.
B) Staphylococcus.
C) Streptococcus.
D) Mycoplasma.
E) Saccharomyces.

Question 13

Enzymes that modify the supercoiling of a DNA molecule are called

A) ligases.
B) primases.
C) transferases.
D) topoisomerases.
E) acetylases.

Question 14

A collection of genes and operons whose expression is controlled by a single protein is called a(n)

A) regulon.
B) monocistronic message.
C) polycistronic message.
D) intron.
E) exon.

Question 15

The term ________ describes a polycistronic messenger RNA whose expression is under control of a promoter.

A) enhancer
B) regulon
C) operon
D) amplicon
E) attenuator

Question 16

Which of the following is true in the DNA double helix?

A) The strands are parallel.
B) Phosphate groups are located at the 5'-ends of both strands.
C) Adenine complements cytosine.
D) Guanine complements thymine.
E) Only major grooves can be formed.

Question 17

The movement of genetic material from one cell into another is called

A) vertical gene transfer.
B) horizontal gene transfer.
C) recombination.
D) transformation.
E) expression.

Question 18

In the figure below, which models DNA semiconservative replication, the numeral I points to ________, II points to ________, and III points to _______.

A) origin of replication; new daughter strands; replication fork
B) termination sequences; replication fork; new daughter strands
C) replication fork; new daughter strands; origin
D) new daughter strands; termination sequences; replication fork
E) new daughter strands; origin; replication fork

Question 19

Bacteria and archaea that grow at extreme pH or temperature possess which feature to protect their DNA from denaturation?

A) pseudogenes
B) Okazaki fragments
C) DNA-binding proteins
D) major grooves
E) minor grooves

Question 20

When preparing Escherichia coli cells for electron microscopy by osmotic disruption, their chromosome was released, revealing a length ________ as long as a single cell.

A) 0.5X
B) 2X
C) 10X
D) 100X
E) 1,500X

Question 21

Besides the nucleoid, two other kinds of DNA molecules that may be present in the cytoplasm of a bacterial cell are ________ and the genomes of ________.

A) bacteriophages; pseudogenes
B) introns; bacteriophages
C) plasmids; bacteriophages
D) plasmids; introns
E) introns; exons

Question 22

Plasmids are NOT

A) found in archaea.
B) found in bacteria.
C) found in eukaryotes.
D) supercoiled.
E) usually circular.

Question 23

The sliding clamp is used to ________ and is loaded by ________.

A) open the helix; clamp-loading complex
B) open the helix; DNA polymerase III
C) tether the DNA polymerase to the chromosome; clamp-loading complex
D) tether the DNA polymerase to the chromosome; DNA polymerase I
E) tether the polymerase to the chromosome; DNA primase

Question 24

Which of the following terms refers to gene duplications that have decayed into nonfunctional entities?

A) introns
B) contigs
C) orthologs
D) pseudogenes
E) transposons

Question 25

Which molecule is responsible for removing torsional stress during DNA replication?

A) DNA primase
B) single-stranded binding proteins
C) RNase H
D) DNA gyrase
E) DNA ligase

Question 26

The main replication DNA polymerase in E. coli is Pol III. What type of bonds do DNA polymerases form?

A) aminoacyl-tRNA
B) peptide
C) phosphodiester
D) hydrogen
E) disulfide

Question 27

Which of the following is NOT a mechanism by which plasmids increase the possibility of being present in the new generation of cells?

A) They can be present at a high number so that some copies will end up in each new cell after cell division.
B) They encode traits such as antibiotic resistance that are required for growth in some environments.
C) They have an exponential amount of genes needed for replication.
D) They participate in the physiological processes of the host cell.
E) They carry host survival genes and self-preservation genes.

Question 28

Eukaryotic chromosomes are ________, contained within a nucleus, and they contain DNA associated to a core of histone proteins called the ________.

A) linear; proteasome
B) linear; nucleosome
C) circular; centromere
D) circular; nucleosome
E) circular; capsid

Question 29

What is the approximate size of Okazaki fragments in E. coli?

A) 10 bp
B) 50 bp
C) 100 bp
D) 1,000 bp
E) 10,000 bp

Question 30

Which of the following is an INCORRECT statement?

A) Reproduction in archaea is predominantly asexual.
B) RNA polymerase components of the archaeon Sulfolobus are homologous to those of eukaryotic RNA Pol II.
C) All known archaea have a single circular chromosome and genes organized in operons.
D) Archaeal DNA-packing proteins and ribosomal components closely resemble those of eukaryotes.
E) Both archaeal and eukaryotic genomes encode metabolic pathways of methanogenesis.

Question 31

In the figure below, which depicts the activation step in bacterial DNA replication, the letter Q points to ________, and the letters R and S point to ________, respectively.

A) DnaA-ATP proteins; 9-mer repeats within oriC and 13-mer sequences
B) Primase; oriC and 13-mer repeats
C) SeqA protein; 13-mer repeats and 9-mer basepairs within oriC
D) DamA methylase; 9-mer repeats within oriC and 13-mer repeats
E) gyrase; 13-mer repeats and 9-mer sequences within oriC

Question 32

The first steps in bacterial DNA replication are represented in the figure below, in which the letters T and U point to ________, respectively.

A) strand separation at GC-rich regions and binding of gyrase at oriC
B) strand separation at the 13-mer repeats and binding of DnaA-ATP proteins at the 9-mer repeats
C) strand separation at the 9-mer repeats and binding of DamA proteins at the 9-mer repeats
D) strand separation at the 13-mer repeats and binding of SeqA proteins at the 9-mer repeats
E) synthesis of RNA primer and binding of primase

Question 33

When double-stranded DNA replicates, the newly made strand is related to its template strand because the two strands have

A) identical sequences and are parallel to each other.
B) complementary sequences and are parallel to each other.
C) identical sequences and are antiparallel to each other.
D) complementary sequences and are antiparallel to each other.
E) identical sequences and are antiparallel to each other, except that U replaces T.

Question 34

Errors during replication are corrected by the DNA proofreading activity intrinsic to DNA Pol

A) I.
B) II.
C) III.
D) IV.
E) V.

Question 35

What region of the chromosome in E. coli is involved in the replication termination process?

A) oriC
B) ter
C) TATA box
D) att
E) dif

Question 36

Which of the following is NOT true about histones?

A) They are rich in arginine and lysine.
B) They bind to negatively charged DNA.
C) They are positively charged.
D) They are used to control expression of bacterial operons.
E) They form units with DNA called nucleosomes.

Question 37

Which of the following is an INCORRECT statement about pseudogenes?

A) Portions of their DNA sequences are similar to those of genes with known functions.
B) RNA can be transcribed from some pseudogenes, but the protein products will not have an obvious function.
C) Pseudogenes are lost more quickly in bacteria because of their faster replication processes.
D) Bacterial pseudogenes account for less of the genome than in eukaryotes.
E) Pseudogenes have not been found in bacteria.

Question 38

Which of the following is a process that involves cell-to-cell contact to move a plasmid from a donor cell to a recipient cell?

A) transformation
B) lysogeny
C) generalized transduction
D) conjugation
E) lysis

Question 39

________ is an enzyme that may have evolved from ancient progenitor cells with an RNA genome, and it functions as a ________.

A) Primase; helicase
B) Primase; reverse transcriptase
C) Telomerase; helicase
D) Telomerase; reverse transcriptase
E) Telomerase; methylator and acetylator

Question 40

Bacterial type II topoisomerases are the targets of antibiotics such as ________, which has been used to treat ________.

A) ampicillin; urinary tract infections
B) rifamycin; bacterial meningitis
C) tetracycline; Lyme disease
D) ciprofloxacin; anthrax pneumonia
E) streyptomycin; tuberculosis

Question 41

Describe the role of the two RNA polymerases that are involved in the early stages of bacterial DNA replication.

Question 42

When gently released from an E. coli cell, the nucleoid was found to contain 30 to100 domain loops. How are these loops kept together, and what type of studies have demonstrated their independence?

Question 43

What role does lysozyme play when isolating DNA from bacterial cells?

A) It degrades the lipids in the cell membranes.
B) It breaks down the peptidoglycan cell wall.
C) It hydrolyzes cytoplasmic proteins.
D) It prevents DNA degradation after elution from DNA-binding columns.
E) It degrades contaminating RNA.

Question 44

Use the figure below and describe the general mechanism of how supercoiling can be introduced in a double-stranded, circular DNA molecule. In this example, this DNA is about 300 bp.

Question 45

The natural function of ________ is to cut the DNA of invading plasmids and phages at specific sequences.

A) topoisomerases
B) restriction endonucleases
C) ligases
D) RNases
E) gyrases

Question 46

Thermostable DNA polymerases are used in PCR because they

A) bind DNA more efficiently than thermolabile DNA polymerases.
B) do not have a proof-reading activity.
C) are less expensive than E. coli DNA Pol III.
D) can survive at the high temperatures used to denature DNA.
E) are water soluble.

Question 47

What determines the timing of DNA replication in Escherichia coli?

Question 48

What are the similarities and differences between DNA and RNA?

Question 49

Pieces of DNA that have been cut with restriction enzymes can anneal and then be covalently bonded using the enzyme

A) DNA gyrase.
B) DNA ligase.
C) DNA primase.
D) RNA polymerase.
E) reverse transcriptase.

Question 50

DNA sequencing by synthesis is a powerful contemporary technique that allows the generation of up to 600 gigabases (Gb) of sequence per run. Which process is part of sequencing by synthesis?

A) The sequencing products are separated by polyacrylamide gel electrophoresis.
B) [32P]-DNA fragments are developed using X-ray film or phosphoimaging.
C) The release of pyrophosphate during the incorporation of dNTPs into a growing DNA chain is detected by a complex reaction system that emits light from oxyluciferin.
D) About one thousand identical copies of each individual template DNA form a tight cluster (at the mm-level) on the surface of a flow cell prior to sequencing.
E) Whole large DNA molecules, such as plasmids or BACs, are used as templates.

Question 51

Describe how the name of bacterial genes and their gene product are denoted.

Question 52

Refer to the figure below and describe the mechanism of action for type I topoisomerases.

Question 53

Many restriction enzymes recognize palindromic sequences on double-stranded DNA. Among the following, which is a palindromic sequence?

A) 5'-GATTACCTAGG-3'
3'-CCTAGGTAATC-5'
B) 5'-ATTACTTTA-3'
3'-TAATGAAAT-5'
C) 5'-GCCTAGGA-3'
3'-CGGATCCT-5'
D) 5'-CTAATGGATCC-3'
3'-GATTACCTAGG-5'
E) 5'-GGATCC-3'
3'-CCTAGG-5'

Question 54

In early cloning techniques, E. coli was ________ with the DNA of interest contained in a plasmid or phage vector. This cloned DNA could then be transferred to another organism using a ________.

A) conjugated; contig
B) conjugated; vector
C) transformed; vector
D) transformed; contig
E) transformed; polymerase chain reaction

Question 55

What is the main difference between structural genes and control sequences in bacteria? Cite examples for both.

Question 56

Which of the following are DNA chain-terminator molecules and were used in the original biochemical approach to DNA sequencing devised by Frederick Sanger in the 1970s?

A) 2'-Deoxyribonucleotides
B) 3'-Deoxyribonucleotides
C) 2', 3'-Dideoxyribonucleotides
D) 2'-Deoxyuridine and 2'-deoxyadenosine
E) Uridine and adenosine

Question 57

Agarose gel electrophoresis separates pieces of linear DNA based on

A) size.
B) charge.
C) sequence.
D) degree of supercoiling.
E) extent of methylation.

Question 58

The ability of cohesive ends of DNA from different organisms to ________ constitutes the basis of recombinant DNA technology.

A) be methylated
B) be specifically cut
C) form complementary base pairs
D) repel each other
E) be sequenced

Question 59

What is horizontal gene transfer and how does it differ from vertical gene transfer? Is horizontal gene transfer limited to bacteria and archaea?

Question 60

The target of fluoroquinolone drugs is topoisomerase II. What is the mechanism of action of this antibiotic?

Question 61

In addition to primases and polymerases, name three other proteins required for initiation and elongation during replication. Describe their functions.

Question 62

Use the figure below to describe the process of RNA primer elimination in the synthesis of the lagging strand. What are the names of the enzymes indicated by the numbers?

Question 63

How are archaeal genomes and gene expression mechanisms similar to both bacterial and eukaryotic genomes?

Question 64

What is metagenomics? How have the methods of metagenomics allowed discovery of so many new species? How is it possible to know about these organisms without being able to grow them in a laboratory?

Question 65

Describe the functions of DNA Pol III.

Question 66

Cite three examples of the use of metagenomics in the advancement of our knowledge of microbiomes.

Question 67

Describe three practical applications of the polymerase chain reaction (PCR) and possible pitfalls.

Question 68

How can plasmids ensure that they are passed on from one generation to the next?

Question 69

How does a restriction-modification system avoid the destruction of a bacterium¢s own genome while breaking down foreign DNA?

Question 70

Why is replication of the lagging DNA strand a problem, and how is this problem overcome?