BROCK BIOLOGY OF MICROORGANISMS 13TH EDITION BY MADIGAN – TEST BANK

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BROCK BIOLOGY OF MICROORGANISMS 13TH EDITION BY MADIGAN – TEST BANK

 

 

Chapter 6

 

MULTIPLE CHOICE.  Choose the one alternative that best completes the statement or answers the question.

 

1)

 

The functional unit of genetic information is called the

 

1)

 

_______

 

  1. A)

 

gene.

 

  1. B)

 

chromosome.

 

  1. C)

 

nucleotide.

 

  1. D)

 

protein.

 

 

 

2)

 

The process whereby RNA specifies a DNA sequence is known as

 

2)

 

_______

 

  1. A)

 

RNA translation.

 

  1. B)

 

reverse transcription.

 

  1. C)

 

RNA transcription.

 

  1. D)

 

the central dogma of molecular biology.

 

 

 

3)

 

Proteins interact predominantly within which portion of a double-stranded DNA helix?

 

3)

 

_______

 

  1. A)

 

telomere

 

  1. B)

 

supercoil

 

  1. C)

 

minor groove

 

  1. D)

 

major groove

 

 

 

4)

 

AT-rich DNA will denature/melt

 

4)

 

_______

 

  1. A)

 

in accordance with the animal or plant from which it was taken.

 

  1. B)

 

at a higher temperature than GC-rich DNA.

 

  1. C)

 

at a lower temperature than GC-rich DNA.

 

  1. D)

 

usually at the same temperature as GC-rich DNA, with some minor variations.

 

 

 

5)

 

In Bacteria and most Archaea, the enzyme that introduces negative supercoils into DNA is known as

 

5)

 

_______

 

  1. A)

 

supercoiling gyrase.

 

  1. B)

 

prokaryotic gyrase.

 

  1. C)

 

DNA gyrase.

 

  1. D)

 

prokaryotic supercoilase.

 

 

 

6)

 

Ciprofloxacin, nalidixic acid, and novobiocin are effective antibiotics because they inhibit the activity of

 

6)

 

_______

 

  1. A)

 

DNA gyrase.

 

  1. B)

 

prokaryotic supercoilase.

 

  1. C)

 

reverse gyrase.

 

  1. D)

 

RNA topoisomerase.

 

 

 

7)

 

Most plasmids are

 

7)

 

_______

 

  1. A)

 

replicated in conjunction with the chromosome.

 

  1. B)

 

double-stranded DNA, though a few are not.

 

  1. C)

 

found in eukaryotic cells, though a few are found in prokaryotic cells.

 

  1. D)

 

linear, though a few are circular.

 

 

 

8)

 

Housekeeping genes are present in

 

8)

 

_______

 

  1. A)

 

neither chromosomes nor plasmids.

 

  1. B)

 

plasmids.

 

  1. C)

 

chromosomes and plasmids.

 

  1. D)

 

chromosomes.

 

 

 

9)

 

The precursor of each new nucleotide in a strand of DNA is a

 

9)

 

_______

 

  1. A)

 

deoxynucleoside 3′-triphosphate.

 

  1. B)

 

deoxynucleoside 3′-diphosphate.

 

  1. C)

 

deoxynucleoside 5′-diphosphate.

 

  1. D)

 

deoxynucleoside 5′-triphosphate.

 

 

 

10)

 

DNA replication always proceeds from the ________ of the incoming nucleotide to the ________ of the previously added nucleotide.

 

10)

 

______

 

  1. A)

 

3′-hydroxyl /5′-phosphate

 

  1. B)

 

5′-hydroxyl / 3′-phosphate

 

  1. C)

 

5′-phosphate / 3′-hydroxyl

 

  1. D)

 

3′-phosphate / 5′-hydroxyl

 

 

 

11)

 

During DNA synthesis, the RNA primer is removed by a(n)

 

11)

 

______

 

  1. A)

 

Pol I exonuclease.

 

  1. B)

 

Okazaki fragment.

 

  1. C)

 

DNA ligase.

 

  1. D)

 

replisome.

 

 

 

12)

 

The template for RNA polymerase is ________, and the RNA chain growth is ________ the chain growth of DNA.

 

12)

 

______

 

  1. A)

 

DNA / the opposite of

 

  1. B)

 

DNA / identical to

 

  1. C)

 

an independent RNA segment / identical to

 

  1. D)

 

an independent RNA segment / the opposite of

 

 

 

13)

 

Promoters are specific sequences of ________ that are recognized by ________.

 

13)

 

______

 

  1. A)

 

RNA / DNA polymerase

 

  1. B)

 

DNA / RNA polymerase

 

  1. C)

 

DNA / sigma factor

 

  1. D)

 

RNA / RNA polymerase

 

 

 

14)

 

An example of nucleotide pairing is

 

14)

 

______

 

  1. A)

 

G and U.

 

  1. B)

 

A and T.

 

  1. C)

 

T and U.

 

  1. D)

 

C and U.

 

 

 

15)

 

Stop codons are also called ________ codons.

 

15)

 

______

 

  1. A)

 

degeneracy

 

  1. B)

 

release factor

 

  1. C)

 

conversion

 

  1. D)

 

nonsense

 

 

 

16)

 

There are about ________ different tRNAs in bacterial cells and about ________ in mammalian cells.

 

16)

 

______

 

  1. A)

 

40 / 70

 

  1. B)

 

100-110 / 140

 

  1. C)

 

200 / 200

 

  1. D)

 

60 / 100-110

 

 

 

17)

 

tRNA is released from the ribosome at the ________ site.

 

17)

 

______

 

  1. A)

 

E

 

  1. B)

 

A

 

  1. C)

 

R

 

  1. D)

 

P

 

 

 

18)

 

Which statement is generally TRUE regarding protein synthesis?

 

18)

 

______

 

  1. A)

 

The 23S rRNA plays a role in translocation; the 16S rRNA plays a role in elongation.

 

  1. B)

 

The 23S rRNA plays a role in termination; the 16S rRNA plays a role in elongation.

 

  1. C)

 

The 23S rRNA plays a role in translocation; the 16S rRNA plays a role in initiation.

 

  1. D)

 

The 23S rRNA plays a role in elongation; the 16S rRNA plays a role in translocation.

 

 

 

19)

 

Streptomycin inhibits ________ of protein synthesis, whereas tetracycline inhibits ________ of protein synthesis.

 

19)

 

______

 

  1. A)

 

maturation / protein folding

 

  1. B)

 

initiation / elongation

 

  1. C)

 

initiation / maturation

 

  1. D)

 

elongation / protein folding

 

 

 

20)

 

In all cells, genes are composed of

 

20)

 

______

 

  1. A)

 

proteins.

 

  1. B)

 

nucleic acids.

 

  1. C)

 

mRNA.

 

  1. D)

 

chaperones.

 

 

 

21)

 

Which of the following is an example of one codon?

 

21)

 

______

 

  1. A)

 

CCGUAA

 

  1. B)

 

CATT

 

  1. C)

 

CAG

 

  1. D)

 

GCCATT

 

 

 

22)

 

In all cells a gene encodes for

 

22)

 

______

 

  1. A)

 

a tRNA.

 

  1. B)

 

an rRNA.

 

  1. C)

 

a protein (via mRNA).

 

  1. D)

 

all of the above.

 

 

 

23)

 

Which of the following is NOT correct regarding DNA and RNA synthesis?

 

23)

 

______

 

  1. A)

 

DNA is the template for both DNA and RNA synthesis.

 

  1. B)

 

The template strand is antiparallel to the newly synthesized strand.

 

  1. C)

 

The overall direction of chain growth is from the 5′ to 3′ end.

 

  1. D)

 

Both processes require an RNA primer to begin.

 

 

 

24)

 

Termination of RNA synthesis is ultimately determined by

 

24)

 

______

 

  1. A)

 

special protein factors.

 

  1. B)

 

CG-rich sequences followed by AT-rich sequences.

 

  1. C)

 

specific nucleotide sequences on the template strand.

 

  1. D)

 

exhaustion of RNA polymerase activity.

 

 

 

25)

 

GTP provides energy for

 

25)

 

______

 

  1. A)

 

protein folding.

 

  1. B)

 

translation.

 

  1. C)

 

DNA replication.

 

  1. D)

 

transcription.

 

 

 

26)

 

Transcription of chaperonins is greatly accelerated when a cell is stressed by

 

26)

 

______

 

  1. A)

 

excessive heat.

 

  1. B)

 

extremes in pH value.

 

  1. C)

 

excessive osmotic pressure.

 

  1. D)

 

lack of oxygen.

 

 

 

27)

 

The flow of biological information begins with

 

27)

 

______

 

  1. A)

 

mRNA translation.

 

  1. B)

 

DNA replication.

 

  1. C)

 

RNA transcription.

 

  1. D)

 

transcriptional regulation.

 

 

 

TRUE/FALSE.  Write ‘T’ if the statement is true and ‘F’ if the statement is false.

 

28)

 

Most prokaryotic genomes are double-stranded circular DNA.

 

28)

 

______

 

 

 

29)

 

Inverted repeats can lead to stem-loop structures in the DNA molecule.

 

29)

 

______

 

 

 

30)

 

In nature, the predominant form of DNA is supercoiled in a negative direction.

 

30)

 

______

 

 

 

31)

 

A polymerase chain reaction (PCR) amplifies a specific DNA sequence up to a billion-fold.

 

31)

 

______

 

 

 

32)

 

The genetic material in a virus is technically called a plasmid.

 

32)

 

______

 

 

 

33)

 

DNA replication is bidirectional in prokaryotes with circular chromosomes.

 

33)

 

______

 

 

 

34)

 

RNA acts at both the genetic and the functional levels.

 

34)

 

______

 

 

 

35)

 

Sometimes it appears that bases in tRNA loops are actually paired with bases in other tRNA loops, which is not the case because pairing occurs exclusively within a given loop.

 

35)

 

______

 

 

 

36)

 

Aminoacyl-tRNA synthetase catalyzes the reaction between the appropriate amino acid and ATP to form an activated amino acid: amino acid + ATP ↔ aminoacyl-AMP + P-P

 

36)

 

______

 

 

 

37)

 

One high-energy phosphate bond is required for the activation of an aminoacyl-tRNA.

 

37)

 

______

 

 

 

38)

 

rRNA has a functional role in all stages of protein synthesis.

 

38)

 

______

 

 

 

39)

 

Proteins known as chaperones are found only in Bacteria, and their sequences vary from organism to organism.

 

39)

 

______

 

 

 

40)

 

Throughout the living world, the genetic code is generally universal; however, there are some slight variations.

 

40)

 

______

 

 

 

41)

 

DNA replication involves the synthesis of an RNA primer on one strand of the DNA.

 

41)

 

______

 

 

 

SHORT ANSWER.  Write the word or phrase that best completes each statement or answers the question.

 

42)

 

DNA participates in protein synthesis through a(n) ________.

 

42)

 

_____________

 

 

 

43)

 

A DNA double helix occurs when ________.

 

43)

 

_____________

 

 

 

44)

 

The artificial construction of a double-stranded nucleic acid by complementary base pairing of two single-stranded nucleic acids is known as ________.

 

44)

 

_____________

 

 

 

45)

 

In Bacteria, a chromosome can be distinguished from a plasmid, because by definition a chromosome is a genetic element whose genes encode for ________.

 

45)

 

_____________

 

 

 

46)

 

A transposable element is the general term for ________.

 

46)

 

_____________

 

 

 

47)

 

In complementary base pairing of DNA, adenine pairs with ________ (or ________ in RNA) and cytosine always pairs with ________.

 

47)

 

_____________

 

 

 

48)

 

The function of the DNA polymerase is to ________.

 

48)

 

_____________

 

 

 

49)

 

DNA replication is started with a(n) ________, which, in most cases, in vivo is a short stretch of ________.

 

49)

 

_____________

 

 

 

50)

 

The function of RNA polymerase is to ________.

 

50)

 

_____________

 

 

 

51)

 

If a transcription unit contains two or more genes, these genes are then ________, giving a single RNA molecule.

 

51)

 

_____________

 

 

 

52)

 

A group of genes that are transcribed together is called a(n) ________, which synthesizes a(n) ________.

 

52)

 

_____________

 

 

 

53)

 

Bacterial proteins that kill closely related strains or species are collectively called ________, and the genes that encode for them are usually present on ________.

 

53)

 

_____________

 

 

 

54)

 

The genetic code is conventionally written as ________ rather than ________, because that is the molecule with which the translation process occurs.

 

54)

 

_____________

 

 

 

55)

 

The universal start codon is ________, and it codes for ________ in Bacteria.

 

55)

 

_____________

 

 

 

56)

 

The structure and function of a protein are determined by its ________ sequence.

 

56)

 

_____________

 

 

 

57)

 

The sequence of three to nine nucleotides upstream of the start codon that helps bind the mRNA to the ribosome is known as the ________.

 

57)

 

_____________

 

 

 

58)

 

When several ribosomes are simultaneously translating a single mRNA molecule, the complex is called a(n) ________.

 

58)

 

_____________

 

 

 

59)

 

To fold properly or to assemble into larger complexes, many proteins require assistance from other proteins called ________.

 

59)

 

_____________

 

 

 

60)

 

The twenty-first and twenty-second genetically encoded amino acids are ________ and ________.

 

60)

 

_____________

 

 

 

61)

 

________ is an enzyme that adds phosphodiester bonds between nicked regions of DNA.

 

61)

 

_____________

 

 

 

62)

 

A triplet of bases on an mRNA molecule is known as a(n) ________.

 

62)

 

_____________

 

 

 

63)

 

Each adenine-thymine base pair has ________ hydrogen bonds, while each guanine-cytosine base pair has ________ hydrogen bonds.

 

63)

 

_____________

 

 

 

64)

 

DNA synthesis occurs continuously on the ________ strand, while on the ________ strand DNA synthesis occurs discontinuously.

 

64)

 

_____________

 

 

 

ESSAY.  Write your answer in the space provided or on a separate sheet of paper.

 

65)

 

Name and give one characteristic feature of each of the three major types of transposable elements.

 

 

 

66)

 

Define genome in terms of the various DNA components of the cell or virus.

 

 

 

67)

 

Explain why DNA, RNA, and proteins are often called informational macromolecules.

 

 

 

68)

 

Explain the difference between transcription and translation.

 

 

 

69)

 

Explain the concept of semiconservative replication.

 

 

 

70)

 

Discuss the initiation of DNA synthesis in Bacteria using the terms origin of replication, replication fork, and theta structures.

 

 

 

71)

 

Explain the function of the helicases.

 

 

 

72)

 

In DNA replication, relate the leading strand to the lagging strand.

 

 

 

73)

 

Explain the role of sigma factors in RNA synthesis.

 

 

 

74)

 

Explain the process of RNA transcription using the terms upstream, Pribnow box, and consensus sequence.

 

 

 

75)

 

Explain the difference between an intrinsic terminator and a Rho-dependent termination site.

 

 

 

76)

 

How can an open reading frame (ORF) be used to determine the location of a protein-encoding gene?

 

 

 

77)

 

Describe protein synthesis in terms of initiation, elongation, and termination/release.

 

 

 

78)

 

Explain the A site, the P site, and the E site in terms of the ribosomal subunits.

 

 

 

79)

 

Explain the role of the signal recognition particle (SRP) in protein secretion compared to SecA.

 

 

 

80)

 

Explain how Escherichia coli can grow with a doubling time of 20 minutes when chromosome replication takes 40 minutes.

 

 

 

81)

 

Speculate on why the half-life of mRNA is short, while the half-lives of rRNA and tRNA are long.

 

 

 

82)

 

Speculate on why it may be problematic to clone a gene from a prokaryote into a eukaryote.

 

 

 

83)

 

Explain why GC-rich DNA requires a higher temperature to denture or melt than AT-rich DNA.

 

 

 

84)

 

Explain why a cell needs both type I and type II topoisomerases.

 

 

 

85)

 

Explain the differences between viruses and plasmids.

 

 

 

1)

 

A

 

2)

 

B

 

3)

 

D

 

4)

 

C

 

5)

 

C

 

6)

 

A

 

7)

 

B

 

8)

 

D

 

9)

 

D

 

10)

 

C

 

11)

 

A

 

12)

 

B

 

13)

 

C

 

14)

 

A

 

15)

 

D

 

16)

 

D

 

17)

 

A

 

18)

 

C

 

19)

 

B

 

20)

 

B

 

21)

 

C

 

22)

 

D

 

23)

 

D

 

24)

 

C

 

25)

 

B

 

26)

 

A

 

27)

 

B

 

28)

 

TRUE

 

29)

 

TRUE

 

30)

 

TRUE

 

31)

 

TRUE

 

32)

 

FALSE

 

33)

 

TRUE

 

34)

 

TRUE

 

35)

 

FALSE

 

36)

 

TRUE

 

37)

 

FALSE

 

38)

 

TRUE

 

39)

 

FALSE

 

40)

 

TRUE

 

41)

 

TRUE

 

42)

 

RNA intermediate

 

43)

 

two long antiparallel polynucleotide chains whose purine and pyrimidine bases are held together by hydrogen bonds

 

44)

 

hybridization

 

45)

 

products necessary for essential cellular functions

 

46)

 

a molecule of DNA that can move from one site on a DNA molecule to another site on the same molecule or on a different DNA molecule

 

47)

 

thymine / uracil / guanine

 

48)

 

catalyze the addition of deoxynucleotides

 

49)

 

primer / RNA

 

50)

 

catalyze the formation of phosphodiester bonds between ribonucleotides

 

51)

 

cotranscribed

 

52)

 

operon / polycistronic mRNA

 

53)

 

bacteriocins / plasmids

 

54)

 

mRNA / DNA

 

55)

 

AUG / N-formylmethionine

 

56)

 

amino acid

 

57)

 

Shine-Dalgarno sequence

 

58)

 

polysome

 

59)

 

chaperones (or chaperonins)

 

60)

 

selenocysteine / pyrrolysine

 

61)

 

DNA ligase

 

62)

 

codon

 

63)

 

two / three

 

64)

 

leading / lagging

 

65)

 

Insertion sequences are the smallest, and no additional genetic information is carried other than what is required to move about the chromosome. Transposons are larger with additional genes being potentially transposable. Certain viruses such as Mu are also bacteriophages.

 

66)

 

Answers will vary but should include a statement that the genome includes the entire complement of genes in a cell or virus, and that it includes the chromosome as well as other genetic elements.

 

67)

 

Answers will vary but should focus on the central dogma of molecular biology and how each of these three macromolecules holds discrete information in its amino acid (protein) or nucleotide (DNA and RNA) sequences.

 

68)

 

Transcription is the process in which mRNA (transcripts) is synthesized from DNA, whereas translation uses RNA as a template to synthesize peptides (or proteins).

 

69)

 

During replication, only one of the two strands is used as a template (called the parental strand) to form a complementary strand called the progeny (or daughter) strand. Therefore, because only one of the two parental strands is needed for replication, it is considered partially (or semi-) conservative.

 

70)

 

The initiation protein DnaA binds to the origin of replication (oriC gene) where DnaB and DnaC proteins help unwind the DNA. This unwound and accessible region of DNA, called the replication fork, is where DNA synthesis occurs. Theta structures are used to describe the appearance of the DNA replication during bidirectional circular DNA replication.

 

71)

 

Helicase enzymes require energy from ATP to unwind double-stranded DNA into single-stranded (ss) DNA. Its function is necessary during the initiation of DNA synthesis, because the polymerase can operate only on ssDNA as the template.

 

72)

 

Figure 6.16 in the textbook illustrates these two strands during DNA replication. The leading strand always has a 3′-hydroxyl group nearest to the replication fork, where a new nucleotide can be added continuously. The other strand lags during replication because the 3′-hydroxy group is at the opposite end of the replication fork, and therefore primase must make new RNA primers to add on new nucleotides to the growing strand of DNA.

 

73)

 

A sigma factor is one of five subunits within an RNA polymerase involved exclusively in transcription of DNA to RNA. It identifies and binds to a promoter (initiation) site, notably the highly conservative -10 and -35 sites, which creates an RNA polymerase-DNA template complex that facilitates transcription initiation. A sigma factor then dissociates from the template after a short stretch of RNA is synthesized. They are also subject to regulation by anti-sigma factor proteins that temporarily inactivate a sigma factor and thus halt RNA synthesis.

 

74)

 

RNA polymerase holoenzyme initiates transcription without the need for a primer. The sigma factor component of RNA polymerase easily dissociates from the holoenzyme to first recognize the promoter region by specifically binding to the Pribnow box and consensus sequence, which are both upstream of the transcriptional start site.

 

75)

 

Intrinsic terminators occur at the nucleotide (DNA) level and require no additional protein involvement. They can develop into secondary structures such as loops, which freely form through base pairing with itself to ultimately halt transcription of RNA. Rho-dependent termination also stops RNA transcription but requires the protein Rho, which interacts with the DNA template-RNA polymerase complex to dissociate the complex at specific nucleotide sequences.

 

76)

 

Answers will vary, but an ORF is often predicted by identifying a start codon, followed by a nucleotide sequence, and a terminating nonsense codon in the same reading frame. Once an ORF is predicted using computational (i.e., bioinformatics) methods, it then is possible for a geneticist to identify the mRNA transcript to confirm the ORF is a gene. From the ORF sequence, the amino acid sequence can be predicted, which aids in the biochemical characterization of the translated protein.

 

77)

 

Answers should describe Figure 6.35b in the textbook where initiation involves a complex formation of the ribosome, initiation proteins, formylmethionine-tRNA, GTP, and mRNA. Elongation uses elongation factors, GTP, and tRNAs to extend a peptide, and termination occurs when release factors are recruited to a nonsense codon that breaks apart the tRNA and polypeptide to release the newly synthesized protein.

 

78)

 

A theme to this answer should be how a ribosome can interact with and translocate several molecules (e.g., tRNAs) all at once by having structurally distinct subunits (A, P, and E). During translation, an incoming tRNA attaches to the A site of the ribosome in the presence of elongation factor (EF)-Tu. The P site of the ribosome binds the previous tRNA used with the growing polypeptide chain, and the E site serves as an exit/release point for the previously used tRNA.

 

79)

 

SecA and SRP both carry proteins to the membrane secretion system. A protein to be transported contains a signal sequence, which allows for the binding of either SecA or SRF depending on the sequence. SRP carries proteins to remain in the cell membrane, and SecA binds proteins that are to be secreted out of the membrane.

 

80)

 

Answers will vary, but the principle idea is that essential genes are made earlier during the replication of its chromosome. When E. coli is placed in a nutrient rich medium, many pathways, such as amino acid biosynthesis, are not evoked.

 

81)

 

An important feature present in rRNA and tRNA yet lacking in mRNA is the secondary structures that make them more difficult to degrade by ribonucleases. These additional bonds also require more energy input to degrade them.

 

82)

 

Answers will vary, but one issue is that the universal genetic code does have exceptions. This means some mRNA could be translated into different proteins in different cells or not terminated at the correct location. Codon bias is another problem that can influence translational efficiency. The machinery and methods of post-translational modification are also very different and can therefore make interdomain cloning difficult.

 

83)

 

The overall increase in stability of G-C pairing should be emphasized over A-T binding. A DNA strand with high GC content (low AT) has more triple H bonds compared to an AT rich (low GC) strand of the same length contains mostly double H bonds. More energy is therefore required to break more H bonds, and thus GC rich DNA is more heat resistant to denaturation.

 

84)

 

Prokaryotes use topoisomerase II (DNA gyrase) to negatively supercoil DNA, which is critical for packaging large quantities of DNA into a small volume. DNA gyrase also can work in the opposite way to unwind a supercoil by breaking both strands for DNA replication. Topoisomerase I instead makes only a break on one of the two DNA strands, and this nicking process unwinds a coiled region of DNA.

 

85)

 

A major difference between a plasmid and a virus is that viruses infect other cells to propagate, and plasmids do not. Viruses also can lyse and kill its host, and plasmids cann

Chapter 7

 

 

 

  1. Chapter 7

 

 

MULTIPLE CHOICE.  Choose the one alternative that best completes the statement or answers the question.

 

1)

 

Histones are positively charged ________ that bind to and neutralize the charge of ________, which is caused by the presence of phosphate groups.

 

1)

 

_______

 

  1. A)

 

DNA / DNA

 

  1. B)

 

DNA / RNA

 

  1. C)

 

proteins / DNA

 

  1. D)

 

RNA / RNA

 

 

 

2)

 

The processes of transcription and translation are coupled processes in

 

2)

 

_______

 

  1. A)

 

prokaryotic cells.

 

  1. B)

 

eukaryotic cells.

 

  1. C)

 

both eukaryotic and prokaryotic cells.

 

  1. D)

 

neither eukaryotic nor prokaryotic cells.

 

 

 

3)

 

Compared with the amount of DNA in a single yeast chromosome, the amount of DNA in a single prokaryotic chromosome is

 

3)

 

_______

 

  1. A)

 

greater.

 

  1. B)

 

less.

 

  1. C)

 

not discernible without comparing specific species.

 

  1. D)

 

about the same.

 

 

 

4)

 

Protein-encoding genes are often split into two or more coding regions called ________ and noncoding regions known as ________.

 

4)

 

_______

 

  1. A)

 

introns / exons

 

  1. B)

 

exons / inteins

 

  1. C)

 

exons / introns

 

  1. D)

 

introns / exteins

 

 

 

5)

 

The Archaea were originally regarded as members of the Bacteria because

 

5)

 

_______

 

  1. A)

 

neither has membrane-bound organelles.

 

  1. B)

 

neither has a nucleus.

 

  1. C)

 

both typically contain a single circular chromosome.

 

  1. D)

 

all of the above are correct.

 

 

 

6)

 

An mRNA transcript may be polycistronic in

 

6)

 

_______

 

  1. A)

 

eukaryotic cells.

 

  1. B)

 

prokaryotic cells.

 

  1. C)

 

both eukaryotic and prokaryotic cells.

 

  1. D)

 

neither eukaryotic nor prokaryotic cells.

 

 

 

7)

 

Intron removal and exon joining are accomplished by the

 

7)

 

_______

 

  1. A)

 

spliceosome.

 

  1. B)

 

microtubules.

 

  1. C)

 

cytoskeleton.

 

  1. D)

 

telomerase enzyme.

 

 

 

8)

 

Which enzyme aids in replication of DNA at the guanine-rich 3′ end of a strand of DNA?

 

8)

 

_______

 

  1. A)

 

DNA polymerase

 

  1. B)

 

telomerase

 

  1. C)

 

RNAse

 

  1. D)

 

hydrolase

 

 

 

9)

 

The antibiotic rifampicin inhibits RNA polymerase from which domain?

 

9)

 

_______

 

  1. A)

 

Eukarya

 

  1. B)

 

Bacteria

 

  1. C)

 

Archaea

 

  1. D)

 

Rifampicin does not inhibit RNA polymerase from any of these domains.

 

 

 

10)

 

Which statement is TRUE?

 

10)

 

______

 

  1. A)

 

Large amounts of protein are bound to eukaryotic DNA in a very regular fashion, whereas proteins are absent from prokaryotic DNA.

 

  1. B)

 

Proteins are not associated with either prokaryotic or eukaryotic chromosomes.

 

  1. C)

 

Proteins are equally associated with prokaryotic and eukaryotic chromosomes.

 

  1. D)

 

Large amounts of protein are bound to prokaryotic DNA in a very regular fashion, whereas proteins are absent from eukaryotic DNA.

 

 

 

11)

 

Which statement is TRUE?

 

11)

 

______

 

  1. A)

 

Introns are the exception rather than the rule in eukaryotic encoding genes, and the lower eukaryotes have fewer and smaller introns than the higher eukaryotes.

 

  1. B)

 

Introns are the exception rather than the rule in eukaryotic encoding genes, and the higher eukaryotes have fewer and smaller introns than the lower eukaryotes.

 

  1. C)

 

Essentially all eukaryotic encoding genes have introns, and the higher eukaryotes have more introns than the lower eukaryotes.

 

  1. D)

 

Essentially all eukaryotic encoding genes have introns, and the lower eukaryotes have fewer introns than the higher eukaryotes.

 

 

 

12)

 

Both Bacteria and Archaea share the trait of

 

12)

 

______

 

  1. A)

 

transcribing several genes onto the same polycistronic mRNA.

 

  1. B)

 

lacking a nucleus.

 

  1. C)

 

the genome being typically a single circular chromosome.

 

  1. D)

 

all of the above.

 

 

 

13)

 

An important sequence in the initiation of transcription in Archaea is the

 

13)

 

______

 

  1. A)

 

start codon.

 

  1. B)

 

TATA box.

 

  1. C)

 

Pribnow box.

 

  1. D)

 

polysome site.

 

 

 

14)

 

Archaeal introns are excised by

 

14)

 

______

 

  1. A)

 

restriction endonucleases.

 

  1. B)

 

the spliceosome.

 

  1. C)

 

a ribozyme.

 

  1. D)

 

a specific endoribonuclease.

 

 

 

15)

 

The first amino acid in an archaeal protein is

 

15)

 

______

 

  1. A)

 

N-formylmethionine.

 

  1. B)

 

N-formylserine.

 

  1. C)

 

methionine.

 

  1. D)

 

pyrrolysine.

 

 

 

16)

 

Telomeres are

 

16)

 

______

 

  1. A)

 

regions that provide an attachment site for the spindle fibers that pull paired chromosomes apart during mitosis.

 

  1. B)

 

the complex assemblage of proteins that links the DNA of the centromere region to the spindle fibers.

 

  1. C)

 

specific proteins that bind to the ends of linear chromosomes and provide DNA polymerase with a free hydroxyl group onto which the first nucleotide can be added.

 

  1. D)

 

repetitive DNA sequences that are used to replicate the ends of eukaryotic chromosomes.

 

 

 

17)

 

Healthy eukaryotic cells contain all of the following EXCEPT

 

17)

 

______

 

  1. A)

 

dsDNA.

 

  1. B)

 

dsRNA.

 

  1. C)

 

ssRNA.

 

  1. D)

 

proteins.

 

 

 

18)

 

RdRP is an enzyme that copies siRNA in

 

18)

 

______

 

  1. A)

 

Bacteria.

 

  1. B)

 

plants.

 

  1. C)

 

humans.

 

  1. D)

 

Archaea.

 

 

 

19)

 

Chromosomal DNA at regular intervals contains condensed DNA complexes, in which DNA is wrapped around a histone tetramer in Archaea and a histone octamer in Eukarya, and are called

 

19)

 

______

 

  1. A)

 

histonosomes.

 

  1. B)

 

nucleosomes.

 

  1. C)

 

chromatin.

 

  1. D)

 

supercoiled DNA.

 

 

 

20)

 

Which of the following statements is NOT true regarding transcription?

 

20)

 

______

 

  1. A)

 

The TATA box is unique to Archaea, Eukarya, and the Pribnow promoter region in Bacteria.

 

  1. B)

 

Relatively little is understood about how an archaeon terminates a transcript except that Rho-like proteins are involved.

 

  1. C)

 

All promoters in Archaea and Eukarya require transcription factors for RNA polymerase recruitment.

 

  1. D)

 

Archaea use only one type of RNA polymerase, which is similar to the eukaryotic RNA polymerase II.

 

 

 

21)

 

During eukaryotic RNA processing methylated guanine nucleotides are added at the ________ terminus in a process called ________.

 

21)

 

______

 

  1. A)

 

5′ / polytailing

 

  1. B)

 

3′ / capping

 

  1. C)

 

5′ / capping

 

  1. D)

 

3′ / polytailing

 

 

 

22)

 

Archaeal and bacterial mRNA often serve as templates for several different proteins to be co-transcribed, however eukaryotic mRNA that makes only a single protein are

 

22)

 

______

 

  1. A)

 

unique during meiosis.

 

  1. B)

 

a result of too much splicing.

 

  1. C)

 

monocistronic.

 

  1. D)

 

called inteins.

 

 

 

23)

 

The assemblage of proteins that serve as a binding site for spindle fibers and bind to chromosomal DNA at the centromere region are called

 

23)

 

______

 

  1. A)

 

chromatids.

 

  1. B)

 

telomeres.

 

  1. C)

 

kinetochore complexes.

 

  1. D)

 

mitotic spindle complexes.

 

 

 

TRUE/FALSE.  Write ‘T’ if the statement is true and ‘F’ if the statement is false.

 

24)

 

Histones are universally present in prokaryotic cells.

 

24)

 

______

 

 

 

25)

 

In eukaryotes, DNA is wound around clusters of histones, forming structures known as nucleosomes.

 

25)

 

______

 

 

 

26)

 

Comparative rRNA gene sequencing has revealed a closer genetic relationship between Archaea and Bacteria than between Archaea and Eukarya.

 

26)

 

______

 

 

 

27)

 

Positive supercoiling protects archaeal DNA against ultraviolet (UV) radiation.

 

27)

 

______

 

 

 

28)

 

The translational machinery of Archaea is more similar to Bacteria than to Eukarya.

 

28)

 

______

 

 

 

29)

 

Both intron and exon regions are transcribed into the primary transcript.

 

29)

 

______

 

 

 

30)

 

Reverse gyrase introduces negative supercoils into DNA.

 

30)

 

______

 

 

 

31)

 

All organisms possess multiple DNA polymerases in part due to their functional diversity that all cells require.

 

31)

 

______

 

 

 

32)

 

Proteins resembling the Rho proteins in Bacteria have been detected in Archaea.

 

32)

 

______

 

 

 

33)

 

Introns and exons are found in Eukarya, but they are extremely rare in both Bacteria and Archaea.

 

33)

 

______

 

 

 

34)

 

Regulation of transcription in Archaea is more similar to that which occurs in eukaryotes than in bacteria.

 

34)

 

______

 

 

 

35)

 

Ribosomes contain rRNA plus proteins. All of the proteins contained in the ribosome are common to Archaea, Bacteria, and Eukarya.

 

35)

 

______

 

 

 

36)

 

Technically, telomerase is an unusual type of reverse transcriptase.

 

36)

 

______

 

 

 

37)

 

The RISC complex recognizes and destroys ssRNA (e.g., mRNA) that corresponds in sequence to siRNA.

 

37)

 

______

 

 

 

38)

 

RNAi is triggered by dsDNA of greater than 20 bp in length.

 

38)

 

______

 

 

 

SHORT ANSWER.  Write the word or phrase that best completes each statement or answers the question.

 

39)

 

The guanine-rich sequence that can base pair with the 3′ end of a complementary RNA present in telomerase is found on the ________ strand of DNA.

 

39)

 

_____________

 

 

 

40)

 

Regulation of transcription in Archaea shares major similarities with that of Bacteria, perhaps because of ________ and ________.

 

40)

 

_____________

 

 

 

41)

 

RNA polymerase I transcribes genes for ________, RNA polymerase II transcribes genes for all of the ________, and RNA polymerase III transcribes genes for ________.

 

41)

 

_____________

 

 

 

42)

 

From the standpoint of molecular biology, two similarities between the Archaea and the Eukarya are ________ and ________.

 

42)

 

_____________

 

 

 

43)

 

Cells that have two of each chromosome are ________, whereas cells that have only one copy of each chromosome are ________.

 

43)

 

_____________

 

 

 

44)

 

________ is the enzyme that introduces positive supercoils into DNA that is found in the ________ domain(s).

 

44)

 

_____________

 

 

 

45)

 

Archaeal transcript splicing first uses a(n) ________ to excise introns and lastly joins the exons together with ________.

 

45)

 

_____________

 

 

 

46)

 

________ is the process that occurs in each haploid Saccharomyces cerevisiae cell before cell division.

 

46)

 

_____________

 

 

 

47)

 

RNA processing in eukaryotic cells removes ________.

 

47)

 

_____________

 

 

 

48)

 

During mRNA processing, nucleotide sequences are removed as a(n) ________.

 

48)

 

_____________

 

 

 

49)

 

The guanosine cap that is formed during mRNA processing is needed for translation because ________.

 

49)

 

_____________

 

 

 

50)

 

Transcription and translation are spatially separate processes in ________, because the ________ are located in the nucleus and the ________ are in the cytoplasm.

 

50)

 

_____________

 

 

 

51)

 

________ are introns that fold up to generate three-dimensional structures with ________ activity.

 

51)

 

_____________

 

 

 

52)

 

________ is a specific type of regulatory RNA that minimizes sequence repeats in ________ of higher animals.

 

52)

 

_____________

 

 

 

53)

 

With rare exceptions, reverse gyrase is present only in ________.

 

53)

 

_____________

 

 

 

54)

 

Bacteria use DNA polymerases of family C as their ________, whereas DNA polymerases of families A and B are used mostly in ________.

 

54)

 

_____________

 

 

 

55)

 

Archaea contain ________ RNA polymerase(s), which have roughly three times more subunits than those found in ________.

 

55)

 

_____________

 

 

 

56)

 

Regulation of transcription in Archaea is similar to that of ________, while the transcription apparatus of Archaea is similar to that of ________.

 

56)

 

_____________

 

 

 

57)

 

The 5.8S rRNA is a ribosomal protein found in ________ but not in ________.

 

57)

 

_____________

 

 

 

58)

 

The ________ is ________ that contains both introns and exons.

 

58)

 

_____________

 

 

 

59)

 

Several genes encoding ________ and ________ of Archaea possess introns that must be removed following transcription to generate the mature molecules.

 

59)

 

_____________

 

 

 

60)

 

The complex of DNA plus histones is known as ________ and when highly condensed is called ________.

 

60)

 

_____________

 

 

 

61)

 

All DNA polymerases must add each nucleotide to a(n) ________, which is often denoted as the ________ end.

 

61)

 

_____________

 

 

 

62)

 

snRNPs are involved in the process of ________.

 

62)

 

_____________

 

 

 

63)

 

The ________ stabilizes mRNA and indicates to the translation machinery that the RNA is mRNA rather than some other form of RNA.

 

63)

 

_____________

 

 

 

64)

 

The conserved sequence of the ________ in eukaryotes somewhat resembles the Pribnow box in the promoters of Bacteria.

 

64)

 

_____________

 

 

 

65)

 

Eukaryotic chromosomes contain both ________ and ________ that Archaea and Bacteria lack.

 

65)

 

_____________

 

 

 

66)

 

Monocistronic mRNA occurs in domain ________, while polycistronic mRNA occurs in domain ________.

 

66)

 

_____________

 

 

 

67)

 

The presence of dsRNA usually indicates the presence of ________ within a cell; this molecule is eliminated from eukaryotes through a mechanism known as ________.

 

67)

 

_____________

 

 

 

ESSAY.  Write your answer in the space provided or on a separate sheet of paper.

 

68)

 

Explain the necessity for a protein primer during replication of linear DNA.

 

 

 

69)

 

Speculate on why more than 90% of the total DNA encodes protein in Bacteria, while in eukaryotic organisms, this fraction is much lower.

 

 

 

70)

 

Explain the necessity and function of telomeres and telomerase.

 

 

 

71)

 

Explain how eukaryotic chromosomes are formed.

 

 

 

72)

 

Explain why a mutation in the gene that encodes telomerase would be a lethal mutation.

 

 

 

73)

 

Diagram the process of meiosis.

 

 

 

74)

 

Prokaryotes have almost no introns. What is the significance of this?

 

 

 

75)

 

Explain why multiple origins of replication are seen in the chromosomes of Archaea and Eukarya.

 

 

 

76)

 

DNA packaging in Archaea resembles both Bacteria and Eukarya. In what way(s) is DNA packaging analogous to Bacteria and in what way(s) is it analogous to Eukarya?

 

 

 

77)

 

Compare and contrast RNA interference (RNAi) and restriction endonucleases.

 

 

 

78)

 

Suppose you are comparing the protein-encoding DNA from two species. In one species, 92% of the DNA encodes proteins, while in the second species, only 7.5% of the DNA encodes proteins. To what domain does each species belong? Explain your answer fully.

 

 

 

79)

 

Using humans as an example, explain the terms haploid and diploid and state when each is present.

 

 

 

80)

 

Compare and contrast the processes of meiosis and mitosis.

 

 

 

81)

 

Discuss the three steps involved in the processing of eukaryotic mRNA.

 

 

 

82)

 

Compare and contrast enzymes and ribozymes of self-splicing introns.

 

 

 

83)

 

Explain why it is unsurprising that mitochondria and chloroplasts contain RNA polymerase, which is bacterial in origin.

 

 

 

84)

 

Compare and contrast the activities of “dicers” and “slicers.”

 

 

 

85)

 

Consider the lifetime of an mRNA transcript within an archaeon, a bacterium, and a eukaryote. In which cell type might these last the longest and why?

 

 

 

1)

 

C

 

2)

 

A

 

3)

 

B

 

4)

 

C

 

5)

 

D

 

6)

 

B

 

7)

 

A

 

8)

 

B

 

9)

 

B

 

10)

 

A

 

11)

 

D

 

12)

 

D

 

13)

 

B

 

14)

 

D

 

15)

 

C

 

16)

 

D

 

17)

 

B

 

18)

 

B

 

19)

 

B

 

20)

 

A

 

21)

 

C

 

22)

 

C

 

23)

 

C

 

24)

 

FALSE

 

25)

 

TRUE

 

26)

 

FALSE

 

27)

 

FALSE

 

28)

 

FALSE

 

29)

 

TRUE

 

30)

 

FALSE

 

31)

 

TRUE

 

32)

 

FALSE

 

33)

 

TRUE

 

34)

 

FALSE

 

35)

 

FALSE

 

36)

 

TRUE

 

37)

 

TRUE

 

38)

 

FALSE

 

39)

 

leading

 

40)

 

the overall small circular genome size / lack of a nucleus (either order)

 

41)

 

the two large rRNA molecules / mRNA / tRNA, 5S rRNA, and other small RNA molecules

 

42)

 

the use of histones for DNA packaging / the detailed mechanism of mRNA translation /chromosome replication (any two)

 

43)

 

diploid / haploid

 

44)

 

Reverse gyrase / Archaea

 

45)

 

endonuclease / ligase

 

46)

 

Mitosis

 

47)

 

introns

 

48)

 

lariat structure

 

49)

 

it promotes the formation of the initiation complex between the mRNA and the ribosome

 

50)

 

eukaryotes / chromosomes / ribosomes

 

51)

 

Self-splicing introns / ribozyme

 

52)

 

piRNA / reproductive cells

 

53)

 

hyperthermophilic archaea

 

54)

 

main replicative enzymes / DNA repair

 

55)

 

a single / Bacteria

 

56)

 

Bacteria / Eukarya

 

57)

 

Eukarya / Archaea and Bacteria

 

58)

 

primary transcript /mRNA

 

59)

 

tRNA / rRNA (either order)

 

60)

 

chromatin / heterochromatin

 

61)

 

free hydroxyl (OH) group / 3′

 

62)

 

RNA splicing

 

63)

 

poly(A) tail

 

64)

 

TATA box

 

65)

 

centromeres / telomeres (either order)

 

66)

 

Eukarya / Bacteria

 

67)

 

an RNA virus genome / RNA interference

 

68)

 

Much like an RNA primer, protein primers bind to specific sequences in linear DNA at the 5′ terminus, which is critical to ensure the primed sequences are not lost during replication.

 

69)

 

Answers will vary, but in general eukaryotes have more duplicated genes and introns. The RNA splicing mechanism also allows a cell to make several different proteins from the same region of introns and exons simply by removing different sequences.

 

70)

 

Eukaryotic linear chromosomes have repetitive sequences at the ends called telomeres, which serve as a unique binding sites for telomerase enzymes. Telomerase contains a short primer within its complex and once bound to the telomere region begins synthesizing the leading DNA strand from the RNA template.

 

71)

 

Chromosomes are formed as a product of DNA replication in eukaryotes much like they are in bacteria in that they both use DNA polymerase. Eukaryotes contain more than one origin of replication, which means there are several different regions; they can use a protein primer rather than an RNA primer.

 

72)

 

The function of the telomerase enzyme is to replicate DNA at the end of eukaryotic chromosomes, and therefore a mutation that prevents telomerase from being active would halt DNA replication in eukaryotes.

 

73)

 

The diagram should contain two major cell division steps that convert one diploid cell to four haploid gametes. The first cell division involves separation of homologous chromosomes and the generation of two haploid cells from a diploid cell. The second division forms four haploid gametes from the two haploid cells.

 

74)

 

A lack of introns for prokaryotes means that they also lack the necessary machinery involved in RNA splicing. The splicesomes that mediate this process are found in the nucleus of eukaryotes, which prokaryotes lack.

 

75)

 

The overall genome sizes for Archaea and Eukarya are large relative to Bacteria, and only one origin of replication would mean the time required for a full genome to be replicated would be very long. Containing several origins of replication allows for the simultaneous replication of chromosomal DNA, which increases the overall replication speed.

 

76)

 

Bacteria use supercoiling to densely package their genome; Archaea also use this packaging method. Eukaryotes instead have their DNA wound around proteins called histones; Archaea do this as well.

 

77)

 

Eukaryotes lack restriction endonuclease systems, but Archaea and Bacteria both use these to defend against foreign DNA by cleaving it apart. RNAi is also a mechanism to defend again foreign nucleic acids but unlike restriction endonucleases, RNAi targets foreign RNA (e.g., RNA viruses) and cleaves them. The RNAi mechanism is exclusive to the Eukarya domain.

 

78)

 

Eukaryotes have the lowest percentage of protein-encoding DNA, and Bacteria tend to have the highest. The 7.5% protein-encoding DNA likely corresponds to a bacterium and the 92% to a eukaryote.

 

79)

 

Diploid cells contain two homologous copies of each chromosome and therefore can be conceptualized as mature cells, such as those found in a developed human. Haploid gametes contain only one copy for each chromosome and are reproductive structures such as eggs and sperm in humans.

 

80)

 

Mitosis is an asexual process used to produce two identical daughter cells from one parent cell. It maintains the number of chromosome sets in a cell where the chromosomes are segregated and condensed after DNA is replicated. Meiosis also produces cells from one parent cell but does not maintain the same number of chromosome sets and instead gives half of the chromosome set to one daughter cell and another set to the other daughter cell. The meiosis process undergoes two cell divisions where four daughter cells are produced rather than two cells produced from one cell division in mitosis. The fate of the daughter cells is different after the two processes where mitosis generates more mature cells and meiosis makes gametes for sexual reproduction.

 

81)

 

All three RNA processing steps occur within a nucleus to generate a mature mRNA transcript. First, a cap is placed onto the 5′ end to prevent degradation of the transcript. Next, introns not to be in the transcript are removed. Finally the 3′ end is clipped to add on several adenine nucleotides called a poly(A) tail.

 

82)

 

RNA strands that fold into complex structures and act as an enzyme, called ribozymes, splice one intron for each ribozyme (1:1). Unlike the ribozymes involved in self-splicing, one proteinaceous enzyme is capable of catalyzing many splicing events (1>1).

 

83)

 

Recognizing the endosymbiotic theory, where these organelles in eukaryotes were the result of assimilating bacterial cells into a eukaryotic cell, it is unsurprising. The RNA polymerases outside of the chloroplasts and mitochondria are unlike bacteria, but the ones found within these structures do resemble the bacterial enzyme, which further corroborates the theory.

 

84)

 

Both destroy RNA transcripts and therefore halt protein translation, but dicers and slicers target different RNA to achieve this result. Dicer is an endonuclease that cleaves dsRNA strands into small (21—23 bp) fragments called siRNA through the process of RNAi in Eukarya. The RNA-induced silencing complex (RISC) contains slicer nucleases that target ssRNA, which bind to siRNA and again are cleaved.

 

85)

 

Answers will vary, but if endo- or exonuclease composition is compared, the eukaryote would have the longest lived mRNA transcript because the eukaryotes lack them. Another possible answer could mention the poly(A) tail unique in Eukarya that stabilizes the transcript and prevents degradation, which would again point to the eukaryote for maintaining the mRNA longest.