Microbiology unit 3

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1

RNA retroviruses use_____________.

viral reverse transcriptase to make a DNA copy that is integrated into the host genome and then host RNA polymerase transcribes it.

2

What recognizes viral mRNA and prevents further viral gene expression.

RNAi

3

A _____ virus cycle leads only to cell lysis, and a _____ virus cycle involves phage genome integration into the host genome.

lytic; lysogenic

4

List the steps from HIV retroviral genome replication to protein synthesis.

  1. (+)ssRNA genome
  2. Reverse transcriptase
  3. dsDNA genome
  4. Integration into host genome
  5. RNA polymerase II transcription
  6. Translation of viral proteins by host ribosomes
5

In the________the phages have transition host cell machinery for phage progeny production, as a consequence of diverted resources the host cell replication slows.

slow-release cycle

6

Prion diseases, which affect the brain, are thought to be caused by_____________.

misfolded proteins that act as a template for further protein misfolding

7

HIV, which only infects humans, is considered to have a______host range, whereas rabies virus, which can infect a number of animals and humans, is considered to have a______host range.

narrow; broad

8

Human papillomavirus (HPV) is a double-stranded DNA virus that enters the cytoplasm before undergoing uncoating. Although the virus is replicated by host DNA polymerase in the nucleus, viral replication is closely tied to epithelial cell differentiation. In particular, viral DNA replication is inhibited until_______are differentiated into_________, which are ready to be shed from the epithelial layer, increasing the likelihood that HPV will be transmitted to a new host.

basal cells; keratinocytes

9

The enzyme reverse transcriptase (RT) is found in__________.

some DNA and some RNA viruses.

10

PrPSc does have a higher proportion of__________, and this could be a viable hypothesis as to why this protein is more resistant to methods of control.

beta pleated sheets

11

What is a prophage?

A phage genome integrated into a host genome.

12

What type of virus can integrate into the host genome to form a prophage.

Lysogenic viruses

13

________are naked nucleic acids, usually RNA, devoid of a protein capsid. Some plant viroids are ribozymes, capable of catalytic action.

Viroids

14

Viroids lack________.

proteins

15

The Baltimore classification of viral genomes is based on what?

The composition of the genome, and the route used to express messenger RNA (mRNA).

16

Viral genomes may comprise____________.

double or single-stranded DNA or double or single-stranded RNA.

17

The innate immune system recognizes double-stranded RNA (dsRNA), an indicator of viral replication in the host cell, and signals the immune response with________.

interferons

18

A gene for a __________ is likely to be encoded in the viral genome.

capsid protein

19

What is the ability to infect a particular type of cell within the host?

Tropism

20

What is a set of short DNA sequences that allow the bacterium to “remember” past infections?

CRISPR

21

Reverse transcriptase catalyzes _____ production from a _____ template.

DNA; RNA

22

Which viral genome is likely to require an RNA-dependent RNA polymerase for transciption upon viral entry?

(–) sense single-stranded RNA

23

All strains of human papillomavirus (HPV) are capable of integrating their double-stranded DNA viral genome into host basal cells while waiting for keratinocyte differentiation before initiating viral replication for virion shedding. As a consequence of the integrated genome, HPV strains that more readily transform host cells are more likely to cause an increased expression of viral_________.

oncogenes.

24

A temperate phage is one that___________.

can undergo lysogeny.

25

_________is a process by which bacteria transfer DNA via formation of a pilus. This process requires cell-to-cell contact.

Conjugation

26

What is a structural gene?

A string of nucleotides that can be used as a template to produce an RNA that codes for a protein.

27

A collection of prokaryotic genes and operons located at different positions on a chromosome but that have a unified biochemical function is known as a__________.

regulon

28

Eukaryotic genomes comprise mostly __________, whereas prokaryotes have mostly __________.

noncoding DNA; coding DNA

29

Functional units of DNA sequences include structural genes, which are nucleotide sequences that encode an RNA molecule, and_________sequences that regulate the expression of structural genes.

DNA control

30

During rolling-circle replication, RepA binds to the ori and nicks one strand of the DNA. The_____ end of the nicked DNA serves as a primer and is extended by DNA polymerase, while the_____ end is coated with single-stranded DNA-binding proteins and replicated using RNA and DNA polymerases.

3’OH; 5’PO4

31

What are constitutive genes?

"Housekeeping genes"; they are always expressed.

transcribed continually as opposed to a facultative gene, which is only transcribed when needed.

32

What are the types of regulatory proteins?

Represses and activators; repression/ induction/ corerepressor/ derepression

33

Repressor+inducer=

Inactive repressor= gene expression

34

To induce or derepress is to_______

Turn on gene expression.

35

Induction involves the______operon

Lac operon

36

Derepression involves the______operon

Trp operon

37

The activator can only itself become active through the use of_______.

Ligand

38

A low level of______transcription always occurs. Why?

lacZYA; Lactose permease (lacY) transports lactose must be expressed.

39

Absence of lactose= ?

Repression, transcription blocked

40

Presence of allolactose=?

Induction, RNA polymerase binds; transcription allowed.

41

lac operon transduction is also controlled by_______, a regulatory molecule that binds to cAMP regulatory protein (CRP)

Cyclic AMP

42

cAMP-CRP complexes________.

bind lac promoter, increasing transcription

43

Cellular cAMP levels fluctuate based on the cell's_______.

Energy level

44

As [glucose] increases [cAMP]______

Decreases

45

Glucose turns off the lac operon via________.

Inducer exclusion

46

What occurs during inducer exclusion?

Glucose blocks the entry of lactose

47

Genes of a biosynthetic pathway for tryptophan synthesis.

Tryptophan operon

48

Low or no tryptophan present=

Derepression; transcription proceeds.

49

Tryptophan present=

Acts as corepressor; binds aporepressor

50

Transcriptional attenuation________.

Is a secondary strategy for regulating tryptophan synthesis.

51

In order to transfer, an F factor must have what?

OriT and tra genes

52

The recipient of Hfr conjugation_______becomes an F+ cell

rarely

53

Genes for the capsid proteins are found in the________.

Viral genome

54

In the CRISPR system of bacteria, the spacer is a(n)______________.

Piece of phage DNA

55

Most structural genes of bacteria are grouped together and transcribed from a single________; immediately following this sequence is the_______that interacts with a regulatory protein to affect transcription of the genes.

promoter; operator

56

The difference between generalized and specialized transduction is____________.

that in generalized transduction, any DNA can be moved, but with specialized transduction, only certain DNA near the phage site can be moved.

57

The operator of an bacterial operon serves was a_______element.

regultory/control

58

Bacterial operons possess a______promoter.

single

59

The transcript of a bacterial operon will be an_______of all the structural genes contained in a single polynucleotide sequence.

RNA copy

60

The information flow of retroviruses is____________.

RNA to DNA to RNA to protein

61

Retroviruses can form a_________.

Provirus

62

Retroviruses can remain in the proviruses state while simultaneously_____________.

initiating production of new viral particles.

63

________is a mechanism of virus exit that leads to acquisition of the envelope around the viral particles

Budding

64

________is a mechanism that allows for the viral genome to be freed from the capsid.

Endospore formation

65

Within a host, receptor molecules can also determine the_________, or tendency to infect a particular tissue type.

Tropism

66

Formation of daughter cells is an example of_________.

vertical gene transfer or transmission?

67

Slow release of bacteriophage progeny from a bacterial host cell__________and___________.

does not kill the host cell; is a feature particular to filamentous phage.

68

Define tropism.

Tissue specificity; relevant for animal viruses

69

_________are proteins that infect animals; they have no nucleic

acid component.

Prions

70

In cows prions cause degenerative brain disease called________or mad cow disease. In humans it causes_______.

spongiform encephalopathy; Creutzfield‐ Jacob disease

71

Viroids alter gene expression in____________.

plants

72

The international committee of taxonomy of viruses is based on what?

Genome, Capsid ssymmetry, Envelope, host range, and viroid size.

73

_____________dictate when lysogeny converts to the lytic cycle.

Environmental cues

74

Define Vertical gene transfer.

the generational passing of genes from parent to offspring

75

__________is type of horizontal gene transfer that involves transfer of genes by bacteriophages. There are two types: generalized and specialized.

Transduction

76

Which of the following events must precede transfer of chromosomal genes by specialized transduction?

site-specific recombination

77

___________is a simple transposable element that consists of a transposase gene flanked by short, inverted repeats that are the target of transposase.

An insertion sequence (IS)

78

An insertion sequence contains a gene for which enzyme?

Transposase

79

__________are mobile DNA elements that can rearrange with in a larger DNA molecule.

Transposable elements

80

Transposable elements differ from plasmids in that only plasmids________.

may exist autonomously, not integrated into host DNA.

81

Which type of DNA uptake is dependent on viruses?

Transduction (requires bacteriophages)

82

Define Conjugation

direct transfer of DNA from one bacterial cell to another

83

Define transformation

the uptake of DNA from the environment

84

during conjugation, the orientation of the will determine which of the flanking chromosomal genes are transferred first.

integrated F factor

85

regions exhibiting_____________would be suggestive of recently acquried foreign DNA.

different codon usage and GC content

86

________refers to the ability to perform transformation.

Competence

87

Natural transformation requires specific protein complexes called__________.

transformasomes

88

Which specific feature of replicative transposition distinguishes it from nonreplicative transposition?

During replicative transposition, the entire transposon is replicated.

89

In bacteria, a partially diploid strain may result from_____________.

acquisition of an F' factor or specialized transduction.

90

__________probably evolved first as a DNA repair mechanism, but it also determines the fate of sequences acquired by transformation, conjugation, and transduction.

recombination

91

Which type of DNA uptake is dependent on transferable plasmids?

Conjugation

92

_________acts to terminate transcription that is already underway, but unnecessary, under conditions of excess tryptophan.

attenuation

93

Phase variation is when______________.

reversible flipping of a DNA segment enables a pathogen to turn on and off cell surface proteins.

94

What is the fastest and most easily reversible way for a cell to alter its physiology?

modification of an existing protein

95

“Virulent” phages only carry out______.

lytic cycle

96

During_______Phage particles reproduce & exit without harming the host cell. Host cells grow slowly, but don’t die

slow release cycle

97

Bacterial host defenses may include__________which cleaves viral DNA sequences lacking methylation

Restriction endonucleases

98

For RNA viruses Genome replication; synthesis of viral proteins; and viral assembly all occur__________.

outside the nucleus

99

The genome of (+) RNA viruses can serve as a template for__________.

Translation

100

The genome of (-) RNA viruses can serve as a template for__________.

mRNA synthesis

101

The genome of retroviruses can serve as a template for__________.

DNA synthesis

102

“Innate immunity”

interferons

103

“Adaptive immunity”

antibodies

104

Lysogeny occurs in certain bacteria; the equivalent process in an animal cell is best represented by a_________

retrovirus infection.

105

promoter + operator + structural genes=

Operon

106

Define Fertility factor or F factor

conjugative/transferable plasmids

107

F’ (F prime) factor formation:

integrated F factor is excised from host chromosome along with some host DNA; extra genes expressed as part of the F’ plasmid.

108

_________is high‐frequency recombination strain

Hfr

109

For Hfr Formation___________.

integration occurs at insertion sequences (IS); areas of homo‐ logy between plasmid & chromosome.

110

Define Specialized Transduction.

transfer of a few closely linked genes.

111

_________the process of mobilizing the transposable element within or between DNA molecules.

Transposition

112

Control sequences in DNA do not code for proteins, but rather____________

they serve to regulate gene function

113

Plasmids that are copied vie rolling circl replication do not undergo____________.

bidirectional replication

114

The presence of competence factors, the formation of translocation in the cell membrane, and the presence of extracellular DNA all indicate_____________.

the cell is ready to carry out transformation