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Microbiology > Horizontal Gene Transfer and CRISPR/Cas > Flashcards

Horizontal Gene Transfer and CRISPR/Cas Flashcards

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Biology 101 flashcards
1
Q

Mutation

A

Heritable change in DNA sequence

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2
Q

Alleles

A

Alternate forms of genes

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3
Q

Mutation can give rise to new ____.

A

Phenotypes

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4
Q

Vertical gene transfer: what is it, what domain of life can use it

A

Sexual reproduction: new combinations of genes arise when gates from parents fuse
Eukarya

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5
Q

How do bacteria and archaea generate genetic variability without sexual reproduction?

A

Horizontal gene transfer

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6
Q

Horizontal gene transfer: how it works

A

Genes are transferred from one independent organism to another

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7
Q

3 mechanisms of horizontal gene transfer

A

Conjugation
Transduction
Transformation

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8
Q

Conjugation

A

DNA transfer through direct cell-cell contact

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9
Q

What 2 things does conjugation require?

A

Pili

Plasmids

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10
Q

Conjugation is the major mode of spreading what kind of genes?

A

Antibiotic resistance

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11
Q

Plasmids: single or double stranded DNA? Linear or circular?

A

Double stranded, circular

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12
Q

Do plasmids rely on chromosomes, or are they separate?

A

Separate/ extrachromosomal

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13
Q

Plasmids carry genes that confer _____.

A

Advantage

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14
Q

Plasmids can be transferred by ______.

A

Conjugation

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15
Q

Plasmids are replicons. What does that mean?

A

They have their own ori

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16
Q

Episomes

A

Plasmids that exist with or without integrating into chromosome

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17
Q

Well-known example of conjugative plasmid: name and species that has it

A

F (fertility) factor

E. coli

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18
Q

Conjugation can also be referred to as _____.

A

Mating

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19
Q

Step 1 of conjugation

A

Pilus extension from donor (F+) to recipient (F-)

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20
Q

Step 2 of conjugation

A

Pilus retracts

F factor begins replication and transfer

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21
Q

Step 3 of conjugation

A

Plasmid-encoded endonuclease nicks one strand of F factor
F factor is replicated and transferred
Single strand enters recipient

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22
Q

Step 4 of conjugation

A

New complementary strand is made through rolling circle replication in both donor and recipient

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23
Q

Hfr cell: what does Hfr stand for?

A

High frequency of recombination

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24
Q

An Hfr cell does what with the F factor plasmid? What does this mean for gene transfer?

A

Integrates it into chromosome

Integrated F factor can also be excised out of chromosome, taking part of chromosome with it

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25
Q

Example of bacteria that can conjugate with plant cells

A

Argobacterium tumefaciens

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26
Q

Argobacterium tumefaciens causes what disease in plants?

A

Crown gall disease

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27
Q

What type of plasmid does Argobacterium tumefaciens have?

A

Tumor-inducing plasmid (Ti)

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28
Q

How does Argobacterium tumefaciens’s Ti plasmid work (3 steps)?

A

Piece of Ti called T DNA is transferred by conjugation from bacterium into plant cell
T DNA integrates into plant genome
Ti genes are expressed, causing tumor growth

29
Q

What does the 2-component system of Argobacterium tumefaciens do?

A

Senses compounds released by wounded plant, then activates transcription of transfer genes

30
Q

T DNA genes of Argobacterium tumefaciens perform what 2 functions?

A

Direct plant cells to overproduce phytohormones (uncontrolled growth leads to tumor formation)
Stimulate plant cells to make opines (carbon and nitrogen source for bacteria)

31
Q

If T DNA was replaced with drought resistance gene, what would happen to plant? This mechanism can be used for____ ______ of plants.

A

Plant would become drought resistant

Genetic engineering

32
Q

Transformation

A

Uptake of free DNA from environment

33
Q

Competent cell

A

Can naturally take up DNA from environment

34
Q

What 4 bacteria genera are known to be naturally competent?

A

Gram positive: Streptococcus, Bacillus

Gram negative: Haemophilus, Neisseria

35
Q

Artificial transformation

A

Making bacteria competent that aren’t naturally competent

36
Q

2 techniques of artificial transformation

A
  1. Calcium chloride: makes cells more permeable

2. Electroporation: pulsing high voltage that creates temporary holes in cell wall and plasma membrane

37
Q

Artificial transformation is a critical step in what?

A

Cloning

38
Q

2 possible outcomes of DNA transformation

A
  1. Stable transformation: DNA is integrated into chromosome by homologous recombination
  2. Unsuccessful transformation: DNA isn’t integrated into chromosome and is instead degraded
39
Q

Protein that integrates DNA by homologous recombination in transformation

A

RecA

40
Q

What bring DNA into the cell during transformation?

A

Membrane-bound protein complexes

41
Q

How is DNA changed when being brought into the cell during transformation? What is the significance of this change?

A

Nuclease converts double stranded DNA into single stranded DNA
Single stranded DNA is easier to incorporate into genome

42
Q

Bacteriophages

A

Viruses that infect bacteria

43
Q

Bacteriophages are _____ and _____.

A

Abundant

Diverse

44
Q

How many bacteriophages per liter of sea water?

A

10 billion

45
Q

Bacteriophages impact _____ and _____ of microbial communities

A

Composition

Behavior

46
Q

Transduction

A

Bacterial gene transfer by phages

47
Q

2 major phage types

A

Virulent

Temperate

48
Q

Virulent phages reproduce through what type of cycle?

A

Lytic (causes bacterial cell lysis)

49
Q

Temperate phages reproduce through what type of cycle?

A

Lysogenic

50
Q

Steps of lytic cycle

A
  1. Attachment of phage to host cell receptor
  2. Phage injects DNA into cytoplasm
  3. Phage DNA directs synthesis of many new phages; degradation of bacterial genome
  4. Cell lyses and releases new phages
51
Q

Steps of lysogenic cycle

A
  1. Attachment of phage
  2. Phage injects DNA into cytoplasm
  3. Prophage is created: phage genome is integrated into bacterial chromosome
  4. Prophage DNA is copies when cell divides
52
Q

What triggers excision of phage DNA from host genome in lysogenic cycle?

A

Environmental stressors such as UV light

53
Q

Generalized transduction occurs during which cycle?

A

Lytic

54
Q

Generalized transduction: how does it work?

A

During viral assembly, pieces of degraded host DNA are mistakenly packaged into phage

55
Q

During generalized transduction, is just bacterial DNA packaged into phage, or can it be a mixture of viral and bacterial DNA? Can any part of bacterial genome be transferred?

A

Can be just bacterial DNA or mixture of viral and bacterial DNA packaged into phage
Any part of bacterial genome can be transferred

56
Q

Specialized transduction occurs during which cycle?

A

Lysogenic

57
Q

Specialized transduction: how does it work?

A

Prophage incorrectly excises, taking part of bacterial genome with it

58
Q

3 defense strategies of bacteria against bacteriophages

A
  1. Surface alterations (prevent phage attachment)
  2. Restriction-modification systems (modify bacterial genome, then use restriction enzymes to degrade unmodified foreign DNA)
  3. CRISPR/Cas systems
59
Q

CRISPR/Cas system acts as prokaryotic _____ system.

A

Immune

60
Q

CRISPR/Cas system is DNA or RNA based?

A

RNA

61
Q

CRISPR: what does it stand for?

A

Clustered regular interspaced short palindromic repeats

62
Q

CRISPR: what is it?

A

Clusters of short DNA sequences found in genomes of many bacteria and archaea

63
Q

Upon phage infection, bacteria do what with sequences of viral DNA?

A

Capture and integrate them into their own genetic material, placing them in between the CRISPR repeats

64
Q

Next time bacteria encounter the phage, what do they do?

A

Transcribe DNA in CRISPR clusters, making RNAs complementary to infecting viral DNA sequences

65
Q

Complementary RNAs synthesized from CRISPR clusters guide what kind of proteins to viral DNA? What do those proteins do to the DNA?

A

Cas proteins

Cut invading DNA

66
Q

How do Cas proteins enable integration of phage DNA into CRISPR locus?

A

Cleave phage DNA into bits

67
Q

6 steps of CRISPR/Cas operation

A
  1. Phage injects its DNA into bacterial cell
  2. DNA is cleaved and integrated into CRISPR locus as spacers in between repeats
  3. CRISPR locus is transcribed into pre-crRNA
  4. Pre-crRNA is cleaved into many transcripts, each containing a different phage’s genetic material
  5. Cas protein takes up crRNA, which guides Cas to phage
  6. Cas cuts phage’s DNA
68
Q

6 steps of CRISPR/Cas-mediated gene editing

A
  1. Make synthetic guide RNA that matches DNA to be cut from genome
  2. Add Cas nuclease
  3. Deliver both guide RNA and Cas into cells
  4. Guide RNA directs Cas to genomic sequence to be cleaved
  5. Cas cuts DNA at desired site that is homologous to guide RNA
  6. Donor DNA is used to repair cut
69
Q

What is an alternate method of injecting separate guide RNA and Cas into cells?

A

Injecting a plasmid that encodes both Cas and guide RNA into cells

Microbiology (24 decks)

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