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Microbiology > Chapter 10 > Flashcards

Chapter 10 Flashcards

1
Q

What are the four reasons bacteria has been a workhorse of genetic research?

A
  1. Rapid growth
  2. Small, haploid genomes- mutations
  3. Excellent tools- plasmids etc
  4. Genetic information of all cellular organisms is encoded in the same way
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2
Q

Why does genetic variation matter?

A

The Central Dogma of Molecular Biology: DNA to RNA to Protein

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3
Q

Any change in the DNA sequence is a ___

A

Mutation

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4
Q

What are mutations? What do they lead to?

A

Changes in the DNA sequence. Either spontaneous or induced. They may lead to a different phenotype.

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5
Q

Most prokaryotes are ___

A

Haploid

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6
Q

Types of mutants based on phenotype are __

A

Observable change in appearance or function of a strain carrying the mutation.

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7
Q

Spontaneous changes in DNA sequence:

A

Generally low

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8
Q

Mutagens change in DNA sequence:

A

Increases the rate.

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9
Q

What are the four types of changes in the DNA sequence?

A

Spontaneous, mutagens, transposons, horizontal gene transfer.

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10
Q

How do we find mutations? (3 ways)

A
  1. Direct selection, like antibiotic resistance, reversion mutants.
  2. Enrichment method.
  3. Screening method- replica plating.
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11
Q

Direct Selection Diagram:

A
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12
Q

Enrichment method diagram:

A
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13
Q

Replica plating diagram:

A
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14
Q

What are transposable elements?

A

Jumping genes.
*likely to disrupt genes

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15
Q

How are transposable/mobile elements catalyzed?

A

By transposase encoded in the transposon.

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16
Q

What are Terminal Inverted repeats?

A

Recognition sites for transposase.

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17
Q

What happens when transposable/mobile elements carry extra genes?

A

Antibiotic resistance.

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18
Q

What are transposable/mobile elements likely to do?

A

Disrupt genes.

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19
Q

What is site-directed mutagenesis for?

A

To mutate a gene of interest exactly how we want.

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20
Q

What are the steps of site-directed mutagenesis? (5)

A
  1. Start with PCR and a modified primer
  2. Introduce into microbial strain of interest
  3. Recombination
  4. Characterize
  5. Genetic complementation to confirm
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21
Q

What are the 4 methods of mutation repair?

A
  1. Direct repair- photolyases
  2. Excision repair
  3. Recombination repair
  4. SOS repair
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22
Q

What are the four genetic differences between prokaryotes and eukaryotes?

A
  1. DNA exchange not prerequisite for reproduction in prokaryotes.
  2. If DNA exchange occurs, generally only small section of DNA exchange in prokaryotes.
  3. Several mechanisms of DNA exchange in prokaryotes- only one in eukaryotes.
  4. Prokaryotes are usually haploid and higher, eukaryotes are usually diploid.
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23
Q

When does vertical gene transfer occur?

A

Occurs during reproduction between generations of cells.

24
Q

What is horizontal gene transfer?

A

The transfer of genes between cells of the same generation.

25
Q

What is transformation in DNA transfer, and what are the three types?

A

Transformations are DNA from the environment.
Genes are transferred from one bacterium to another as “naked” DNA in solution. Few species are able to transform.
Natural, artificial, and competent.

26
Q

What is transduction in DNA transfer and what are the two types?

A

Bacteriophage transfers DNA. Generalized and specialized.

27
Q

What is conjugation in DNA transfer and what are the types?

A

Direct cell-cell contact is required.
Opposite mating sites.
Donor (plasmid) and recipient.
Gram-positive, gram-negative (F+, F-, Hfr)

28
Q

What does competent mean in transformations?

A

Alterations in the cell wall that make it permeable to large DNA molecules.

29
Q

Natural transformation: What do single strands come in and do?

A

Recombine with DNA in chromosome- stretch of hybrid DNA. (RecA proteins)

30
Q

What DNA is released from donor in natural transformation?

A

Dead cells
Alive: Quorum sensing/biofilms

31
Q

Artificial transformation:

A

Generate “competent” cells by some treatment to permeabilize the cell membrane.
Chemical competent (Ca2+ treatment, heat shock), electroporation.

32
Q

What is artificial transformation generally restricted to and why?

A

Generally restricted to plasmids (self-replicating, circular DNA that contains genes) because of exonucleases in cytoplasm,

33
Q

What are plasmids?

A

Self-replicating, circular DNA that contains genes.
1-5% the size of the bacterial chromosome.

34
Q

Transducing particles:

A

Bacterial DNA is transferred from a donor cell to a recipient cell inside a bacteriophage.

35
Q

Generalized transduction:

A

All genes contained within a bacterium are equally likely to be packed in a phage.

36
Q

Specialized transduction:

A

Only certain bacterial genes are transferred.
Distinct from generalized, not due to packaging errors. Due to excision errors when going from lysogenic phase to lytic phase.

37
Q

What are the types of phage replication?

A

Virulent/Lytic Phages

Temperate phages: lysogenic or lytic pathway, lysogeny at att sites, prophage (excised due to environmental cues).

38
Q

What percent of progeny in a P22 lysate are generalized transducing particles?

A

2%
Some recombined into host, most circularized.

39
Q

Is one or two crossovers more stable in specialized transduction?

A

Two crossovers.

40
Q

Conjugative plasmid:

A

Carries genes for sex pili and transfer of the plasmid.
F factor

41
Q

Dissimilation plasmids:

A

Encode enzymes for catabolism of unusual compounds.

42
Q

R factors of plasmids:

A

Encode resistance to antibiotics, heavy metals, and cellular toxins.

43
Q

What secretion system type do gram negatives use?

A

Type IV secretion system.

44
Q

Common F factor in plasmids of conjugation:

A
  • Transfer within the enterics (intestinal)
  • Contains 13 tra genes required for its transfer
    – Including encoding subunits for the sex pili
  • Cells with F factor (F+)
  • No F plasmid are F-
  • F+ cells attach to F- cells with the pilus, pull the two together, transfer copy of the plasmid, both cells are now F+
  • Hfr (High freq of recombination): F plasmid becomes inserted into the chromosome
    – Now transfers chromosomal genes with itself.
45
Q

Hfr (high freq of recombination:

A

F plasmid becomes inserted into the chromosome.

46
Q

Conjugation:
Mating gram positives __

A

Clump together.

47
Q

Conjugation (gram-positive):
Pilus mediated conjugation seemingly __

A

Absent.

48
Q

CRISPR/Cas:

A

Prokayotix mechanism for immunity. Vaccine for microbes. Foreign DNA into the cell.

49
Q

How is DNA processed in CRSPR?

A

Cas system: cleaves foreign DNA
Cleaved DNA “archived” within organized clusters aka CRISPRs.

50
Q

What is CRSPR transcribed as?

A

A long precursor RNA (pre crRNA)
- Spacers- complementary sequences to foreign DNA.
- Palindromic repeats that form hairpins.

51
Q

CRSPR is processed by __ to __

A

Processed by Cas enzymes to crRNAs

52
Q

Other uses for CRSPR: (4)

A
  1. Silence or downregulate the expression of specific genes- target specific mRNAs
  2. Cas proteins role in adaptive immunity, stress response- repair proteins and refold proteins.
  3. Immunize industrial strain of bacteria
  4. Genome editing and transcriptional regulation in microbes and eukaryotes- genetic engineering.
53
Q

What is CRSPR ready to recognize and do?

A

Ready to recognize foreign DNA and target for
degradation

54
Q

What is CRSPR inherited by?

A

Progeny.

55
Q

CRSPR is FDA approved to treat what?

A

Sickle cell disease.

56
Q

What do genomes tell us about bacteria and archaea? (6)

A
  1. DNA sequencing and genomics
  2. Thousands of DNA sequences available
  3. A lot of information
  4. Many ORKs without known functions (putative functions)
  5. Metagenomics: microbes present, genes present, metabolism
  6. Phylogenetic analysis: relatedness/similarity of organism (tracking sources of epidemics/ disease epidemiology, changes in microbes over time.)

Microbiology (22 decks)

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