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Microbiology - BIO214 > Exam 3 > Flashcards

Exam 3 Flashcards

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1
Q

What is a promoter?

A

A DNA sequence that is needed for the initiation of transcription

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2
Q

The role of tRNA is to deliver __________ during protein synthesis.

A

An amino acid

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3
Q

Which of the following statements about operons are TRUE?

A

Genes within an operon encode proteins that function together in the same cellular process (ex. Lac operon, trp operon)

The structure of an operon ensures that all structural genes are expressed at the same time and same level

Operons are common in bacteria but not eukaryotes

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4
Q

In an inducible operon, an inducer binds to the ______________, pulling it off the operator and enabling transcription of the structural genes

A

repressor

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5
Q

In a repressible operon, a(n) _________________ binds to the repressor, which prevents transcription of the structural genes.

A

Co-repressor

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6
Q

The structural genes in the lac operon are involved in the __________ of lactose. The structural genes in the trp operon are involved in the __________ of tryptophan

A

Breakdown, synthesis

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7
Q

Which of the following statements about mutations are TRUE

A

Mutations are changes in the existing genetic information of an organism

Mutations can occur spontaneously when organisms reproduce

Mutation rate can be increased by mutagens.

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8
Q

A gene that moves to various different sites within a bacterial chromosome is likely positioned within a:

A

Transposon

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9
Q

Horizontal gene transfer refers to DNA that is:

A

acquired from an external source

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10
Q

Which of the following is necessary for the integration of foreign DNA into a host chromosome?

A

Recombination

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11
Q

The enzyme SwbP1 recognizes the sequence 5’-TTCGAA-3’ and cuts between the ‘TT’ within the sequence to produce a sticky end. What single-stranded overhang is produced as a result? (hint: DNA is double-stranded)

A

5’-TCGA-3’

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12
Q

Which enzymes are commonly used by molecular biologists to amplify a gene of interest and insert it into a plasmid for the purposes of genetic engineering/cloning?

A

DNA polymerase, Restriction enzymes, Ligase

  • DNA polymerase synthesizes DNA in PCR
  • Restriction enzymes recognize a DNA sequence and cut it
  • Ligase seals the DNA backbone

In bacteria: DNA polymerase replicate DNA in bacteria, RE’s cut foreign DNA/threats, ligase stitches okazaki fragments

KNOW HOW EACH ENZYME IS IN BACTERIAL ENGINEERING AND BACTERIA NORMALLY

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13
Q

3 stages in transcription

A

Initiation, Elongation, Termination

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14
Q

Initiation

A

RNA polymerase binds to DNA at a promoter (a DNA sequence that directs RNA polymerase to the start of a gene)

Start of transcription is at the promoter

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15
Q

Elongation

A

RNA polymerase adds RNA nucleotides to the 3’ end of the growing RNA strand

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16
Q

Termination

A

Release of RNA polymerase and RNA from the DNA

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17
Q

constitutively expressed

A

Genes that are always expressed

These are ‘housekeeping genes’ that encode proteins that are always needed for a cell to remain alive and functional

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18
Q

Explain why the expression of most genes can be regulated

A

Allows the cell to produce proteins that are needed in a given environment/situation and not waste resources by expressing proteins that aren’t currently needed

Not all genes are expressed at the same time

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19
Q

Induce

A

increase expression

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20
Q

Repress

A

decrease expression

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21
Q

Operon

A

Group of adjacent genes (back to back to one another) that are transcribed together and controlled by a single promoter

Genes within an operon encode proteins that function together in the same cellular process

Ensures that all genes are expressed at the same time and same level

Common in bacterial chromosomes, not eukaryotes

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22
Q

The genes within an operon are controlled by a _________ and an _________

A

promoter, operator

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23
Q

Promoter

A

region upstream of the gene(s) where the RNA polymerase binds

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24
Q

Sigma factor

A

the part of the RNA polymerase subunit that is responsible for binding to the promoter

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25
Q

Operator

A

Region upstream of the gene(s) where a repressor binds

By binding the operator, repressors influence the ability of the RNA polymerase (sigma factor) to bind the promoter

Where regulatory protein(s) bind and impact transcription

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26
Q

Regulatory gene

A

Encodes a regulatory protein (e.g. repressor), LacI

Repressors are DNA-binding proteins that bind to the operator and turn off transcription of the structural genes

Is always expressed (constitutively) → means that the repressor is always being made

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27
Q

Structural genes

A

Genes that make up operon

Expression is regulated (may or may not be expressed)

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28
Q

In an inducible operon, the default state (of the operon) is ___

A

Off

The repressor is bound to the operator, preventing transcription of the structural genes

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29
Q

Mutations

A

Changes to existing (endogenous) genetic information

Are inevitable

An uncorrected ‘error’

May or may not affect the encoded protein

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30
Q

Horizontal gene transfer

A

acquisition of new (exogenous) genetic information

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31
Q

What two things are largely responsible for the fact that genomes are dynamic – constantly changing through

A

Mutations and Horizontal gene transfer

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32
Q

Genome Evolution

A

Genomes are dynamic – constantly changing through

Create the diversity that is the raw material for evolution

Natural selection acts on populations of organisms to ensure the survival of organisms fit for a particular environment

Explains why bacteria evolve (i.e. antibiotic resistance)

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33
Q

Vertical gene transfer

A

When a cell divides, it passes its DNA onto its offspring

DNA getting passed down from generation to generation

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34
Q

3 mechanisms of HGT

A

Transformation
Conjugation
Transduction

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35
Q

Transformation

A

Uptake of DNA from the environment

Usually from cells that had died

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36
Q

Competency

A

the ability to perform transformation

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37
Q

Natural Competency

A

some bacteria have specialized machinery that bind to DNA outside cell and bring it inside; naturally perform transformation

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38
Q

Induced Competency

A

Make bacteria do transformation

Via electrical or chemical means

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39
Q

Electrical (electroporation) means for induced competency

A

shock bacteria, shock opens holes in membrane so outside DNA can float in

40
Q

Chemical means for induced competency

A

put bacteria in chemicals (salt) with preheat shock that opens holes in the membrane like electrical

41
Q

Transduction

A

DNA transfer mediated by a bacteriophage (“offshoot” of bacteriophage infection)

A bacteriophage is a virus that infects bacteria

After infecting a bacterial cell, bacteriophage package their DNA into a capsid so they can infect other cells

Sometimes DNA from bacterial chromosome gets packaged into the capsid instead

Results in the transfer of bacterial DNA from the donor to the recipient

42
Q

Biotechnology

A

The use of microbes, cells, or cell components to make a product

Convert cells into factories

Involves recombinant DNA technology (genetic engineering)

Modifying an organism’s genetic material

ex. Food (fermented foods), Vaccine, Antibiotics, Vitamins

43
Q

Why are restriction sites palindromic?

A

The 2 identical copies bind as a dimer

RE’s function as dimers; one binds at the top, one at the bottom, then they cut

44
Q

Polymerase Chain Reaction (PCR)

A

Technique for amplifying DNA

Used to produce millions of copies of a gene for insertion into a vector (plasmid)

Also commonly used as diagnostic tests (genetic and infectious diseases)

Done with thermocycler machine

45
Q

Endosymbiotic theory

A

Eukaryotes evolved from a pre-eukaryote that engulfed and ‘domesticated’ a prokaryote

The prokaryote evolved to be an endosymbiont that we now call the mitochondrion

Still today, mitochondria contain their own genome (which resembles a bacterial genome)

Eukaryotic cell kept bacteria with mitochondria around because it generates energy very well

Chloroplasts kept around → harvest energy from light (photosynthesis)

46
Q

Bioremediation

A

Use of microbes to detoxify or degrade pollutants (ex. oil spill cleanup)

Evolved naturally

47
Q

Bioaugmentation

A

Addition of specific microbes to degrade a pollutant

Purposefully placed by man

48
Q

Composting

A

Arranging organic waste to promote microbial degradation by thermophiles (ex. Compost bin; gets hot inside)

Convert plant remains into the equivalent of natural humus

49
Q

Benefits of fermentation

A

Preservation: fermentation results in conditions (acid + alcohol production) that very few microbes can tolerate, especially human pathogens

Improve digestibility of the food: microbes break down fibers

Add nutrients (such as vitamins) and flavor (such as esters and sulfur compounds)

50
Q

Food spoilage

A

A process in which food becomes unsuitable for consumption

‘Goes bad’

Often due to microbial activity (mold, fungi)

Humans are in competition with microbes for the nutrients in food

51
Q

Conjugation

A

Direct transfer of DNA between two bacterial cells

Involves a donor and a recipient

Initiated by a sex pilus protruding from the donor cell

Donor creates a bridge (sex pilus), reaches out and touches the recipient, pulls in close, then transfers DNA

52
Q

Sex pili are encoded on…

A

conjugative plasmids

53
Q

Conjugative plasmids

A

Mediate their own transfer from the donor cell to a recipient cell

Conjugative plasmid benefits; it stays in the original cell and transfers a copy of itself

HGT occurs when some of the recipient’s DNA is transferred along with the conjugative plasmid

A donor contains a conjugative plasmid where, on it, is a gene that encodes a sex pilus

It’s the conjugative plasmid that makes the decision to perform conjugation

54
Q

Plasmids

A

Self-replicating circular pieces of DNA

Maintained within a cell, inherited without the need for chromosomal integration

100x smaller than bacterial chromosomes

DO NOT encode essential genes (main difference plasmid vs chromosome)

Can be lost and the bacterial cell will still survive b/c there are no essential genes on the plasmid, only specialty genes ( Antibiotic resistance, virulence)

55
Q

Recombination

A

Exchange of DNA between two DNA molecules

Most efficient when regions are homologous (similar DNA sequence); Allows DNA to integrate into the chromosome

Is NOT a mechanism of horizontal gene transfer

DNA that is acquired through HGT must be maintained by the recipient cell or it will be lost

If the DNA is a plasmid, it will be maintained on its own

If the DNA is not a plasmid, it has to integrate into the chromosome or it will be degraded by the cell before it can be passed down

56
Q

Explain the process/steps to recombination

A
  1. DNA from one cell aligns with DNA in the recipient cell (there is a nick in the donor DNA)
  2. DNA from the donor aligns with complementary base pairs in the recipient’s chromosome. This can involve thousands of base pairs.
  3. RecA protein catalyzes the joining of the two strands
  4. Result is the recipient’s chromosome contains new DNA
    Complementary base pairs between the two strands will be resolved by DNA polymerase and ligase. The donor DNA will be destroyed. The recipient may now have one or more new genes.
57
Q

Restriction enzymes

A

Enzymes that cut specific DNA sequences

How we go about Recombinant DNA Technology; we need to cut DNA in a convenient matter so that we can put it in a plasmid

Naturally produced by bacteria as a defense mechanism

Used in bacteria as a defense mechanism but in the lab are used to cut DNA in a specific way for biotech

Different RE’s cut at different locations within recognition site; different DNA sequences

58
Q

Explain how RE’s are naturally produced by bacteria as a defense mechanism

A

Bacteria cut up bacteriophage DNA or any foreign DNA

Bacterial DNA is protected because it is methylated
RE’s can’t cut methylated DNA → chromosomal DNA is left alone

59
Q

blunt ends

A

Some RE’s cut DNA at the same location on both strands

Cuts right across from each other

60
Q

sticky ends

A

RE cuts DNA in a staggered manner, producing an overhang

61
Q

3 Stages to PCR

A
  1. Denaturation
  2. Annealing
  3. Extension
62
Q

Denaturation (1st step in PCR)

A

Separating target DNA into individual strands

High temperature

63
Q

Annealing (2nd step in PCR)

A

Primers bind to target DNA in a sequence-specific manner; needed to allow DNA polymerase to start synthesizing

Low temperature

64
Q

Extension (3rd step in PCR)

A

DNA polymerase synthesizes DNA

Intermediate temperature

65
Q

Model Microbes

A

Common model systems for recombinant DNA technology

Prokaryotes (bacteria) - E. coli
Eukaryotes – S. cerevisiae (budding yeast)

Easily cultured, well-characterized, maintain plasmids

66
Q

Taxonomy

A

Classification system (for organisms) based on evolutionary relatedness

We assign scientific name based on taxonomy

Names are based on binomial nomenclature – genus and species

67
Q

Three Domain System

A

1978 proposal by Carl Woese based on rRNA sequence (since ribosomes are a requirement of cellular life and differences in RNA sequence can provide information on evolutionary relatedness)

3 domains:
Eukaryotes
Bacteria
Archaea

68
Q

How methods of taxonomy have changed over time

A

Carl Linnaeus originally placed all life into 2 kingdoms: plants and animals

The discovery of microbes led to disagreements around their classification

Fungi were placed in their own kingdom in 1959

Prokaryotes were placed in their own kingdom in 1968

Mitochondria and chloroplasts are derived from bacteria; DNA looks like bacteria more than host cell (eukaryote) → evidence of endosymbiotic theory

69
Q

Why are viruses not included in the three domains of life?

A

They lack cellular structure (and aren’t considered living/organisms)

Viruses still have genomes so they can be classified in respect to one another

70
Q

Where did viruses come from in the first place [if they’re not living things]?

A

We don’t know fully

Possibly arose from independently-replicating strands of nucleic acids (e.g. plasmids)

Possibly developed from degenerative cells that got whittled down to genetic material and capsid

71
Q

Symbiosis

A

Close association between two different organisms that is beneficial to one or both of them

72
Q

Indicator organisms

A

Used to detect fecal contamination of water

73
Q

Coliforms

A

Aerobic or facultatively anaerobic, gram-negative,
non–endospore-forming rods

Ferment lactose with acid and gas within 48hrs at 35°C

Predominantly E. coli

Presence of coliforms determined by Most Probable Number (MPN) method

74
Q

Botulism

A

Food-borne disease caused by consumption of the botulism toxin secreted by the bacterium Clostridium botulinum

C. botulinum forms endospores (heat tolerant), toxin is heat stable (boiling doesn’t destroy it), packaging swells due to gas production by C. botulinum

Avoid bulging cans (due to gas → expanding), no need to avoid a dented can

The toxin inhibits fusion of synaptic vesicles → prevents activation of muscle cells → leads to flaccid paralysis (muscles constantly in weakened position)

Botulism toxin makes us sick, not the bacteria

75
Q

Where do the fermenting microbes come from?

A

Indigenous flora or Starting cultures

76
Q

Indigenous flora

A

Microbes naturally found on the food

Common for traditional fermented foods
E.g. wines and cheeses aged in caves

77
Q

Starter cultures

A

Microbes added to the food

Often transferred from a previous fermentation

Strains can be engineered for desirable traits and re-used

78
Q

Ethanolic Fermentation

A

Pyruvate –> ethanol + carbon dioxide

Essential part of bread, beer, and wine making

Production of beer and wine involves the same yeast: Saccharomyces cerevisiae (Brewer’s yeast)

79
Q

Beer [ethanolic fermentation]

A

Alcoholic fermentation of grain (starting substance)

80
Q

Wine [ethanolic fermentation]

A

Alcoholic fermentation of fruit (starting substance, e.g. grapes)

81
Q

Synonymous mutation

A

no change to protein sequence (silent)

82
Q

Frameshift mutation

A

Shifts the reading frame

All subsequent codons are out of frame

83
Q

Frameshift and nonsense cause underlying protein to not be…

A

functional anymore

84
Q

Codon

A

3 mRNA nucleotides that code for an amino acid

64 total (61 sense, 3 nonsense)

85
Q

Replicative transposon

A

makes a copy of itself, original piece stays, copy gets put elsewhere

86
Q

Non Replicative transposon

A

picks up and moves

87
Q

Insertion sequence (IS)

A

the simplest version of a transposons composed of only inverted repeats and transposase gene

88
Q

How are plasmids vectors

A

They transfer genes between organisms

Able to self-replicate (ori) independently from the chromosome
Ori = origin of replication

89
Q

Phylogenetic trees

A

Display evolutionary relatedness

Utilized for taxonomy

Closely-related organisms should have similar names

Originally based on observable characteristics (e.g. cell morphology)
But the same characteristic can evolve independently in different organisms
Sharing a trait does not mean relatedness

All things are related, it’s a matter or how closely
Now based on genetic relatedness (DNA sequence); more accurate

90
Q

If bacteria don’t have sex, how do they achieve diversity?

A

By acquiring DNA through HGT

91
Q

Horizontal Gene Transfer (HGT)

A

DNA comes into cell from some outside source

Allows traits to be shared between unrelated bacteria; Unrelated cells that aren’t offspring

Ex. Antibiotic resistance can be shared with other bacteria

92
Q

Transcription

A

RNA synthesis

Accessing the information stored within DNA and converting to an intermediate form (mRNA) that will soon be translated into protein

On a gene by gene basis

Cell asks do we want to express the gene and at what level

93
Q

Non-synonymous mutation

A

changes protein sequence

94
Q

Missense (type of non-synonymous)

A

changes an amino acid to another amino acid

95
Q

Nonsense (type of non-synonymous)

A

Changes an amino acid to a stop codon

Cause underlying protein to not be functional anymore

Microbiology - BIO214 (7 decks)

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