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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
Operator
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
26
Regulatory gene
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
27
Structural genes
Genes that make up operon Expression is regulated (may or may not be expressed)
28
In an inducible operon, the default state (of the operon) is ___
Off The repressor is bound to the operator, preventing transcription of the structural genes
29
Mutations
Changes to existing (endogenous) genetic information Are inevitable An uncorrected ‘error’ May or may not affect the encoded protein
30
Horizontal gene transfer
acquisition of new (exogenous) genetic information
31
What two things are largely responsible for the fact that genomes are dynamic – constantly changing through
Mutations and Horizontal gene transfer
32
Genome Evolution
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)
33
Vertical gene transfer
When a cell divides, it passes its DNA onto its offspring DNA getting passed down from generation to generation
34
3 mechanisms of HGT
Transformation Conjugation Transduction
35
Transformation
Uptake of DNA from the environment Usually from cells that had died
36
Competency
the ability to perform transformation
37
Natural Competency
some bacteria have specialized machinery that bind to DNA outside cell and bring it inside; naturally perform transformation
38
Induced Competency
Make bacteria do transformation Via electrical or chemical means
39
Electrical (electroporation) means for induced competency
shock bacteria, shock opens holes in membrane so outside DNA can float in
40
Chemical means for induced competency
put bacteria in chemicals (salt) with preheat shock that opens holes in the membrane like electrical
41
Transduction
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
Biotechnology
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
Why are restriction sites palindromic?
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
Polymerase Chain Reaction (PCR)
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
Endosymbiotic theory
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
Bioremediation
Use of microbes to detoxify or degrade pollutants (ex. oil spill cleanup) Evolved naturally
47
Bioaugmentation
Addition of specific microbes to degrade a pollutant Purposefully placed by man
48
Composting
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
Benefits of fermentation
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
Food spoilage
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
Conjugation
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
Sex pili are encoded on...
conjugative plasmids
53
Conjugative plasmids
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
Plasmids
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
Recombination
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
Explain the process/steps to recombination
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
Restriction enzymes
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
Explain how RE's are naturally produced by bacteria as a defense mechanism
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
blunt ends
Some RE's cut DNA at the same location on both strands Cuts right across from each other
60
sticky ends
RE cuts DNA in a staggered manner, producing an overhang
61
3 Stages to PCR
1. Denaturation 2. Annealing 3. Extension
62
Denaturation (1st step in PCR)
Separating target DNA into individual strands High temperature
63
Annealing (2nd step in PCR)
Primers bind to target DNA in a sequence-specific manner; needed to allow DNA polymerase to start synthesizing Low temperature
64
Extension (3rd step in PCR)
DNA polymerase synthesizes DNA Intermediate temperature
65
Model Microbes
Common model systems for recombinant DNA technology Prokaryotes (bacteria) - E. coli Eukaryotes – S. cerevisiae (budding yeast) Easily cultured, well-characterized, maintain plasmids
66
Taxonomy
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
Three Domain System
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
How methods of taxonomy have changed over time
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
Why are viruses not included in the three domains of life?
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
Where did viruses come from in the first place [if they’re not living things]?
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
Symbiosis
Close association between two different organisms that is beneficial to one or both of them
72
Indicator organisms
Used to detect fecal contamination of water
73
Coliforms
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
Botulism
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
Where do the fermenting microbes come from?
Indigenous flora or Starting cultures
76
Indigenous flora
Microbes naturally found on the food Common for traditional fermented foods E.g. wines and cheeses aged in caves
77
Starter cultures
Microbes added to the food Often transferred from a previous fermentation Strains can be engineered for desirable traits and re-used
78
Ethanolic Fermentation
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
Beer [ethanolic fermentation]
Alcoholic fermentation of grain (starting substance)
80
Wine [ethanolic fermentation]
Alcoholic fermentation of fruit (starting substance, e.g. grapes)
81
Synonymous mutation
no change to protein sequence (silent)
82
Frameshift mutation
Shifts the reading frame All subsequent codons are out of frame
83
Frameshift and nonsense cause underlying protein to not be...
functional anymore
84
Codon
3 mRNA nucleotides that code for an amino acid 64 total (61 sense, 3 nonsense)
85
Replicative transposon
makes a copy of itself, original piece stays, copy gets put elsewhere
86
Non Replicative transposon
picks up and moves
87
Insertion sequence (IS)
the simplest version of a transposons composed of only inverted repeats and transposase gene
88
How are plasmids vectors
They transfer genes between organisms Able to self-replicate (ori) independently from the chromosome Ori = origin of replication
89
Phylogenetic trees
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
If bacteria don’t have sex, how do they achieve diversity?
By acquiring DNA through HGT
91
Horizontal Gene Transfer (HGT)
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
Transcription
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
Non-synonymous mutation
changes protein sequence
94
Missense (type of non-synonymous)
changes an amino acid to another amino acid
95
Nonsense (type of non-synonymous)
Changes an amino acid to a stop codon Cause underlying protein to not be functional anymore

Microbiology - BIO214 (7 decks)

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