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microbiology 201+202 > final material > Flashcards

final material Flashcards

1
Q

an inherited change in the nucleotide base sequence of a genome

A

mutations

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2
Q

how are mutations a driving force of nature

A

they allow the opportunity for change on a genetic level

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3
Q

why are mutations rare

A

every 10^8, 10^9bp, proofreading abilities of polymerase, cells want to keep dna conserved so they keep up dna repair mechanisms

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4
Q

why are mutations more common in prokaryotes

A

their replication rate if faster and haploid means there’s no backup gene to express so it has to express the mutation

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5
Q

bac strain carrying a mutation where genotype differs, but phenotype may or may not

A

mutant strains

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6
Q

three types of mutations

A

point, frame shift, and reversion

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7
Q

one bp is subbed for another

A

point mutation

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8
Q

three kinds of point mutations

A

silent -> diff seq but same aa, usually third is diff
nonsense -> adding a stop codon = incomplete protein
missense -> different aa = evolutionary change

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9
Q

multiple bps deleted or inserted throwing off reading frame creating a domino effect on reading the entire rest of the transcript

A

frame shift mutation

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10
Q

reversion mutation

A

an earlier mutation is corrected by a second mutation either corrected at the same site or a secondary site

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11
Q

How do mutations occur

A

either spontaneous or induced

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12
Q

random change in DNA from errors in replication

A

spontaneous

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13
Q

physical or chemical agent that interacts w DNA

A

induced

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14
Q

structurally similar enough to normal bases they are incorporated into replicating chain (active culture) causing a point mutation (faulty pairing)

A

base analogs, stable mutation

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15
Q

mutagens change a base structure, altering its pairing, doesn’t need to be active, point mutation

A

DNA modifying agents

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16
Q

planar molecules that insert themselves (intercalate) btw stacked bases of the helix to induce single nucleotide pair insertions and deletions (frameshift),

A

intercalating, disrupts DNA polymerases ability to see what’s there

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17
Q

two kinds of radiation

A

non ionizing and ionizing

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18
Q

describe non ionizing radiation

A

excites atoms to a higher energy state, ex UV radiation (not very penetrating), absorbed by DNA and targets pyrimidine forming pyrimidine dimers (bases break across molecule to bind to Nextdoor base), good for tissue cultures, wl 260nm

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19
Q

describe ionizing radiation

A

causes ions to form by ejecting orbital e-, ex from most to least gamma, X-rays, cathode; more likely to see a DNA break (single or double stranded doesn’t matter)

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20
Q

three repair mechanisms

A

excision, direct, SOS

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21
Q

two kinds of excision repair

A

nucleotide excision and base excision

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22
Q

describe nucleotide ex repair

A

UvrABC uses polymerase I (endonuclease) to cut out an entire mutation-containing segment, DNA ligase to reconnect

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23
Q

describe bas ex repair

A

DNA glycosylase picks off an individual mutated base - yielding an apurinic/apyrimidic site (AP site); AP nuclease nicks the back bone for polymerase I to readd and ligase to reconnect

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24
Q

describe direct repair

A

photo activation uses photolyase to repair altered bonding from UV damage (pyrimidine dimer repair) (no polymerase or ligase)

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25
describe SOS repair system
last resort effort bc mutations keep occurring; stalls in replication or too many breaks in DNA (from mutation repairs) triggers RecA (effector) to remove LexA (repressor) so SOS genes can be transcribed
26
SOS genes that are made
UvrABC -> nucleotide ex repair (fixing segments) SfiA -> temporary block on cell division allows repair mechanisms more time to work Translation DNA synthesis genes -> use polymerase 4 and 5 to fill gaps without proofreading
27
two kinds of isolating mutants
selection -> confers some type of advantage like antibiotic resistance screening -> involves examining large numbers of colonies for certain types of mutations (non selectable); harder to determine
28
what isolating technique is used to detect autotrophic mutations like nutritional mutations
replica plating
29
replica plating organism example
Auxotroph, lysine auxotroph only grows if lysine is supplemented in media
30
replica plating process
1) grow on a master plate (complete media) and stamp with a sterile velvet stamp 2) stamp velvet on new complete plate and new minimal plate 3) incubate 4) growth -> all colonies grow on complete, only non mutants grow on minimal (process of elimination)
31
physical exchanges of genes between genetic elements is
genetic recombination
32
quorum sensing
cell communication
33
most common recombination involving exchange of 2 similar pieces of DNA btw diff sources
Homologous recombination, occurs in all domains, uses RecA as main enzyme
34
genetic recombination differs between euks and proks how
euks -> use vertical gene transfer, during meiosis proks -> horizontal gene transfer
35
DNA transfer mediated by bacteriophage (viruses affecting prok cells)
Transduction
36
two kinds of phage infection
lytic -> get in, explode, get out lysogenic -> either lyse or hide out in the cell, benefit of hiding out is waiting until environmental conditions are favorable then blow it up
37
two method of transduction
generalized or specialized
38
describe generalized transduction
- lytic component - phage is taking over host cell facilities to make viral proteins instead - host DNA is deteriorating into fragments, some are taken up by phage bc the phage is only checking for size requirements - normal phages and traducing phages are made, cell is lysed when a transducing phage goes to inject a new cell with a viral protein, the bac DNA fragment is injected and homologous recombination occurs
39
describe specialized transduction
- only hiding out - phages become closely associated with host genome - phages cut themselves out taking some bac DNA with them - new phage either lost some viral genome or has additional bac dna - when it goes to infect a new cell it is unproductive
40
what plasmids can be transferred to one cell from another and contain a specific set of genes
conjugative plasmids
41
conjugative plasmid gene set
Tra region contains TraI = nicking gene relaxosome Pilus = allows genetic exchange Type IV secretion system = inject DNA into pilus
42
two kinds of conjugative plasmids
resistance plasmids - antibiotic resistance, encode proteins to either inactivate a substance OR inhibit a substance virulence plasmids - genes allow attachment to specific cells and/or form a substance that damages host
43
recombination due to the movement of DNA sequences from one part of the genome to another
Transposable elements, no origin of replication, discovered by Barbara McClintock
44
two kinds of transposable elements, both have inverted repeats (50-100bps) and transposase encoding exons
insertion sequences - simpler, shorter, just the transposase exons transposons - longer, additional genes beyond transposase
45
what does transposase do
recognizes, cuts, pastes back in for transposable elements
46
transposase mechanisms
conservative - cut out an area and relocate it somewhere else replicative - copy an area and paste the copy somewhere else
47
describe viruses
- they lack enzymes for metabolic processes (no glycolysis, ETC, TCA etc..), - lack machinery for synthesizing proteins (no ribosomes) - not considered cells, non living - obligate intracellular parasite (debated bc parasite insinuates its alive) - size is tiny, nanometer range 22-250 nm
48
virus structure
- simpler than bacteria - just need a genome and something to protect the genome - all have a nucleic acid and capsid, only animal viruses have envelopes (makes its own phospholipid bilayer out of host plasma)
49
describing the viral capsid
- protein encompassing genetic material - composed of capsomeres that spontaneously self assemble - structure is inherent (coded for)
50
what are the three kinds of viral capsid shapes
helical - elongated icosahedral - spherical, 20 triangular faces, 12 vertices, symmetrical atypical/complex - not helical or icosahedral - poxvirus - polysaccharide capsid glycoprotein w fibril shape - and bacteriophage has extra appendages
51
describe viral nucleic acid
- the genome - number of genes is much smaller than bac - contain DNA OR RNA NOT BOTH - four kinds, DNA single or double stranded or RNA single or double stranded
52
retroviruses
RNA genome with a DNA phase
53
two kinds of classification of viruses
International committee on taxonomy of viruses and Baltimore scheme
54
how is the international committee organized
- host range, structural morphology, replication cycle, genome, seq of genome - classified 2000 species - order, family, subfamily, genus, species - 3 orders - viralis - fam - virile - gen - includes virus in the name - sp - virus
55
describe the Baltimore scheme
- viral genome type and its relationship with mRNA - 7 classes
56
what are the three parts of the replication cycle
adsorption, penetration + unceasing, replication + protein synthesis - technically 6 steps, 8-40 hrs
57
first step in viral replication
adsorption - virus attaches to its host by binding to specific cell receptors - tissue specific
58
first method used in penetration and uncoating
method 1 - virus is engulfed (endocytose) and enclosed in a vesicle - enzymes in the vesicle begin to break down capsid/envelope - virus mediates breakdown of vesicle, unceasing the genetic material - euk endozomal path: big change decrease in pH uncoats capsid
59
second method used in penetration and uncoating
- direct fusion of viral envelope with host cell membrane - capsid released into cytoplasm - cytoplasm is a reducing environment so capsid will uncoat
60
how do dna viruses replicate
they use host machinery in nucleus to replicate and assemble
61
why does positive sense need RNA-dependent RNA polymerase for replication but not protein synthesis
because it can act as its own mRNA to transcribe proteins, but not to copy its genome
62
how do negative sense deal without DNA
- RNA polymerase only know hoe to make RNA from DNA - viral RNA- dependent RNA polymerase is within the capsid
63
Retroviruses (positive sense)
- synthesize DNA using their RNA genome - RNA is immediately used to transcribe DNA using virally packaged reverse transcription enzyme (reverse transcriptase is able to use RNA to make DNA) - rely on RNase H that can break down the RNA strand, allowing DNA to be double stranded + integrate into chromosome (integrase)
64
viral proteins
early - taking over + genome replication proteins late - structural proteins assembly - viral particles are constructed from the growing pool of parts
65
release of viral proteins
two options cell lysis - cytoplasmic membrane is completely disrupted = cell death membrane budding/swelling - association w enveloped viruses; endocytosis to bud off of cell membrane taking a portion with it; use lipid rafts
66
what are lipid rafts
- enriched cholesterol + sphingolipids which change density of membrane in that specific area - more inclusive environment, only going to take what can handle the new environment - uses it a lot with signal cascades

microbiology 201+202 (5 decks)

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