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Microbiology > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

Microbiome

A
  • human body is 100 trillion cells
  • educate immune system
  • metabolize food
  • prevent harmful microbes from invading
  • maintain a healthy state
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2
Q

Microbe

A
  • cannot be seen by the naked eye
  • <150 um
  • bacterium, viruses, parasites, bacteriophages (virus that only infects bacteria)
  • NOT all microbes are prokaryotes
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3
Q

Prokaryotes

A
  • no nucleus
  • circular DNA (1 or 2 chromosomes)
  • DNA in nucleoid, not membrane bound
  • DNA replication, transcription, and translation in the cytoplasm
  • Coupled processes for rapid growth and adaptation
  • small in size
  • no organelles
  • binary fission
  • may have several external layers
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4
Q

Eukaryotes

A
  • DNA in nucleus
  • linear DNA
  • membrane bound organelles and nucleus
  • DNA replication and transciption in the nucleus
  • translation inthe cytoplasm
  • uncoupled process (slower)
  • larger in size
  • mitosis and meiosis
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5
Q

Pathogen

A

organism/microbe that causes disease

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6
Q

Endosymbiosis

A
  • symbiotic - both organisms benefit
  • endosymbiotic - both benefit when one organism lives inside of the other (gut bacteria/humans)
  • give rise to eukaryotes
  • Lynn Margulis
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7
Q

Commensal

A
  • organisms that dont cause disease
  • could be opportunistic pathogen that attacks weakened systems
  • typically do NOT cause disease
  • antibiotics kill commensals and extra nutrients cause over growth
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8
Q

Lynn Margulis

A
  • pre-eukaryotes ate bacteria
  • cyanobacteria - bacteria created energy (ATP) via light
  • proteabacteria - bacteria created energy (ATP) via respiration
  • evidence - chloroplasts and mitochondria have circular DNA and their own membrane
  • evidence - similar DNA found in chloroplast and cyanobacteria also in mitochondria and antient proteabacteria
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9
Q

Spallanzani

A
  • disprove spontaneous generation
  • heated broth left open lead to growth
  • heated broth that was sealed did not show growth, but then showed growth after being opened
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10
Q

Discovery of Microbes

A

Robert Hooke and Antoine van Leeuwenhoak

-24/7 partners because microbes influence metabolism, nutrinet extraction, and improve our immune system

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11
Q

Pasteur 1859

A
  • work after Spanllanzani
  • open broth flask lead to growth
  • cotton plug lead to sterile broth
  • swan neck lead to sterile broth, bacteria stuck in the bottom of swan neck
  • Important for wine and beer
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12
Q

Florence Nightingale

A
  • nurse that documented battlefield deaths on pie charts
  • battle wounds, infection, other deaths
  • large portion was infection
  • didnt know that microbes were causing infections
  • motivation for research in order to improve troops
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13
Q

Koch’s Postulates

A

OVERALL: Microbes cause disease

  1. Association - microbe found in diseased animal, but NOT health animal
  2. Isolation - microbe is isolated in pure culture (ONE potential infectious agent in the culture, nondisease causing cells may be present)
  3. Causation - microbe introduced into healthy animal and cause SAME disease
  4. Reisolation - isolate the same microbe from the diseased animal
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14
Q

Limitations to Koch’s Postulate

A
  • 2nd animal may not develop the same disease or symptoms
  • lack high pathogenicity, asymptomatic carriers
  • requires an accurate test animal
  • viruses need host cells, makes harder to pure culture
  • microbe may need specific growth conditions that are hard or impossible in the lab
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15
Q

Edward Jenner

A
  • Variolation - rub dried pustules into open wound, observed by Mary Montagu
  • Jenner built off of Montagu - create cowpox vaccination that worked on smallpox
  • cowpox and smallpox are similar so immune system recognizes smallpox after exposure to cowpox
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16
Q

Pasteur 1879

A
  • attenuated Cholera vaccine
  • attenuated - weakened vaccine, cannot cause disease
  • provide protection against virulent form
  • chickens - fresh cholera killed chicken. old cholera didnt kill chicken, use same chicken with fresh cholera and they survived
  • attenuated pathogens can protect against virulent form
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17
Q

Joseph Lister

A
  • recognized that most disease in patients originated from the doctors
  • suggest washing hands with antiseptic
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18
Q

Alexander Fleming

A
  • Penicillium was on plate and the Staph colony did not grow around it
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19
Q

Fredrick Griffith

A
  • Worked with Streptococcus pneumoniae
  • Discovered “transformation” where harmless bacteria became virulent
  • No capsule - mouse lives, avirulent
  • With capsule - mouse dies, virulent, capsule allows bacteria to avoid detection and engulfment by the immune cells
  • heat killed with capsule - membrane ruptures and the contents are released. Mouse lives
  • Mix of avirulent noncapsule and heat killed with capsule - mouse dies, bacteria with capsules were found in the mouse. Something transformed the noncapsule to have a capsule
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20
Q

Oswald Avery

A
  • use enzymes that degrades components of the cell and expose to mice
  • enzyme that degraded DNA allowed the mice to survive
    • failed to find live capsule bacteria in mouse
  • Extention of Griffith research
  • DNA contained the genetic information that was responsible for transformation
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21
Q

Double Helix Discovery

A

Franklin - first image of double helix

Watson and Crick - Nobel Prize for structure

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22
Q

Cell envelope

A
  • cell membrane, cell wall, maybe a capsule, outer membrane in a gram neg cell
  • capsule is advantageous when causing disease
  • Prevent immune calls from recognizing bacteria, harder for phagocytosis
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23
Q

Cell Membrane

A
  • selectively permeable - only lets certain things in and out
  • transmembrane protein - transporters in and out
  • Passive transport - no ATP
    • Diffusion - no membrane proteins, with gradient, small uncharged ions
    • Facilitated diffusion - added by pore or carrier protein, with gradient
      • pores carry ions
      • carrier proteins carry larger molecules (sugars, AA)
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24
Q

Gram Positive Cell Envelope

A
  • Peptidoglycan (PGN) makes up cell wall. Several layers thick, Impedes antibiotics
  • Lipoteichoic acid (LTA) - anchored in the cell membrane, only in Gram +
  • Teichoic acid (TA) - linked to PGN, only in Gram +
  • Thick PGN, TA and LTA cause inflammation that enhances disease by improving access to blood flow and tissue
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25
Q

Cell Wall (Gram +)

A
  • Several layers of peptidoglycan
  • turgor pressure pushes on wall
  • made of alternating N-Acetylglucosamine and N-Acetylmuramic acid
  • D-alanine on the end of the stem peptides that connect the NAM’s (cross bridge)
  • Penecillin binding protein - cleaves one d alanine and connects stem peptides
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26
Q

Penicillin and Vancomycin

A
  • Penicillin binds to teh PBP and prevents cross bridges
  • Vancomycin binds to both D alanine and blocks PBP
  • Growing cells lyse
  • Resistance
    • PBP mutates where penicillin cant bind to it
    • Multiples versions of PBP
    • Slightly modify the step peptide, can still form cross bridge but resists vancomycin
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27
Q

Primary Active Transport

A
  • Requires ATP
  • can go against the gradient
  • resist antibiotics by effluxing antibiotics out of the cell
  • Larger or charged molecules
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28
Q

Secondary Active Transport

A

“Coupled”

  • NO ATP
  • 2 molecules move simultaneously, energy provided by 1 molecule moving with the gradient and the second molecule against the gradient
  • Antiport - molecules move in opposite direction
  • Symport - molecules move in the same direction
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29
Q

Sortase

A
  • attaches proteins to the cell wall
  • recognizes signal sequence and links it to the PGN
  • Covalent link
  • mostly in Gram +
  • Not reponsible for bringing protein across the membrane
  • Uses a signal sequence
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30
Q

Gram Negative Cell Envelope

A
  • outer membrane, periplasm, cell wall(thin), inner membrane, maybe a capsule
  • Different than Gram + because thinner PGN, has an OM, has lipopolysaccharides
  • OM is less selective than the IM
  • OM has LPS, IM does not
  • Porins or outer membrane proteins are less specific than IM proteins
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31
Q

Lipopolysaccharides (LPS)

A
  • endotoxin
  • in the OM
  • stimulates the immune cellls
  • bactericidal - antibiotic that kills cells via lysis could cause harm and septic shock
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32
Q

murein lipoprotein

A
  • In Gram neg cells
  • 3 fatty acid chains insert into inner leaflet of OM
  • docks stem peptide to link PGN to OM
  • outpocketing occurs when murein lipoprotein doesnt work
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33
Q

Nucleid and Plasmids

A
  • Nucleoid is larger, plasmids more mobile and can easily transfer DNA
  • Accessory genes on the plasmid and essential genes on the nucleoid
  • supercoiling compacts DNA
  • Transcription and translation are coupled processes - they can occur concurrently because the nucleus is not membrane bound. Major difference between pro and eukaryotes
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34
Q

Polysomes

A
  • single mRNA and many ribosomes
  • allows for rapid adaptation to new environments
  • make proteins quickly in order to change functions and adapt to surroundings
  • make many polypeptides at a time
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35
Q

Signal Recognition Particle/Protein

A
  • recognize protein and puts it into membrane
  • recognize hydrophobic groups
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36
Q

Bacteriostatic

A
  • impede process for bacteria to survive
  • rifampicin - inhibit RNA polymerase
  • attack transcription and translation
  • Erythromycin and tetracycline attack 50S and 30S subunits (ribosome)
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37
Q

No antibiotics for viral infections?

Why do antibiotics not kill human cells?

A
  • viruses do not transcribe and translate so the antibiotics cant attack these functions
  • do not have a cell wall
  • No cell wall
  • ribosomes and RNA polymerase are different in pro and eukaryotes
38
Q

Capsule

A
  • Gram + and - bacteria can have capsules
  • avoid detection from the immune system
    • hide LPS in Gram -
    • hide PGN, LTA, and TA in Gram +
  • Hinderance
    • hard to detect new environment
    • capsule is energetically expensive to make
    • slower growth
39
Q

Flagella

A
  • Stimulate movement - lack of nutrients
  • Chemotaxis - move to chemical stimulants
  • move away from toxin, bad environments, immune response
  • power - proton movement across membrane, called the Proton Motive Force
40
Q

Non-sex Pili

A
  • made of pilin (protein)
  • stick to abiotic and biotic structures
  • improve survival in environments with stress due to movement
  • twitching motility - glide next to each other and improve movement
  • microbial piggy backing - nonmotil bacteria attach to motil bacteria and move with them
41
Q

Biofilm

A
  • form on biotic and abiotic surfaces
  • more resistant to antibiotics
  • composed of polysaccharides that surround and prevent penetration (exopolysaccharides EPS)
  • grow slower and limit susceptibility to abx
  • planktonic - motil in solution
  • sessile - in place and stationary
  • severial species in one film
42
Q

sex pilus

A
  • bacterial conjugation - contact dependent sharing of info
  • genetic donor with sex pilus gives to genetic recipient (no sex pilus)
  • typically transmit plasmid (becomes linear then sex pilus then recircularize)
  • normally transmission is benefitial to the recipient
43
Q

DNA replication

A
  • DNA gyrase - uncoil DNA
  • Begins at the ori (origin) and ends at the termination sequence
  • semiconservative - half old and half new
  • bidirectional - circular DNA replication occurs in both directions
  • can only occur 5’ to 3’
44
Q

Replisomes

A
  • main machine for replicating DNA
  • DNA polymerase is the enzyme that does replication
  • other accessory proteins
  • each replisome has 2 DNA polymerases and each dividing nucleoid has 2 replicsomes
  • when reach the terminus it disassembles and falls off
  • initiate septation (FtsZ)
  • More replisomes may attach to new DNA before division, divide more rapidly, but energy expensive
45
Q

Leading and Lagging Strand

A
  • Only 5’ to 3’ replication
  • leading strand is replicated continuously
  • lagging strand is made via okazaki fragments
46
Q

Septation

A
  • Begins when replisone reaches terminus and FtsZ is recruited
  • FtsZ at the septum and other proteins are required for more membrane and cell wall in order to divide
  • older cell wall on the outer edge of the division
  • new cell wall is more susceptible to antibiotics
47
Q

Cell Arrangement

A
  • how cells group due to division septum
  • streptococci - chains, divide only on the vertical plane
  • diplococci - 2 cell chain
  • staphylococci - clusters, many planes for division
48
Q

Influence on Doubling Time

A
  • temperature
  • pH
  • nutrient levels
  • salinity
  • pressure
  • oxygen
  • biproduct conc.
49
Q

Closed system

A

Fixed volume

nutrients

space

O2

temperature

50
Q

Batch Culture Steps

A
  1. Lag phase - preparing for growth, adjust to environment
  2. log phase/exponential phase - post acclimation, grow rapidly
  3. stationary phase - nutrients consumed, filled space, flat line. Stop because 1. death = cell division 2. stop growing
  4. Death Phase - maybe due to metabolic products or lack of nutrients and space
51
Q

sporulation

A
  • adapt to poor conditions
  • mostly Gram +
  • Highly coordinated event
  • spores are dormant and survive w/o nutrients/growing conditions
  • vegetative growth during favorable conditions
  • Symmetric septum during veg growth with origins near septum
  • sporulation - asymmetrical septum (larger area for mother cell) and origins on opposite ends
52
Q

Sporulation Steps

A
  1. Asymmetric septum forms, origins at opposite poles
  2. Forespore and mother cell
  3. Mother cell engulfs forespore and makes double membrane around the forespore
  4. Mother cell degrades
  5. Cortex is PGN between membranes
  6. Diplicolinic acid stabilizes and protects spore DNA
  7. Spore is released
53
Q

Endospores

A

Resistant to radiation, pH, dessication, hot/cold, low oxygen, long period of dormancy

Botulinum toxin and anthrax

54
Q

Bio mitigation

A

Use oil eating bacteria to clean up oil spill

55
Q

Anabolism, catabolism, metabolism

A
  • anabolism - build stuff up
    • proteins, nucleic acids, lipids
  • catabolism - break down
  • metabolism - sum of anabolic and catabolic in an organism
56
Q

Essential Nutrients

A
  • CNPHOS
  • Make new biomass
  • lipids, DNA, RNA, proteins, carbohydrates
  • Co-factors are required for optimal function of enzymes
    • M 2+
  • Micronutrients - needed in smaller amounts
57
Q

Growth Factor

A
  • nutrient that only a particular bacteria needs
  • makes bacteria harder to grow in lab
  • viable but not culterable
  • Can use the DNA sequence to ID the growth factors
    • transport carbs gene - live in high carb environment
  • Energy expensive to make growth factors, would prefer to bring them in from the environment
58
Q

Autotroph/Heterotroph

A

Autotroph - make own food and build larger molecules

Heterotrophs - “eat” other organisms to make carbon molecules

  • benefit to metabolizing food is it produces energy
  • consequence of metabolizig food is it produces waste products
59
Q

Heterotroph and Autotroph cycle

A
  • autotrophs use by products from heterotrophs
  • Heterotrophs produce CO2 and H2O from polysaccharides
  • Autotrophs produce sugar via photosynthesis or lithotrophy (mineral oxidation) using H2O and CO2
60
Q

ABC Transporters

A
  • ATP Binding Cassette
  • sugar into cell (food)
  • solute binding protein, membrane embedded transporter, ABC
  • ATP hydrolized to power
  • uptake or efflux (possibly abx)
  • in Gram + or -
61
Q

Sidephores

A
  • forms Fe 3+
  • brings Fe 3+ into the cell
  • secretes siderophores in order to bring in Fe 3+
  • complex and through OMP to periplasm
  • Complex bound by solute binding protein and the SBP brings it through the the ABC transporter
62
Q

PTS System

A
  • phosphotransferase system
  • Uses PEP (phosphoenol pyruvate) that is made during glycolysis
  • Use PO4 in order to bring glucose into the cell against the gradient
  • Does NOT use ATP, but does use hte products of metabolism
  • High glucose conc inside of the cell. PO4 disguises glucose to avoid gradient detection
63
Q

Niche

A

physical location or place

64
Q

Stress Response

A
  • accomplish via transcription factors - proteins that effect what genes are expressed/transcribed
    • membrane composition
    • chaperone proteins
    • cofactors
65
Q

Cold Shock Response

A

governs expression of RNA chaperones and ribosomal factors

66
Q

Stress Response: Polysomes

A
  • one mRNA and many ribosomes
  • make protein quickly in order to adapt
  • can be more active during stress
67
Q

Thermal Impacts

A
  • effects membrane fluidity, enzyme function, integrity of protein structure
  • Microbes must adapt to the temperature of the environment
  • Psychrophiles - cold
  • mesophiles - humans
  • thermophiles - warm
  • extreme thermophiles - extreme heat, special adaptations - enzymes more stable and different membrane composition
  • Psychrophiles used to clean up oil. also in some unpasteurized cheeses
68
Q

Heat Shock Response

A
  • sense increased misfolded proteins - triggers response
  • transcription factors are made/activated
  • proteins used to stabilize proteins
  • alter membrane composition
69
Q

Pressure Impacts

A
  • membrane fluidity is a challenge
  • barosensitive - die with increase pressure
  • barophiles - need high pressure, but die due to extreme pressure
  • barotolerant - grow up to a certain pressure and then die
70
Q

Autoclave

A

Sterilization technique that uses high temperature and pressure

71
Q

Osmolarity Impacts

A
  • bacteria are 70% water, 0.5-2.5% NaCl
  • water cannot be used if it is complexed
  • Water activity - amount of water available (not complexed)
  • High osmolarity - lots of solutes and little water available
  • hypertonic - solution high, cell low, water out
  • hypotonic - solution low, cell high, water in
72
Q

Halophile

A
  • 10-20% NaCl
  • specialized Na+/K+ pump to rid excess Na+
  • Different level of salinity will have different dominate species, different colors
73
Q

Aquaporins

A
  • facilitated diffusion
  • no ATP
  • faster movement of water into and out of the cell
    • bacteria can make more aquaporins to adapt to the environment
74
Q

Hyperosmotic Shock

A
  • prevent shell shrinkage
  • compatible solutes (osmoprotectants) - cells can make certain solutes that increase the intracellular solute conc. Do not disturb normal cell function
  • prevent water from leaving
  • make chaperone proteins to protect against denaturing
75
Q

Hypoosmotic shock

A
  • mecahnosensitive channels - high turgor pressure causes activation
  • leak solutes
76
Q

pH Impact

A
  • acidophiles - prefer low pH
  • neutralophiles - 6-8 pH
  • alkaphiles - prefer high pH
  • alkaphiles use other ions (not H+) to power many processes
  • pH effects hydrogen bonds (proteins and DNA pairs)
  • some bacteria sense a pH change that triggers growth due to favorable conditions (human gut)
  • enzymes need pH 5 - 8.5
  • selectively permeable especially for charged ions
    • allows for control over H+ and OH- ions
77
Q

Oxygen Impact

A
  • Aerobic versus anaerobic
  • Aerobic - uses O2 as terminal electron acceptor in electron transport chain (aerobic respiration). Makes lots of ATP
  • Anaerobes - use alternative terminal electron acceptor (anaerobic respiration), lack electron transport chain
    • release acids, gases, alcohol
    • ethanol, lactic acid
  • Facultative anaerobe - live in presence or abscence of O2
    • can produce ATP via fermentation or respiration
  • Aerotolerant - can grow with or without O2, can only generate ATP via fermentation
78
Q

Environmental Factors Overall

A
  • global changes in gene expression to adapt
    • transciption factors
    • chaperone proteins
  • temperature, pH, osmolarity, pressure
    • adapt to maintain membrane integrity
    • maintain protein structure and function
    • mechanisms for osmotic stresses
79
Q

About Viruses

A
  • are microbes
  • are NOT cells, not prokaryotes and eukaryotes
  • viruses are not alive
  • can infect many organisms
  • small genome - live off host, dont need to make up proteins themselves
80
Q

Virion Structure

A
  • spike proteins - bind to host proteins, determine what host cells are infected, determines host range
  • tegument - between envelope and capsid. contains proteins needed for viral processes
  • Nucleocapsid - genome and the surrounding capsid
  • envelope - contains everything, spike proteins attached. Not on all virions
81
Q

Icosahedral

A
  • “naked” - lacks an envelope
  • viral genome - DNA or RNA (single or double)
    • needed to mkae progeny virions
    • maintanence
    • evade detection and hijack host machinery
  • capsid - icosahedral is made of 20 identical triangles
    • protects the genome
  • “enveloped” - Envelope - made of lipids and proteins from combo of host and viral components
  • Spike proteins - bind to host receptors
    • determine what cells are infects - “bacteria range”
  • tegument - proteins needed for viral processes
82
Q

Helical Capsid

A
  • normally RNA
  • non-enveloped or enveloped
  • similar to icosahedral
83
Q

Complex Capsid

A
  • aka bacteriophage
  • head, neck, tail sheath, tail fibers
  • target bacteria
  • DNA only
  • must inject DNA in order to get through the cell envelope
  • tail fibers determine the bacteria selected
84
Q

asymmetrical capsid

A
  • larger
  • less rigid outer membrane instead of envelope
  • has protein spikes on core envelope inside of the OM
  • accessory proteins stabalize the genome
85
Q

Virus Life Cycle

A
  1. attachment - spike proteins bind to host cell membrane
  2. enter/uncoat - capsid enters cytoplasm. caspid uncoats and releases DNA/RNA and enters nucleus
  3. Replicate/assemble - used host cell machinary
  4. Exit - takes some of the host membrane and viral membrane. Buds off of the host cell

Unenveloped - does not need to enter the nucleus. Does NOT bud but causes host cell to lyse

86
Q

HIV

A
  • gp120 binds to CD4 on the host cell (immune cell)
  • CD4 on host cell serves other purposes, NOT just there to accept HIV
  • Viral tropism - virus has affinity for certain receptors on host cells
  • spike protein attaches to the receptor
    • fuse with membrane, genetic content release
87
Q

H1N1

A
  • Hemaglutanin (H) - the spike protein
  • does not fuse to membrane
  • enters via endocytosis and forms an endosome in the cell
  • virion envelope fuses with endosome membrane in order to release the nucleic acid
  • Neuraminidase (N) - helps the virus leave the cell and damages sialic acid (receptor)
    • prevents virus from reinfecting the same cell
  • Tamiflu - antiviral, neuraminidase inhibitor, completes all steps before, cannot exit, stuck in cell
88
Q

Naked Viruses

A
  • capsid proteins binds and attach
  • genetics into cell
  • could occur via endocytosis
  • lyse the cell to release
89
Q

Lytic Phage Replication

A
  • Phage attaches and injects DNA genome
  • phage proteins made
  • degrades host DNA and hijacks replication machinery
    • limits chance of cell rejecting/degrading genome
  • phae heads packaged with DNA
  • additional assembly of collars and tail fibers
  • bacterium lyses and phages are released
    • lysin is the protein that causes lysis
      • could be used to kill bacteria in food
90
Q

Temperate phages - lysogenic replication

A
  • phages attaches and injects DNA
  • phage DNA inserted as a prophage into bacterial chromosome
  • phage replicated with bacterial DNA
  • Binary fission; phage DNA now incorporated
  • Degrades host, DNA hijacks replication machinery
  • phage proteins made
  • phage heads packaged with DNA
  • additional assembly collars, tail fibers
  • lyse, phage release

Microbiology (6 decks)

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