First Half Flashcards
(205 cards)
1
Q
characteristics of prokaryotes
A
- small
- no membrane- bound organelles
- 1-2 circular chromosomes
- divide by binary fission
- 70S ribosomes
- complex cell walls
- rudimentary cytoskeleton
- simple appendages
2
Q
characteristics of eukaryotes
A
- larger
- membrane-bound organelles
- multiple linear DNA with histones
- divide by mitosis
- 80S ribosomes
- simple cell walls (when present)
- complex cytoskeleton
- complex appendages
3
Q
similar feature in prokaryote and eukaryote cell structure
A
- cytoplasm
- DNA
- cell division
- ribosomes
- cell wall
- cytoskeleton of some form
4
Q
they “typical” prokaryotic cell
A
- cytoplasm is a gel-like network
- 70S ribosomes and NO mitochondria
- nucleoid contains the bacterial chromosome
- have 1 or several plasmids present
- thick/complex cell wall
- motile bacteria have flagellum
5
Q
what are Pili
A
small hairlike protein filaments used for motility, attachmet and exchange of genetic material
- pathogens use them to attach to and hosts so they can invade
- sex pili: transfer DNA during conjugation from donor to recipient
6
Q
what are stalks
A
extensions of the cell envelope and cytoplasm
- secrete adhesion factors to form “holdfast” to attach bacterium in envelope
- allows formation of biofilms in water streams
7
Q
what are flagella
A
helical bacterial “tails” used for motility
- not all bacteria have them
- arrangements allows them for swimming the direction they need to go
- can use formation to tell microbes apart
8
Q
what is the nucleoid
A
contains most prokaryotic genetic material, not membrane bound
- 1-2 chromosomes, typically haploid
- DNA is packaged into supercoiled domains by NAPs
- may also contain extrachromosomal DNA that is found in plasmids
9
Q
what are plasmids
A
are extra-chromosomal DNA elements typically not required for “everyday” survival, replicate autonomously
- smaller than chromosomes
- circular double stranded DNA
10
Q
horizontal gene transfer
A
transfer of genetic material between organisms, outside of traditional reproduction
- exclusive to prokaryotes
11
Q
types of horizontal gene transfer
A
- transformation
- transduction
- conjugation
12
Q
vertical gene transfer
A
transmission of genes from the parental generation to the offspring by asexual reproduction
- e.g. binary fission
13
Q
transformation
A
allows cell to uptake DNA from the environment
14
Q
transduction
A
allows DNA to transfer through bacteriophages that infect bacteria
15
Q
conjugation
A
allows bacteria to directly transfer DNA between cells via pili
16
Q
prokaryotic ribosomes
A
- made up of a large and small subunit
- smaller weight than eukaryotes (70S vs 80S)
17
Q
cell membrane
A
- anchor site for proteins
- selectively facilitates transport in and out of the cell
- site for proton motive force for energy conversion (ATP synthesis)
18
Q
proton motive force
A
electrochemical gradient of protons drives ATP synthesis from ADP at the F1F0-ATP synthase
19
Q
membrane phospholipids
A
- prevent free movement of polar or charged molecules across the membrane
- amphipathic
- vary in their head groups and fatty acid side chains
20
Q
saturated side chains of phospholipids
A
- only single bonds
- melt at higher temp, increase order/rigidity
- Better for organisms in warm environments
21
Q
unsaturated side chains of phospholipids
A
- contains one or more double bonds
- melt at lower temp, increase fluidity
- Bette for organisms in cold environments
22
Q
membranes also include planar molecules that fill gaps between hydrocarbon chains…
A
help control membrane structure
- in eukaryotes = sterols
- in bacteria = hopanoids
- in other prokaryotes they are a mix of these different membrane lipids and hopanoid
23
Q
bacterial vs. Archaea membrane
A
lipid tail:
Bacteria = straight chains of fatty acid without branches
archaea = long, branched isoprene chains with a methyl side chain every 4 carbons
Bond that joins lipid tail to glycerol:
Bacteria = glycerol-ester-lipids
Archaea = glycerol-ether-lipids
- enantiomers of each other
- archaea can be monolayer or bilayer
24
Q
types of membrane proteins
A
- membrane-spanning proteins (integral)
- Membrane-anchored proteins
- Peripheral membrane proteins
25
functions of membrane proteins
- structure
- detection of signals
- secrete factors for communication
- ion transport and energy generation - electron transport
26
3 transport mechanisms across the membrane
1. diffusion (simple and facilitated)
2. active transport
3. osmosis
27
diffusion across the membrane
Simple
- small uncharged molecules easily pass through
- Substrate moves DOWN its concentration gradient directly through the membrane
Facilitated
- integral memb proteins form membrane spanning channels
- Substrate moves DOWN its concentration gradient
- Premiase opens to bind the substrate then closes as it moves through
28
active transport
- requires input of energy
- coupled substrate transport is most common - export 2 different substrates simultaneously
- Energy released by one substrate moving down its gradient is used to move a different solute UP its gradient
29
symporters vs antiporters
symporter: move 2 molecules in the same direction
antiporter: move 2 molecules in the opposite direction
30
ABC transporters
- a type of active transport
- ATP-binding-cassette, biggest family of ATP dependent transport
2 types...
uptake ABC transporters: transport nutrients
Efflux ABC transporters: are used as multi drug efflux pumps
31
osmosis
- same principle as diffusion but specific to water
- Water moves from region of lower concentration of solutes to higher concentration
- facilitated by aquaporins
32
cell envelope
protective layer for most prokaryotes, includes cell wall and associated layers
exception: Mycoplasma species = no cell envelope
33
bacterial cell wall
- made up of peptidoglycan sugar chains and cross-bridges
- peptidoglycan consists of alternating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
- NAM is bound to a short peptide that crosslinks to connect the parallel glycan strands
34
peptidoglycan
- unique to bacterial cell walls - good target for antibiotics
- provides structure and support
35
antibiotics that target peptidoglycan in bacterial cell walls
Penicilin: inhibits the transpeptidase that cross-links the peptides
Vancomycin: prevents cross-bridge formation by binding to d-Ala-d-Ala dipeptide
36
Cross-linking differs between cell walls of gram-positive and gram-negative…
gram-positive: peptides in neighbouring chains are bound to each other by another peptide (pentapeptide and tetrapeptide)
gram-negative: direct link
37
thickness or gram-positive and negative bacterial cell wall
gram-positive: thick cell wall - thicker peptidoglycan layer, no outer membrane
Gram-negative: thin cell wall, has outer membrane
Mycobacteria: complex multilayered cell wall - extra associated proteins and lipids, can differentiate by staining for mycelia acids
38
structure of gram-positive bacteria
- cell wall has multiple layers of peptidoglycan
- Some have an additional cell capsule exterior to the cell wall - made of polysaccharides and glycoprotein (protect from phagocytosis)
39
pros and cons of gram-positive bacteria structure
Pros
- gram stain purple
- Strong: very thick cell wall with added strength due to threading
- Protection agains osmotic lysis
Cons
- susceptible to lysozyme and other things that attack the cell wall, which is readily accessible
- More susceptible to antibiotics than gram-negative
40
examples of gram-positive bacteria
- Bacillus cereus
- Streptococcus pyogenes
- Sthaphylococcus aureus
41
structure of gram-negative bacteria
- 2 membranes separated by periplasm that contains peptidoglycan
- outermembrane has lipopolysaccharides (LPS)
- outermsmbrane contains porins
- Lipoproteins on OM that anchor peptidoglycan in place
42
lipopolysaccharides (LPS)
- present in gram-negative outer membranes
- works as an endotoxin: harmless when pathogen is intact, but become toxic and activate immune response when released from a lysed cell
- used for stereotyping (classification of species)
43
3 regions of LPS as a permeability layer
1. O-antigen: repetitive polysaccharide (varies by strain)
2. Core polysaccharide (conserved)
3. Lipid A: anchors core polysaccharide to outer membrane
44
pros and cons of gram-negative bacteria structure
Pros
- OM is an excellent selective barrier
- Able to defend itself agains a wide range or toxic molecules
- Peptidoglycan is protected
Cons
- energetically expensive to build and maintain
- Usually have larger genomes - genes for outer membrane components
45
examples of gram-negative bacteria
- Escherichia coli
- treponema pallidum
46
Mycobacteria
- complex envelope structure
- Characteristics of both gram positive and negative and its own features
- Extreme resistance to environmental impacts
47
components unique to mycobacteria
mycolic acids: Cell wall consists of hydrophobic “waxy” mycomembrane tech in mycolic acids
arabinogalactan polysaccharide: holds together the mycolic acid layer and peptidoglycan layer of the cell wall
48
pros and cons of mycobacteria cell structure
Pros
- thick, waxy outer mycomembrane
- Resistance to dryness, osmotic stress, detergents, antiseptics, many antibiotics, phagocytosis
Cons
- grows slowly
- Cell envelope is energetically expensive to synthesize and maintain
49
Prokaryotic cell wall add ons
- S layer
- capsule
50
S layer
- monomolecular layer of identical proteins of glycoproteins
- fits together like tiles
- flexes at central pores in subunits to allow movement of molecules
- additional protection against osmotic stress, viruses and predators
- assists adherence and biofilm formation
51
difference between S layer in gram negative and positive
gram positive: S layer is below the glycosyl chains
gram negative: s layer is the most exterior layer
52
Archaeal cell wall features different from bacteria
- no peptidoglycan
- have a proteinaceous S-layer considered a part of the cell wall
- a few species contain pseudomurein with NAT rather than NAM - forms stronger peptide interbridges
- methanochondroitin is a cell wall polymer in some archaea
53
what is the capsule
- coat of polysaccharides loosely bound to the cell envelope - binds water to form a hydration layer
- can occur in gram negative and positive
- found external to S layer if they exist together
- functions: prevent phagocytosis, assist with adherence, protect from dehydration
54
what are thylakoids
- membrane structures in the cytosol of bacteria that maximize photosynthetic capability
- only available in gram negative phototrophs (e.g cyanobacteria)
55
what are carboxysomes
- found in cytosol of gram negative bacteria
- polyhedral-shaped selectively permeable protein shell containing CO2 fixing enzymes
- found in all cyanobacteria and some chemotrophs
56
Prochlorococcus Marinus bacteria
- marine cyanobacteria
- one of the earths most plentiful organisms
- responsible for 20% of oceanic photosynthesis
57
photosynthesis
- oxidation of water, with O2 produced as a by-product
- reduction of CO2 to form carbohydrates (CO2 fixing enzymes)
58
Gas vesicles
- allow microbes to float (aquatic phototrophs and some heterotrophs)
- collect gases produced by metabolism (H2 and CO2)
allow microbe to maintain a set buoyancy optimal to its preferred conditions in the water column
59
major phyla of the domain bacteria
- oxygenic phototrophs
- gram positive
- gram negative
- PVC super phylum
60
oxygenic phototrophs
- produce oxygen
- photoautotrophic prokaryotes
e.g. cyanobacteria
61
cyanobacteria as an oxygenic phototroph
- earths atmospheric oxygen comes from cyanobacteria
- contains chlorophyll and associated pigments: commonly appear green because of blue and red absorption
- also called "blue-green algae" for phycocyanin accessory pigments that some possess
62
cyanobacteria cell structure
- thylakoids (for photosynthesis)
- carboxysomes (to fix CO2)
- gas vesicles (to maintain buoyancy)
- heterocysts (to fix N2)
63
single celled and filamentous cyanobactreia
single celled include...
- synechococcus and prochlorococcus: most abundant in oceans
- microcystis: fresh water microbe, produces dangerous toxins
64
cyanobacteria in real life
- some may have red pigments
- some produce highly potent toxins
- used as food/dietary supplement
- used in production of eco-friendly renewable biodiesel/fuels
- can make bricks out of them
65
phylum apart of gram positive bacteria
- firmicutes (low GC)
- actinobacteria (high GC)
66
Phylum Firmicutes (gram +ve): order Bacillales
- consists of large rod-shaped cells
- B. subtitles = model system for gram positives
- B. anthracis = causative agent of anthrax, found in soil
- vegetable cells develop inert endospores in times of starvation and stress - released spores germinate in favourable conditions
67
Phylum Firmicutes: order clostridiales: genus Clostridium
- rod shaped cells, form endospore which swell forming a "drumstick"
- found in soil, can contaminate food
- species include: C. botulinum, C. retain, C. difficile
- botox is used to relax muscle spasms
68
non-spore-forming firmicutes
Staphylococcus
- facultative anaerobes
- cocci in clusters
Streptococcus
- aerotolerant
- cocci in chains
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Phylum actinobacteria (gram +ve): order Actinomycetales
- form complex multicellular filaments resembling branched "fuzzy" of fungi
- streptomyces: soil dwelling organisms, obligate aerobes, major antibiotic producers - form hyphae and mycelia that fragment into spores
70
3 phylums of gram-negative bacteria
Superphylum proteobacteria
Spirochetes
Bacteroidetes
71
proteobacteria
consists of 5 major classes considered to be phyla: alpha, beta, gamma, delta and epsilon
- all share common structure: triple layered gram-negative cell envelope (membrane, thin peptidoglycan, periplasm)
72
phylum alphaproteobacteria
- known as endosymbionts: nitrogen fixers at plant roots including Rhizobium
- rod-shaped with aerobic metabolism
- within the host cell the bacteria lose their cell wall and become bacteria's specialized for N fixation
73
examples of alphaproteobacteria
Agrobacterium: plant pathogens closely related to the rhizobia
Rickettsias: obligate intracellular pathogens
- cause Rocky Mountain spotted fever, spread by ticks
- includes methane-oxidizing bacteria
74
Phylum Betaproteobacteria
- heterotrophic, require nutrient rich environment
Examples...
Neisseria gonorrhoeae: forms diplococci, causes gonorrhea
Burkholderia cepacia: major opprotunistic invaders of the lungs of CF patients
75
Phylum Gammaproteobacteria
- include enteric bacteria (toxic in lakes) that colonize the colon
- rod shaped, motile by flagella
- tolerant to bile salts
- facultative anaerobes & fermentation
- include methane-oxidizing bacteria
Examples: Escherichia coli, Salmonella Shigella, Campylobacter
76
Phylum Spirochaetes (gram -ve)
- heterotrophic bacteria
- consist of sheathed spiral cells with internal flagella (endoflagella)
Examples: Treponemea palladium (syphilis), Borrelia burgdoferi
77
Phylum Bacteroidetes (gram -ve)
- non-spore forming
- rod shaped
- aerobic and anaerobic species
- contains genera such as Bacteroides and Flavobacterium
- break down toxins in foods
- can be opportunistic pathogens`
78
what are expremeophiles
organism tolerant to environmental extremes
- primarily prokaryotes
- defined by environmental conditions they grow in
- some extremophiles adapt to multiple stresses, e.g. thermoacidophiles and haloalkaliphiles
79
defining extremophiles by their environment...
acidophilic: grow between pH 1-5
alkaliphilic: grow above pH 9
halophilic: grow in high salt concentrations
thermophilic: grow between 60-80 degrees
psychrophilic: grow at 15 degrees or lower
endolithic: grow within rocks
barophilic: grow at high hydrostatic pressure
xerophilic: grow in dry conditions
80
bacterial thermophiles
- have similar physiology to archaea and are found in the same habitats
- fast growth rates and high rates of mutation
- most are hypertherophiles (grow at 70-95 degrees)
- extensive horizontal transfer of archaea genes
81
examples of bacterial thermophiles
aquifex pyrophilus: flagellated rod
thermocrinis ruber: forms filamentous mats in hydrothermal vents
Thermotoga maritima: uses anaerobic respiration, respired on sulfur
82
archaea genomes
- resemble those of bacteria in gene size and density
- certain tRNA genes are interrupted by introns
- DNA and RNA polymerases and TFs are similar to those in eukaryotes
- histone homologs
- large portions derived from bacteria by horizontal gene transfer
83
how did we determine archaea were separate from bacteria
- based on both the small subunit 16S rRNA and genome sequences
- many species live in extreme conditions
several taxa group into super phyla: Euryarchaeota = most divergent
84
Euryarchaeota phylum: methanogens
- contain several clades of methanogens
- energetic role in ecosystems for anaerobic removal of H2 - produce methane
- found in soil, ruminant digestive tract, landfills, marine floor
- major environment: anaerobic soil of wetlands, especially rice paddies; landfills
85
Methane deposit in the earth
- methane produced by methanogens deep underground is trapped in ice as methane hydrates
- global warming is causing the permafrost to melt, releasing CH4
- CH4 is 20x more potent than CO2
- CH4 is the cleanest burning natural gas
86
structure of methanogens
- rigid cell walls made up of pseudopeptidoglycan (sulphated polysaccharides or proteins)
- S layer
- cells either come in rods, cocci or spiral form
87
Archaea Halophiles
E.g. Haloquadratum walsbyi
- likes hypersaline pools - survive easy at high salt conc.
- phototroph that forms fragile sheets that float near surface of water
- supplement metabolism with light-driven ion pumps called bacteriorhodopsin for ATP-synthesis
- use gas filled vesicles to float
use pigment bacterioruberin to protect against light
88
archaea thermophiles
anaerobe that metabolizes sulfur to H2S
e.g. Pyrococcus furiosus: lives in deep sea in hydrothermal vents - hyperthermophile and barophile
89
use of archaea in biotechnology
- extremophiles make enzymes with novel ranges of stability "extremosymes" - e.g. Pfu polymerase
- archaea lipids make great vaccine adjuvants
90
Domain Eukarya
- most diverse kingdom
- animals, plants, fungi and protists kingdoms
- fungi contain micro and macroscopic organisms
- protists are single-celled and colonial eukaryotes other than fungi
- protists divide into clades of protozoa and algae
91
Kingdom Fungi
- diverse groups of heterotrophs - decomposers
- largest phyla: Basidiomycota, ascomycota
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micro vs. macro fungi
microfungi: Yeasts and moulds
macrofungi: mushrooms, puffballs, truffles
93
most Distinctive traits of fungi
CELL WALL- contains glucans and chitin
- ergosterol-containing cell membrane
94
fungi cell wall
- inner cell wall is conserved - made up of chitin and branched B-1,3-glucan
- chitin = unique component
- outer cell wall is variable
- many yeasts have an outer cell wall of manna and mannoproteins
- cryptococcus makes a capsule - not present in other fungi
95
fungi are heterotrophs with absorptive nutrition...
- principle decomposers of dead/decaying organic matter - feed off CO2 and minerals
- environmental nutrient cycling, convert organic matter to inorganic molecules
- cannot inject food - have to absorb it
- secrete enzymes for extracellular degradation
96
growth of fungi
- hyphae: grow as extended multinucleate cellular filaments
- mycelium: extending and branching form a mass of hyphae
*spore germinates to form hypha; extends/branches into mycelium which can further differentiate into fruiting bodies
97
Spores of fungi
- micro and macro fungi produce spores
- making spores is how fungi reproduce
- sexual spores: meiospores such as basidiospore and ascospores in sexual fruiting bodies
- asexual spores: mitospores such as conidiophores and sporangiospores in asexual fruiting bodies
98
sexual reproduction of fungi example: ascomycota
- sexual ascospores are endospores: form within a sac-like meiocyte that form an ascus
- sexual fruiting body = ascoma
- asci undergo meiosis internally
99
Yeasts
- unicellular organisms
- grow via budding
- some form strings of connected budding cells or hyphae
- best characterized yeast = Saccharomyces cerevisiae
100
yeasts that are important pathogens
- Candida albicans (dimorphic)
- Cryptococcus neoformans (capsule)
- Aspergillus
101
fungal symbiomts
mycorrhiza: relationship with plants
lichens: relationship with algae
102
fungal diversity as pathogens
ustilago maydis: causes corn smut
dermatophytes: causes ring worm and athletes foot (skin)
candida: causes yeast infections (mucosal)
chytrid and cordyceps fungus: animal [pathogens
103
Kingdom Protists
eukaryotes that divide into algae and protozoa
protozoa: single-celled heterotrophs
algae: photosynthetic eukaryotes, secondary endosymboiant containing chloroplasts
104
features of algae
- single-celled and simple multicellular protists
- metabolism include phototrophs: phytoplankton feed aquatic ecosystems
- rigid cell walls: cellulose and or glycoprotein layer (except diatoms)
- often have motile structures (flagella or cilia)
105
Primary algae
primary endosymbiosis: pre-eukaryote engulfment of cyanobacterium to give rise to chloroplast and primary algae
- chloroplast surrounded by 2 membranes
- includes red and green algae
106
secondary algae
secondary endosymbiosis: engulfment of primary algae by protists give rise to secondary algae
- chloroplasts surrounded by more than 2 membranes
- metabolism includes heterotrophy (due to protists) to supplement photosynthesis
- include diatoms, brown algae, dinoflagellata
107
Primary algae: chlorophyta
- also known as green algae
- chlorophyll reflects green light
- live in shallower waters
108
Primary algae: rhodophyta
- also known as red algae
- colours red with phycoerythrin pigment
- absorbs green and blue light
- lives in deeper waters
- sulfated polygalactans include agar and agarose
109
Secondary algae: Diatoms
- unusual algae
- large component of fresh water marine plankton
- diverse shapes, bipartite shells as "cell walls"
- shells of dead diatoms make up 26% of earths crust
110
Secondary algae: brown algae
- kelp: long brown blades that root near beaches
- sargassum weeds: unrooted, floating seaweed forests
- support complex food web for marine life
111
secondary algae: dinoflagellata
- major marine phytoplankton, primary producers
- predatory phototroph that can engulf prey to supplement photosynthesis
- triple membrane around chloroplasts, 2 flagella
- arbor-plated appearance of cell wall consists of stiff cellulose and carotenoid pigment
- some produce toxins: red algae blooms
- some grazers not affected
112
what is symbiosis
relationships/associations of organisms that live together
- can be positive or negative
- both partners evolve in response to each other
113
Mutualism
2 organisms grow in an intimate species-specific relationship, both symbionts benefit and may fail to grow if separated
- e.g. Lichens: consist of fungi and algae
114
synergism
both species benefit from growing together but can be separated and still grow independently
- e.g. human colonic bacteria and methanogens
115
commensalism
one species benefits, the other species is neither benefited or harmed
- e.g. Beggiatoa and H2S
116
Amensalism
one species benefits by harming the other, relationship is nonspecific
- e.g. Streptomyces bacteria and species living in soil
117
Parasitism
one species benefits at the expense of another, specifically a host
118
examples of highly evolved mutualisms
- lichens
- gut microbiome of plant/wood digesting animals
119
Lichens
- a mutualistic relationship between algae or cyanobacteria and fungi
- algae/cyanobacteria acts as a photobiont
- fungi receive carbs produced by the photosynthetic algae/cyanobacteria
- photobiont receives water and minerals from fungi
- fungi physically protect the photobiont
- nutrient exchange at photobiont layer
120
the termite wood-digesting microbe
- termites feed on wood, completely dependent on its mutualistic gut microbes to breakdown plant components for nutrients
- the protist mixotricha is composed of 5 different organisms: 3 bacterial ectosymbionts (for locomotion), at least one endosymbiont lives inside to help digest cellulose in wood
121
Endophytes (in mutualism)
- symbionts or pathogens that grow WITHIN cells - can be bacterial or fungal
- Rhizobium is a nitrogen-fixing bacteria that is an endophyte
- the bacterium enters and adapts to life within the plant tissues
- the plant forms nitrogen-fixing nodules and the endophyte bacteria are fed by the plant host
122
types of microbial metabolism
phototrophs: get energy from sunlight
chemotrophs: get energy from chemical compounds
autotrophs: get carbon from inorganic sources
heterotrophs: get carbon from organic compounds
123
examples of phototrophs: autotrophs
- cyanobacteria
- vascular plants
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examples of phototrophs: heterotrophs
- heliobacteria
- most green non-sulfur bacteria
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examples of chemotrophs: autotrophs
aka chemolithotroph
- sulfur-oxidizing bacteria
- hydrogen bacteria
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examples of chemotrophs: heterotrophs
aka chemoorganotroph
- most bacteria
- animals
127
how chemoorganotrophs get energy
- organic molecules are broken down (oxidized)
- main carbon source = glucose
128
released energy from catabolism is captured in...
1. the bonds to ATP
2. through the reduction of electron carries NADH and FADH2
129
Electron carriers (how cells survive)
NADH and FAHD2
- NADH is the reduced form (has already accepted an e-)
- NADH carries more energy than ATP
- oxidation of FADH2 and HADN allows electrons and energy to be transferred
130
glycolysis and the Krebs cycle
Glycolysis
- start with 2 glucose (6 carbons), become 2 glyceraldehyde 3-phosphate (3 carbons), become 2 pyruvate (3 carbons)
Kreb's Cycle
- where we capture the most energy in metabolism
- form lots of NADH
131
2 ways to generate ATP from glucose in chemoorganotrophs
1. substrate level phosphorylation
- hydrolysis releases energy to phosphorylate ADP to ATP
2. oxidative phosphorylation
- chemical energy is transferred first to electron carriers that create an electrochemical gradient to power ATP synthesis
132
Stages of glucose catabolism and energy capture
stage 1 = glycolysis: fuel molecules broken down producing ATP and electron carriers
stage 2 = pyruvate oxidation
stage 3 = citric acid cycle: fuel molecules are fully broken-down, produce some ATP and lots of electron carriers
stage 4 = oxidative phosphorylation: electron carriers donate electrons
133
what is respiration
set of metabolic reactions that convert chemical energy from nutrients into ATP, then release waste products
aerobic: oxygen is the terminal electron acceptor (inorganic)
anaerobic: uses inorganic molecule other than
134
fermentation
non-respiration based mechanism to generate ATP via glycolysis
- terminal electron acceptor is organic, substrate level phosphorylation
- allows oxidation of NADH produce during glycolysis to NAD+ so it can continue
- occurs in anaerobic environments
135
lactic acid vs alcoholic fermentation
lactic acid: happens by lactobacillus - produces cheese, yogurt, etc.
alcoholic: happens by saccharomyces cerevisiae - produces cheese, yogurt etc.
136
electron transport chain and proton motive force
- electrochemical gradient of protons drives ATP synthesis at ATP synthase
- electron donors (NADH/FADH2) donate e- to be transported from protein to protein in the ETC with concomitant export of H+
- the H+ gradient generates the PMF
- terminal electron acceptor = O2
137
oxidative phosphorylation
oxidation of NADH/FADH2 generates the PMF which leads to the phosphorylation of ADP to ATP
138
what is microbial growth defined as
increase in both the cell mass and cell numbers
139
essential nutrients for microbe growth
macronutrients: include major elements (C, O, H, N, P, S) and cations for protein function (Mg2+, Ca2+, Fe2+, K+)
micronutrients: needed in trace elements (Co, Cu, Mn, Zn)
140
microbial growth cycle
- most bacteria divide by binary fission - parent cell increases in size/cell volume and mass, then splits into 2 equal cells
- population doubles
- some bacteria divide asymmetrically, yeast divide by asymmetrical budding
141
germination time
the time it tales for a population to double
- in a favourable environment bacteria divide at a constant interval
- fastest fermentation = clostridium perfringens
- slowest germination = mycobacterium leprae
142
2 forms of culture media
1. liquid media: cells are in suspension, best for obtaining large numbers of cells
2. solid media: gel/solidified agar, cells grow as CFU, good for isolating a pure culture, study diversity in a sample
143
complex/rich media
- nutrient rich
- contain general extracts of yeast cell, plant and animal tissue
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minimal defined media
- contain only essential nutrients for growth of a given microbe
- concentrations are known
145
enriched media
- specific factors are added, microbes are not capable of making them but they need them to grow
- blood proteins, nucleotides, vitamins etc.
146
selective media
- favour the growth of one organism over another
- high or low pH, plus antimicrobials, specific nutrients
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differential media
- exploit biochemical/physiological differences between 2 species that grow equally well
- contain a dye that changes colour when bacteria produce specific byproducts - differentiate based on metabolic activities
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techniques to isolate pure cultures
dilution streaking and spread plating
149
what is the objective when we isolate pure cultures
- to obtain single colonies which can be used to establish pure cultures or estimate total number of bacteria in a sample
150
steps in dilution streaking
- sterilized loop picks up a small amount of sample
- drag it across the surface of an agar plate
- flame loop to sterilize/kill bacteria and let cool
- touch to end of last streak to pick up some bacteria and repeat the streaking
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result of dilution streaking
a dilution of the sample increases which the probability of obtaining separation of single bacterium producing a visible colony
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spread plating
- set up 10-fold dilutions in a liquid culture
- small amount of each dilution is plated on an agar medium
- goal is to obtain dilutions with nicely separated colonies to calculate the number of bacteria in the original sample
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Robert Hooke
- first to see and record microbes
- gave birth to microbiology
- coined the term cell
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Antonie van Leeuwenhoek
- first person to see single-celled organisms
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what disproved spontaneous generation theory
Francesco Redi: proved that maggots in decaying meat were the offspring of flies
Lazzaro Spallanzani: showed that meat broth sterilized by boiling and not exposed to air failed to grow a life source
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spontaneous generation theory
living creatures could arise from non-living matter
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Bubonic Plague
- caused by Yersinia pestis
- spread by fleas and rodents
- causes infection of the lymph nodes
- Black Death: 45-50% of European population died due to bubonic plague
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small pox
- caused by various virus
- causes small skin lesions, highly contagious, airborne
- infects multiple organs
- evidence from Egyptian mummies
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Cholera
- caused by the bacterium vibrio cholerae
- causes infection of the small intestine, severe diarrhea, vomiting and dehydration
- transmuted through contaminated food and water
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miasma theory
diseases were caused by "bad air" or "night air"
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germ theory
some diseases are caused by microorganisms
- promoted the idea of sanitation and hygine
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who contributed to germ theory
- John Snow
- Ignaz Semmelweis
- Louis Pasteur
- Joseph Lister
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John Snow
- determined that a water pump was at the centre of a cholera outbreak
- first concrete evidence for a contaminant causing disease - "founding event" for epidemiology
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Florence Nightingale
- tracked causes of deaths in crimean war, found more soldiers died of microbial infections than of battle wounds
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Louis Pasteur
- discovered microbial fermentation produces lactic acid or alcohol
- showed that microbes fail to appear spontaneously using swan neck flasks
- developed the first artificial vaccine (against anthrax)
- developed pasteurization techniques for milk
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Rober Koch
- founder of the scientific method of microbiology!
- first to use animal model system and developed pure-culture technique
- used techniques to prove that tuberculosis is caused by mycobacterium tuberculosis
- discovered specific bacteria responsible for TB, anthrax and cholera
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Julius Petri
discovered the petri dish
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Angelina and Walther Hess
first to develop solid medium to culture bacteria
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Joseph Lister
- realized gangrene and death after surgery was due to infection
- antiseptic practice during surgery: sterilize surgical instruments, made surgeons wash hands and wear gloves
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Edward Jenner
- found milkmaids exposed to cowpox are immune to smallpox
- first person to provide evidence for the use of vaccination to control infectious disease
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Discovery of viruses
Dimitri Ivanovsky: discovered small disease causing agent
Martinus Beijerinck: proposed this agent was not a bacterium but a virus
Wendell Stanley: purified and crystallized the agent, using electron microscopy identified the tobacco mosaic virus
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Alexander Flemming
- found mould Penicillium not inhibits growth of Staphylococcus bacteria - isolates penicillin
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Carl Woese
- studied bacteria that adapted to life in environmental conditions
- coined the name archaea to distinguish them from bacteria
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Global concerns for infection and disease
- emergence and re-emergence
- changing susceptibilities
- population density and globalization
- climate change/global warming
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antibacterial drug targets...
- cell wall
- DNA and RNA synthesis
- plasma membrane
- ribosomes
- metabolic pathways
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antibacterial drug resistance
- efflux pump
- inactivation of enzymes
- blocked penetration
- target modifications
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antimicrobial drug resistance
- increased antibiotic use is creating a crisis of drug resistance
- E coli anf Staphylococcus aureus are recent pathogens associated with resistance
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microbes and human health (microbiome)
- gut microbiome is essential for longevity
- alteration to the microbiome can result in metabolic disorder, cancer, neurodegenerative diseases and more
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3 domains of life
bacteria
archaea
eukarya (divide into e more categories)
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hierarchy of increasingly specific level of organisms...
Kingdom - Phylum - Class - Order - Family - Genus - Species
"kids play catch over farmer green's shed"
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Basics of bacteria
- most are harmless or beneficial, but some are pathogens
- most have cell walls containing peptidoglycan
- non-photosynthetic or photosynthetic (cyanobacteria)
- enormous metabolic diveristy
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Basics of Archaea
- found in nearly every habitat, mostly extremes
- none have been shown to be human pathogens
- cell walls contains pseudopeptidoglycan
- different evolution history than bacteria
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eukaryotic microorganisms
- protists: algae or protozoa
- Fungi: yeasts and moulds/filamentous fungi
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moulds vs yeast
Yeasts
- unicellular
- impacts in food production and safety
- can cause gonadal infections and oral thrush
Moulds
- multicellular
- impacts on pharmaceuticals
- role in decomposition and nutrient cycling
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basics of viruses
- acellular microorganisms that consist of protein and genetic material
- inert outside of the host cell
- by incorporating themselves into host they can infect other cells
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wavelength of light limits the size of the object that can be resolved, resolution requires...
contrast: able to distinguish object from its surrounding
wavelength: needs to be equal to or smaller than the object to be resolved
magnification: spreading light rays apart allows access to information
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how does light interact with an object
- absorption: light is absorbed by object
- reflection: light is reflected off object
- refraction: light passes through object and changes angle when it comes out the other end
- scattering: light goes in all directions
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commonly used microscope terms
Resolution: the ability to tell that 2 different points are separate - low resolution appears fuzzy while high resolution appears sharp
Contrast: need to increase contrast to detect different structures in a specimen
Magnification: ability of a lens to enlarge the image of an object when compared to the real object
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light vs electron microscopy
light: resolves images according to absorption of light
electron: uses beams of electrons to resolve smaller details
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types of light microscopy
1. bright field
2. dark field
3. phase-contrast
4. fluorescence
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compound microscopes (for light microscopy)
- has a system of multiple lenses to focus correct
- ocular lense = 10x magnification
- objective lens = 10, 40 and 100x magnification
- total magnification = magnification of ocular lens x magnification of objective lens
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bright field microscopy
- most common
- object appears as dark silhouette blocking passage of light
- oil immersion lens is putting a drop of oil between lens and object to minimize loss of refracted light
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impacts of staining with bright field microscopy
simple stain: adds dark colour specifically to cells, but not to anything surrounding
differential stain: stains one kind of cell but not another
- advantage = observation of cells in natural state
- disadvantage = little contrast between cell and background
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what is gram staining
- a differential stain
- differentiates between 2 type of bacteria: gram positive and gram negative
- gram positive will retain the purple stain (due to thicket peptidoglycan layer in cell wall)
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acid fast staining
- differentiates 2 types of gram-positive cells: those that have waxy mycolic acid in their cell walls and those that don't
- mycobacteria have mycolic in their cell walls therefore they will stain red
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capsule staining: negative staining
- determines bacteria that contain a protective outer capsule
- the medium around will be stained, not the organism itself
- capsule will appear like a white rig around the cell
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endospore staining
- endospores are structures within bacterial cells that allow them to survive harsh conditions
- endospores will resist staining if present - Bacillus species form highly resistant endospores
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dark field microscopy
- microbes appear as halos of bright light against darkness
- well suited for live and unstained biological samples
- object scatters light and is collected by the objective lens
- extra opaque lens under the condenser lens created a central blacked-out area
- only light scattered by the sample reaches the objective lens, all other light misses the objective
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phase contrast microscopy
- exploits differences in refractive index between the cytoplasm and surrounding medium OR between different organelles
- reveals differences in refractive index as patterns of light and dark
- can be used to view live, unfixed cells and cellular organelles
- good for visualizing unstained samples
small differences in refractive index = big differences in contrast
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fluorescence microscopy
- good for detecting "parts" of a cell
- specimen absorbs light of defined wavelength and emits light of lower energy ("fluoresces")
- specificity is determined by chemical affinity, labelled antibody, DNA hybridization, GFPs
-
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what is immunofluorescence
identifies certain disease-causing microbes by observing whether antibodies bind to them
1. antigen is fixed to a surface
2. patient serum is added, if antibodies present they bind to antigen
3. secondary antibody is added (with fluorescent label), if patient antibodies are present it binds and fluoresces
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electron microscopy
- uses beams of electrons instead of visible light
- can produce very sharp image
- scanning electron microscope (SEM): detects reflected electrons (3D)
- transmission electron microscopy (TEM): uses electrons passing through thin sections to create image
- used to detect bacteriophages (viruses)
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Koch's "Postulates"
the basis explaining why all disease is caused by microbes
1. microbe is found in all cases of disease
2. microbe is isolated from diseased host and grown in pure culture
3. when the microbe is introduced into healthy host, the same disease will occur
4. the same strain of microbe is obtained from the newly diseased host
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how do cells live?
the oxidation of NADH and FADH2 allows electrons to be transferred which allows the generation of ATP to provide energy for the cell
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