Term
|
Definition
A process used to clean up human pollution.
1) by introducing specific microorganisms to polluted environment
2) by adding nutrients that stiumlate pre-existing microorganisms to degrade the pollutants |
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Term
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Definition
| the science of the identification and analysis of genomes |
|
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Term
| As they exist in nature, why can it be said that microbial cells differ fundamentally from the cells of higher organisms? |
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Definition
| Microorganisms are independent entities that carry out their life processes independently of other cells. |
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Term
| Why are microbial cells useful tools for basic science? |
|
Definition
1) microbial cells share many characteristics with cells of multicellular organisms
2) MO's can be grown to extremely high densities in small-scale laboratory cultures. |
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Term
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Definition
| In microbiology, growth refers to an increase in the number of cells. |
|
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Term
| Major properties of cells. Which are universal of all cells? |
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Definition
*Properties of all cells*
1) Compartmentalization and metabolism
2) Growth
3) Evolution
*Properties of some cells*
4) Motility
5) Differentiation
6) Communication |
|
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Term
| Compare catalytic and genetic functions of a microbial cell. Why is neither of value to a cell without the other? |
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Definition
Genetic functions: DNA - replication, transcription and translation
Catalytic functions: Energy conservation, metabolism and enzymes.
You need energy and enzymes in order to efficiently complete the genetic functions. Without the genetic functions, you would have no enzymes or mitochondria. |
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Term
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Definition
| Populations of cells that interact with other populations of cells. |
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Term
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Definition
| A population is a group of cells derived from a single parental cell by successive cell divisions. |
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Term
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Definition
| Collectively, all the living organisms, together with the physical and chemical components of their environment |
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Term
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Definition
| The immediate environment in which a microbial population lives |
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Term
|
Definition
Last Universal common Ancestor.
Because all cells are constructed in similar ways, it is thought that all cells are descended from LUCA. |
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Term
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Definition
| oxygenated the primordial earth. |
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Term
| Where are most microbial cells found? |
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Definition
| Most are found in the terrestrial subsurface, up to 10 km under is clearly suitable for microbial life. |
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Term
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Definition
| Bacteria, Archaea, Eukarya |
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Term
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Definition
| Microorganisms that cause infectious diseases |
|
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Term
| Who were the giants of the early days of MB and their major contributions |
|
Definition
Robert Hooke (1664) - discovery of MO
Antoni Van Leeuwenhoek (1684) - discovery of bacteria
Edward Jenner (1798) - Vaccination (smallpox)
Louis Pasteur (mid to late 1800s) - mechanism of fermentation, defeat of spontaneous generation**
Robert Koch - Koch's postulates, pure culture microbiology |
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Term
| Defeat of Spontaneous Generation |
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Definition
| Louis Pasteur used a swan-necked flask to prove that MO's came from outside the flask to populate the broth. |
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Term
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Definition
1) The disease-causing organism must always be present in animals suffering from the disease, but not in healthy animals.
2) The O must be cultivated in a pure culture away from the animal body
3) the isolated o must cause the disease when inoculated into healthy suceptible animals
4) the O must be isolated from the newly infected animals and cultured again |
|
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Term
|
Definition
| When a pathogen is isolated and grown away from other MO |
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Term
| Enrichment culture technique |
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Definition
| MO are isolated from natural samples using highly selective techniques of adjusting nutrient and incubation conditions to favor a particular metabolic group of O. |
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Term
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Definition
| The oxidation of inorganic compounds to yield energy |
|
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Term
| life cycle of endospore forming bacteria |
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Definition
| vegetative cell - endospore - vegetative cell |
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Term
|
Definition
| The ability to distinguish between two adjacent objects as distinct and separate. |
|
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Term
| What are light microscopys resolution limits? |
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Definition
|
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Term
| types of light microscopes |
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Definition
| bright-field, phase-contrast, differential interference contrast, dark-field, fluorescence |
|
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Term
| Resolution is highest when what light is used? Why? |
|
Definition
When Blue light is used.
The diameter of the smallest object resolvable by any lens is equal to
0.5(lambda)/numerical aperture |
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Term
|
Definition
| bind strongly to negatively charged cell components |
|
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Term
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Definition
| After staining, gram positive bacteria appear purple-violet |
|
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Term
|
Definition
| after staining, gram negative bacteria appear pink |
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Term
| Phase contrast microscopy |
|
Definition
Based on the principle that cells differ in refractive index.
This subtle difference is amplified by a device in the objective lens of the PC microscope called a phase ring. |
|
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Term
|
Definition
| light reaches the speciment from the sides only. |
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Term
| Differential interference microscopy |
|
Definition
employs a polarizer in the condenser to produce polar light, which then passes through a prism that generates two distinct beams.
these beams transverse the speciment and enter the objective lens where they are recombined into one.
*visibly enhances subtle diff in structure |
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Term
|
Definition
| tiny stylus is positioned extremely close to specimen such that weak repulsive forces are establish between the atoms and stylus. |
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Term
| Transmission Electron Microscopy |
|
Definition
resolving power is about 0.2 nanometers.
cells must be cut into many, very thin slices which are then examined individually by TEM |
|
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Term
| Scanning Electron Microscope |
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Definition
| The specimen is coated with a thin film of heavy metal, such as gold. Then electron beam scans across specimen. electrons scattered activate a viewing screen to produce the image. |
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Term
|
Definition
| Eukaryotes house their DNA in a membrane-enclosed nucleus and are typically much larger and more complex that prokaryotic cells. |
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Term
|
Definition
DNA resides in the cytoplasm as small, compact genomes and is not enclosed within a nucleus.
Most employ their Cyt. Membrane in energy-conservation reactions. |
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Term
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Definition
| Much smaller than cells and is not a true live organism. Lacks key function of replication until it infects a host cell. |
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Term
|
Definition
nucleoid - A dense aggregation of DNA filled chromosomes found in prokaryotic cytoplasm.
nucleus - a membrane bound organelle that contains eukaryotic organisms DNA |
|
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Term
|
Definition
| small circles of DNA distinct from that of the chromosome. Typically contain genes that confer a special property on a cell (like unique metabolism) |
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Term
|
Definition
the evolutionary relationship between organisms
signs of it: Ribosomes |
|
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Term
|
Definition
| Organisms that conserve energy from organic chemicals. |
|
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Term
|
Definition
| require organic comopunds as their carbon source |
|
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Term
|
Definition
| Use carbon dioxide as their carbon source. |
|
|
Term
| What is the largest phylum of bacteria? |
|
Definition
|
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Term
|
Definition
| A type of Archaea cell, from Euryarchaeota, which cannot tolerate any oxygen. STRICT ANAEROBE. |
|
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Term
|
Definition
| Unified by their requirement for very large amounts of salt for metabolism and reproduction. |
|
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Term
|
Definition
| Protists (algae and protozoa), fungi and slime molds. |
|
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Term
|
Definition
|
|
Term
| What are the different morphologies of bacteria? |
|
Definition
Coccus (sphericle or ovid)
Rod or Bacillus (cylindrical)
Spirillum (road twisted into spiral shapes)
Spirochete (tightly coiled bacteria)
Budding and appendaged bacteria (stalks and hyphas)
Filamentous bacteria |
|
|
Term
| What limits size of cells? What does this mean for prokaryotes? |
|
Definition
Cell size is limited by the surface area to volume ratio.
Because prokaryotes are smaller, their metabolism is faster and therefore their productivity is greater than eukaryotes. |
|
|
Term
|
Definition
CM - phospholipid bilayer
- width of membrane ~ 6-8 nm
- enriched with membrane protins (trans, integral, peripheral membrane proteins) |
|
|
Term
| What makes archael membranes different? |
|
Definition
They are a MONOLAYER.
Archaeal lipids lack true fatty acid side chains instead are compose of repeating units of isoprene.
Many also contain rings within the HC chains. |
|
|
Term
| what are the functions of the cytoplasmic membrane? |
|
Definition
Permeability barrier,
Anchor for many proteins,
Site of energy conservation (proton motive force) |
|
|
Term
| What are the classes of transport systems? |
|
Definition
Simple transport - driven by the energy in the proton motor force
group translocation - chemical modification of the transported substance driven by phosphenolpyruvate
ABC transporter - Periplasmic binding proteins are involved and energy comes from ATP. |
|
|
Term
| what are the different types of transport events ? |
|
Definition
uniporters - transport a molecule unidirectionally
symporters - cotransporters that transport one molecule with another substance. (proton)
Antiporters - transport one molecule into the cell and simultaneously one molecule out of the cell. |
|
|
Term
|
Definition
ATB = ATP binding casette
- exist for the uptake of organic compounds
- consist of three components: a substrate binding protein, a membrane-integrated transporter and an ATP-hydrolyzing protein. |
|
|
Term
|
Definition
it is a polysaccharide composed of two sugar derivatives- N-acetylglucosamine and N-acetylmuramic acid
- only present in species of bacteria.
- thick in gram + bacteria.
- Thin in gram - bacteria.
**keeps bacteria from bursting from osmotic pressure |
|
|
Term
|
Definition
| acidic components of gram + bacteria's cell walls. |
|
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Term
|
Definition
Found in gram - bacteria. On the outside of the layer of peptidoglycan.
is effectively a second phospholipid bilayer.
**its this that is toxic to animals |
|
|
Term
| what is the structure of a LPS of a gram negative bacteria? |
|
Definition
Lipid A embedded into periplasm,
Core polysaccharide
O-specific polysaccharide |
|
|
Term
|
Definition
| refers to the outer membrane of a gram - bacteria |
|
|
Term
|
Definition
located between the outer surface of the cytoplasmic membrane and the inner surface of the outer membrane.
contains different types of proteins: hydrolytic enzymes, binding proteins, chemoreceptors |
|
|
Term
|
Definition
The most common cell wall in species of Archaea.
consists of interlocking protein or glycoprotein molecules that show an ordered appearance when viewed with an electron microscope.
Always outermost cell wall. |
|
|
Term
|
Definition
polysaccharide layer found around bacterial cells that excludes small particles.
capsules typically adhere firmly to the cell wall or are covalently linked to the peptidoglycan |
|
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Term
|
Definition
| A type of layer found around bacterial cells that is hard to see, more easily deformed than capsules, and will not exclude small particles. |
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Term
|
Definition
Filamentous structure composed of protein that extends from the surface of a cell.
They enable a cell to stick to surfaces or to form pellicles or biofilms. |
|
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Term
|
Definition
Similar to Fimbriae, but are typically longer and only one or a few pili are present on the surace of a cell.
- facilitates genetic exchange during conjucation
- adhedes pathogens to specific host tissues and subsequent invasion. |
|
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Term
|
Definition
| Reduce the concentration of molecules by sectioning off particles into a larger structure to use later. |
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Term
|
Definition
fixed by sulphur using bacteria and archaea.
the globules are actually in the periplasm. |
|
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Term
|
Definition
Intracellular particles of the iron mineral magnetite.
Aids bacteria in orientating themselves within a magnetic field. |
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Term
|
Definition
bacteria that live a floating existence within the water column of lakes and oceans.
they are kept afloat because they contain gas vesicles. |
|
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Term
|
Definition
produced by bacteria during a process called sporulation.
They are extremely resistant to heat, harsh chemicals and radiation.
possibly can survive tens of tousands of years |
|
|
Term
| what are the steps in endospore revival? What environmental factors are required? |
|
Definition
activation,
- occurs when endospores are heated for several minutes at an elevated but sublethal temp.
germination,
occurs when placed in the presense of specific nutrients. Typically rapid process.
outgrowth,
visible swelling due to water uptake and synthesis of RNA, proteins and DNA. |
|
|
Term
| what substance is characteristic of endospores but missing from vegetative cells? |
|
Definition
|
|
Term
| How/why is an endospore so resistant to heat, radiation and chemicals? |
|
Definition
SASP's - small acid-soluble proteins - bind to DNA and protect from UV damage, desiccation and dry heat. (changes its molecular structure)
Dehydration of the vegetative cell (and thus cytoplasm) greatly increases heat resistence and resistence to chemicals. |
|
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Term
| peritrichous flagellation |
|
Definition
| flagella are inserted at many locations around the cell surface. |
|
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Term
|
Definition
| When flagella is attached at one or both ends of a cell. |
|
|
Term
|
Definition
| A type of polar flagella, where a tuft is attached at one or both ends of a cell. |
|
|
Term
| What are the components of Flagella? |
|
Definition
Gram - (from base to flagella)
C ring below MS ring. Both surrounded by Mot proteins.
Above MS ring is P ring and L ring then the hook then the filament.
a rod is going through all the rings.
In gram + bacteria, it is missing the P and L ring because it has no outer membrane. |
|
|
Term
| What is the "basal body" of a flagella? |
|
Definition
| The Basal Body consists of the L, P, MS and C rings. (MS and C rings in gram + bacteria) |
|
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Term
|
Definition
| generate torque for flagellar movement |
|
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Term
|
Definition
through slime excretion
twitching motility - repeated extension and retraction of type IV pili. |
|
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Term
|
Definition
| the reaction/process o responding to a stimuli by either moving towards or away from it. |
|
|
Term
| what elements make up the bulk of living organisms? |
|
Definition
| Carbon, Hydrogen, Oxygen and Nitrogen |
|
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Term
|
Definition
| Iron-binding molecules that function to bind Fe*3 (ferric) iron and transport it into the cell. |
|
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Term
|
Definition
Organic compounds that are required only in very small amounts.
GF are vitamins, amino acids, purines, pyrimidines or various other organic molecules |
|
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Term
|
Definition
| the nutrient solutions used to grow microorganisms in the lab. |
|
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Term
|
Definition
Prepared by adding precise amounts of highly purified inorganic and organic chemicals to distilled water.
exact quantities are known |
|
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Term
|
Definition
a culture medium made of digests of microbial, animal or plant products such as casin (mlik protein), beef, soy-beans, yest cells
**imprecise nutritional composition. |
|
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Term
|
Definition
| Culture medium that starts with a complex base and is embellished with additional nutrients such as serum, blood etc. |
|
|
Term
|
Definition
| Contains compounds that inhibit growth of some microorganisms but not others. |
|
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Term
|
Definition
| One in which an indicator, typically a reactive dye, is added that reveals whether or not a particular chemical reaction has occured during growth. |
|
|
Term
Energy, what are its units.
what is FREE ENERGY? |
|
Definition
Measure in KJ (kilojoules)
Free energy - the energy available to do work |
|
|
Term
| how do you calculate the (delta G 0 naught) of a reaction? (IE change in free energy) |
|
Definition
Products minus reactants using the values for free energies of formation
(G) = (Gf){C + D} - (Gf)[A + B) |
|
|
Term
| Do exergonic reactions have a negative or positive change in free energy? |
|
Definition
| They have a negative change in free energy. This means that they release energy and could occur spontaneously. |
|
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Term
|
Definition
| Activation energy is the energy required to bring all molecules in a chemical reaction into the reactive state. |
|
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Term
|
Definition
A catalyst is a substance that lowers the activation energy of a reaction
Biological catalysts are enzymes |
|
|
Term
|
Definition
All enzymes are protein catalysts.
they are highly specific for the reactions they ccatalyze - each often only catalyzing one reaction.
Enzyme combines with substrate (reactant) |
|
|
Term
|
Definition
Loosely bound to enzymes and a single coenzyme molecule may associate with a number of different enzymes.
Most are derivatives of vitamins and NAD or NADH |
|
|
Term
|
Definition
| Groups that bind very tightly to their enzymes, usually covalently and permenantly. |
|
|
Term
| To catalyze a specific reaction, what must an enzyme do? |
|
Definition
1) bind its substrate
2) position the substrate relative to the catalytically active |
|
|
Term
|
Definition
Oxidation is the removal of an electron or electrons from a substance.
The substance oxidized donates electrons. |
|
|
Term
|
Definition
Reduction is the addition of an electron or electrons to a substrate.
Can involve an electron or electron and proton.
The substrate reduced (often O2) is the electron acceptor. |
|
|
Term
|
Definition
| An expression of a compounds or atoms tendency to be electron donors or electron acceptors. Ranges from -1 to +1. |
|
|
Term
| How do redox reactions work? |
|
Definition
| The reduced substance of a redox couple, who's E0' is more negative, donates electrons to the oxidized substance of a redox couple whose Eo' is more positive. |
|
|
Term
| What type of phosphate bond yields the most energy? (is the most "energy rich") |
|
Definition
| Anhydride bonds in phosphoenolpyruvate yields -51.6kJ/mol |
|
|
Term
| How much energy is released per mole of ATP converted to ADP + pi under standard conditions? |
|
Definition
|
|
Term
|
Definition
| The form of anaerobic catabolism in which an organic compound is both an electron donor and electron acceptor and ATP is produced by substrate level phosporylation |
|
|
Term
|
Definition
| The catabolism in which compound is oxidized with O2 (or an O2 substitute) as the terminal electron acceptor, usually accompanied by oxidative phosphorylation. |
|
|
Term
| Substrate-Level phosphorylation |
|
Definition
| In this process, ATP is synthesized directly from energy-rich intermediates during steps in the catabolism of the fermentable substrate. |
|
|
Term
| Oxidative phosphorylation |
|
Definition
| ATP is produced at the expense of the proton motive force. |
|
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Term
|
Definition
Breaks down glucose into pyruate.
Three stages:
1) preperatory reactions - not redox reactions, do not release energy, but lead to the production of a key intermediate.
Stage II - ATP synthesized when each molecule of (1,3-bisphosphoglyeric acid) is converted to (3-phosphoglyceric acid) + each molecule of phosphoenolpyruvate is converted to pyruvate.
stage III - NADH must be oxidized back to NAD+ accomplished when pyruvate is reduced (by NADH) to fermentation products (ethanol, CO2, Lactate)
**2 ATP yield!! |
|
|
Term
|
Definition
Hydrophobic molecules that lack a protein component.
Free to move about within the membrane.
They accept two electrons and two protons (H+) but transfer only two electrons to the next carrier in the electron transport chain. |
|
|
Term
| Generation of the proton motor force: |
|
Definition
1) NADH + H+ form FMNH2, 4 H+ ions are extruded to outer surface when FMNH donates 2 e- to Complex 1.
2) 2 H+ donate to quinone from dissociation of H2O into 2 H+ and O
3) Complex 2 donates and receives electrons from quinone cycle as well as donating electrons to the Cytochrome (n complex IV)
4)Quinone cycle pumps out 4 H+ to outer membrane.
5) Cytochrome feeds electrons through to Complex IV, which reduces 1/2 O2 to H2O and pumps out 2 H+.
# H+ pumped out = 10 |
|
|
Term
| What features are characteristic of all transport chains? |
|
Definition
1) arrangement of carriers in order of increasingly more positive Eo'
2) Alternation of electon-only and electon-plus-proton carriers in the chain
3) generation of a proton motor force |
|
|
Term
| What is the proton motor force for? How does it do this? |
|
Definition
It uses the electrochemical gradient produced by the pumping of H+ ions onto the outside of the cell (and the retention of OH molecules from the break down of water) to drive a large protein complex called ATP synthase (ATPase).
**Driving ATPase backwards can generate a proton motor force! |
|
|
Term
|
Definition
| The pathway by which pyruvate is completely oxidized into CO2 |
|
|
Term
| For each pyruvate molecule oxidized through the CAC, how many CO2 molecules are released? |
|
Definition
| three CO2 molecules are released. |
|
|
Term
| Explain respiration of glucose and explain how much ATP it gives you. |
|
Definition
Electrons from NADH and FADH are fueld for electron transport chain, ultimately resulting in the reduction of electron acceptor O2 to H2O ... this allows for a complete oxidation of glucose to CO2.
A total of 38 ATP can be made by respiring the Glucose molecule to CO2 + H2O |
|
|
Term
|
Definition
| The time that it takes for one cell to eventually separate into two cells. |
|
|
Term
| Fts (Filamentous Temperature Sensitive) Z proteins |
|
Definition
Fts Z polymerizes to form a ring around the middle of the cell.
the Zip A anchor connects the FtsZ ring to the cytoplasmic membrane and stabilizes it. |
|
|
Term
| Which type of protein is the FtsZ and FtsA proteins related to? |
|
Definition
FtsZ --> related to tubulin
FtsA --> related to Actin |
|
|
Term
|
Definition
Fascilitate the midpoint for the FtsZ.
There's Min C, D, E.
Min D forms a spiral structure on the inner surface of the CM and oscillates back and forth from pole to pole. |
|
|
Term
|
Definition
The protein that is a major shape-determining factor in prokaryotes.
Forms a spiral shape around the inside of the cell, just underneath the CM.
Assists in segregation of the replicated chromosome such that one copy is distributed to each cell. |
|
|
Term
|
Definition
| A hydrophobic alchohol that transports peptidoglycan precursers across the CM by rendering them sufficiently hydrophobic to pass through the membrane interior. |
|
|
Term
| Explain peptidoglycan synthesis, |
|
Definition
Beginning at FtsZ ring, small gaps in the wall are made by enzymes called autolysins.
Bactoprenol transports peptidoglycan precursors across the CM by rendering them sufficeintly hydrophobic to pass through the membrane interior.
Then, transpeptidation |
|
|
Term
|
Definition
| The junction or ridge formed between new and old peptidoglycan of a cell. |
|
|
Term
|
Definition
| Forms the peptide cross-links between muramic acid residues in adjacent glycan chains. |
|
|
Term
| What process is blocked by penicillin? |
|
Definition
|
|
Term
| What are the phases of the microbial growth cycle? |
|
Definition
Lag
Exponential
Stationary
Death |
|
|
Term
|
Definition
| An organism growing in an enclosed vessel. |
|
|
Term
|
Definition
- During New Growth
- after damage to cell material
- when transferred from rich to poor nutrient concentration |
|
|
Term
| What is stationary phase? |
|
Definition
| When exponential growth ceases and there is no net increase or decrease in cells. |
|
|
Term
|
Definition
| A continuous culture device that maintains a constant volume to which fresh medium is added at a constant rate while an equal volume of spent culture medium (containing cells) is removed at the same rate. |
|
|
Term
| What factors govern the growth rate and cell density in a chemostat? |
|
Definition
| Two factors govern: 1) The dilution rate 2) the concentration of a limiting nutrient. |
|
|
Term
|
Definition
For every MO there is a minimum temperature below which growth is not possible,
an optimum temperature at which growth is most rapid,
and a maximum temperature above which growth is not possible.
*these are the cardinal temperatures. |
|
|
Term
| What is the range for any organisms cardinal temps? |
|
Definition
|
|
Term
| What are the different temperature classes of organisms? |
|
Definition
Psychrophile (below zero - *4 - 15)
Psychrotolerant (0 - *20 - 40 )
Mesophile (Optima 39)
Thermophile (Optima 45-80)
Hyperthermophile Bacteria/Archaea (Opt 88)
Hyperthermophile Archaea - (Opt 106) |
|
|
Term
|
Definition
Water availability is expressed in physical terms. It is defined as the ratio of the vapor pressure of the air in equilibrium with a substance or solution to the vapor pressure of pure water.
Values vary between 0 and 1 |
|
|
Term
|
Definition
The solute used inside the cell for adjustment of cytoplasmic water activity. It's noninhibitory to macromolecules within the cell.
Typically highly water soluble molecules, such as sugars, alchohols or amino acid derivitaves. |
|
|
Term
What's the difference between
Aerobes
Microaerophiles
Facultative
Anaerobes
Aerotolerant Anaerobes
Obligate Anaerobes |
|
Definition
Aerobes - Grow at full oxygen tension, respire o2 in their metabolism
Microaerophiles, Aerobes that can use o2 only when it is present at levels reduced from that in air (microoxic conditions) (facultative)
Anaerobes - cannot respire oxygen
Strict or Obligate anaerobes - Die if they respire oxygen
Aerotolerant Anaerobes - Can tolerate o2 and grow in its presence |
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