question

microbial bioremediation

answer

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

question

Genomics

answer

the science of the identification and analysis of genomes

question

As they exist in nature, why can it be said that microbial cells differ fundamentally from the cells of higher organisms?

answer

Microorganisms are independent entities that carry out their life processes independently of other cells.

question

Why are microbial cells useful tools for basic science?

answer

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.

question

Growth

answer

In microbiology, growth refers to an increase in the number of cells.

question

Major properties of cells. Which are universal of all cells?

answer

*Properties of all cells*
1) Compartmentalization and metabolism
2) Growth
3) Evolution
*Properties of some cells*
4) Motility
5) Differentiation
6) Communication

question

Compare catalytic and genetic functions of a microbial cell. Why is neither of value to a cell without the other?

answer

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.

question

Microbial community

answer

Populations of cells that interact with other populations of cells.

question

Microbial population

answer

A population is a group of cells derived from a single parental cell by successive cell divisions.

question

Ecosystem

answer

Collectively, all the living organisms, together with the physical and chemical components of their environment

question

Habitat

answer

The immediate environment in which a microbial population lives

question

LUCA

answer

Last Universal common Ancestor.
Because all cells are constructed in similar ways, it is thought that all cells are descended from LUCA.

question

Cyanobacteria

answer

oxygenated the primordial earth.

question

Where are most microbial cells found?

answer

Most are found in the terrestrial subsurface, up to 10 km under is clearly suitable for microbial life.

question

Major Lineages of Cells

answer

Bacteria, Archaea, Eukarya

question

Pathogens

answer

Microorganisms that cause infectious diseases

question

Who were the giants of the early days of MB and their major contributions

answer

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

question

Defeat of Spontaneous Generation

answer

Louis Pasteur used a swan-necked flask to prove that MO's came from outside the flask to populate the broth.

question

Koch's postulates

answer

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

question

Pure culture

answer

When a pathogen is isolated and grown away from other MO

question

Enrichment culture technique

answer

MO are isolated from natural samples using highly selective techniques of adjusting nutrient and incubation conditions to favor a particular metabolic group of O.

question

Chemolithotrophy

answer

The oxidation of inorganic compounds to yield energy

question

life cycle of endospore forming bacteria

answer

vegetative cell - endospore - vegetative cell

question

Resolution

answer

The ability to distinguish between two adjacent objects as distinct and separate.

question

What are light microscopys resolution limits?

answer

around 0.2 micrometers.

question

types of light microscopes

answer

bright-field, phase-contrast, differential interference contrast, dark-field, fluorescence

question

Resolution is highest when what light is used? Why?

answer

When Blue light is used.
The diameter of the smallest object resolvable by any lens is equal to
0.5(lambda)/numerical aperture

question

Basic dyes

answer

bind strongly to negatively charged cell components

question

Gram + Bacteria

answer

After staining, gram positive bacteria appear purple-violet

question

Gram - Bacteria

answer

after staining, gram negative bacteria appear pink

question

Phase contrast microscopy

answer

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.

question

dark field microscopy

answer

light reaches the speciment from the sides only.

question

Differential interference microscopy

answer

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

question

Atomic Force Microscopy

answer

tiny stylus is positioned extremely close to specimen such that weak repulsive forces are establish between the atoms and stylus.

question

Transmission Electron Microscopy

answer

resolving power is about 0.2 nanometers.
cells must be cut into many, very thin slices which are then examined individually by TEM

question

Scanning Electron Microscope

answer

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.

question

Eukaryote

answer

Eukaryotes house their DNA in a membrane-enclosed nucleus and are typically much larger and more complex that prokaryotic cells.

question

Prokaryotic cells

answer

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.

question

Viruses

answer

Much smaller than cells and is not a true live organism. Lacks key function of replication until it infects a host cell.

question

nucleus vs nucleoid

answer

nucleoid - A dense aggregation of DNA filled chromosomes found in prokaryotic cytoplasm.
nucleus - a membrane bound organelle that contains eukaryotic organisms DNA

question

plasmids

answer

small circles of DNA distinct from that of the chromosome. Typically contain genes that confer a special property on a cell (like unique metabolism)

question

phylogeny

answer

the evolutionary relationship between organisms
signs of it: Ribosomes

question

Chemoorganotrophs

answer

Organisms that conserve energy from organic chemicals.

question

heterotrophs

answer

require organic comopunds as their carbon source

question

autotrophs

answer

Use carbon dioxide as their carbon source.

question

What is the largest phylum of bacteria?

answer

Proteobacteria

question

Methanogens

answer

A type of Archaea cell, from Euryarchaeota, which cannot tolerate any oxygen. STRICT ANAEROBE.

question

Extreme Halophiles

answer

Unified by their requirement for very large amounts of salt for metabolism and reproduction.

question

Microbial Eukarya

answer

Protists (algae and protozoa), fungi and slime molds.

question

morphology

answer

cell shape.

question

What are the different morphologies of bacteria?

answer

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

question

What limits size of cells? What does this mean for prokaryotes?

answer

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.

question

cytoplasmic membrane

answer

CM - phospholipid bilayer
- width of membrane ~ 6-8 nm
- enriched with membrane protins (trans, integral, peripheral membrane proteins)

question

What makes archael membranes different?

answer

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.

question

what are the functions of the cytoplasmic membrane?

answer

Permeability barrier,
Anchor for many proteins,
Site of energy conservation (proton motive force)

question

What are the classes of transport systems?

answer

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.

question

what are the different types of transport events ?

answer

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.

question

ABC Transport Systems

answer

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.

question

peptidoglycan

answer

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

question

Techoic acids

answer

acidic components of gram + bacteria's cell walls.

question

The outer membrane

answer

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

question

what is the structure of a LPS of a gram negative bacteria?

answer

Lipid A embedded into periplasm,
Core polysaccharide
O-specific polysaccharide

question

endotoxin

answer

refers to the outer membrane of a gram - bacteria

question

periplasm

answer

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

question

S-layers

answer

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.

question

Capsule

answer

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

question

slime layer

answer

A type of layer found around bacterial cells that is hard to see, more easily deformed than capsules, and will not exclude small particles.

question

Fimbriae

answer

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.

question

Pili

answer

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.

question

Cell inclusions

answer

Reduce the concentration of molecules by sectioning off particles into a larger structure to use later.

question

Sulphur Globules

answer

fixed by sulphur using bacteria and archaea.
the globules are actually in the periplasm.

question

magnetosomes

answer

Intracellular particles of the iron mineral magnetite.
Aids bacteria in orientating themselves within a magnetic field.

question

planktonic

answer

bacteria that live a floating existence within the water column of lakes and oceans.
they are kept afloat because they contain gas vesicles.

question

endospores

answer

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

question

what are the steps in endospore revival? What environmental factors are required?

answer

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.

question

what substance is characteristic of endospores but missing from vegetative cells?

answer

Dipicolinic acid.

question

How/why is an endospore so resistant to heat, radiation and chemicals?

answer

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.

question

peritrichous flagellation

answer

flagella are inserted at many locations around the cell surface.

question

polar flagella

answer

When flagella is attached at one or both ends of a cell.

question

lochotrichous

answer

A type of polar flagella, where a tuft is attached at one or both ends of a cell.

question

What are the components of Flagella?

answer

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.

question

What is the "basal body" of a flagella?

answer

The Basal Body consists of the L, P, MS and C rings. (MS and C rings in gram + bacteria)

question

what do Mot proteins do?

answer

generate torque for flagellar movement

question

gliding motility

answer

through slime excretion
twitching motility - repeated extension and retraction of type IV pili.

question

-taxis

answer

the reaction/process o responding to a stimuli by either moving towards or away from it.

question

what elements make up the bulk of living organisms?

answer

Carbon, Hydrogen, Oxygen and Nitrogen

question

Siderophores

answer

Iron-binding molecules that function to bind Fe*3 (ferric) iron and transport it into the cell.

question

Growth Factors

answer

Organic compounds that are required only in very small amounts.
GF are vitamins, amino acids, purines, pyrimidines or various other organic molecules

question

Culture Media

answer

the nutrient solutions used to grow microorganisms in the lab.

question

Defined Media

answer

Prepared by adding precise amounts of highly purified inorganic and organic chemicals to distilled water.
exact quantities are known

question

Complex Media

answer

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.

question

Enriched medium

answer

Culture medium that starts with a complex base and is embellished with additional nutrients such as serum, blood etc.

question

Selective Medium

answer

Contains compounds that inhibit growth of some microorganisms but not others.

question

Differential medium

answer

One in which an indicator, typically a reactive dye, is added that reveals whether or not a particular chemical reaction has occured during growth.

question

Energy, what are its units.
what is FREE ENERGY?

answer

Measure in KJ (kilojoules)
Free energy - the energy available to do work

question

how do you calculate the (delta G 0 naught) of a reaction? (IE change in free energy)

answer

Products minus reactants using the values for free energies of formation
(G) = (Gf){C + D} - (Gf)[A + B)

question

Do exergonic reactions have a negative or positive change in free energy?

answer

They have a negative change in free energy. This means that they release energy and could occur spontaneously.

question

Activation Energy

answer

Activation energy is the energy required to bring all molecules in a chemical reaction into the reactive state.

question

Catalyst

answer

A catalyst is a substance that lowers the activation energy of a reaction

Biological catalysts are enzymes

question

enzymes

answer

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)

question

Coenzymes

answer

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

question

Prosthetic Group

answer

Groups that bind very tightly to their enzymes, usually covalently and permenantly.

question

To catalyze a specific reaction, what must an enzyme do?

answer

1) bind its substrate
2) position the substrate relative to the catalytically active

question

Oxidation

answer

Oxidation is the removal of an electron or electrons from a substance.
The substance oxidized donates electrons.

question

Reduction

answer

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.

question

Reduction potential

answer

An expression of a compounds or atoms tendency to be electron donors or electron acceptors. Ranges from -1 to +1.

question

How do redox reactions work?

answer

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.

question

What type of phosphate bond yields the most energy? (is the most "energy rich")

answer

Anhydride bonds in phosphoenolpyruvate yields -51.6kJ/mol

question

How much energy is released per mole of ATP converted to ADP + pi under standard conditions?

answer

32.8 kJ/mol

question

Fermentation

answer

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

question

Respiration

answer

The catabolism in which compound is oxidized with O2 (or an O2 substitute) as the terminal electron acceptor, usually accompanied by oxidative phosphorylation.

question

Substrate-Level phosphorylation

answer

In this process, ATP is synthesized directly from energy-rich intermediates during steps in the catabolism of the fermentable substrate.

question

Oxidative phosphorylation

answer

ATP is produced at the expense of the proton motive force.

question

Glycolysis

answer

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!!

question

Quinones

answer

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.

question

Generation of the proton motor force:

answer

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

question

What features are characteristic of all transport chains?

answer

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

question

What is the proton motor force for? How does it do this?

answer

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!

question

Citric Acid Cycle

answer

The pathway by which pyruvate is completely oxidized into CO2

question

For each pyruvate molecule oxidized through the CAC, how many CO2 molecules are released?

answer

three CO2 molecules are released.

question

Explain respiration of glucose and explain how much ATP it gives you.

answer

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

question

Generation Time

answer

The time that it takes for one cell to eventually separate into two cells.

question

Fts (Filamentous Temperature Sensitive) Z proteins

answer

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.

question

Which type of protein is the FtsZ and FtsA proteins related to?

answer

FtsZ --> related to tubulin
FtsA --> related to Actin

question

Min Proteins

answer

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.

question

MreB

answer

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.

question

Bactoprenol

answer

A hydrophobic alchohol that transports peptidoglycan precursers across the CM by rendering them sufficiently hydrophobic to pass through the membrane interior.

question

Explain peptidoglycan synthesis,

answer

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

question

Wall-Band

answer

The junction or ridge formed between new and old peptidoglycan of a cell.

question

Transpeptidation

answer

Forms the peptide cross-links between muramic acid residues in adjacent glycan chains.

question

What process is blocked by penicillin?

answer

Transpeptidation.

question

What are the phases of the microbial growth cycle?

answer

Lag
Exponential
Stationary
Death

question

Batch Culture

answer

An organism growing in an enclosed vessel.

question

When is Lag observed?

answer

- During New Growth
- after damage to cell material
- when transferred from rich to poor nutrient concentration

question

What is stationary phase?

answer

When exponential growth ceases and there is no net increase or decrease in cells.

question

Chemostat

answer

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.

question

What factors govern the growth rate and cell density in a chemostat?

answer

Two factors govern: 1) The dilution rate 2) the concentration of a limiting nutrient.

question

Cardinal Temperatures

answer

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.

question

What is the range for any organisms cardinal temps?

answer

25-40 degrees

question

What are the different temperature classes of organisms?

answer

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)

question

Water Activity

answer

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

question

Compatible Solutes

answer

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.

question

What's the difference between
Aerobes
Microaerophiles
Facultative
Anaerobes
Aerotolerant Anaerobes
Obligate Anaerobes

answer

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

BMSC 210 – Microbiology – Flashcards

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