Can be used to study surfaces of objects at high magnification by moving a probe over the specimen's surface

microscope that illuminates the specimen directly with bright light and forms a dark image on a brighter background

light microscope in which laser-derived light scans across the specimen at a single plane of focus; stray light from other parts of the specimen is blocked out to give an image with excellent contrast and resolution

microscope that brightly illuminates the specimen while leaving the background dark

Differential Interference Contrast Microscopy

combines two beams of plane-polarized light after passing through a specimen; their interference is used to create the image

type of microscopy that exposes a specimen to light of a specific wavelength and then forms an image from the fluorescent light produced; usually the specimen is stained with a fluorescent dye (fluorochrome)

describes a microscope that retains proper focus when the objectives are changed

microscope that converts slight differences in refractive index and cell density into easily observed differences in light intensity

electron microscope that scans a beam of electrons over the surface of a specimen and forms an image of the surface from the electrons that are emitted by it

microscope in which an image is formed by passing an electron beam through a specimen and focusing the scattered electrons with magnetic lenses

Electron microscopy:

ability to observe physical characteristics in fine detail;

biochemical and physiological characteristics;

sequences of nucleic acids and proteins

describes a precellular stage in the evolution of life in which RNA was capable of storing, copying, and expressing genetic information, as well as catalyzing other chemical reactions

discovery of an RNA molecule in a protist that could cut out an internal section of itself and splice the remaining sections back together; since then, other catalytic RNA molecules have been discovered, including an RNA found in ribosomes that is responsible for forming peptide bonds

RNA and DNA are structurally similar, RNA could have given rise to double-stranded DNA

1. Isolation of DNA

2. PCR of SSU rRNAs

3. line up the sequences

4. determine evolutionary distance (different nucleotides over total nucleotides)

5. correct evolutionary distance

6. computer program constructs the tree

1. Redi: conducted a series of experiments on decaying meat and its ability to produce maggots spontaneously

2. Leeuwenhoek: boiled meat and hay extracts and then corked them; still gave rise to microorganisms

3. Spallanzani: sealed flasks, boiled them, no growth took place as long as flasks were corked; could be attributed to microorganisms already in the medium needing air to grow

4. Pasteur: drew the necks out on glass flasks, no growth because microbes in the air got trapped in the necks; still had access to air

the belief that living organisms could develop from nonliving matter

1. Microorganism must be present in every case of the disease but absent from healthy organisms,

2. suspected microorganism must be isolated and grown in a pure culture,

3. same disease must result when isolated microorganism is inoculated into a healthy host,

4. same microorganism must be isolated again from diseased host

use of only one dye, the purpose of which is simply to determine cell size, shape, relative number, and arrangement

uses more than one dye and multiple steps to distinguish between organisms based on unique staining properties

cell wall outer membrane, large periplasmic space, thin peptidoglycan layer, plasma membrane; contains Braun's lipoproteins and lipopolysaccharides (LPSs) and porins

very thick outer peptidoglycan layer, little periplasmic space, internal plasma membrane; usually contain large amounts of secondary cell wall polymers (teichoic acids)

theory is that alcohol shrinks the pores of the thick PG layer of gram positive bacteria, which prevents the loss of the CV dye; gram negative PH is too thin and not as crosslinked, so the stain washes out

capsules: most are composed of polysaccharides; not required for growth and reproduction in laboratory cultures, but confer several advantages when bacteria grow in normal habitats – help resist phagocytosis, contain water that protects against desiccation

slime layers: zone of diffuse, unorganized material that is removed easily; usually composed of polysaccharides; aids in attachment to surfaces and helps glide

plasma membrane (permeability barrier, metabolic activities), cytosol (absence of other organelles), ribosomes (free floating; protein synthesis), nucleoid (generalized location of genetic material), DNA chromosomes (genetic material in nucleoid), inclusions (storage), possibly capsule, slime layer, s-layer (protection), possibly ciliar/flagella (motility)

mitochondria (energy source), ER (contains ribosomes for protein synthesis), golgi apparatus (packaging and modifying materials for secretion), lysosome (intracellular digestion), nucleolus (location of rRNA synthesis and assembly of ribosomal subunits), nucleus (contains cell chromosomes)

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  • origin of Eukaryotic cells is due to engulfment of bacteria by ancestral eukaryote; these bacteria became dependent on the host eukaryote and evolved into mitochondria and chloroplasts

double membrane in mitochondria and chloroplasts – one from organelle, one from host that engulfed it; mitochondria and chloroplasts both possess their own DNA and ribosomes; genome of Rickettsia powazekii is more closely related to modern mitochondrial DNA than modern bacteria

endosymbiont was anaerobic bacteria that produced H2 and CO2, engulfed by host that became dependent on the H2

lipid A embedded in outer membrane, core polysaccharide and O antigen that project from the surface of the bacteria

contributes to negative charge on bacterial surface, helps stabilize outer membrane structure, may contribute to attachment to surfaces and biofilm formation, helps create a permeability barrier, protecting pathogenic gram negative bacteria from host defenses via O antigen, lipid A portion is toxic – act as an endotoxin

archaea often have an S-layer and only an S-layer comprising the cell wall

Phospholipid conformation!

every fifth carbon has a branch, ether links in archaea (ester in bacteria), can cyclize chains, form tetraethers

Storage: glycogen inclusions, polyhydroxyalkonate granules, polyphosphate granules, sulfur globules

microcompartments: carboxysomes, magnetosomes, gas vacuoles

outside in:

exosporium

coat

cortex

core wall

core

microbial population is reduced to levels that are considered safe by public health strandards

chemical fixatives penetrate cells and react with cellular components to render them inactive, insoluble, and immobile

used to protect fine cellular substructure and morphology

transmission:

electrons are illuminating beam, can be focused to create a high resolution image, useful magnification is well over 100,000x; heated tungsten filament generates a beam of electrons that is focused on a specimen by a condenser; forms an enlarged image on a fluorescent screen; denser region in the specimen scatters more electrons and appears darker in the image since fewer electrons strike that area

scanning:

produces an image from electrons released on an object's surface; hit the specimen with a beam of electrons; when the beam strikes a particular area, surface atoms discharge showers of electrons, which are trapped by a detector; when electron beams strikes a raised area, large number of electrons enter the detector; fewer electrons escape depressive areas and are darker

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  • Hotter: saturated tails with few kinks to keep close together, longer tails to interact more

  • Colder: shorter tails and unsaturated tails to maintain fluidity

  • archaea can also adjust length with cyclic rings and create monolayers to increase stability

use CO2 as sole or principal carbon source

use reduced, preformed organic molecules as carbon source

light as energy source

energy from oxidation of chemical compounds (either organic/inorganic)

reduced inorganic substances as electron source

reduced organic compounds as electron source

organic compounds that cannot be synthesized by an organism but are essential for its growth; must obtain them from the environment

process by which molecules move from a region of higher concentration to one of lower concentration; rate depends on the size of the concentration gradient

the use of carrier proteins embedded in the plasma membrane for diffusion, creating channels through which substances pass; rate plateaus above a specific gradient value because carrier proteins are saturated – transporting as many solute molecules as possible

transport of solute molecules to higher concentration with the input of metabolic energy; involves transport proteins which bind solutes with great specificity; divided into two types – primary and secondary transporters

use the energy provided by ATP hydrolysis to move substances against concentration gradient; example is ATP-binding cassette transporters (ABC transporters) – solute-binding protein binds solute and then approaches the ABC transporter, where it attaches and releases the solute – energy released by hydrolysis of ATP drives movement of the solute across the membrane

couple potential energy of ion gradients to transport of substances

linked transport of two substances in the same direction (ion + molecule)

transported substances move in opposite directions

only one molecule is being moved (as in primary active transport, facilitated diffusion, and passive diffusion)

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  • Group translocation chemically modifies the molecule as it is brought into the cell

  • best example is the phosphoenolpyruvate: sugar phosphotransferase system – transports a variety of sugars while phosphorylating them, using phosphoenolpyruvate (PEP) as the phosphate donor

  • this is an example of a phosphorelay system – phosphate from PEP transferred to Hpr via Enzyme I, yielding pyruvate – phosphate transferred to enzyme IIB via enzyme IIA – enzyme IIB is connected to enzyme IIC, which is embedded in the membrane – as glucose enters cell, becomes phosphorylated

siderophores are released when iron in the media is scarce; they scavenge for iron and bind it; the iron bound siderophores will enter the cell via a transporter

a medium in which all chemical components are known

media that contain some ingredients of unknown chemical composition; useful in cases when one media can then meet all nutritional requirements of many different microorganisms; also useful when nutritional requirements of an organism are unknown

sustains the growth of many microorganisms; blood and other nutrients can be added to encourage growth of finicky microbes (in which case the media is called enriched)

favors the growth of particular microorganisms

peptones, meat extracts, and yeast extracts

can meet nutritional requirements of many different microorganisms and can also meet nutritional requirements of organisms whose nutritional requirements are unknown

commonly used solidfying agent; cannot be degraded by microorganisms; solid media; can be used to isolate different microbes from each other to establish pure cultures

liquid; all microorganisms in same environment, cannot be isolated

MinCDE system limits Z-ring formation to the center of the cell – oscillate from one end of the cell to the other; oscillation keeps high concentrations of MinC at the poles, where it prevents formation of the Z-ring; thus Z-ring formation can only occur at midcell, which lacks MinCDE

in the cytoplasm, attachment of UDP to NAM and NAG (forms UDP-NAM and UDP-NAG); NAM-UDP links to NAG (NAM-NAG-UDP); bactoprenol proteins carry this unit to the periplasm; autolysins located at divisome degrade glycosidic linkages between specific NAG-NAM molecules and amino acid cross bridges – this permits the insertion of new peptidoglycan subunits

new cell wall is made along the side of the cell but not at poles

as division begins, FtsZ polymerization forms Z ring and new cell wall growth is confined to midcell; daughter cells are formed with one new pole and one old pole

cells are synthesizing new components necessary for growth to occur

microorganisms are growing and dividing at the maximal rate possible given their genetic potential, the nature of the medium, and environmental conditions; rate of growth is constant; balanced growth – all cellular constituents are manufactured at constant rates relative to each other

number of viable cells often declines at an exponential rate; was assumed that detrimental environmental changes caused irreparable harm to the cells; however, some microbiologists think the cells are temporarily unable to grow – viable but nonculturable (VBNC); possibly also programmed cell death

attribute this to the appearance of subpopulations of microbes that are better able to use the released nutrients and accumulated toxins to survive – continually evolving to adapt

constant environmental conditions maintained and constant removal of wastes; can observe the growth of microorganisms in an environment closer to that of their natural habitat – mimic natural conditions; can also control growth rate by controlling supply rate of a given nutrient

solutes and water activity, pH, temperature, oxygen level, pressure, and radiation

in a hypertonic environment, the concentration of the solutes outside the cell is more than inside the cell – the concentration of water in the cell is greater than outside the cell – this will cause water to move out of the cell and the cell will shrink – the plasma membrane will shrink away from the rest of the cell wall

in a hypotonic environment, the concentration of solutes is less outside the cell, and the concentration of water is higher – this will cause water to move into the cell and the cell can swell and possibly burst

in a hypotonic environment, the mechanosensitive channels will open up and let solutes flow out

many microorganisms will keep their osmotic pressure above that in the habitat, this way the plasma membrane is always pressed firmly against the cell wall; they do this by compatible solutes – they are chemicals that can be kept at high intracellular concentrations and cannot interfere with any other reactions occurring in the cell

require NaCl over 0.2 M

require NaCl over 2M;

intracellular K & Cl ions much greater in extreme halophiles than other bacteria to compensate for the extreme salt concentration extracelluarly

if the polymerase can't withstand the heat of the denaturation step, it will need to be added before every annealing step of every round of PCR → time consuming!

Some reactions occur spontaneously and have negative ΔGs, others do not occur spontaneously and have positive ΔGs; by coupling a reaction with a positive delta G to one with a negative delta G of greater magnitude, it can make the overall delta G negative, causing both reactions to occur spontaneously

ATP -

it has a lotttt of energy stored up to be released - All of those negatively charged oxygens want to get away from each other, but they cannot because of the covalent linkage between oxygen and phosphate atoms – therefore, there is a lot of strain – ie energy between those bonds, which allows a lot of energy to be released when the bond is broken

monocarboxylic acid with long alkyl chains that usual have an even number of carbons

glycerol backbone, broadly classified as “triesters of glycerol,” 3 ester linkages with fatty acids, make up fats stored in our bodies and most dietary fats and oils, major source of biochemical energy, can be saturated or unsaturated

no double bonds → as many hydrogens as possible saturate the carbon chain

polar/hydrophilic head; nonpolar, hydrophobic tail

organisms can grow as members of large complexes on surfaces called biofilms – most often seen as slime on rocks or at other solid surface water interfaces – this is a specialized type of bacterial growth – biofilms are of concern to the medical community because they can form on devices used for join replacements

morphovars: differ morphologically

biovars: differ biochemically/physiologically

serovars: differ in antigenic properties

skin: dry dead cells - pathogens cannot get the nutrients they need and skin cells are sloughed off before they get a foothold; skin secretions also contain natural antibiotics;

mucous membranes: secrete mucous containing antibacterial enzymes, physically trap pathogens, coughed/sneezed out

most common - link between D-alanine of one strand and DAP on adjacent strand

another is peptide interbridge - series of GLYs that link them

caveolin-dependent

clatherin-dependent

porins

Braun's lipoproteins

lipopolysaccharides

capsules

s-layers

advances in molecular biology - obtaining sequence data, eg

microscopy - morphological and biological differences are much more well known

gram neg: outside outer membrane

gram pos: outside peptidoglycan

complex

NOT defined

oxygen in aerobic

something else in anaerobic