Microbiology

capsules and slime layers

Capsules typically adhere firmly to the cell wall, and some are even covalently linked to peptidoglycan. Slime layers, by contrast, are loosely attached and can be lost from the cell surface

Defined media

prepared by adding precise amounts of pure inorganic or organic chemicals to distilled water

respiration

the form of aerobic or anaerobic catabolism in which an electron donor is oxidized with O2 or an O2 substitute as the terminal electron acceptor.

functions of cytoplasmic membrane

- permeability barrier protein anchor energy coservation

endospore germination

. Cells do not sporulate when they are actively growing but only when growth ceases owing to the exhaustion of an essential nutrient. Thus, cells of Bacillus, a typical endospore-forming bacterium, cease vegetative growth and begin sporulation when, for example, a key nutrient such as carbon or nitrogen becomes limiting. An endospore can remain dormant for years but can convert back to a vegetative cell rapidly. This process involves three steps: activation germination and outgrowth Activation occurs when endospores are heated for several minutes at an elevated but sublethal temperature. Activated endospores are then conditioned to germinate when supplied with certain nutrients,such as certain amino acids. Germination, typically a rapid process (on the order of minutes), involves loss of refractility of the endospore, increased ability to be stained by dyes, and loss of resistance to heat and chemicals. The final stage, outgrowth, involves visible swelling due to water uptake and synthesis of RNA, proteins, and DNA. The vegetative cell emerges from the broken endospore and begins to grow, remaining in vegetative growth until environmental signals once again trigger sporulation.

a scanning electron microscope (SEM)

. In scanning electron microscopy, the specimen is coated with a thin film of a heavy metal, typically gold. An electron beam then scans back and forth across the specimen. Electrons scattered from the metal coating are collected and projected on a monitor to produce an image In the SEM, even fairly large specimens can be observed, and the depth of field (the portion of the image that remains in sharp focus) is extremely good. A wide range of magnifications can be obtained with the SEM, from as low as 15* up to about 100,000*, but only the surface of an object is typically visualized

S-layer

. S-layers consist of interlocking molecules of protein or glycoprotein (Figure 2.31). The paracrystalline structure of S-layers can form various symmetries, including hexagonal, tetragonal, or trimeric, depending upon the number and structure of the subunits of which it is composed. S-layers have been found in representatives of all major lineages of Archaea

Characteristics of ETC

1) the carriers are arranged in order of increasingly more positive E0′, (2) there is an alternation of electron-only and electron-plus-proton carriers in the chain, and (3) the net result is reduction of a terminal electron acceptor and generation of a proton motive force.

Koch's postulates

1. should find organism in question 2.culture organism in pure form 3.does bacterium introduced to animal cause disease? 4. do you find the bacterium in the animal.

oxidative phosphorylation

ATP is synthesized here at the expense of the proton motive force

Proton Motor force

As a result of the separation of H+ and OH-, the two sides of the membrane differ in both charge and pH; this forms an electrochemical potential across the membrane. This potential, along with the difference in pH across the membrane, is called the proton motive force (pmf) and causes the membrane to be energized, much like a battery

net yield in glycolysis

During Stages I and II of glycolysis, two ATP molecules are consumed and four ATP molecules are synthesized Thus, the net energy yield in glycolysis is two molecules of ATP per molecule of glucose fermented.

The cytoplasmic membrane of Archaea

In the tetraether lipid, the ends of the phytanyl side chains that point inward from each glycerol molecule are covalently linked. This forms a lipid monolayer instead of a lipid bilayer membrane

substrate-level phosphorylation

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

Inclusions

Inclusions functionas energy reserves and/or carbon reservoirs or have special functions. Inclusions can often be seen directly with the light microscope and are usually enclosed by single-layer (nonunit) membranes that partition the inclusion off in the cell. reduces the osmotic stress that would occur should the same amount of the substance be dissolved in the cytoplasm glycogen

iron-sulfur proteins

Like cytochromes, nonheme iron-sulfur proteins carry electrons only.

nonspecific porins

Nonspecific porins form water-filled channels through which any small substance can pass

phase-contrast microscope

Phase-contrast microscopy is based on the principle that cells differ in refractive index (a factor by which light is slowed as it passes through a material) from their surroundings. Light passing through a cell thus differs in phase from light passing through the surrounding liquid. This subtle difference is amplified by a device in the objective lens of the phase-contrast microscope called the phase ring, resulting in a dark image on a light background. The ring consists of a phase plate that amplifies the variation in phase to produce the higher-contrast image

periplasm

This space, located between the outer surface of the cytoplasmic membrane and the inner surface of the outer membrane

What is the difference between Gram stain positive and Gram stain Negative cell walls?

The gram-negative cell wall, or cell envelope as it is often called, consists of at least two layers, whereas the gram-positive cell wall is typically much thicker and consists primarily of a single type of molecule.

bright-field microscope,

The light microscope uses visible light to illuminate cell structures.With the bright-field microscope, specimens are visualized because of the slight differences in contrast that exist between them and their surroundings, differences that arise because cells absorb or scatter light to varying degrees. Bacterial cells are typically difficult to see well with the bright-field microscope because the cells themselves lack significant contrast with their surrounding medium.

importance of LPS

The lipid portion of the LPS, called lipid A, is not a typical glycerol lipid, but instead the fatty acids are connected through the amine groups from a disaccharide composed of glucosamine phosphate. The disaccharide is attached to the core polysaccharide through KDO ( ketodeoxyoctonate). LPS replaces much of the phospholipid in the outer half of the outer membrane and functions as an anchor tying the outer membrane to peptidoglycan. Thus, although the outer membrane is technically a lipid bilayer, its structure is distinct from that of the cytoplasmic membrane.

porins

The outer membrane is relatively permeable to small molecules (even hydrophilic molecules) because of proteins called porins.that function as channels for the entrance and exit of solutes Several porins are known, including both specific and nonspecific classes. transmembrane proteins made up of three identical subunit

Toxicity and LPS

Toxicity is associated with the LPS layer, in particular, lipid A. The term endotoxin refers to this toxic component of LPS. Some endotoxins cause violent symptoms in humans, including gas, diarrhea, and vomiting, and the endotoxins produced by Salmonella and enteropathogenic strains of E. coli transmitted in contaminated foods are classic examples of this.

transport proteins

Transport proteins have a saturation effect and high specificity and their synthesis is often highly regulated.

biofilm

When the opportunity arises, bacteria of all types typically bind to solid surfaces, often forming a thick layer of cells

Is petidoglycan only present is bacteria?

Yes

A confocal scanning laser microscope (CSLM)

a computer controlled microscope that couples a laser to a fluorescent microscope. The laser generates a bright three-dimensional

Fermentation

a form of anaerobic catabolism in which an organic compound is both an electron donor and an electron acceptor.

Differential interference contrast (DIC) microscopy

a form of light microscopy that employs a polarizer in the condenser to produce polarized light (light in a single plane). The polarized light then passes through a prism that generates two distinct beams.These beams pass through the specimen and enter the objective lens where they are recombined into one. Because the two beams pass through substances that differ in refractive index, the combined beams are not totally in phase but instead interfere with each other, and this effect enhances subtle differences in cell structure. Thus, by DIC microscopy, cellular structures such as the nucleus of eukaryotic cells (Figure 2.7 or endospores, vacuoles, and inclusions of bacterial cells, appear more three-dimensional.

Peptidogylcan

a rigid layer that is primarily responsible for the strength of the wall. It is a polysaccharide composed of two sugar derivatives—N-acetylglucosamine and N-acetylmuramic acid—and a few amino acids, including L-alanine, D-alanine, D-glutamic acid, and either L-lysine or a structurally similar molecule,diaminopimelic acid (DAP).

ABC transport systems

a substrate binding protein, a membrane integrated transporter, and an ATP hydrolyzing protein. "ABC" standing for ATP-binding cassette, a structural feature of proteins that bind ATP

twitching motility

a type of gliding motility, movement along a solid surface In twitching motility, extension of pili followed by their retraction drags the cell along a solid surface, with energy supplied by ATP.

Simple transport

an ion is transported with substance using proton motive force

type IV pili,

assist cells in adhesion but also allow for an unusual form of cell motility called twitching motility. Type IV pili are present only at the poles of those rod-shaped cells that contain them Type IV pili are also thought to mediate genetic transfer by the process of transformation in some bacteria, which, along with conjugation and transduction, are the three known means of horizontal gene transfer in prokaryotes

outer surface layers

capsules slime layers biofilm pros- acting as virulence factors in certain bacterial diseases and preventing the cell from suffering dehydration outer surface layers of virtually any type bind water and likely protect the cell from desiccation in periods of dryness.

6 types of cell morphology

coccus- circular rod spirillum- bent rods spirochete- swigily budding and appendaged filamentous bacteria

cytochromes

cytochromes are proteins that contain heme prosthetic groups . Cytochromes undergo oxidation and reduction through loss or gain of a single electron by the iron atom in the heme of the cytochrome.

endospores

during a process called sporulation. Endospores (the prefix endo means "within") are highly differentiated cells that are extremely resistant to heat, harsh chemicals, and radiation.Endospores function as survival structures and enable the organism to endure unfavorable growth conditions, including but not limited to extremes of temperature, drying, or nutrient depletion. Endospores can thus be thought of as the dormant stage of a bacterial life cycle: vegetative cell S endospore S vegetative cell. Endospores are also easily dispersed by wind, water, or through the animal gut. Endospore-forming bacteria are commonly found in soil, and species of Bacillus are the best-studied representatives.

Fimbriae

enable cells to stick to surfaces, including animal tissues in the case of pathogenic bacteria, or to form pellicles (thin sheets of cells on a liquid surface) or biofilms on solid surfaces.

glycolysis stage 1

glucose is phosphorylated by ATP= glucose 6-phosphate. The latter is then isomerized to fructose 6-phosphate, and a second phosphorylation leads to the production of fructose 1,6-bisphosphate. The enzyme aldolase then splits fructose 1,6-bisphosphate into two 3-carbon molecules, glyceraldehyde 3-phosphate and its isomer, dihydroxyacetone phosphate which is converted into glyceraldehyde 3-phosphate. To this point, all of the reactions, including the consumption of ATP, have proceeded without any redox changes.

How does peptidogylcan contribute to cell wall strength?

glycan tetrapeptide-Long chains of peptidoglycan are biosynthesized adjacent to one another to form a sheet surrounding the cell. The individual chains are connected by cross-links of amino acids. The glycosidic bonds connecting the sugars in the glycan strands are covalent bonds, but these provide rigidity in only one direction. Only after cross-linking is peptidoglycan strong in both the X and Y directions.

Quinones

hydrophobic molecules that lack a protein component. Because they are small and hydrophobic, quinones are free to move about within the membrane. Like the flavins ,quinones accept 2 e- + 2 H+ but transfer only 2 e- to the next carrier in the chain; quinones typically participate as links between iron-sulfur proteins and the first cytochromes in the electron transport chain

citric acid cycle

in respiration, pyruvate is oxidized to CO2. The pathway by which pyruvate is oxidized to CO2 is called the citric acid cycle

fluorescence microscope

is used to visualize specimens that fluoresce, emitting light of one color after absorbing light of another color

dark-field microscope,

light reaches the specimen from the sides only. The only light that reaches the lens is that scattered by the specimen, and thus the specimen appears light on a dark background. Dark-field microscopy is a particularly good way to observe microbial motility, as bundles of flagella (the structures responsible for swimming motility) are often resolvable with this technique

teichoic acids covalently bound to membrane lipids

lipoteichoic acids

flagella

long, thin appendages free at one end and attached to the cell at the other end. Flagella can attach to cells in different locations. In polar flagellation, the flagella are attached at one or both ends of a cell. Occasionally a group of flagella (called a tuft) may arise at one end of the cell, a type of polar flagellation called lophotrichous When a tuft of flagella emerges from both poles of the cell, flagellation is called amphitrichous.

How can peptidoglycan be destroyed?

lysozyme, a protein that cleaves the β-1,4-glycosidic bonds between N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan (Figure 2.25), thereby weakening the wall. When this occurs, water can enter the cell and cause cell lysis.

Complex media

made from digests of microbial, animal, or plant products, such as casein (milk protein), beef (beef extract), soybeans (tryptic soy broth), yeast cells (yeast extract), or any of a number of other highly nutritious substances. the disadvantage of a complex medium is that its nutritional composition is not known precisely

What to do gram negative cells have that gram negative positive cells don't have?

most of the wall is composed of the outer membrane. This layer is effectively a second lipid bilayer, but it is not constructed solely of phospholipid and protein, as is the cytoplasmic membrane (Figure 2.15). Instead, the outer membrane also contains polysaccharide, and the lipid and polysaccharide are linked to form a complex. Because of this, the outer membrane is often called the lipopolysaccharide layer, or simply LPS for short.

prokaryotes that survive in nature without their cell walls

mycoplasmas. Thermoplasma and its relatives, species of Archaea that naturally lack cell walls. These organisms are able to survive without cell walls because they either contain unusually tough cytoplasmic membranes or because they live in osmotically protected habitats such as the animal body. Most mycoplasmas have sterols in their cytoplasmic membranes, and these molecules function to add strength andrigidity to the membrane as they do in the cytoplasmic membranesof eukaryotic cells. Thermoplasma membranes contain molecules called lipoglycans that serve a similar strengthening function.

Group translocation

needs a conformational change ( glucose)

Pili

similar to fimbriae, but are typically longer and only one or a few pili are present on the surface of a cell. Because pili can be receptors for certain types of viruses, they can best be seen electron microscope. Two very important functions of pili include facilitating genetic exchange between cells in a process called conjugation and enabling the adhesion of pathogens to specific host tissues that they subsequently invade

specific porins

specific porins contain a binding site for only one or a small group of structurally related substances

gas vesicles

structures that confer buoyancy that allow the cells to position themselves in a water column in a particular location.The most dramatic examples of gas-vesiculate bacteria are cyanobacteria that form massive accumulations called blooms in lakes or other bodies of water Gas vesicles are conical-shaped structures made of protein; they are hollow yet rigid and of variable length and diameter Gas vesicles may number from a few to hundreds per cell and are impermeable to water and solutes but permeable to gases. Gas vesicles are composed of two different proteins. The major protein, called GvpA, forms the watertight vesicle shell itself and is a small, hydrophobic, and very rigid protein, copies of which align to form the parallel "ribs" of the vesicle. The rigidity is essential for the structure to resist the pressures exerted on it from outside. The minor protein, called GvpC, functions to strengthen the shell of the gas vesicle by cross-linking and binding the ribs at an angle to group several GvpA molecules together gas vesicles decrease a cell's overall density and thereby increaseits buoyancy

What acid does gram-positive cell wall contain that gram negative does not?

teichoic acids-"teichoic acids" includes all cell wall, cytoplasmic membrane, and capsular polymers composed of glycerol phosphate or ribitol phosphate. These polyalcohols are connected by phosphate esters and typicallycontain sugars or D-alanine (Figure 2.27b). Teichoic acidsare covalently bonded to muramic acid in the wall peptidoglycan. Because the phosphates are negatively charged, teichoic acidsare in part responsible for the overall negative electrical charge of the cell surface.

structural difference of gram stain positive and negative gram stain cell wall

the Gram stain, an insoluble crystal violet-iodine complex forms inside the cell. This complex is extracted by alcohol from gram-negative but not from grammpositive bacteria gram-positive bacteria have very thick cell walls consisting primarily of peptidoglycan. During Gram staining, the gram-positive cell wall is dehydrated by the alcohol, causing the pores in the walls to close and preventing the insoluble crystal violet-iodine complex from escaping. in gram-negative bacteria, alcohol readily penetrates the lipid-rich outer membrane and extracts the crystal violet-iodine complex from the cell. After alcohol treatment, gram-negative cells are nearly invisible unless they are counterstained with a second dye, a standard procedure in the Gram stain.

the polysaccharide portion of LPS consists of two components, what are they?

the core polysaccharide and the O-specific polysaccharide

The transmission electron microscope (TEM)

used to examine cells and cell structure at very high magnification and resolution. The resolving power of a TEM is much greater than that of the light microscope, even allowing one to view structures at the molecular level (Figure 2.10). This is because the wavelength of electrons is much shorter than the wavelength of visible light, and, as we have learned, wavelength affects resolution Unlike photons, electrons are very poor at penetrating; even a single cell is too thick to penetrate with an electron beam. Consequently, to view the internal structure of a cell, thin sections of the cell are needed, and the sections must be stabilized and stained with various chemicals to make them visible. To obtain sufficient contrast, the sections are treated with stains such as osmic acid, or permanganate, uranium, lanthanum, or lead salts. Because these substances are composed of atoms of high atomic weight, they scatter electrons well and thus improve contrast.

magnetosomes

yield intracellular inclusions.Some bacteria can orient themselves within a magnetic field because they contain magnetosomes.These structures are intracellular particles of the iron oxide mineral magnetite—Fe3O4. Magnetosomes impart a magnetic dipole on a cell, allowing it to orient itself in a magnetic field. Bacteria that produce magnetosomes exhibit magnetotaxis, the process of migrating along Earth's magnetic field lines. Magnetosomes have been found in several aquatic organisms that grow best at low O2 concentrations. It has thus been hypothesized that one function of magnetosomes may be to guide these primarily aquatic cellsdownward (the direction of Earth's magnetic field) toward thesediments where O2 levels are lower.