Microbiology Unit 1 Key Terms

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Microbiology

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The study of microorganisms - microscopic organisms consisting of single, independent cells.

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Prokaryote

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a cell that lacks a membrane-enclosed nucleus and other organelles.

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Eukaryote

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a cell having a membrane-enclosed nucleus and usually other membrane-enclosed organelles.

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Bacteria

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one of two known domains for prokaryotes; compare with Archaea.

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Archaea

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One of two known domains of prokaryotes; compare with Bacteria. Chemotrophic.

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Eukarya

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the domain of life that includes all eukaryotic cells.

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Virus

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a genetic element that contains either a DNA or an RNA genome, lacks ribosomes, has an extracellular form (the virion), and depends on a host cell for replication.

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Bacterial chromosome

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Chromosome - a genetic element containing genes essential to cell function.

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Haploid, Diploid

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Haploid - a single copy of each gene.
Diploid - two copies of each gene.

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Nucleoid, Nucleus

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Nucleoid - the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea.
Nucleus - a membrane-enclosed structure that contains the chromosomes in eukaryotic cells.

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Plasmid

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an extrachromosomal genetic element nonessential for growth.

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Binary fission

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Cell division when a cell grows by intercalary growth to twice its minimum size and then divides to form two cells. Example: E.coli's rod shape that elongates, then a septum forms to pinch the two daughter cells apart. Time required for this is generation time.

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Mitosis, Meiosis

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Mitosis - Normal form of nuclear division in eukaryotic cells in which chromosomes are replicated and partitioned in to two daughter nuclei.
Meiosis - Specialized form of nuclear division that halves the diploid number of chromosomes to the haploid number, for gametes of eukaryotic cells.

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Phylogenetics

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Phylogeny - the evolutionary relationships between organisms.

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Endosymbiosis

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the theory that mitochondria and chloroplasts originated from Bacteria.

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Chemoorganotroph

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an organism that obtains its energy from the oxidation of organic compounds

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Chemolithotroph

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an organism that obtains its energy from the oxidation of inorganic compounds

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Phototroph, Heterotroph, Autotroph

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Phototroph - an organism that obtains its energy from light.
Heterotroph - an organism that requires organic carbon as its carbon source.
Autotroph - an organism able to grow with carbon dioxide (CO2) as its sole carbon source.

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Mutualism

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A type of symbiosis in which both organisms in the relationship benefit.

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Molecule

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Two or more atoms chemically bonded to one another.

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Covalent bond

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A nonionic bond chemical bond formed by a sharing of electrons between two atoms.

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Hydrogen bond

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A weak chemical bond between a hydrogen atom and a second, more electronegative element, usually oxygen or nitrogen. Can be broken without use of enzymes.

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Van der Waals force

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Attractive force occurring between two or more atoms when they become very close (3-4 angstroms)
-Substrate enzyme binding
- Protein-nucleic acid interactions
[Not a permanent bond. Strong enough for something to happen, but weak enough to move on.]

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Hydrophobic interaction

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Water repelling molecules tend to cluster in an aqueous environment leading to associating of non-polar portions of a macromolecule
-Protein folding
-Substrate-enzyme binding

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Carbohydrate

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Polysaccharide Sugars. C:H:O ratio of 1:2:1.
C4, C5, C6 and C7 are particularly important.
Pentoses (five-carbon sugars) are important for the backbones of RNA and DNA- Ribose and Deoxyribose.
Derviatives of hexoses (glucose and fructose) are important as energy sources.

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Glycosidic bond

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Bonds between polymers, an oxygen connecting the polysaccharides.

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Lipid

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Long chains of fatty acids. They are hydrophobic.
Simple lipids (triglycerides): Fatty acids linked to glycerol by ester linkage.

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Nucleic acid

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A polymer of nucleotides.
Ribonucleic acid (RNA): A polymer of nucleotides connected via a phosphate-ribose backbone; involved in protein synthesis or as genetic material of some viruses.
Deoxyribonucleic acid (DNA) - A polymer of nucleotides connected via a phosphate-deoxyribose sugar backbone; the genetic material of cells and some viruses.

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Protein (primary, secondary, tertiary, and quaternary structures)

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Protein - A polymeric molecule consisting of one or more polypeptides.
Primary - Linear array of amino acids.
Secondary - Twist and sheets; H-bonds do not occur in R-groups but between atoms in peptide bond. a-helix and b-sheets.
Tertiary - more folding, unique 3D confirmation
Quaternary - Two or more polypeptides where each subunit contains primary, secondary, and tertiary structure.

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Peptide bond

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Bonds found between amino acids. (H2O is a released out, and the peptide bond is between a carbonyl and a nitrogen.

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Denaturation

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Destruction of the folding properties of a protein usually leading to loss of functionality. Destroyed if you boil - will not destroy primary structure. Gentle vs. Harsh Denaturation. Denature a little bit to remove urea before reactivation. Harsh will render an inactive protein.

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Magnification

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Product of the ocular and objective magnification (compound microscope).

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Aberration and Distortion

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Due to imperfection in lens resulting in failure to focus in a single plain.

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Resolution

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The ability to distinguish two objects as distinct and separate under the microscope. Why we can't just layer lens upon lens.
Resolving power is a function of the wavelength of light used and an innate lens property called the numerical aperture (measure of light gathering ability). Limit of 0.2 micrometers (smallest distance between two points) for light microscopes.

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Contrast or Differentiation

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Achieved by staining. LIGHT MICROSCOPY.

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Simple stain, Differential stain

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Contrast staining.
Simple stain is a single stain of dye used to increase contrast. Usually positive. Examples: methylene blue, crystal violet, safranin.
Differential stain is used to differentiate on basis of cellular characteristics. Example: Gram stain.

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Phase contrast microscopy

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LIGHT MICROSCOPY.
Advantage: View living material. No staining.
This is based on the bending of light, like how a straw appears in water.
Cells differ in their refractive index from their surroundings, light passing through refractive material is slowed down and becomes out of phase causing intracellular features to appear light on a dark background.

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Dark field microscopy

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LIGHT MICROSCOPY.
Advantage: Great for looking at flagella. Living.
Based on lighting system modifications so that light reaches the specimen from the sides only. Light reaching the lens is scattered by specimen; specimen appears on a dark background.

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Fluorescence microscopy

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LIGHT MICROSCOPY.
Advantage: Living. With DAPI fluorescent dye, cells can be stained bright blue because it complexes with cell's DNA. [E.coli]
Based on visualizing specimens that fluoresce (emit light of one color when light of another color shines on them).
There are naturally fluorescent substances such as chlorophyll - autofluorescence.

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Differential interference microscopy (DIC)

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3D IMAGING.
Form of light microscopy that employs a polarizer to produce polarized light.
Polarized light then passes through a prism generating two beams. One direction. Not all over.
Beams recombine in objective lens, but are not entirely in phase, hence 3D appearance.

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Atomic force microscopy

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3D IMAGING.
Atomic forces are established between probe and specimen. Uses Van de Waals forces.
Probe scans surface of specimen in horizontal and vertical dimensions.
Pattern detected by computer.
Images like Electron Microscopy, but ADVANTAGE: Specimens can be alive.

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Transmission electron microscopy (TEM)

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ELECTRON MICROSCOPY.
Advantage: grand image.
Disadvantage: Expensive, & specimen is dead.
Organism is sectioned into very thin slices (20-60 nm).
Sections are treated with electron-dense stains such as osmic acid, uranium, etc.

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Scanning electron microscopy (SEM)

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ELECTRON MICROSCOPY.
Disadvantage: Dead specimen. A bit pricey.
Use of heavy metal to cover specimen, usually gold.
Electron beam scans back and forth (e- hit specimen and bounce back).
Scattered e- are collected to produce an image.
Dyes can be used.

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Macronutrient, Micronutrient

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Macronutrient - nutrients that are required in large amounts. Like: Carbon, Nitrogen, P, S, K, Mg, Ca, Na.
Micronutrients - nutrients that are required in trace amounts. Like: Iron.

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Defined media, Undefined/complex media

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Defined media - Cultures whose precise chemical composition is known.
Undefined/complex media - General growth media in which the exact composition and amounts of ingredients are unknown.

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Selective media, Differential media

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Selective media - Contains compounds that inhibit the growth of some microorganisms but enhance others.
Differential media - An indicator, usually a reactive dye, is added to reveal whether a particular chemical reaction has occurred during growth. Useful for distinguishing different species of bacteria.

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Liquid media, Solid media

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Liquid media - Liquid cultures can be solidified by adding a gelling agent.
Solid media - Cells are immobilized, allowing them to grow and form visible, isolated masses called colonies.

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Aseptic technique

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A series of steps to prevent contamination during manipulations of cultures and sterile culture media.
Loop is heated, Tube is uncapped and the tube is run through the flame, Sample is removed on sterile loop for transfer to a sterile medium, Tube is reflamed and recapped, Loop is reheated.

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cyanobacteria

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prokaryotic oxygenic phototrophs. Generated oxygen into the atmosphere that provided multicellular organisms to grow.

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Morphology
(Coccus, Rod, Spirillum, Spirochete, Filamentous, Appendaged)

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Morphology = shape.
Coccus = spherical or ovoid, like Micrococcus & Staphylococcus.
Rod = cylindrical, like Bacillus.
Spirillum = rod that is curved and forms a spiral pattern, like Rhodospirillum.
Spirochete = tightly coiled, like Spirochaeta.
Filamentous = long, thin cells, like Chloroflexus.
Appendaged = possess extensions of cell as long tubes or stalks, like Rhodomicrobium. (Budding from stalk).

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Cytoplasmic membrane

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1. Thin structure surrounding the cell.
2. Barrier about 8 nm thick that separates cytoplasm from external environment.
3. It is a highly selective permeable barrier: Regulates nutrient concentration and excretes wastes.
ALSO: Protein anchor, energy conservation.

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Phospholipid bilayer

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1. Hydrophobic region (fatty acid) - the tail.
2. Hydrophilic region (glycerol) - the head.

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Sterol

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Found in eukaryotic membranes, like cholesterol.

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Hopanoids

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Found in membranes of Bacteria, but not in Archael membranes and are for strength and flexibility.
Example: diplotene.

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Cell wall

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1. Serves to withstand pressure exerted by internal solutes and give shape and rigidity.
2. Has features that distinguishes between gram - and gram + Bacteria.

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Peptidoglycan

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Found in Bacteria. Rigid polysaccharide layer that provides strength.

In Gram +, Peptidoglycan is thick.
In Gram -, there's an outer membrane (LPS and protein), and then periplasm (like cytoplasm) which has a thin layer of peptidoglycan inside.

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Flagellum

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Flagellum - specialized structure for locomotion.
Arrangement: Peritrichous - located all around surface; Polar - attached at ONE or BOTH ends of cell; Lophotrichous - grouped at one end of cell; Amphitrichous - tufts at BOTH poles.

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Flagellum Structure

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Helical. Composed of protein subunits called flagellin.
The hook consists of a single type of protein. Connects filament to motor portion of base.
The motor is anchored in cytoplasmic membrane and cell wall. Consists of: Central rod, L ring (lipopolysaccharide layer), P ring (peptidoglycan layer), MS ring (cytoplasmic membrane), and C ring (cytoplasm).

Gram - Bacteria: All 4 rings are present.
Gram + Bacteria: Lack L and P rings.

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Flagellar Movement & Synthesis

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Two elements: Rotor and Stator.
Synthesis: FLAGELLA GROWS FROM THE TIP. 20,000 flagellins per one flagellum. MS/C rings, Motor proteins, P ring, L ring, Cap, Hook, and Filament synthesis.

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Gliding motility

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Gliding motility - another method of locomotion.

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Gas vesicle

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For buoyancy.
Characteristics: Spindle-shaped, Gas-filled, Hollow, Rigid, Variable lengh
Made of 2 proteins: GvpA (hydrophobic) for rigidity. GvpC for strength.

Found in: Cyanobacteria, Some Archael organisms, Purple & Green Phototrophic bacteria, Nonphototrophic bacteria.

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Endospore

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Dormant stage of bacterial life cycle. Heat resistant by dehydration (only 10% to 25% water).
Process: Sporulation.
Also resistant to harsh chemicals and radiation.
Ideal for wind, water, animal gut dispersion.
Bacillus and Clostridium are highly studied (best).

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Endospore Details

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Exosporium, Spore Coats, Cortex, Core (Core wall, Cytoplasmic membrane, Cytoplasm, Nucleoid, Ribosomes, DIPICOLINIC ACID complexed with CALCIUM - reduces water availability).

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Divisome

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A complex of proteins that directs cell division processes.
1. FtsZ
2. FtsA
3.ZipA
4. FtsI
5. FtsK

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Divisome
1. FtsZ

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Analogous to tubulin in eukaryotic cells.
Forms rings along midline of cell to initiate cell division.
Formation of ring attracts other proteins.

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Divisome
2. FtsA

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Related to actin.
ATPase. Energy.

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Divisome
3. ZipA

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Anchors FtsZ ring to cytoplasmic membrane.

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Divisome
4. FtsI

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Penicillin-binding protein.
Peptidoglycan biosynthesis protein.
Important because penicillin kills bacteria. Without this, bacteria can't make the peptidoglycan it needs for defense.

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Divisome
5. FtsK

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Assists in chromosome separation. 2 copies.

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Divisome
FtsZ's helper to locate middle of cell

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Min proteins. MinC & MinD (oscillates back and forth between poles).
Together, these two prevent formation of FtsZ ring.
So when they dwell longer at the poles, the center of the cell has the lowest concentration, and is the best site for FtsZ ring to assembly.
MinE sweeps MinC/D aside as it oscillates.

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Bactoprenol

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Lipid carrier molecule assists in synthesis of new peptidoglycan by inserting peptidoglycan precursors as preexisting peptidoglycan is cut by autolysins.

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Transpeptidation

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Final step in cell wall synthesis. Forms cross links between muramic acid residues in adjacent glycan chains.
Key protein is FtsI.
In Gram -, cross-link b/w DAP and D-Alanine.

This is what penicillin attacks.

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Microbial Growth Cycle

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Four phases: lag, exponential, stationary, death.
Lag: No increase.
Exponential: Uphill climb (Take viability count0
Stationary: Standstill (Turbidity - optical density)
Death: decline.

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Microbial Growth Cycle
1. Lag phase

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Period when essential metabolites are being synthesized.
Cells have been damaged, but not killed.
Like when transferring to new or poorer medium.
***THERE IS NO LAG PHASE WHEN THEY ARE TRANSFERRED DURING EXPONENTIAL GROWTH PHASE.

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Microbial Growth Cycle
2. Exponential phase

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Period when organism is experiencing exponential growth.
The rate is dependent on generation time, available resources, and environmental factors (temp, composition of media, etc.)
Healthiest state of culture; therefore the best time to run biochemical tests.

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Microbial Growth Cycle
3. Stationary phase

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Occurs when growth is limited.
Essential nutrients are used up. Waste products have built to toxic levels. Cells continue to metabolize, but no production of new cells.

Take turbidity reading here. It's the optical density. When cells die, they burst.

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Microbial Growth Cycle
4. Death phase

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Occurs when cells start to die.
Rate of cell death is much slower than rate of exponential growth.

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Measuring Microbial Growth

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1. Total count - solids and liquids (mL = cm3)
Problem: Count dead, too. Some are too small to see, Precision is difficult, Must stain cells.
2. Viable cell counting - Count of cells that are able to divide and produce offspring. Spread plate or pour-plate methods - make a lawn. All colonies come from 1 cell. Or the dilution method. Sample to be counted is placed in broths continuously.

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Environmental Factors that Affect Microbial Growth

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Temperature, pH, Osmotic effects, Oxygen

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Temperature & Microbial Growth
Cardinal Temperatures

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Minimum, Optimum, Maximum
(on graph, looks like an incline slope that just drops straight down at maximum).
Optimum is where cells like to grow best.

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pH and Microbial Growth

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Acidophiles - pH 6 and below
Examples: Fungi, Archael organisms

Alkaliphiles - pH 9 and above
Examples: Bacillus

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Osmotic Effects
!!!

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Water availability is expressed in physical terms as water activity (aw).
Water activity (aw) is the ratio of vapor pressure of air in equilibrium with a substance or solution to the vapor pressure of pure water.
aw = 1.00 for pure water
aw = 0.98 for sea water
aw = 0.75 for salt lakes
aw = 0.995 for human blood, and it's the most preferred aw (water activity) for most pathogens.

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Osmotic Effects
!!!!

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Most cells are unable to cope with environments of lowered water activity (higher solute concentrations) and either die, become dehydrated or dormant.

What they do in lowered water activity:
Increase internal solute concentration to maintain positive water balance - but can only increase concentration of compatible solutes.

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Oxygen
Anerobe

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1. Obligate - requires oxygen for growth.
2. Microaerophile - can only grow in reduced oxygen levels (below atmospheric levels).
3. Facultative - can grow under either oxic or anoxic conditions.

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Oxygen
Anaerobe

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1. Aerotolerant anaerobe - can tolerate and grow in presence of oxygen, but cannot use it.
2. Obligate anaerobe - inhibited or killed by the presence of oxygen.

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Minimum Inhibitory Concentration (MIC)

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The smallest amount of an agent needed to inhibit the growth of a test organism.
To determine, use disk diffusion technique.

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Chemical Antimicrobials
In vitro

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1. Sterilant - kills all forms of life, including endospores.
2. Disinfectant - kills micoorganisms, but not endospores.
3. Sanitizers - Reduce microbial numbers, but do not eliminate
4. Antiseptics - kill or inhibit microorganisms but are nontoxic enough to be applied to living tissue.

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History
Johannes and Zacharias Jannsen

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1590: Credited with compound microscope design

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History
Robert Hooke

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1665: First description of microorganisms.

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History
Antoni van Leeuwenhoek

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1676: Discovered bacteria
"wee animacules"

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History
Ferdinand Cohn

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1866: Describes sulfur bacteria, heat resistance of spores associated with Bacillus, Laid groundwork for system of classification.

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History
Louis Pasteur

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1864: Performed his swan-necked flask (Pasteur flask) experiment.

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Koch's Postulates

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1. Organism must be present in diseased host and absent in healthy individuals.
2. Causative organism must be isolated and grown in pure culture.
3. Isolated organism must be able to cause disease in a susceptible host.
4. Causative pathogen must be re-isolated and demonstrated to be identical with the original pure culture.

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Limitation of Koch's Postulates

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Some hosts may have immunity, ethical issues, some microbes are opportunists, and many fastidious organisms and all viruses cannot be grown in pure culture.