Microbiology

Microbiology

Domains of life
1. Prokaryotes
  Annotations:
  - Unicellular organisms that lake a nucleus and membrane bound organelles.
  1. Bacteria
    Annotations:
    - A domain of prokaryotic life.
    1. Structure
      1. Cell Envelope
        Peptidoglycan
        Annotations:
          Polysaccharide crosslinked with peptide chains. A major component of bacterial cell walls.
        Penicillin
        Annotations:
        β-lactam antibiotic discovered by Alexander Fleming. Produced by Penicillium species of Fungi. Prevents cross linking of peptidoglycan.
        Gram positive
        Annotations:
        Descriptive of a bacterium that stains purple when performing the Gram stain. Indicates that the organism has cell envelope that consists of one membrane and a thick peptidoglycan layer.
        Lipoteichoic acid
        Annotations:
        A component of Gram positive cell walls. Consist of chains of teichcoic acid linked covalently linked to lipids in the cell membrane.
        Teichoic acid
        Annotations:
        Component of Gram-positive cell wall. A polymer of glycerol/ribitol phosphates and carbohydrates.
        Gram negative
        Annotations:
        Descriptive of a bacterium that stains pink when performing the Gram stain. Indicates that the organism has cell envelope that consists of two membranes either side of a thin peptidoglycan layer.
        Periplasm
        Annotations:
        Space between the cytoplasmic and outer membranes in Gram negative bacteria.
        Porin
        Annotations:
        Protein channels in outer membrane of Gram-negative bacteria that allow passive diffusion into the periplasm and environment.
        Lipopolysaccharide
        Annotations:
           Molecule of lipid covalently linked to a polysaccharide (O-antigen), present in the outer membrane of Gram-negative bacteria.
        O-antigen
        Annotations:
        The saccharide component of lipopolysaccharide.
        Endotoxin
        Annotations:
        Refers to the O-antigen of lipopolysaccharide in the outer membrane of Gram-negative bacteria. Can induce an immune response.
        Capsule
        Annotations:
        A polysaccharide layer that exists outside of the cell envelope.
        Slime
        Annotations:
        Descriptive of a bacterial capsule that is diffusing into the surrounding medium. Slime layer is looser than a capsule.
        Sheath
        Annotations:
        Extracellular structure produced by certain bacteria for protection. A single sheath may contain 100s of cells.
      2. Appendages
        Pilus
        Annotations:
          Prokaryotic appendage usually required for conjugation.
        Fimbria
        Annotations:
        Prokaryotic appendage for attachment (to other organisms, surfaces or hosts).
        Flagella
        Annotations:
        Prokaryotic appendage for motility.
      3. Inclusion bodies
        Annotations:
        An aggregate of a substance that occurs in the cytoplasm.
        Polyphospahtes
        Annotations:
        Phosphate storage moleule
        Sulfur granules
        Annotations:
        Inclusions of insoluble sulfur, generated by sulfide oxidation
        Gas vesicles
        Annotations:
        Prokaryotic inclusion body, used to help organisms float
        Magnetosomes
        Annotations:
        Inclusion body present in certain bacteria consisting of magnetic iron particles.
        Polyhydroxybutyric acid
        Annotations:
        Polymer produced by bacteria for storage of carbon.
        Endospores
        Annotations:
        A structure produced by some Gram-positive bacteria. Are a dormant form of the cell, that are highly resist to heat, UV, desiccation, etc.
      4. Morphology
        Coccus
        Annotations:
        A spherical-shaped cell
        Bacillus/rod
        Annotations:
        Descriptive of a rod-shaped cell
        Spirulum
        Annotations:
        Descriptive of a spiralled cell morphology
        Spirochete
        Annotations:
        Descriptive of a cell with ‘corkscrew’ morphology.
    2. Genetics
      1. Horizontal gene transfer
        Annotations:
        Non-inherited transfer of genetic material between organisms; typically between different species/strain.
        Conjugation
        Annotations:
        The transfer of genetical material, typically plasmids, by cell-to-cell contact. Plasmids are plaicated by rolling circle replication.
        Transformation
        Annotations:
        Mechanism of horizontal gene transfer where DNA is taken up from the environment by ‘competent’ cells.
        Electroporation
        Annotations:
        Laboratory technique of inducing transformation of bacteria by electric shock. Important for introducing cloning vectors into hosts.
        Transduction
        Annotations:
        Mechanism of horizontal gene transfer where DNA is transferred from organism to organism by a viral vector. Can be generalized or specialized depending on whether the virus in integrated into the host genome.
        Specialized
        Annotations:
        Specialized transduction occurs when a virus/phage has integrated into a genome. When the virus is excised from the genome, the flanking regions of DNA are co-excised and packaged into the capsid.
        Generalized
        Annotations:
        Occurswhen random fragments of DNA are packaged into the viral capsid.
        Transposon
        Annotations:
        A ‘jumping gene’. In its simplest form a gene encoding a transposase flanked by inverted repeats.
        Transposase
        Annotations:
        Enzyme responsible for moving a transposon.
      2. Genome
        Annotations:
        In bacteria, refers to all the chromosomes and plasmids in a cell.
        Plasmid
        Annotations:
        Extrachromosomal DNA present in certain prokaryotes. Typically small, circular and contain non-essential genes.
        Chromosome
        Annotations:
        In bacteria, a usually circular piece of DNA that encodes genes that are essential for the organism to grow.
        Megaplasmid
        Annotations:
          A large plasmid, >1 Mb. Could be considered a small chromosome in some circumstances.
        ori
        Annotations:
        The origin of replication in bacterial chromosomes and plasmids.
        Nucleoid
        Annotations:
        Organisation of nucleic acid in a bacterial cell, consisting of supercoiled DNA and nucleoid proteins.
        Supercoiled DNA
        Annotations:
           Descriptive of DNA that is overwound. Helps 'package' DNA.
        DNA gyrase
        Annotations:
        Enzyme responsible for DNA supercoiling.
      3. Operon
        Annotations:
        A functioning unit of DNA containing a cluster of genes under the control of a single promoter.
        Polycistron
        Annotations:
        mRNA that contains the transcribed sequences of multiple genes
    3. Growth
      1. Binary Fission
        Annotations:
        Process of cell division in bacteria
        Septum
        Annotations:
        Region of a bacterial cell that constricts during binary fission.
      2. Temperature
        Cardinal temperature
        Annotations:
        The temperature at which an organism ceases to grow.
        Hyperthermophile
        Annotations:
        Organism (from Archaea and Bacteria) that grows optimally above 80 °C.
        Thermophile
        Annotations:
        Organism that grows optimally above 60°C.
        Mesophile
        Annotations:
        Organism that grows optimally between 20 and 45°C.
        Psychrophile
        Annotations:
        Organism that grows optimally below 20°C.
      3. pH
        Acidophile
        Annotations:
        Organism that grows optimally at acidic pH; typically below pH 4.
        Neutrophile
        Annotations:
        An organism that grows optimally around pH 7.
        Alkaliphile
        Annotations:
        Organism that grows optimally at alkali pH; typically above pH 10.
      4. Salt
        Halphile
        Annotations:
        Organism that grows optimally in high concentrations of salt.
        Halotolerant
        Annotations:
        Organism that can grow in high concentrations of salt but grows optimally at low salt concentrations.
      5. Oxygen
        Aerobe
        Annotations:
        An organism that requires oxygen for growth.
        Microaerobe
        Annotations:
        Descriptive of an organism that only grows in the presence of low concentrations of oxygen.
        Anaerobe
        Annotations:
        An organism that does not require oxygen for growth.
      6. Metabolism
        Energy
        Phototrophy
        Annotations:
        The use of light as an energy source
        Anoxygenic photosynthesis
        Annotations:
        Photosynthetic process which doesn’t generate oxygen, i.e. use something other than water as the electron donor.
        Oxygenic photosynthesis
        Annotations:
        Photosynthetic process which generates oxygen, i.e. uses water as the electron donor.
        Chemotrophy
        Annotations:
        The use of chemicals as an energy source
        Lithotrophy
        Annotations:
        The use of inorganic compounds as electron donors in respiration.
        Organotrophy
        Annotations:
        The use of organic compounds as sources of electrons (usually via NADH).
        TCA cycle
        Annotations:
        Cycle of reactions that generates converts acetate to CO2 generating NADH.
        Respiration
        Annotations:
          The process in which electrons are transferred from an electron donor (e.g. NADH; H2) to electron acceptor (e.g. O2; NO3) to generate a proton motive force, which in turn is used to generate ATP by oxidative phosphorylation.
        Electron transport chain
        Annotations:
        A chain of proteins, mostly in the cell membrane, that is responsible for electron transfer from a donor to an acceptor, generating a proton gradient across the membrane which is used for oxidative phosphylation (ATP) production.
        Fermentation
        Annotations:
        The process which produces ATP by substrate-level phosphorylation. The substrate is both the electron donor and the electron acceptor.
        ATP
        Annotations:
        Adenosine TriPhosphate. Energy currency in the cell.
        NAD
        Annotations:
        Nicotin Adenine Dinucleotide. Used as electron currency in cells. Oxidised - NAD+; reduced NADH.
        Carbon
        Autotrophy
        Annotations:
        Where organisms derive cell carbon from fixing CO2.
        Heterotrophy
        Annotations:
        Where organisms derive cell carbon from organic sources
        Nutrients
        Macronutrients
        Annotations:
        Nutrients required in large amounts
        Micronutrients
        Annotations:
        Nutrients required in trace amounts
        Growth facotrs
        Annotations:
        Organic micronutrients e.g. vitamins.
    4. Techniques
      1. Identification
        Phenotypic tests
        Staining
        Gram stain
        Annotations:
        A staining procedure that allows the differentiation of bacteria based on the structure of their cell envelope.
        Acid Fast Stain
        Annotations:
        Staining procedure used for Mycobacterium. Also called Ziehl-Neelsen stain.
        Spore stain
        Annotations:
        Staining procedure that allows differentiation between spores and vegetative and dead stain.
        Biochemical tests
        Annotations:
        Tests that often use dyes to determine the presence of certain enzymes or metabolic capabilities, such as catalase, cytochomre oxidase, tryptophanase, coagulase, B-galactosidase etc. These test require culturing of the organism and the dye is often present in the growth medium.
        API strips
        Annotations:
        Commercially available strips that combine multiple biochemical tests.
        MALDI-TOF
        Annotations:
        Matrix-Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry. A method that analyses complex samples giving a bacterial species a ‘finger-print’ based on its protein profile.
        Immunoassays
        Annotations:
        A procedure for detecting or measuring antigens or antibodies, which can be specific for individual strains of bacteria.
        Immunofluorescence
        Annotations:
        A technique used for visualising biological samples using antibodies linked to a fluorescent probe.
        Immunodiffusion
        Annotations:
        An immunoassay for detecting or measuring antibodies and antigens by their precipitation when diffused together through a gel.
        Agglutination
        Annotations:
        The process that occurs if an antigen is mixed with its corresponding antibody.
        Radioimmunoassay
        Annotations:
        Immunoassay using a radiolabelled (radioactive) antibody.
        ELISA
        Annotations:
        Enzyme-Linked ImmunoSorbent Assay. Immunoassay that uses antibodies linked to enzymes to detect the presence of antigen or other antibodies.
        Antigen
        Annotations:
        A component (particularly of a pathogen) that produces an immune response. Typically protein or polysaccharide.
        Antibody
        Annotations:
        A large Y-shaped protein produced by the immune system to neutralize pathogens.
        Genotypic tests
        Nucleic acid hybridization
        Annotations:
        Technique used to identify microorganisms or the presence certain genes. Nucleotide probes linked to a fluorescent probe are added to cells and hybridise to complementary sequences in the genome, if they are present.
        DNA Sequencing
        16S rRNA
        Annotations:
        Subunit of prokaryotic ribosome that is used to identify organisms and determine evolutionary relationships between them.
        Whole genome sequencing
        Annotations:
        The whole genome of an organism is sequenced (chromosomes and plasmids) to give accurate information about identity and metabolic capabilities (e.g. antibiotic resistance).
        NGS
        Annotations:
        Next Generation Sequencing. Sequencing technologies that produce large amounts of high-throughput data. Allows the identification of multiple organisms in a complex sample without culturing.
      2. Aceptic technique
        Annotations:
        The practice and procedures used to prevent contamination by microorganisms.
        Culture of bacteria
        Solid
        Agar
        Annotations:
        Inert gelling agent used to provide a solid growth medium for microorganisms.
        Colony
        Annotations:
        A visible mass of microorganisms all originating from a single cell, therefore a colony consists of bacteria that are all genetically identical.
        Liquid
        Batch culture
        Annotations:
        A culture of organisms in a fixed volume of medium with fixed amounts nutrients.
        Lag phase
        Annotations:
        Period on a bacterial growth curve where little to no increase in number is observed. Cells are adjusting to a new environment at this stage.
        Stationary phase
        Annotations:
        Stage of growth in batch culture when cells stop dividing due to exhausting nutrients.
        Exponential phase
        Annotations:
        Period of growth in a batch culture where cells are dividing. Also called log phase.
        Death phase
        Annotations:
          The phase in batch culture when organisms die off.
        Lysis
        Annotations:
        The bursting of cells, releasing contents of the cytoplasm.
        Continuous culture
        Annotations:
        A technique for culturing microorganisms in a steady state; cells are harvested at the same rate that nutrients are added. Other factors such as pH are also kept constant.
        Medium
        Annotations:
        A liquid or solid containing the components to support growth of microorganisms.
        Selective
        Annotations:
        A type of growth media which allows growth of a specific organism but inhibits growth of others.
        Differential
        Annotations:
        A type of growth media which allows differentiation between properties; typically contain an indicator such as dye.
        Complex
        Annotations:
          A type of growth media which does not contained defined amounts of nutrients; typically contain digests of plant and animal products e.g. casein (from milk), yeast extract, beef extract, etc.
        Defined
        Annotations:
        A type of growth media which contains defined amounts of nutrients.
        Enumeration
        Generation time
        Annotations:
        The time it takes for a population of organisms to double in size.
        Counting chamber
        Annotations:
        A specialist slide that allows counting of cells under a microscope.
        Viable cell counts
        Annotations:
        A measure of cells that are alive and capable of growth. Involves plating cultures onto solid media and counting colonies.
        Turbidity
        Annotations:
        Enumeration method that equates light absorbance in a spectrophotometer to cell nubmer/biomass.
        Laminar flow cabinet
        Annotations:
        Enclosed bench designed to prevent contamination of biological samples by blowing filtered air towards the user.
  2. Archaea
    Annotations:
    - A domain of prokaryotic life.
    1. Cell envolope
      Annotations:
      - Single membrane Cell Wall in most, but not all species
      1. Membrane
      2. Cell wall
        Annotations:
        Consists of an S-layer
2. Eucharyotes
  Annotations:
  - Unicellular or multicellular organisms that have DNA surrounded by a nucleus and possess membrane bound organelles.
  1. Structure
    1. Cell envelope
      Annotations:
      - Consist of a single membrane with/without a cell wall.
      1. Chitin
        Annotations:
        Cell wall present in fungi.
      2. Cellulose
    2. Appendages
Viruses
1. Bacteriophage
  Annotations:
  - A virus that infects bacteria.
  1. Prophage
    Annotations:
    - A phage that has integrated into the host genome.
  2. Lytic
    Annotations:
    - Phage/viral life cycle where the DNA remains separate from the host DNA.
  3. Lysogenic
    Annotations:
    - Phage/viral life cycle where the viral DNA is incorporated into the host genome. The lytic cycle is then activated at later time.
2. Morphology
  1. Icosahedral
  2. Helical
  3. Complex
3. Enzymes
  1. Lysozyme
    Annotations:
    - Enzyme that catalyses catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan.
  2. Neuramoindase
    Annotations:
    - Protein on the surface of some viruses that facilitates its release from the cell.
4. Baltimore classification
Prions
Annotations:
- An infectious protein particle that causes (typically) neurodegenerative disease.
Microbiome
Annotations:
- All the microorganisms in a particular environment (e.g. gut, soil etc).

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	Created by Tom Osborne over 6 years ago