Microbiology

1. Prokaryotes

   Nota:

   • Unicellular organisms that lake a nucleus and membrane bound organelles.
   1. Bacteria

      Nota:

      • A domain of prokaryotic life.
      1. Structure
         1. Cell Envelope
            1. Peptidoglycan

               Nota:

               •   Polysaccharide crosslinked with peptide chains. A major component of bacterial cell walls.   
               1. Penicillin

                  Nota:

                  • β-lactam antibiotic discovered by Alexander Fleming. Produced by Penicillium species of Fungi. Prevents cross linking of peptidoglycan.
            2. Gram positive

               Nota:

               • 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.     
               1. Lipoteichoic acid

                  Nota:

                  • A component of Gram positive cell walls. Consist of chains of teichcoic acid linked covalently linked to lipids in the cell membrane.   
               2. Teichoic acid

                  Nota:

                  • Component of Gram-positive cell wall. A polymer of glycerol/ribitol phosphates and carbohydrates.   
            3. Gram negative

               Nota:

               • 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.     
               1. Periplasm

                  Nota:

                  • Space between the cytoplasmic and outer membranes in Gram negative bacteria.
               2. Porin

                  Nota:

                  • Protein channels in outer membrane of Gram-negative bacteria that allow passive diffusion into the periplasm and environment.   
               3. Lipopolysaccharide

                  Nota:

                  •    Molecule of lipid covalently linked to a polysaccharide (O-antigen),  present in the outer membrane of Gram-negative bacteria.   
                  1. O-antigen

                     Nota:

                     • The saccharide component of lipopolysaccharide.
                     1. Endotoxin

                        Nota:

                        • Refers to the O-antigen of lipopolysaccharide in the outer membrane of Gram-negative bacteria. Can induce an immune response.
            4. Capsule

               Nota:

               • A polysaccharide layer that exists outside of the cell envelope.
            5. Slime

               Nota:

               • Descriptive of a bacterial capsule that is diffusing into the surrounding medium. Slime layer is looser than a capsule.    
            6. Sheath

               Nota:

               • Extracellular structure produced by certain bacteria for protection. A single sheath may contain 100s of cells.   
         2. Appendages
            1. Pilus

               Nota:

               •   Prokaryotic appendage usually required for conjugation.   
            2. Fimbria

               Nota:

               • Prokaryotic appendage for attachment (to other organisms, surfaces or hosts).   
            3. Flagella

               Nota:

               • Prokaryotic appendage for motility.   
         3. Inclusion bodies

            Nota:

            •  An aggregate of a substance that occurs in the cytoplasm.   
            1. Polyphospahtes

               Nota:

               • Phosphate storage moleule
            2. Sulfur granules

               Nota:

               • Inclusions of insoluble sulfur, generated by sulfide oxidation
            3. Gas vesicles

               Nota:

               • Prokaryotic inclusion body, used to help organisms float
            4. Magnetosomes

               Nota:

               • Inclusion body present in certain bacteria consisting of magnetic iron particles.   
            5. Polyhydroxybutyric acid

               Nota:

               • Polymer produced by bacteria for storage of carbon.
            6. Endospores

               Nota:

               • 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
            1. Coccus

               Nota:

               • A spherical-shaped cell
            2. Bacillus/rod

               Nota:

               • Descriptive of a rod-shaped cell
            3. Spirulum

               Nota:

               • Descriptive of a spiralled cell morphology
            4. Spirochete

               Nota:

               • Descriptive of a cell with ‘corkscrew’ morphology. 
      2. Genetics
         1. Horizontal gene transfer

            Nota:

            • Non-inherited transfer of genetic material between organisms; typically between different species/strain.    
            1. Conjugation

               Nota:

               • The transfer of genetical material, typically plasmids, by cell-to-cell contact. Plasmids are plaicated by rolling circle replication.    
            2. Transformation

               Nota:

               • Mechanism of horizontal gene transfer where DNA is taken up from the environment by ‘competent’ cells.   
               1. Electroporation

                  Nota:

                  • Laboratory technique of inducing transformation of bacteria by electric shock. Important for introducing cloning vectors into hosts.   
            3. Transduction

               Nota:

               • 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.   
               1. Specialized

                  Nota:

                  • 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. 
               2. Generalized

                  Nota:

                  • Occurswhen random fragments of DNA are packaged into the viral capsid.
            4. Transposon

               Nota:

               •  A ‘jumping gene’. In its simplest form a gene encoding a transposase flanked by inverted repeats.   
               1. Transposase

                  Nota:

                  • Enzyme responsible for moving a transposon.
         2. Genome

            Nota:

            • In bacteria, refers to all the chromosomes and plasmids in a cell.   
            1. Plasmid

               Nota:

               • Extrachromosomal DNA present in certain prokaryotes. Typically small, circular and contain non-essential genes.   
            2. Chromosome

               Nota:

               • In bacteria, a usually circular piece of DNA that encodes genes that are essential for the organism to grow.   
            3. Megaplasmid

               Nota:

               •   A large plasmid, >1 Mb. Could be considered a small chromosome in some circumstances.   
            4. ori

               Nota:

               • The origin of replication in bacterial chromosomes and plasmids.
            5. Nucleoid

               Nota:

               • Organisation of nucleic acid in a bacterial cell, consisting of supercoiled DNA and nucleoid proteins.   
               1. Supercoiled DNA

                  Nota:

                  •    Descriptive of DNA that is overwound. Helps 'package' DNA.   
                  1. DNA gyrase

                     Nota:

                     • Enzyme responsible for DNA supercoiling.
         3. Operon

            Nota:

            • A functioning unit of DNA containing a cluster of genes under the control of a single promoter.
            1. Polycistron

               Nota:

               • mRNA that contains the transcribed sequences of multiple genes
      3. Growth
         1. Binary Fission

            Nota:

            •   Process of cell division in bacteria   
            1. Septum

               Nota:

               • Region of a bacterial cell that constricts during binary fission.   
         2. Temperature
            1. Cardinal temperature

               Nota:

               • The temperature at which an organism ceases to grow.   
               1. Hyperthermophile

                  Nota:

                  • Organism (from Archaea and Bacteria) that grows optimally above 80 °C.
               2. Thermophile

                  Nota:

                  • Organism that grows optimally above 60°C.
               3. Mesophile

                  Nota:

                  • Organism that grows optimally between 20 and 45°C.   
               4. Psychrophile

                  Nota:

                  • Organism that grows optimally below 20°C.   
         3. pH
            1. Acidophile

               Nota:

               • Organism that grows optimally at acidic pH; typically below pH 4.   
            2. Neutrophile

               Nota:

               • An organism that grows optimally around pH 7.   
            3. Alkaliphile

               Nota:

               • Organism that grows optimally at alkali pH; typically above pH 10.   
         4. Salt
            1. Halphile

               Nota:

               • Organism that grows optimally in high concentrations of salt.   
            2. Halotolerant

               Nota:

               • Organism that can grow in high concentrations of salt but grows optimally at low salt concentrations.   
         5. Oxygen
            1. Aerobe

               Nota:

               • An organism that requires oxygen for growth.
            2. Microaerobe

               Nota:

               •  Descriptive of an organism that only grows in the presence of low concentrations of oxygen.   
            3. Anaerobe

               Nota:

               • An organism that does not require oxygen for growth.   
         6. Metabolism
            1. Energy
               1. Phototrophy

                  Nota:

                  • The use of light as an energy source
                  1. Anoxygenic photosynthesis

                     Nota:

                     • Photosynthetic process which doesn’t generate oxygen, i.e. use something other than water as the electron donor.   
                  2. Oxygenic photosynthesis

                     Nota:

                     • Photosynthetic process which generates oxygen, i.e. uses water as the electron donor.   
               2. Chemotrophy

                  Nota:

                  • The use of chemicals as an energy source
                  1. Lithotrophy

                     Nota:

                     • The use of inorganic compounds as electron donors in respiration.   
                  2. Organotrophy

                     Nota:

                     • The use of organic compounds as sources of electrons (usually via NADH).   
                     1. TCA cycle

                        Nota:

                        • Cycle of reactions that generates converts acetate to CO2 generating NADH.
               3. Respiration

                  Nota:

                  •   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.   
                  1. Electron transport chain

                     Nota:

                     • 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.   
               4. Fermentation

                  Nota:

                  • The process which produces ATP by substrate-level phosphorylation. The substrate is both the electron donor and the electron acceptor.   
               5. ATP

                  Nota:

                  • Adenosine TriPhosphate. Energy currency in the cell.   
               6. NAD

                  Nota:

                  • Nicotin Adenine Dinucleotide. Used as electron currency in cells. Oxidised - NAD+; reduced NADH. 
            2. Carbon
               1. Autotrophy

                  Nota:

                  • Where organisms derive cell carbon from fixing CO2.   
               2. Heterotrophy

                  Nota:

                  • Where organisms derive cell carbon from organic sources   
            3. Nutrients
               1. Macronutrients

                  Nota:

                  • Nutrients required in large amounts
               2. Micronutrients

                  Nota:

                  • Nutrients required in trace amounts
               3. Growth facotrs

                  Nota:

                  • Organic micronutrients e.g. vitamins.
      4. Techniques
         1. Identification
            1. Phenotypic tests
               1. Staining
                  1. Gram stain

                     Nota:

                     • A staining procedure that allows the differentiation of bacteria based on the structure of their cell envelope.   
                  2. Acid Fast Stain

                     Nota:

                     • Staining procedure used for Mycobacterium. Also called Ziehl-Neelsen stain.
                  3. Spore stain

                     Nota:

                     • Staining procedure that allows differentiation between spores and vegetative and dead stain.   
               2. Biochemical tests

                  Nota:

                  • 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.
                  1. API strips

                     Nota:

                     • Commercially available strips that combine multiple biochemical tests.
               3. MALDI-TOF

                  Nota:

                  • 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.   
               4. Immunoassays

                  Nota:

                  • A procedure for detecting or measuring antigens or antibodies, which can be specific for individual strains of bacteria.   
                  1. Immunofluorescence

                     Nota:

                     • A technique used for visualising biological samples using antibodies linked to a fluorescent probe.   
                  2. Immunodiffusion

                     Nota:

                     • An immunoassay for detecting or measuring antibodies and antigens by their precipitation when diffused together through a gel.   
                  3. Agglutination

                     Nota:

                     • The process that occurs if an antigen is mixed with its corresponding antibody.   
                  4. Radioimmunoassay

                     Nota:

                     • Immunoassay using a radiolabelled (radioactive) antibody.   
                  5. ELISA

                     Nota:

                     • Enzyme-Linked ImmunoSorbent Assay. Immunoassay that uses antibodies linked to enzymes to detect the presence of antigen or other antibodies.     
                  6. Antigen

                     Nota:

                     • A component (particularly of a pathogen) that produces an immune response. Typically protein or polysaccharide.   
                  7. Antibody

                     Nota:

                     • A large Y-shaped protein produced by the immune system to neutralize pathogens.
            2. Genotypic tests
               1. Nucleic acid hybridization

                  Nota:

                  • 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.   
               2. DNA Sequencing
                  1. 16S rRNA

                     Nota:

                     • Subunit of prokaryotic ribosome that is used to identify organisms and determine evolutionary relationships between them.   
                  2. Whole genome sequencing

                     Nota:

                     • The whole genome of an organism is sequenced  (chromosomes and plasmids) to give accurate information about identity and metabolic capabilities (e.g. antibiotic resistance).
                  3. NGS

                     Nota:

                     • 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

            Nota:

            • The practice and procedures used to prevent contamination by microorganisms.   
            1. Culture of bacteria
               1. Solid
                  1. Agar

                     Nota:

                     • Inert gelling agent used to provide a solid growth medium for microorganisms.   
                  2. Colony

                     Nota:

                     • A visible mass of microorganisms all originating from a single cell, therefore a colony consists of bacteria that are all genetically identical.   
               2. Liquid
                  1. Batch culture

                     Nota:

                     •  A culture of organisms in a fixed volume of medium with fixed amounts nutrients.   
                     1. Lag phase

                        Nota:

                        •  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.   
                     2. Stationary phase

                        Nota:

                        • Stage of growth in batch culture when cells stop dividing due to exhausting nutrients.   
                     3. Exponential phase

                        Nota:

                        • Period of growth in a batch culture where cells are dividing. Also called log phase.   
                     4. Death phase

                        Nota:

                        •   The phase in batch culture when organisms die off.   
                        1. Lysis

                           Nota:

                           •  The bursting of cells, releasing contents of the cytoplasm.   
                  2. Continuous culture

                     Nota:

                     •  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.     
               3. Medium

                  Nota:

                  •  A liquid or solid containing the components to support growth of microorganisms.   
                  1. Selective

                     Nota:

                     • A type of growth media which allows growth of a specific organism but inhibits growth of others.
                  2. Differential

                     Nota:

                     • A type of growth media which allows differentiation between properties; typically contain an indicator such as dye.   
                  3. Complex

                     Nota:

                     •   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.   
                  4. Defined

                     Nota:

                     • A type of growth media which contains defined amounts of nutrients.   
               4. Enumeration
                  1. Generation time

                     Nota:

                     • The time it takes for a population of organisms to double in size.   
                  2. Counting chamber

                     Nota:

                     • A specialist slide that allows counting of cells under a microscope.
                  3. Viable cell counts

                     Nota:

                     • A measure of cells that are alive and capable of growth. Involves plating cultures onto solid media and counting colonies.
                  4. Turbidity

                     Nota:

                     • Enumeration method that equates light absorbance in a spectrophotometer to cell nubmer/biomass.
            2. Laminar flow cabinet

               Nota:

               • Enclosed bench designed to prevent contamination of biological samples by blowing filtered air towards the user.   
   2. Archaea

      Nota:

      • A domain of prokaryotic life.
      1. Cell envolope

         Nota:

         • Single membrane Cell Wall in most, but not all species
         1. Membrane
         2. Cell wall

            Nota:

            • Consists of an S-layer
2. Eucharyotes

   Nota:

   • Unicellular or multicellular organisms that have DNA surrounded by a nucleus and possess membrane bound organelles.
   1. Structure
      1. Cell envelope

         Nota:

         • Consist of a single membrane with/without a cell wall.
         1. Chitin

            Nota:

            • Cell wall present in fungi.
         2. Cellulose
      2. Appendages

1. Bacteriophage

   Nota:

   • A virus that infects bacteria.
   1. Prophage

      Nota:

      • A phage that has integrated into the host genome.
   2. Lytic

      Nota:

      • Phage/viral life cycle where the DNA remains separate from the host DNA.
   3. Lysogenic

      Nota:

      • 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

      Nota:

      • 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

      Nota:

      • Protein on the surface of some viruses that facilitates its release from the cell.
4. Baltimore classification

Nota:

• An infectious protein particle that causes (typically) neurodegenerative disease.

Nota:

•    All the microorganisms in a particular environment (e.g. gut, soil etc).