Microbiology

Microbiology

1. Domains of life

   • Prokaryotes
     • Unicellular organisms that lake a nucleus and membrane bound organelles.
     • Bacteria
       • A domain of prokaryotic life.
       • Structure
         • Cell Envelope
           • Peptidoglycan
             •   Polysaccharide crosslinked with peptide chains. A major component of bacterial cell walls.   
             • Penicillin
               • β-lactam antibiotic discovered by Alexander Fleming. Produced by Penicillium species of Fungi. Prevents cross linking of peptidoglycan.
           • Gram positive
             • 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
               • A component of Gram positive cell walls. Consist of chains of teichcoic acid linked covalently linked to lipids in the cell membrane.   
             • Teichoic acid
               • Component of Gram-positive cell wall. A polymer of glycerol/ribitol phosphates and carbohydrates.   
           • Gram negative
             • 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
               • Space between the cytoplasmic and outer membranes in Gram negative bacteria.
             • Porin
               • Protein channels in outer membrane of Gram-negative bacteria that allow passive diffusion into the periplasm and environment.   
             • Lipopolysaccharide
               •    Molecule of lipid covalently linked to a polysaccharide (O-antigen),  present in the outer membrane of Gram-negative bacteria.   
               • O-antigen
                 • The saccharide component of lipopolysaccharide.
                 • Endotoxin
                   • Refers to the O-antigen of lipopolysaccharide in the outer membrane of Gram-negative bacteria. Can induce an immune response.
           • Capsule
             • A polysaccharide layer that exists outside of the cell envelope.
           • Slime
             • Descriptive of a bacterial capsule that is diffusing into the surrounding medium. Slime layer is looser than a capsule.    
           • Sheath
             • Extracellular structure produced by certain bacteria for protection. A single sheath may contain 100s of cells.   
         • Appendages
           • Pilus
             •   Prokaryotic appendage usually required for conjugation.   
           • Fimbria
             • Prokaryotic appendage for attachment (to other organisms, surfaces or hosts).   
           • Flagella
             • Prokaryotic appendage for motility.   
         • Inclusion bodies
           •  An aggregate of a substance that occurs in the cytoplasm.   
           • Polyphospahtes
             • Phosphate storage moleule
           • Sulfur granules
             • Inclusions of insoluble sulfur, generated by sulfide oxidation
           • Gas vesicles
             • Prokaryotic inclusion body, used to help organisms float
           • Magnetosomes
             • Inclusion body present in certain bacteria consisting of magnetic iron particles.   
           • Polyhydroxybutyric acid
             • Polymer produced by bacteria for storage of carbon.
           • Endospores
             • A structure produced by some Gram-positive bacteria. Are a dormant form of the cell, that are highly resist to heat, UV, desiccation, etc.   
         • Morphology
           • Coccus
             • A spherical-shaped cell
           • Bacillus/rod
             • Descriptive of a rod-shaped cell
           • Spirulum
             • Descriptive of a spiralled cell morphology
           • Spirochete
             • Descriptive of a cell with ‘corkscrew’ morphology. 
       • Genetics
         • Horizontal gene transfer
           • Non-inherited transfer of genetic material between organisms; typically between different species/strain.    
           • Conjugation
             • The transfer of genetical material, typically plasmids, by cell-to-cell contact. Plasmids are plaicated by rolling circle replication.    
           • Transformation
             • Mechanism of horizontal gene transfer where DNA is taken up from the environment by ‘competent’ cells.   
             • Electroporation
               • Laboratory technique of inducing transformation of bacteria by electric shock. Important for introducing cloning vectors into hosts.   
           • Transduction
             • 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
               • 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
               • Occurswhen random fragments of DNA are packaged into the viral capsid.
           • Transposon
             •  A ‘jumping gene’. In its simplest form a gene encoding a transposase flanked by inverted repeats.   
             • Transposase
               • Enzyme responsible for moving a transposon.
         • Genome
           • In bacteria, refers to all the chromosomes and plasmids in a cell.   
           • Plasmid
             • Extrachromosomal DNA present in certain prokaryotes. Typically small, circular and contain non-essential genes.   
           • Chromosome
             • In bacteria, a usually circular piece of DNA that encodes genes that are essential for the organism to grow.   
           • Megaplasmid
             •   A large plasmid, >1 Mb. Could be considered a small chromosome in some circumstances.   
           • ori
             • The origin of replication in bacterial chromosomes and plasmids.
           • Nucleoid
             • Organisation of nucleic acid in a bacterial cell, consisting of supercoiled DNA and nucleoid proteins.   
             • Supercoiled DNA
               •    Descriptive of DNA that is overwound. Helps 'package' DNA.   
               • DNA gyrase
                 • Enzyme responsible for DNA supercoiling.
         • Operon
           • A functioning unit of DNA containing a cluster of genes under the control of a single promoter.
           • Polycistron
             • mRNA that contains the transcribed sequences of multiple genes
       • Growth
         • Binary Fission
           •   Process of cell division in bacteria   
           • Septum
             • Region of a bacterial cell that constricts during binary fission.   
         • Temperature
           • Cardinal temperature
             • The temperature at which an organism ceases to grow.   
             • Hyperthermophile
               • Organism (from Archaea and Bacteria) that grows optimally above 80 °C.
             • Thermophile
               • Organism that grows optimally above 60°C.
             • Mesophile
               • Organism that grows optimally between 20 and 45°C.   
             • Psychrophile
               • Organism that grows optimally below 20°C.   
         • pH
           • Acidophile
             • Organism that grows optimally at acidic pH; typically below pH 4.   
           • Neutrophile
             • An organism that grows optimally around pH 7.   
           • Alkaliphile
             • Organism that grows optimally at alkali pH; typically above pH 10.   
         • Salt
           • Halphile
             • Organism that grows optimally in high concentrations of salt.   
           • Halotolerant
             • Organism that can grow in high concentrations of salt but grows optimally at low salt concentrations.   
         • Oxygen
           • Aerobe
             • An organism that requires oxygen for growth.
           • Microaerobe
             •  Descriptive of an organism that only grows in the presence of low concentrations of oxygen.   
           • Anaerobe
             • An organism that does not require oxygen for growth.   
         • Metabolism
           • Energy
             • Phototrophy
               • The use of light as an energy source
               • Anoxygenic photosynthesis
                 • Photosynthetic process which doesn’t generate oxygen, i.e. use something other than water as the electron donor.   
               • Oxygenic photosynthesis
                 • Photosynthetic process which generates oxygen, i.e. uses water as the electron donor.   
             • Chemotrophy
               • The use of chemicals as an energy source
               • Lithotrophy
                 • The use of inorganic compounds as electron donors in respiration.   
               • Organotrophy
                 • The use of organic compounds as sources of electrons (usually via NADH).   
                 • TCA cycle
                   • Cycle of reactions that generates converts acetate to CO2 generating NADH.
             • Respiration
               •   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
                 • 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
               • The process which produces ATP by substrate-level phosphorylation. The substrate is both the electron donor and the electron acceptor.   
             • ATP
               • Adenosine TriPhosphate. Energy currency in the cell.   
             • NAD
               • Nicotin Adenine Dinucleotide. Used as electron currency in cells. Oxidised - NAD+; reduced NADH. 
           • Carbon
             • Autotrophy
               • Where organisms derive cell carbon from fixing CO2.   
             • Heterotrophy
               • Where organisms derive cell carbon from organic sources   
           • Nutrients
             • Macronutrients
               • Nutrients required in large amounts
             • Micronutrients
               • Nutrients required in trace amounts
             • Growth facotrs
               • Organic micronutrients e.g. vitamins.
       • Techniques
         • Identification
           • Phenotypic tests
             • Staining
               • Gram stain
                 • A staining procedure that allows the differentiation of bacteria based on the structure of their cell envelope.   
               • Acid Fast Stain
                 • Staining procedure used for Mycobacterium. Also called Ziehl-Neelsen stain.
               • Spore stain
                 • Staining procedure that allows differentiation between spores and vegetative and dead stain.   
             • Biochemical tests
               • 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
                 • Commercially available strips that combine multiple biochemical tests.
             • MALDI-TOF
               • 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
               • A procedure for detecting or measuring antigens or antibodies, which can be specific for individual strains of bacteria.   
               • Immunofluorescence
                 • A technique used for visualising biological samples using antibodies linked to a fluorescent probe.   
               • Immunodiffusion
                 • An immunoassay for detecting or measuring antibodies and antigens by their precipitation when diffused together through a gel.   
               • Agglutination
                 • The process that occurs if an antigen is mixed with its corresponding antibody.   
               • Radioimmunoassay
                 • Immunoassay using a radiolabelled (radioactive) antibody.   
               • ELISA
                 • Enzyme-Linked ImmunoSorbent Assay. Immunoassay that uses antibodies linked to enzymes to detect the presence of antigen or other antibodies.     
               • Antigen
                 • A component (particularly of a pathogen) that produces an immune response. Typically protein or polysaccharide.   
               • Antibody
                 • A large Y-shaped protein produced by the immune system to neutralize pathogens.
           • Genotypic tests
             • Nucleic acid hybridization
               • 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
                 • Subunit of prokaryotic ribosome that is used to identify organisms and determine evolutionary relationships between them.   
               • Whole genome sequencing
                 • 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
                 • 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.   
         • Aceptic technique
           • The practice and procedures used to prevent contamination by microorganisms.   
           • Culture of bacteria
             • Solid
               • Agar
                 • Inert gelling agent used to provide a solid growth medium for microorganisms.   
               • Colony
                 • 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
                 •  A culture of organisms in a fixed volume of medium with fixed amounts nutrients.   
                 • Lag phase
                   •  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
                   • Stage of growth in batch culture when cells stop dividing due to exhausting nutrients.   
                 • Exponential phase
                   • Period of growth in a batch culture where cells are dividing. Also called log phase.   
                 • Death phase
                   •   The phase in batch culture when organisms die off.   
                   • Lysis
                     •  The bursting of cells, releasing contents of the cytoplasm.   
               • Continuous culture
                 •  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
               •  A liquid or solid containing the components to support growth of microorganisms.   
               • Selective
                 • A type of growth media which allows growth of a specific organism but inhibits growth of others.
               • Differential
                 • A type of growth media which allows differentiation between properties; typically contain an indicator such as dye.   
               • Complex
                 •   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
                 • A type of growth media which contains defined amounts of nutrients.   
             • Enumeration
               • Generation time
                 • The time it takes for a population of organisms to double in size.   
               • Counting chamber
                 • A specialist slide that allows counting of cells under a microscope.
               • Viable cell counts
                 • A measure of cells that are alive and capable of growth. Involves plating cultures onto solid media and counting colonies.
               • Turbidity
                 • Enumeration method that equates light absorbance in a spectrophotometer to cell nubmer/biomass.
           • Laminar flow cabinet
             • Enclosed bench designed to prevent contamination of biological samples by blowing filtered air towards the user.   
     • Archaea
       • A domain of prokaryotic life.
       • Cell envolope
         • Single membrane Cell Wall in most, but not all species
         • Membrane
         • Cell wall
           • Consists of an S-layer
   • Eucharyotes
     • Unicellular or multicellular organisms that have DNA surrounded by a nucleus and possess membrane bound organelles.
     • Structure
       • Cell envelope
         • Consist of a single membrane with/without a cell wall.
         • Chitin
           • Cell wall present in fungi.
         • Cellulose
       • Appendages

2. Viruses

   • Bacteriophage
     • A virus that infects bacteria.
     • Prophage
       • A phage that has integrated into the host genome.
     • Lytic
       • Phage/viral life cycle where the DNA remains separate from the host DNA.
     • Lysogenic
       • Phage/viral life cycle where the viral DNA is incorporated into the host genome. The lytic cycle is then activated at later time.
   • Morphology
     • Icosahedral
     • Helical
     • Complex
   • Enzymes
     • Lysozyme
       • Enzyme that catalyses catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan.   
     • Neuramoindase
       • Protein on the surface of some viruses that facilitates its release from the cell.
   • Baltimore classification

3. Prions

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

4. Microbiome

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