Tamil Nadu HSE First Year Microbiology cheat sheet

Microbiology is the study of organisms too small to be seen clearly by the unaided eye, including bacteria, fungi, algae, protozoa, and viruses; viruses are acellular and are studied as obligate intracellular parasites.

Antonie van Leeuwenhoek (1670s) first observed and described live microorganisms ('animalcules') using single-lens microscopes, making him the father of observational microbiology.

Louis Pasteur disproved spontaneous generation by swan-neck flask experiments, established germ theory, developed pasteurisation, and produced attenuated vaccines (chicken cholera, anthrax, rabies).

Robert Koch established Koch's postulates and identified the causes of anthrax (Bacillus anthracis), tuberculosis (Mycobacterium tuberculosis), and cholera (Vibrio cholerae); he introduced pure culture and solid media techniques.

Koch's postulates: the organism must be found in all diseased hosts, be isolated in pure culture, reproduce disease when inoculated into a healthy host, and be re-isolated from that host.

Alexander Fleming discovered penicillin from Penicillium notatum in 1928; Florey and Chain developed it for clinical use, opening the antibiotic era.

Edward Jenner used cowpox material for smallpox vaccination (1796); Joseph Lister introduced antiseptic surgery with carbolic acid; Dmitri Ivanowski and Beijerinck described the first filterable agents (viruses).

Sergei Winogradsky and Martinus Beijerinck founded environmental microbiology through studies of chemolithotrophy, nitrogen fixation, and enrichment culture techniques.

Prokaryotic cell: no membrane-bound nucleus, 70S ribosomes, single circular chromosome, peptidoglycan cell wall (bacteria), and no mitochondria or endoplasmic reticulum.

Bacterial shapes: coccus (spherical), bacillus (rod), spirillum (rigid spiral), spirochaete (flexible spiral), vibrio (comma); arrangements include diplo-, strepto-, staphylo-, and sarcina.

Gram-positive wall: thick peptidoglycan with teichoic acids, retains crystal violet-iodine complex and stains purple; Gram-negative wall: thin peptidoglycan plus outer membrane with lipopolysaccharide (endotoxin) and stains pink with safranin.

Bacterial appendages: flagella for motility (monotrichous, lophotrichous, amphitrichous, peritrichous), pili for conjugation and adhesion, fimbriae for attachment; capsules resist phagocytosis.

Bacterial endospores (Bacillus, Clostridium) are heat-resistant, dehydrated, dipicolinic-acid-containing dormant forms; they are not reproductive and are destroyed only by autoclaving.

Fungal cell: eukaryotic with chitin-containing cell wall, ergosterol in the membrane, hyphae forming mycelium; yeasts reproduce by budding, moulds by spore formation (conidia, sporangiospores).

Viruses: nucleic acid (DNA or RNA, never both) enclosed in a protein capsid; some have a lipoprotein envelope. They have no ribosomes or metabolism and replicate only inside host cells; bacteriophages infect bacteria.

Algae are photosynthetic eukaryotes with chlorophyll and cell walls of cellulose; protozoa are non-photosynthetic, motile heterotrophs (amoebae, ciliates, flagellates, sporozoa) often causing human disease.

Macronutrients: carbon, nitrogen, phosphorus, sulphur, potassium, magnesium, calcium, iron; micronutrients (trace elements): zinc, manganese, copper, cobalt, molybdenum.

Nutritional types by carbon and energy source: photoautotroph, photoheterotroph, chemoautotroph (chemolithotroph), chemoheterotroph; most medically important bacteria are chemoheterotrophs.

Growth curve phases: lag (adaptation, no net increase), log/exponential (fastest division, constant generation time), stationary (growth rate equals death rate, nutrient depletion and waste accumulation), and death/decline phase.

Generation time is the time for a population to double; in exponential phase N = N0 x 2^n, where n is the number of generations.

Culture media: defined (synthetic) media have known chemical composition; complex media contain peptone, beef extract, or yeast extract; selective media inhibit unwanted organisms (e.g., MacConkey, mannitol salt agar); differential media reveal biochemical differences (e.g., blood agar, MacConkey).

Streak-plate and pour-plate methods yield isolated colonies; serial dilution with plate count gives viable counts; turbidity measured by spectrophotometer estimates total biomass.

Physical growth requirements: temperature classes (psychrophile, mesophile, thermophile, hyperthermophile), pH ranges, osmotic pressure, and oxygen classes (obligate aerobe, facultative anaerobe, obligate anaerobe, microaerophile, aerotolerant).

Anaerobic culture uses anaerobic jars with gas packs or reducing agents (thioglycollate broth); capnophiles require added CO2 (candle jar, 5% CO2 incubator).

Bacterial genome: one circular double-stranded DNA chromosome plus optional plasmids; plasmids are extrachromosomal, self-replicating DNA carrying traits such as antibiotic resistance (R plasmids) and fertility (F plasmid).

DNA structure: antiparallel double helix, base pairing A-T (two hydrogen bonds) and G-C (three hydrogen bonds); replication is semiconservative, catalysed by DNA polymerase.

Central dogma: DNA is transcribed to mRNA by RNA polymerase, then translated to protein on ribosomes using codons (triplets); AUG is the start codon and UAA, UAG, UGA are stop codons.

Transformation (uptake of naked DNA, Griffith/Avery-MacLeod-McCarty), transduction (DNA transfer by bacteriophage), and conjugation (direct transfer through a sex pilus from F+ to F- cells) are mechanisms of horizontal gene transfer.

Mutation types: point substitution (missense, nonsense, silent), frameshift from insertion or deletion, and induced mutations by UV light (thymine dimers) or chemical mutagens; repair by photoreactivation and excision repair.

Operon concept (Jacob and Monod): the lac operon is inducible and the trp operon is repressible; structural genes are controlled by promoter and operator elements.

Genetic engineering tools: restriction endonucleases cut specific palindromic sequences, DNA ligase joins fragments, and plasmids act as cloning vectors; PCR amplifies DNA using Taq polymerase and primers.

Antibiotic resistance spreads by plasmid transfer and transposons; molecular diagnosis uses PCR, nucleic acid hybridisation, and sequencing.

Sterilisation kills or removes all microorganisms including endospores; disinfection destroys pathogens on inanimate objects; antisepsis applies to living tissue; sanitisation reduces counts to safe public-health levels.

Moist heat: autoclave at 121 degrees C, 15 psi (103 kPa), 15-20 minutes kills spores; tyndallisation is fractional sterilisation at 100 degrees C on three successive days; pasteurisation (63 degrees C for 30 min or 72 degrees C for 15 s) kills pathogens without sterilising.

Dry heat: hot-air oven at 160-170 degrees C for 2 hours for glassware; red heat and flaming for loops; incineration for contaminated waste.

Membrane filtration (0.22 micrometre pore) sterilises heat-labile liquids and gases; it removes organisms rather than killing them, so viruses may pass through.

Radiation: UV light (254 nm) damages DNA (thymine dimers) but has poor penetration, so it is used for surface and air disinfection; gamma rays and electron beams penetrate and sterilise disposable plastics.

Chemical agents: alcohols (70% ethanol is more effective than 100%), phenolics, halogens (hypochlorite, iodine), quaternary ammonium compounds, glutaraldehyde, ethylene oxide gas, and hydrogen peroxide; mode of action includes protein denaturation, membrane damage, and nucleic acid damage.

Antibiotics: bactericidal agents kill (penicillins, aminoglycosides, cephalosporins) while bacteriostatic agents inhibit growth (tetracyclines, chloramphenicol); penicillins inhibit cell-wall peptidoglycan cross-linking, so they are ineffective against mycoplasmas.

Antibiotic resistance arises by enzymatic inactivation (beta-lactamase), altered target site, decreased uptake, or efflux pumps; misuse of antibiotics selects resistant strains.

Innate immunity is non-specific and present from birth: physical barriers (skin, mucous membranes), chemical barriers (lysozyme, gastric acid), phagocytes, complement, and inflammation.

Adaptive immunity is specific and has memory: B lymphocytes produce antibodies (humoral immunity) and T lymphocytes mediate cell-mediated immunity (helper CD4 cells, cytotoxic CD8 cells).

Antibody (immunoglobulin) classes: IgG (most abundant, crosses placenta), IgM (first antibody in infection, pentamer), IgA (secretions, milk), IgE (allergy, parasites), IgD (B-cell receptor).

Antigen-antibody reactions used in diagnosis: agglutination (Widal, blood grouping), precipitation, complement fixation, ELISA, immunofluorescence, and Western blot.

Active immunity is produced by the body after natural infection or vaccination; passive immunity is transferred ready-made antibody (maternal IgG/IgA, antiserum) and gives immediate but short-lived protection.

Vaccines: live attenuated (BCG, MMR, oral polio), killed (Salk polio, pertussis), toxoid (tetanus, diphtheria), and subunit/conjugate vaccines; adjuvants such as alum enhance the response.

Hypersensitivity types I to IV: type I immediate IgE-mediated anaphylaxis; type II antibody-mediated cytotoxic; type III immune-complex; type IV delayed cell-mediated (tuberculin test).

Autoimmunity (rheumatoid arthritis, type 1 diabetes), immunodeficiency (HIV/AIDS), and transplant rejection reflect failures or misdirection of immune defences.

Pathogenicity is the ability to cause disease; virulence is its degree; virulence factors include capsules, toxins, adhesins, and enzymes such as coagulase and hyaluronidase.

Exotoxins are heat-labile proteins secreted by living cells (tetanus, diphtheria, botulinum, cholera toxins) and are neutralised by antitoxin; endotoxin is heat-stable lipopolysaccharide of Gram-negative outer membrane causing fever and shock.

Gram-positive cocci: Staphylococcus aureus (pus, food poisoning, toxic shock) and Streptococcus pyogenes (pharyngitis, scarlet fever, rheumatic fever); Streptococcus pneumoniae causes pneumonia and meningitis.

Mycobacterium tuberculosis is acid-fast, grows slowly, and causes tuberculosis; diagnosis uses Ziehl-Neelsen staining, culture on Lowenstein-Jensen medium, and Mantoux test.

Vibrio cholerae causes profuse rice-water diarrhoea via cholera toxin raising cAMP; Salmonella typhi causes enteric fever diagnosed by Widal test and blood culture.

Viruses: influenza (antigenic drift and shift), poliovirus, HIV (retrovirus, CD4 cell destruction), hepatitis B (blood-borne, vaccine-preventable), and rabies (fatal encephalitis, prevented by post-exposure vaccine).

Fungal infections: Candida albicans (candidiasis), dermatophytes (ringworm), Aspergillus, and Cryptococcus; protozoan diseases include malaria (Plasmodium), amoebiasis (Entamoeba histolytica), and leishmaniasis.

Universal precautions, hand hygiene, and safe disposal of sharps limit hospital-acquired (nosocomial) infections; sterilisation of instruments and aseptic technique are essential in patient care.

Biogeochemical cycles depend on microbes: nitrogen fixation (Rhizobium, Azotobacter, cyanobacteria), nitrification (Nitrosomonas, Nitrobacter), denitrification, carbon cycling by decomposers, and sulphur cycling by Thiobacillus.

Sewage treatment: primary (physical settling), secondary (biological oxidation in activated sludge or trickling filters), and tertiary (nutrient removal, disinfection); BOD measures organic load.

Indicator organisms such as coliforms (E. coli) signal faecal contamination of water; the MPN test and membrane filtration are standard detection methods.

Bioremediation uses microorganisms to degrade oil spills, pesticides, and industrial wastes; bioaugmentation adds specific degraders and biostimulation supplies limiting nutrients.

Biofertilisers: Rhizobium, Azospirillum, Azotobacter, and blue-green algae fix nitrogen; phosphate-solubilising bacteria release bound phosphate; mycorrhizae improve nutrient and water uptake.

Biopesticides such as Bacillus thuringiensis (Bt) produce insecticidal crystal proteins; Trichoderma and Pseudomonas act as biocontrol agents against plant pathogens.

Industrial fermentation products: ethanol and citric acid (Aspergillus niger), penicillin, vitamins, enzymes (amylase, protease), and amino acids (glutamic acid by Corynebacterium glutamicum).

Fermenter design controls temperature, pH, aeration, agitation, and sterility; batch, fed-batch, and continuous culture differ in nutrient supply and productivity.

Food spoilage is caused by bacteria, yeasts, and moulds acting on proteins, carbohydrates, and fats; spoilage type depends on water activity, pH, temperature, and oxygen availability.

Food preservation methods: refrigeration, freezing, drying, salting, sugaring, acidification, canning (commercial sterilisation), irradiation, and addition of chemical preservatives.

Food-borne infections (Salmonella, Shigella, Vibrio cholerae, Listeria) differ from food intoxications caused by preformed toxins (Staphylococcus aureus, Clostridium botulinum, Bacillus cereus).

Clostridium botulinum grows in anaerobic low-acid canned foods and produces a neurotoxin; proper canning at 121 degrees C and acidification prevent it.

Milk composition supports microbial growth; raw milk flora includes lactic acid bacteria, coliforms, and pathogens; the methylene blue reduction test and standard plate count measure quality.

Pasteurisation (HTST 72 degrees C for 15 s or LTLT 63 degrees C for 30 min) kills pathogens and most spoilage organisms; UHT treatment plus aseptic packaging gives shelf-stable milk.

Fermented dairy products: curd/yoghurt uses Lactobacillus bulgaricus and Streptococcus thermophilus; cheese uses starter cultures plus rennet; lactic acid lowers pH and inhibits spoilage.

Probiotics are live beneficial microorganisms (Lactobacillus, Bifidobacterium) that improve gut health; food safety relies on HACCP, good manufacturing practice, and hygiene of handlers.

Laboratory attire: closed lab coat, gloves, and safety goggles; tie back long hair; never eat, drink, or apply cosmetics in the laboratory; wash hands before leaving.

Aseptic technique: flame the loop, hold tubes at an angle, sterilise the mouth of tubes, work near a flame in a laminar flow hood, and never place the loop or cap on the bench.

Microscope use: start with the low-power objective, focus with the coarse knob, then switch to high power and use the fine knob; oil immersion (100x) needs immersion oil and lens tissue cleaning.

Smear preparation and Gram staining sequence: heat-fixed smear, crystal violet (1 min), Gram's iodine (1 min), decolourise with alcohol, counterstain with safranin; the decolourisation step is critical.

Autoclave operation: load loosely, ensure steam contact, check temperature and pressure, and use autoclave tape or biological indicators (Geobacillus stearothermophilus spores) to verify sterilisation.

Biosafety: know the location of the first-aid box, fire extinguisher, and eyewash; report spills and injuries immediately; decontaminate surfaces with appropriate disinfectant.

Sharps and biological waste: place needles and broken glass in puncture-proof sharps containers; autoclave contaminated cultures before disposal; never recap needles.

Record keeping: label cultures with organism, date, and name; record observations honestly and accurately; calibrate instruments such as pH meter, balance, and spectrophotometer before use.