General Microbiology & Immunology Notes (Part I)

General Microbiology & Immunology Notes (Part I)

• Microbiology is the study of minute or small organisms not visible to the naked eye.
• Antonie van Leeuwenhoek, known as the "Father of Microbiology", was the first person to observe microorganisms using a simple microscope.
• He observed small swimming organisms in pond water, calling them "animalcules."
• The theory of spontaneous generation (abiogenesis) proposed that life arose from non-living matter.
• Francesco Redi challenged this theory by demonstrating that maggots on decaying meat came from fly eggs, not the meat itself.
• Lazzaro Spallanzani further challenged spontaneous generation by showing that sealed and boiled flasks did not develop microorganisms, suggesting that air carried germs.
• John Needham, however, countered Spallanzani's experiment by stating that vital force was required.
• Louis Pasteur definitively disproved spontaneous generation by demonstrating that broth in swan-necked flasks remained sterile, even though exposed to air.
• He developed the process of pasteurization to prevent spoilage in liquids.
• Edward Jenner pioneered the concept of vaccination by demonstrating that cowpox infection provides immunity to smallpox.
• Robert Koch established postulates for establishing a link between a microorganism and a specific disease. These include proving the microorganism is present in every case of the disease; isolating and culturing the microbe; re-introducing the isolated microorganism into a healthy animal to cause the disease; and isolating the microorganism again from this diseased animal to show its identity.
• Koch also developed culture media and techniques for isolating and cultivating microbes, and identified many pathogens.
• Koch's laboratory helped make significant advancements in microbiology with discoveries like the petri dish, the use of agar, and the gram stain.
• Julius Petri developed the Petri dish.
• Frau Hesse introduced agar.
• Christian Gram developed the Gram stain.
• Paul Ehrlich pioneered chemotherapy using arsphenamine, a 'magic bullet' for treating certain infections.
• Joseph Lister introduced antiseptic surgery by using phenol.

Development of Microbiology

• Before the discovery of microorganisms, all living organisms were classified into two kingdoms: Animalia and Plantae.
• Criteria differentiating plant and animal kingdoms included energy source (light vs. oxidation), presence of chlorophyll, principal reserve materials (starch vs. glycogen), active movement, and cell wall.
• The kingdom Protista was proposed by Haeckel in 1866
• This kingdom comprised unicellular and multicellular organisms that lacked specialization/differentiation of cell types and tissues.
• The kingdom Protista was later modified to include only eukaryotic organisms like algae/chlorophyll containing protists.
• Protozoa were grouped as non-photosynthetic heterotrophic, unicellular eukaryotes.
• Fungi are non-photosynthetic eukaryotes with cell walls.
• Slime molds share features with fungi and protozoa.
• A major taxonomy differentiation occurred with three kingdoms. Eubacteria, Archaea and Eucarya.

Classification of Living Organisms

• Currently, a system of classification using three domains has become prevalent
• Domain Protista includes unicellular eukaryotes like algae. Protozoa, fungi, algae and bacteria were all categorized under this kingdom for a time

Viruses

• Viruses are submicroscopic infectious agents, made of genetic material (DNA or RNA) surrounded by a protein coat (capsid).
• They are obligate intracellular parasites, replicating only inside living cells.
• Viruses can have icosahedral, helical, or complex symmetry.
• Viral cultivation methods include tissue cultures (primary and secondary) and animal inoculation. Steps in viral replication include; attachment, penetration, uncoating, replication, assembly, and release.

Fungi

• Fungi are non-photosynthetic eukaryotic organisms that are heterotrophic, requiring organic compounds for energy and carbon.
• They are commonly aerobic or facultatively anaerobic saprophytes, and frequently decompose plant material.
• Fungi form a mass of branching filaments called hyphae, which together form a mycelium in some fungi.
• Yeasts are unicellular fungi that reproduce by budding.

Protozoa

• Protozoa are unicellular, non-photosynthetic, chemoheterotrophic eukaryotes lacking cell walls.
• They move by cilia or pseudopods and reproduce asexually or sexually.
• Different groups of protozoa including the sarcodina, ciliophora, mastigophora and sporozoa

Bacteria

• Bacteria are a diverse group of prokaryotic microscopic organisms.
• They inhabit various environments and play essential ecological roles (e.g., nutrient recycling).
• Bacteria have a cell wall containing peptidoglycan (except for mycoplasmas).
• Bacteria reproduce by binary fission, except for actinomycetes, which form conidiospores.
• They have three fundamental forms: spherical (coccus), rod-shaped (bacillus), and curved/spiral (vibrio, spirillum, spirochaete)

Bacterial Cell Structure

• A typical bacterium has a cell wall, cell membrane and cytoplasm containing ribosomes, genetic material and other cytoplasmic components like slime layer or capsule.
• Some types of bacteria have dormant spores under adverse environmental conditions.
• The nucleoid carries the cell’s genetic information as a single circular DNA molecule.
• The cytoplasm is an aqueous mixture containing nutrients, metabolites, waste products, enzymes, and reserve food.
• The cell membrane functions in selective permeability, transport, excretion, and biosynthesis. Note: Additional information in the text, like sections on the cell wall, bacterial morphology, special types of bacteria and/or other structural components, are not included in this summary.

Bacterial Metabolism

• Metabolism involves anabolism (building complex molecules) and catabolism (breaking down complex molecules).
• Organisms may obtain their energy via phototrophy (light), or chemotrophy (chemical reactions using organic or inorganic molecules). Different types of chemotrophs exist.
• Most eukaryotic cells and bacteria carry out chemoorganotrophic metabolism by the oxidation of organic molecules.
• The oxidation of organic molecules produces ATP via various pathways such as substrate-level phosphorylation and oxidative phosphorylation.
• Oxygen, nitrate, or other inorganic molecules may serve as the final electron acceptors during respiration.
• When oxygen is not available or when the organism cannot use respiration (e.g., in some bacteria), fermentation occurs.

Nucleic Acids/DNA

• Nucleic acids (DNA and RNA) carry genetic material.
• DNA has a double helix structure with four bases (adenine, guanine, cytosine, and thymine).
• RNA has a single-stranded structure with four bases (adenine, guanine, cytosine, and uracil).

DNA Replication

• DNA replication is semi-conservative; each new DNA molecule contains one original strand and one new strand
• It typically occurs from a specific origin of replication and proceeds bidirectionally; Replication is typically bi-directional.
• DNA polymerases are involved in copying the DNA
• Two growing strands are involved, one leading and the other lagging; DNA nucleotides are added to the 3' end of a growing DNA chain.

Transcription and Prokaryotic Gene Expression

• Transcription is the synthesis of RNA using DNA as a template. This process involves three stages - initiation, elongation, and termination.
• Prokaryotic organisms have only one RNA polymerase consisting of multiple subunits.
• Gene expression is regulated with constitutive enzymes present at relatively constant levels and induced enzymes produced only when substrates are present.

Translation

• Translation is the synthesis of proteins using mRNA as a template. It follows three steps - Initiation, Elongation, and Termination
• Ribosomes that are composed of RNA and protein are essential for this process

Regulation of Gene Expression

• Regulation of gene expression controls the levels of proteins being produced.
• Mechanisms include; induction (an increase in enzyme level) with an inducer; end product repression (decrease in enzyme level) by the effect of an end product) as well as feedback inhibition (the end product of the pathway inhibits the first enzyme)
• Genes and operons are controlled with regulatory proteins.

Bacterial Growth and Growth Curve

• Some prokaryotes grow using a closed system, where the medium and growth is contained in a batch culture.
• In a batch culture, bacterial growth is best characterized by four phases: the lag phase, log phase, stationary phase, and death phase.
• An open system, like a continuous culture system, is a more controllable method for measuring cell growth.

Microbial Variation

• Variation in microorganisms is an important aspect of adaptation and evolution
• Genotype or phenotype changes can be reversible or irreversible.
• Mutation is a permanent change in the genetic material (DNA)
• Environmental factors, like radiation or chemicals, can induce mutations.
• Organisms have repair mechanisms to fix DNA damage

Microbial Control,

• A variety of methods are used to control microorganisms in various environments.

Genetic Transfer

• Genes can be transferred vertically (from parent to offspring) or horizontally (among different organisms).
• Horizontal gene transfer (HGT) in microorganisms occurs through transformation, conjugation, and transduction.

Microbial Growth and Measurement

• Microbial growth is measured using various methods, including; observing cell mass (dry weight or optical density); and viable cell counts (based on the number of live cells).