General Microbiology Lecture Notes

Flashcards for General Microbiology Lecture Notes

Importance of Microorganisms

Microorganisms are fundamental to all life on Earth. They were the first living systems, and it’s through their metabolic and ecological activity that the biosphere was created, enabling multicellular life to evolve.

Microbiology

Organisms too small to be seen clearly by the naked eye. With the exception of viruses, most microorganisms are organized into cells, are unicellular or multicellular without tissues, and are separated from their environment by a cell membrane.

Major groups in Microbiology

Bacteria and Archaea, both prokaryotes; Viruses, virions, satellites, prions which are acellular and non-living; Fungi (yeast, mold), Protists (Algae, and Protozoa) which are eukaryotic. Also within its scope are groups like: Water molds and Slime molds; Chromista, including Yellow-green algae, Brown algae, and Diatoms; Red algae (Rhodophyta) and Green algae (Chlorophyta).

LUCA

A theoretical organism which likely lived around 3.9 to 4 billion years ago. LUCA is thought to have had: A cell wall, cytoplasm, and DNA; A universal genetic code, with transcription and translation systems; Key metabolic features like glutamine synthetase (GS), nitrogenase (Nif), and antiporters (Mrp); Enzymes involved in carbon and nitrogen fixation, such as the Wood–Ljungdahl pathway enzymes; Adaptations to extreme conditions, like H₂- dependence and anaerobic thermophily.

Oxygen Concentration in microbes

Microbes vary in their oxygen requirements: Aerobes require oxygen for growth. Anaerobes cannot tolerate oxygen and may find it toxic. Facultative anaerobes can grow with or without oxygen. Microaerophiles require low levels of oxygen.

Osmotic Concentration and Salinity in Microbes

Based on salt tolerance: Nonhalophiles can’t tolerate salt. Halotolerant microbes can survive in moderate salt conditions. Halophiles (e.g., marine organisms) require salt, while Extreme halophiles, like Halobacterium, thrive in very high salinities.

Temperature ranges for microbes

Microbes have distinct temperature ranges: Psychrophiles grow at ~0–15°C (B. psychrophilus). Psychrotolerant grow at low temperatures but prefer 20–30°C (Pseudomonas fluorescens). Mesophiles grow best at 20–45°C (Escherichia coli). Thermophiles prefer 55–65°C (Thermus aquaticus). Hyperthermophiles thrive at 85–113°C (Sulfolobus acidocaldarius).

Water Activity (aw)

Crucial for enzymatic activity and cell structure stability. Most Gram-negative bacteria need aw > 0.95. Yeasts grow at aw between 0.91–0.88. Halophilic bacteria and Staphylococcus aureus can grow at aw as low as 0.75. Xerophilic molds and osmophilic yeasts like Saccharomyces rouxii thrive at even lower water activities (~0.65).

pH for microbes

Microbes are grouped by their optimal pH range: Acidophiles: pH 0–5.5; Neutrophiles: pH 5.5–8.0; Alkaliphiles: pH 8–11.5

UV Radiation

A powerful disinfectant that damages microbial DNA and membranes. It’s used to sterilize water and surfaces without toxic byproducts and is effective even against chlorine-resistant organisms.

Antony van Leeuwenhoek (1632–1723)

The first to observe and describe microorganisms using a handcrafted microscope. His discovery laid the foundation for microbiology, even though he had no formal scientific training.

Edward Jenner (1749–1823)

Developed the first successful vaccine against smallpox (Poxvirus variolae) in 1798. He used material from cowpox lesions, giving rise to the term “vaccine” (vacca = cow in Latin).

Ignác Semmelweis (1818–1865)

Know as “The savior of mothers,” dramatically reduced maternal deaths by introducing hand washing with chlorinated lime in obstetrics, long before the germ theory of disease was accepted.

Joseph Lister (1827–1912)

Pioneered antiseptic surgery using carbolic acid (phenol), reducing surgical mortality. He introduced the concept of asepsis, preventing microbial contamination.

Louis Pasteur (1822–1895)

Developed vaccines for rabies, anthrax, and chicken cholera. Invented pasteurization, a method to kill pathogens in liquids. Refuted the spontaneous generation theory, proving that life arises only from pre-existing life through the famous swan-neck flask experiment. Showed that specific microbes are linked to specific diseases.

Robert Koch (1843–1910)

Established Koch’s postulates, a set of criteria to link specific pathogens to specific diseases. He discovered the causative agents of tuberculosis (Mycobacterium tuberculosis) and cholera (Vibrio cholerae). He developed pure culture techniques using solid media (gelatin, then agar).

Elie Metchnikoff (1845–1916)

Discovered phagocytosis, a fundamental immune defense mechanism.

Paul Ehrlich (1854–1915)

Studied antibodies and developed the first effective antimicrobial drug, Salvarsan, against syphilis. He’s considered the father of chemotherapy.

Alexander Fleming (1881–1955)

Discovered penicillin from Penicillium notatum, which had a profound impact on medicine.

Griffith’s Transformation (1928)

Showed that a ‘transforming principle’ could turn non-pathogenic bacteria into pathogenic forms. This hinted at DNA as the genetic material.

Oswald Avery (1944)

Confirmed that the transforming principle was DNA, providing direct evidence that DNA carries genetic information.

Luria and Delbrück (1943)

Demonstrated that bacterial mutations occur spontaneously, not as a result of selective pressure.

Lederberg and Tatum (1946)

Discovered bacterial conjugation, the transfer of genetic material between bacteria—a major mechanism of genetic diversity.

Virions

The extracellular, morphologically complete forms of viruses, capable of surviving outside a host and initiating infection. Structurally, they are infectious nucleoproteins, composed of genetic material (either RNA or DNA) surrounded by protein — and sometimes lipids and carbohydrates.

Capsid

A protein coat made of capsomeres that protects the genome and ensures delivery into the host cell. Together, the genome and capsid form the nucleocapsid.

Envelope (in some viruses)

Derived from the host cell membrane and contains virus-encoded glycoproteins (peplomers) for attachment. Makes enveloped viruses sensitive to heat, desiccation, and solvents (e.g., influenza virus, HIV).

Helical symmetry

The capsid proteins wrap around the nucleic acid in a spiral.

Icosahedral (cubical) symmetry

Capsid proteins form a 20-sided polygon with symmetrical facets.

Complex viruses

No clear symmetrical structure, often large and layered.

Binary (bacteriophages)

Combine icosahedral heads and helical tails with tail fibers.

Structural Proteins

External capsid proteins and internal core proteins.

Envelope Glycoproteins

Viral-coded, inserted into host-derived membrane. Involved in receptor binding, membrane fusion, and immune neutralization.

Attachment (Adsorption)

The virus binds to specific receptor molecules on the host cell surface. This interaction determines host specificity and tissue tropism.

Endocytosis

Virus is engulfed by the host membrane.

Membrane fusion

Viral envelope fuses with the host cell membrane.

Injection of nucleic acid

Tail contracts to inject DNA into bacteria.

Uncoating (Decapsidation)

The capsid is broken down, releasing the viral genome into the host cell.

Assembly

Newly synthesized viral genomes and proteins assemble into new virions.

Maturation

Structural rearrangements occur to make the virus infectious. Capsid proteins fold correctly, and the nucleocapsid condenses around the genome.

Release

Non-enveloped viruses typically cause cell lysis, releasing progeny virions. Enveloped viruses bud from the cell membrane or organelles, acquiring their envelope in the process.

Baltimore classification system

Groups viruses (I–VII) based on genome type and replication strategy.

Prokaryotic cell

A simple, unicellular organism lacking a membrane-bound nucleus and organelles. Prokaryotes include Bacteria and Archaea, which were among the first life forms on Earth — appearing about 3.9–4 billion years ago.

Cell membrane

A phospholipid bilayer (no sterols, except in Mycoplasma) with hopanoids for membrane stability.

Cytoplasm

Contains nucleoid (circular dsDNA), ribosomes (70S), plasmids, and inclusions (e.g. glycogen, PHB, sulfur).

Plasmids

Small circular DNA with genes for antibiotic resistance, toxin production, etc.

Cell Wall

Composed of peptidoglycan (murein): repeating units of NAG and NAM linked by peptides. Gives shape and protects against osmotic stress.

Gram-positive (G+) Cell Wall

Thick peptidoglycan layer (10–80 nm) with teichoic and lipoteichoic acids, which act as antigens. No outer membrane or periplasmic space.

Gram-negative (G−) Cell Wall

Thin peptidoglycan layer in a periplasmic space, between: Inner membrane and Outer membrane (contains lipopolysaccharides – LPS).

Glycocalyx

Outer layer of polysaccharides or glycoproteins

Fimbriae

Numerous, short projections for adhesion (e.g., to tissues).

Pili

Longer, fewer – especially sex pilus for conjugation and gene transfer (e.g., R-plasmid transfer)

Flagella

Long, whip-like structures for motility, made of flagellin. Powered by a rotary motor, not ATP

The Cell Membrane

7–8 nm thick phospholipid bilayer without sterols (except Mycoplasma). Instead, hopanoids stabilize the membrane

Bacterial Genetic Material

One circular, double-stranded DNA molecule, located in the nucleoid. No histones, but histone-like proteins compact the DNA. Haploid (one genome copy per cell).

Spore Formation

Extremely resistant to heat, radiation, desiccation, and chemicals. Contain calcium dipicolinate, which helps dehydration and heat resistance.

Gas vacuoles

Provide buoyancy in aquatic photosynthetic bacteria (adjust depth for optimal light and oxygen).

Carboxysomes

Found in cyanobacteria; contain RubisCO enzyme for CO₂ fixation — crucial for autotrophic metabolism.

Magnetosomes

Membrane-bound magnetite (Fe₃ O ₄) crystals help bacteria navigate using the Earth’s magnetic field (e.g., in nutrient-rich sediments).

Chlorosomes

Present in green sulfur bacteria (Chlorobaculum tepidum); contain light-harvesting pigments like bacteriochlorophyll for photosynthesis.

Fungi

Form a distinct kingdom of eukaryotic, heterotrophic, and chemoorganotrophic organisms. Lack chlorophyll, so they don’t perform photosynthesis. Instead, they absorb dissolved nutrients across their entire surface — a process called absorptive nutrition.

Hyphae

Branching filaments which form mycelium. Their cell walls contain chitin and glucan — but not cellulose, which distinguishes them from plants. Some species also have mannan and chitosan in their walls.

Chytridiomycota

Considered the earliest-diverging lineage of fungi. They are aquatic, often unicellular or coenocytic (i.e., without septa in their hyphae). Their hallmark is motile cells: they produce zoospores with a single posteriorly inserted flagellum (opisthokont flagella), which is unique among true fungi.

Zygomycota

Coenocytic, meaning they have aseptate hyphae — septa form only during reproduction. They are mostly terrestrial saprotrophs, but some are facultative pathogens, affecting the lungs or CNS

Ascomycota and Basidiomycota

The two most advanced and diverse groups of the true fungi (Eumycota). Together, they include many ecologically, medically, and industrially important species.

Ascomycota

The most abundant fungal group: approximately 45% of all described fungi. Named after their defining sexual structure: the ascus, a sac-like structure where meiosis and sometimes mitosis produce ascospores.

Plasmogamy

Fusion of compatible hyphae tips from two mating types.

Dikaryotic phase

Two haploid nuclei coexist in the same cell.

Karyogamy

The two nuclei fuse to form a diploid zygote nucleus within the ascus.

Basidiomycota

Known for producing basidiospores on a specialized cell called a basidium.

Antimicrobial drugs

Chemical substances — either natural, semi-synthetic, or synthetic — that, at low concentrations, selectively inhibit or kill microorganisms without causing significant harm to the host.

Antibiotics

Secondary metabolic products produced by microorganisms like fungi and bacteria, which inhibit or destroy other microbes.

Bacteriostatic drugs

Inhibit growth.

Bactericidal drugs

Kill microbes.

Lytic agents

Cause microbial disintegration.

Ideal antimicrobial drug

Microbicidal, not just microbistatic; Soluble and stable in body fluids; Remains active long enough and is not inactivated too quickly; Does not lead to resistance development; Assists host immune defenses; Is active in tissues, reaches the infection site, and is affordable; Does not trigger allergies or secondary infections; Selective toxicity: harms the microbe but not the host.

Synergism

Increases effectiveness.

Antagonism

Can reduce efficacy.

Cell Wall Synthesis Inhibitors

Interfere with peptidoglycan synthesis, leading to cell lysis.

Protein Synthesis Inhibitors

Target ribosomes, which differ structurally from eukaryotic ones.

Nucleic Acid Synthesis Inhibitors

Target DNA replication or RNA transcription.

Cell Membrane Disruptors

Disturb membrane integrity.

Antimetabolites (Folic Acid Synthesis Inhibitors)

Interfere with key metabolic pathways: Sulfonamides and trimethoprim inhibit steps in folate synthesis, essential for nucleotide biosynthesis.

Azoles

Inhibit lanosterol 14α-demethylase, blocking ergosterol synthesis.

Allylamines

Inhibit squalene epoxidase earlier in the same pathway.

Polyenes

Bind ergosterol directly, forming pores in the fungal membrane.

Echinocandins

Inhibit β-1,3-glucan synthase, weakening the fungal cell wall.

Flucytosine

Converted to 5-fluorouracil inside fungal cells → inhibits DNA/RNA synthesis. Often used with amphotericin B for Cryptococcus infections.

Antibiotic resistance

Refers to the ability of a microorganism to withstand the effects of an antibiotic that would normally kill it or inhibit its growth. This can be intrinsic (natural) or acquired (through mutation or horizontal gene transfer).

Sensitivity

The bacterium is affected by the antibiotic at therapeutic concentrations.

Tolerance

The bacterium isn’t killed but its growth is slowed; it requires longer exposure.

Resistance

The bacterium proliferates despite the antibiotic, even at high concentrations.

β-lactamases

Destroy β-lactam antibiotics (e.g., penicillins).

Aminoglycoside-modifying enzymes

Add chemical groups, inactivating the drug.

Efflux pumps

Bacteria actively pump antibiotics out, lowering intracellular concentration

Intrinsic Resistance

Natural property of a species

Acquired Resistance

Through mutations or horizontal gene transfer: Transformation (uptake of naked DNA), Conjugation (plasmid exchange via sex pilus), Transduction (phage-mediated gene transfer).

Disk Diffusion Test (Kirby-Bauer)

Antibiotic discs placed on an agar plate inoculated with bacteria. Zone of inhibition indicates effectiveness.

Broth Dilution Test

Serial dilutions of antibiotics tested in broth cultures. Determines Minimum Inhibitory Concentration (MIC) – the lowest concentration that prevents visible growth.

E-test (Gradient Strip)

Combines diffusion and dilution principles; gives a direct MIC value on a strip.