Comprehensive Study Guide: Microbiology Foundations, Prokaryotic & Eukaryotic Cells, and Viruses

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Introduction to Microbiology

Types of Microorganisms

Microorganisms are diverse life forms studied in microbiology, including both cellular and acellular entities. Understanding their characteristics is foundational for the field.

Bacteria: Prokaryotic, unicellular, lack a nucleus and membrane-bound organelles, cell walls contain peptidoglycan, reproduce by binary fission, can be beneficial or pathogenic.
Viruses: Acellular, contain DNA or RNA (never both), protein capsid, sometimes a lipid envelope, obligate intracellular parasites, replicate only inside host cells.
Fungi: Eukaryotic, includes yeasts (unicellular) and molds (multicellular), cell walls made of chitin, heterotrophic, reproduce by spores.
Protozoa: Unicellular eukaryotes, lack cell walls, often motile (flagella, cilia, pseudopodia), many are parasitic.
Algae: Photosynthetic eukaryotes, produce oxygen, cell walls often contain cellulose, some produce toxins.
Helminths: Multicellular parasitic worms (roundworms, tapeworms, flukes), studied due to microscopic eggs/larvae.
Prions: Infectious proteins, lack nucleic acids, cause fatal neurodegenerative diseases.

Historical Contributors to Microbiology

The development of microbiology involved key experiments and discoveries that shaped our understanding of microorganisms.

Antonie van Leeuwenhoek: First to observe living microorganisms, improved microscopes.
Francesco Redi: Challenged spontaneous generation with meat-and-jar experiment, supported biogenesis.
John Needham: Supported spontaneous generation, but experiments were flawed due to poor sterilization.
Lazzaro Spallanzani: Improved Needham’s experiment, showed no growth with proper sterilization, critics argued air was needed for life.
Louis Pasteur: Swan-neck flask experiment, definitively disproved spontaneous generation, established biogenesis, developed pasteurization.
Robert Koch: Established Koch’s postulates, linked specific microbes to diseases.
Joseph Lister: Introduced antiseptic techniques in surgery.
Ignaz Semmelweis: Demonstrated handwashing reduced puerperal fever.
Florence Nightingale: Improved sanitation and hospital hygiene.
Edward Jenner: Developed the first vaccine (smallpox).
John Snow: Traced cholera outbreak to contaminated water, founder of epidemiology.
Hans Christian Gram: Developed Gram staining technique.
Carl Linnaeus: Developed binomial nomenclature, Father of Taxonomy.

Binomial Nomenclature

Binomial nomenclature is the universal system for naming organisms, consisting of a genus and species name.

Structure: Genus (capitalized) + species (lowercase), both italicized (e.g., Escherichia coli).
Formatting: Italicize when typed, underline when handwritten. Genus may be abbreviated after first use (e.g., E. coli).

The Three Domains of Life

Bacteria: Prokaryotic, peptidoglycan cell walls.
Archaea: Prokaryotic, lack peptidoglycan, often extremophiles.
Eukarya: Eukaryotic organisms (fungi, protozoa, algae, helminths).

Prokaryotic vs. Eukaryotic Cells

Feature	Prokaryotic	Eukaryotic
Nucleus	Absent	Present
Organelles	Absent	Present
DNA	Circular	Linear
Ribosomes	70S	80S
Size	Smaller	Larger

Microbe-Centered Disciplines

Bacteriology: Study of bacteria
Virology: Study of viruses
Mycology: Study of fungi
Parasitology: Study of protozoa and helminths
Immunology: Study of the immune system and defense against pathogens
Serology: Study of blood serum

Roles of Microbes

Beneficial: Normal microbiota (resident vs. transient), vitamin production (e.g., vitamin K), food production, environmental recycling.
Harmful: Cause disease, produce toxins, food spoilage.

Scientific Method

Observation/Question
Hypothesis
Experiment
Data analysis
Conclusion

Key Vocabulary

Pathogen: Disease-causing organism
Virulence: Degree of pathogenicity
Spontaneous generation: Disproven idea that life arises from nonliving matter
Biogenesis: Life arises from existing life
Normal microbiota: Microorganisms that normally inhabit the body

Prokaryotic Cell Structure and Function

Bacterial Cell Walls

The bacterial cell wall provides structural support, maintains shape, and protects against osmotic lysis. Its composition influences pathogenicity, antibiotic susceptibility, and staining behavior.

Gram-Positive: Thick peptidoglycan, no outer membrane, contains teichoic acids, stains purple, more susceptible to penicillin and lysozyme.
Gram-Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), stains pink, increased resistance to antibiotics.

Lipopolysaccharide (LPS) and Endotoxins

Lipid A: Toxic portion (endotoxin)
Core polysaccharide
O antigen: Antigenic variability
Endotoxins cause fever, inflammation, hypotension, septic shock; heat stable and released when cells die or divide.

Acid-Fast Bacteria and Mycolic Acid

Cell walls rich in mycolic acid (waxy lipid), resist Gram staining, require acid-fast staining.
High resistance to disinfectants, slow-growing, difficult to treat.
Example: Mycobacterium tuberculosis

Plasma Membrane Structure

Phospholipid bilayer with proteins
Functions: selective permeability, nutrient transport, energy production, synthesis of cell wall components

Transport Mechanisms

Passive Transport: Simple diffusion, facilitated diffusion (carrier proteins), no ATP required
Active Transport: Moves substances against gradient, uses ATP and transport proteins
Group Translocation: Unique to prokaryotes, substance chemically modified during transport (e.g., phosphorylation of sugars)

Internal Structures

Ribosomes: 70S, site of protein synthesis, target of antibiotics
Nucleoid: Region with circular DNA, not membrane-bound
Inclusion Bodies: Storage granules for nutrients (carbon, phosphate, sulfur)

Endospores

Dormant, non-reproductive, extremely resistant to heat, radiation, chemicals, desiccation
Survive harsh environments, germinate when conditions improve
Genera: Bacillus, Clostridium

External Structures

Glycocalyx: Capsule or slime layer, prevents phagocytosis, aids adhesion, biofilm formation, increases virulence
Fimbriae: Short, numerous, attachment to surfaces
Pili: Longer, involved in conjugation (genetic transfer)
Flagella: Motility, structure includes filament, hook, basal body; arrangements: monotrichous, lophotrichous, amphitrichous, peritrichous

Cell Morphology and Arrangement

Shape	Description
Cocci	Spherical
Bacilli	Rod-shaped
Spirilla	Spiral-shaped

Arrangement	Description
Diplo-	Pairs
Strepto-	Chains
Staphylo-	Clusters
Tetrads	Groups of four
Sarcinae	Cubical packets

Staining Techniques

Gram Stain: Differentiates bacteria by cell wall structure (positive = purple, negative = pink)
Acid-Fast Stain: Detects mycolic acid; acid-fast bacteria retain red stain, non–acid-fast appear blue

Biofilms and Quorum Sensing

Biofilms: Microbial communities attached to surfaces, embedded in extracellular matrix, increased resistance to antibiotics, common on medical devices
Quorum Sensing: Cell-to-cell communication via chemical signals, coordinates group behaviors (biofilm formation, virulence factor production)

Mycoplasmas and L-Forms

Mycoplasmas: Naturally lack cell walls, smallest free-living bacteria, resistant to beta-lactam antibiotics
L-Forms: Bacteria that lost cell walls due to stress or antibiotics, can revert to walled form, associated with chronic infections

Eukaryotic Cell Structure and Function

Characteristics of Eukaryotic Microbes

Eukaryotic microbes possess a true nucleus and membrane-bound organelles, distinguishing them from prokaryotes.

True nucleus with linear DNA
Membrane-bound organelles (mitochondria, ER, Golgi, lysosomes)
Larger and more complex than prokaryotes
80S ribosomes
Cell membranes contain sterols

Major Groups of Eukaryotic Microbes

Fungi: Yeasts (unicellular), molds (multicellular), cell wall of chitin, heterotrophic, reproduce by spores, important decomposers, some pathogenic
Protozoa: Unicellular, lack cell wall, heterotrophic, motile (cilia, flagella, pseudopodia), free-living or parasitic
Algae: Photosynthetic, uni- or multicellular, cell wall of cellulose, contain chloroplasts, produce oxygen
Helminths: Multicellular, complex life cycles, studied due to microscopic eggs/larvae

Eukaryotic vs. Prokaryotic Cells

Feature	Eukaryotic Microbes	Prokaryotes
Nucleus	Present	Absent
DNA	Linear chromosomes	Circular DNA
Organelles	Present	Absent
Ribosomes	80S	70S
Cell size	Larger	Smaller
Cell division	Mitosis/Meiosis	Binary fission

Eukaryotic Cell Structures & Functions

Nucleus: Contains DNA, controls cell activities, nuclear envelope
Ribosomes: Protein synthesis, free or attached to rough ER
Endoplasmic Reticulum (ER): Rough ER (protein synthesis), Smooth ER (lipid synthesis, detoxification, calcium storage)
Golgi Apparatus: Modifies, sorts, packages proteins/lipids
Mitochondria: ATP production, has own DNA
Lysosomes: Digest waste, damaged organelles, pathogens
Cytoskeleton: Maintains shape, movement, intracellular transport

Cell Cycle Overview

Interphase: G₁ (growth), S (DNA replication), G₂ (prep for division)
Cell Division: Mitosis or Meiosis, followed by cytokinesis

Mitosis

Purpose: Growth, repair, asexual reproduction
Produces 2 identical diploid cells
Stages: Prophase, Metaphase, Anaphase, Telophase (PMAT)
Cytokinesis: Division of cytoplasm

Meiosis

Purpose: Gamete production, genetic diversity
Produces 4 genetically diverse haploid cells
Meiosis I: Reduction division, crossing over, independent assortment
Meiosis II: Similar to mitosis, separates sister chromatids

Feature	Mitosis	Meiosis
Occurs in	Somatic cells	Germ cells
Purpose	Growth & repair	Sexual reproduction
Divisions	1	2
Daughter cells	2	4
Genetic makeup	Identical	Diverse
Chromosome number	Diploid (2n)	Haploid (n)
Crossing over	No	Yes

Endocytosis vs. Exocytosis

Endocytosis: Intake of materials via vesicles, requires ATP, includes phagocytosis (solids), pinocytosis (liquids), receptor-mediated (specificity)
Exocytosis: Secretion of materials via vesicle fusion with membrane, requires ATP

Feature	Endocytosis	Exocytosis
Direction	Into the cell	Out of the cell
Energy required	Yes (ATP)	Yes (ATP)
Vesicles used	Yes	Yes
Purpose	Intake of materials	Secretion & waste removal
Membrane action	Folds inward	Vesicle fuses with membrane

Viruses, Viroids, and Prions

Viruses

Viruses are infectious, acellular agents containing DNA or RNA, never both. They are considered nonliving because they lack cellular structure and metabolism, and require host cells for replication.

Structure: Capsid (protein coat), envelope (in some), spikes (attachment), nucleic acid genome (DNA or RNA, single- or double-stranded)
Virion: Complete infectious viral particle
Nucleocapsid: Capsid + nucleic acid
Classification: By shape, genome type, envelope presence, replication cycle
Retroviruses: Use reverse transcriptase (e.g., HIV)

Viroids

Small, circular RNA molecules, no protein coat
Infect plants, cause diseases affecting growth and crop yield
Simpler than viruses; no capsid or envelope

Prions

Infectious misfolded proteins, lack DNA or RNA
Cause fatal neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease, mad cow disease)
Induce misfolding of normal proteins

Viral Replication Cycles

Bacteriophage Replication

Lytic Cycle: Attachment → Penetration → Biosynthesis → Assembly → Release (lysis); results in host cell death, rapid virus production
Lysogenic Cycle: Viral DNA integrates into host genome (prophage), no immediate cell death, can switch to lytic cycle, allows long-term survival and replication with host

Animal Virus Replication vs. Bacteriophage Replication

Feature	Bacteriophages	Animal Viruses
Host	Bacteria	Eukaryotic cells
Entry	Inject nucleic acid	Endocytosis, direct penetration, or membrane fusion
Uncoating	Not required	Capsid must be uncoated
Release	Cell lysis	Budding (enveloped) or lysis (naked)
Replication cycles	Lytic, lysogenic	Varied, often more complex

Proto-Oncogenes vs. Oncogenes

Proto-Oncogenes: Normal genes regulating cell growth, division, and survival; not harmful unless altered.
Oncogenes: Mutated or overexpressed proto-oncogenes causing uncontrolled cell division and cancer.
Mutations: Point mutations, gene amplification, chromosomal translocations.

Feature	Proto-Oncogene	Oncogene
Normal or mutated?	Normal	Mutated/overexpressed
Function	Regulates normal growth	Drives uncontrolled growth
Role in cancer	No	Yes
Mutation effect	None	Gain of function

Neoplasms

Neoplasm: Abnormal mass of tissue from uncontrolled cell division; may be benign or malignant.

Feature	Benign	Malignant
Growth rate	Slow	Rapid
Cell appearance	Normal	Abnormal
Invasion	No	Yes
Metastasis	No	Yes
Cancerous	No	Yes

Key Exam Tips

Pasteur disproved spontaneous generation with swan-neck flasks
Koch’s postulates link microbes to disease
Prokaryotes lack nuclei; eukaryotes have nuclei and organelles
Gram-negative bacteria are more resistant due to outer membrane
Endotoxin = Lipid A
Acid-fast bacteria resist decolorization
Endospores are survival structures
Biofilms increase virulence and resistance
Mycoplasmas lack cell walls permanently
Proto-oncogene → oncogene = uncontrolled growth
Malignant neoplasm = cancer; benign ≠ harmless, but malignant = dangerous

Additional info: Where content was brief, academic context was added for clarity and completeness, especially in the explanations of cell structure, viral replication, and neoplasms.