Comprehensive Study Guide: Microbiology Chapters 1, 3, 4, and 6

Introduction to Microbiology

Types of Microorganisms

Microorganisms are diverse life forms studied in microbiology. They include both prokaryotic and eukaryotic organisms, as well as acellular agents.

• Bacteria: Prokaryotic, unicellular, lack nucleus and membrane-bound organelles, cell walls with peptidoglycan, reproduce by binary fission, can be beneficial or pathogenic.

• Viruses: Acellular, contain DNA or RNA (never both), protein capsid, sometimes lipid envelope, obligate intracellular parasites, replicate only inside host cells.

• Fungi: Eukaryotic, includes yeasts (unicellular) and molds (multicellular), cell walls 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 with 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

Key figures advanced the field through experiments and discoveries:

• Antonie van Leeuwenhoek: First to observe living microorganisms, improved microscopes.

• Francesco Redi: Disproved spontaneous generation with meat-and-jar experiment.

• John Needham: Supported spontaneous generation, but experiments were flawed.

• Lazzaro Spallanzani: Improved Needham's experiment, showed no growth with proper sterilization.

• Louis Pasteur: Swan-neck flask experiment, disproved spontaneous generation, developed pasteurization.

• Robert Koch: Established Koch’s postulates, linking microbes to diseases.

• Joseph Lister: Introduced antiseptic techniques in surgery.

• Ignaz Semmelweis: Demonstrated handwashing reduced puerperal fever.

• Florence Nightingale: Improved sanitation, reduced hospital mortality.

• Edward Jenner: Developed first vaccine (smallpox).

• John Snow: Traced cholera outbreak, founder of epidemiology.

• Hans Christian Gram: Developed Gram staining technique.

• Carl Linnaeus: Developed binomial nomenclature, Father of Taxonomy.

Binomial Nomenclature

Scientific naming uses a two-part system: genus and species.

• Genus: Capitalized (e.g., Escherichia).

• Species: Lowercase (e.g., coli).

• Both italicized when typed, underlined when handwritten.

• Genus may be abbreviated after first use (e.g., E. coli).

The Three Domains of Life

Domain	Characteristics
Bacteria	Prokaryotic, peptidoglycan cell walls
Archaea	Prokaryotic, lack peptidoglycan, often extremophiles
Eukarya	Eukaryotic (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 immune system and defense against pathogens

• Serology: Study of blood serum

Roles of Microbes

• Beneficial: Normal microbiota (resident vs. transient), vitamin production, food production, environmental recycling

• Harmful: Cause disease, produce toxins, food spoilage

Scientific Method

1. Observation/Question

2. Hypothesis

3. Experiment

4. Data analysis

5. 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 cell wall provides structural support, maintains shape, and protects against osmotic lysis. Its composition affects pathogenicity, antibiotic susceptibility, and staining.

• Gram-Positive: Thick peptidoglycan, no outer membrane, teichoic acids, stains purple, more susceptible to penicillin and lysozyme.

• Gram-Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), periplasmic space, stains pink, more resistant 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, released when cells die/divide.

Acid-Fast Bacteria and Mycolic Acid

• Cell walls rich in mycolic acid (waxy lipid), resist Gram stain, require acid-fast stain.

• 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, cell wall synthesis

Transport Mechanisms

• Passive: Simple diffusion, facilitated diffusion (no ATP)

• Active: Uses ATP, moves substances against gradient

• Group Translocation: Unique to prokaryotes, substance chemically modified during transport (e.g., phosphorylation of sugars)

Internal Structures

• Ribosomes: 70S, site of protein synthesis, antibiotic target

• Nucleoid: Region with circular DNA, not membrane-bound

• Inclusion Bodies: Storage granules (carbon, phosphate, sulfur)

Endospores

• Dormant, highly resistant structures (heat, radiation, chemicals, desiccation)

• Formed by Bacillus and Clostridium

• Survive harsh environments, germinate when conditions improve

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: 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	Groups of eight

Staining Techniques

• Gram Stain: Differentiates based on cell wall; Gram-positive (purple), Gram-negative (pink)

• Acid-Fast Stain: Detects mycolic acid; acid-fast bacteria (red), non–acid-fast (blue)

Biofilms and Quorum Sensing

• Biofilms: Microbial communities on 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)

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/antibiotics, can revert, associated with chronic infections

Eukaryotic Cell Structure and Function

Characteristics of Eukaryotic Microbes

Eukaryotic microbes have a true nucleus and membrane-bound organelles, and are generally larger and more complex than prokaryotes.

• True nucleus with linear DNA

• Membrane-bound organelles (mitochondria, ER, Golgi, lysosomes)

• 80S ribosomes

• Cell membranes contain sterols

• Reproduce by mitosis (growth/repair) and/or meiosis (sexual reproduction)

Major Groups of Eukaryotic Microbes

• Fungi: Yeasts (unicellular), molds (multicellular), cell wall of chitin, heterotrophic, reproduce by spores, 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 Microbes

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

Cell Theory

• All living organisms are composed of one or more cells

• The cell is the basic unit of life

• All cells arise from pre-existing cells

Eukaryotic Cell Structures & Functions

• Nucleus: Contains DNA, controls cell activities, nuclear envelope

• Ribosomes: Protein synthesis, free or on rough ER

• Endoplasmic Reticulum (ER): Rough ER (protein synthesis), Smooth ER (lipid synthesis, detoxification, Ca2+ 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 (2n) daughter cells

• Stages: Prophase, Metaphase, Anaphase, Telophase (PMAT)

• Cytokinesis: Division of cytoplasm

Meiosis

• Purpose: Gamete production, genetic diversity

• Produces 4 genetically diverse haploid (n) cells

• Meiosis I: Homologous chromosomes separate, crossing over

• Meiosis II: Sister chromatids separate

Mitosis vs. Meiosis Comparison

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

• Types: Phagocytosis (solids), Pinocytosis (liquids), Receptor-mediated (specific)

• Exocytosis: Secretion of materials via vesicle fusion, requires ATP

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

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 can only replicate inside host cells.

• Structure: Capsid (protein coat), envelope (in some), spikes (attachment), nucleic acid (DNA or RNA, single- or double-stranded)

• Virion: Complete infectious viral particle

• Nucleocapsid: Capsid + nucleic acid

• Classification: 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/yield

• Simpler than viruses

Prions

• Infectious misfolded proteins, no DNA/RNA

• Cause fatal neurodegenerative diseases (e.g., Creutzfeldt-Jakob, 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 as 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 uncoated inside cell
Release	Cell lysis	Budding (enveloped) or lysis (naked)

Proto-Oncogenes vs. Oncogenes

• Proto-oncogenes: Normal genes regulating cell growth, division, survival

• Oncogenes: Mutated/overexpressed proto-oncogenes, cause uncontrolled cell division (cancer)

• Mutations: Point mutations, gene amplification, chromosomal translocations

• Only one mutated copy can drive cancer (gain-of-function)

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

Neoplasms are abnormal tissue masses from uncontrolled cell division. They may be benign or malignant.

Benign vs. Malignant Neoplasms

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