Chapter 01 - Intro To Molecular Microbiology in our Lives

Microbiology is the study of microbes microbes include

• bacteria
• fungi
• protozoa
• microscopic algae
• viruses

1. Bacteria

Definition: Single-celled prokaryotic microorganisms lacking a true nucleus. They reproduce asexually through binary fission.

Key Features:

• Structure: Lacks membrane-bound organelles. Contains ribosomes, a nucleoid region, and often flagella or pili.
• Cell Wall Composition: Composed primarily of peptidoglycan (Gram-positive: thick peptidoglycan layer; Gram-negative: thin layer with an outer membrane).
• Reproduction: Binary fission, spore formation in some cases.
• Metabolism: Wide variety, including aerobic, anaerobic, photosynthetic, and chemotrophic.
• Genetic Material: Circular DNA, sometimes with plasmids (small circular DNA molecules).
• Pathogenicity: Can be pathogenic (e.g., Staphylococcus aureus) or beneficial (e.g., gut flora).

Subtopics:

• Gram Staining: Differences in cell wall structure.
• Endospores: Dormant structures formed by some bacteria.
• Biofilms: Communities of bacteria in protective environments.
• Horizontal Gene Transfer: Mechanisms of genetic exchange (conjugation, transformation, transduction).
• Antibiotic Resistance: Mechanisms and implications in healthcare.
• Bacterial Growth Curve: Phases of growth in culture (lag, log, stationary, death).

2. Fungi

Definition: Eukaryotic organisms that include yeasts, molds, and mushrooms. They play roles in decomposition and nutrient cycling.

Key Features:

• Structure: Contains a true nucleus, membrane-bound organelles, and a rigid cell wall made of chitin.
• Reproduction: Both sexual (spore formation) and asexual (budding in yeasts, spore formation in molds).
• Nutrition: Heterotrophic, absorbing nutrients from organic matter (saprophytic, parasitic, or symbiotic).
• Hyphae and Mycelium: Fungal structures used for growth and nutrient absorption.
• Pathogenicity: Some fungi are pathogens (e.g., Candida albicans) while others are beneficial in symbiosis (e.g., mycorrhizae).

Subtopics:

• Fungal Cell Structure: Including organelles and unique features.
• Fungal Reproduction: Asexual and sexual reproductive cycles.
• Fungal Diseases (Mycoses): Superficial, subcutaneous, and systemic infections.
• Fungal Symbiosis: Relationships with plants (mycorrhizae) and animals.
• Antifungal Resistance: Mechanisms in pathogenic fungi.
• Fungi in Biotechnology: Use in fermentation, pharmaceuticals, and bioremediation.

3. Protozoa

Definition: Single-celled eukaryotes that exhibit animal-like behaviors, such as motility and predation. Some are parasitic.

Key Features:

• Structure: Eukaryotic cells with a nucleus, vacuoles, and contractile organelles. Many protozoa possess flagella, cilia, or pseudopodia for movement.
• Reproduction: Mostly asexual (binary fission), but some exhibit sexual reproduction (e.g., conjugation in Paramecium).
• Feeding: Heterotrophic, ingesting bacteria, other protozoa, or organic particles.
• Pathogenicity: Protozoa can cause diseases such as malaria (Plasmodium), amoebiasis (Entamoeba histolytica), and giardiasis (Giardia lamblia).

Subtopics:

• Protozoan Morphology: Diverse structures for locomotion and feeding.
• Protozoan Life Cycles: Complex cycles, often with multiple hosts (e.g., Plasmodium).
• Protozoan Diseases: Pathogenesis and immune evasion strategies.
• Protozoa in Ecosystems: Role in nutrient cycling and symbiotic relationships.
• Host-Protozoan Interactions: Mechanisms of parasitism and immune response.
• Antiprotozoal Agents: Drug mechanisms and resistance.

4. Microscopic Algae

Definition: Photosynthetic eukaryotic organisms, ranging from single-celled forms (e.g., Chlorella) to multicellular seaweeds. Algae can be found in both freshwater and marine environments.

Key Features:

• Structure: Eukaryotic with chloroplasts, a nucleus, and other organelles. Some have flagella for movement.
• Reproduction: Asexual (binary fission, spore formation) and sexual reproduction.
• Photosynthesis: Algae produce oxygen and fix carbon dioxide using light energy, making them important for global carbon cycles.
• Ecological Roles: Primary producers in aquatic ecosystems, forming the base of the food web.
• Pathogenicity: Rare, but some algae produce harmful toxins (e.g., Karenia brevis causing red tides).

Subtopics:

• Algal Cell Structure: Unique chloroplasts and pigments (e.g., chlorophyll a, b, c, phycobilins).
• Photosynthetic Pathways: Mechanisms of carbon fixation and oxygen production.
• Algal Bloom and Eutrophication: Causes and environmental impacts.
• Algae in Biotechnology: Use in biofuels, pharmaceuticals, and wastewater treatment.
• Symbiotic Algae: Associations with corals (zooxanthellae) and lichens.
• Toxic Algae: Algal toxins and their effects on ecosystems and human health.

5. Viruses

Definition: Acellular, obligate intracellular pathogens. Viruses are composed of genetic material (DNA or RNA) encased in a protein coat (capsid) and, in some cases, a lipid envelope.

Key Features:

• Structure: Composed of nucleic acid (DNA or RNA) and a protein coat. Some viruses have an envelope derived from the host cell membrane.
• Reproduction: Cannot replicate outside a host cell. Utilize host cellular machinery to produce viral particles.
• Pathogenicity: Viruses can infect all forms of life, including bacteria (bacteriophages), plants, and animals.
• Host Range: Specific viruses infect specific hosts (e.g., HIV infects human T cells, while bacteriophages infect bacteria).
• Viral Evolution: High mutation rates, especially in RNA viruses, allowing rapid adaptation.

Subtopics:

• Viral Classification: Based on genome (DNA, RNA, single-stranded, double-stranded), replication mechanisms, and morphology.
• Viral Replication Cycles: Lytic and lysogenic cycles in bacteriophages; viral entry, replication, and assembly in animal viruses.
• Host-Pathogen Interactions: Immune evasion strategies and viral latency.
• Antiviral Therapy: Mechanisms of antiviral drugs and resistance.
• Emerging Viruses: Zoonotic viruses, pandemics (e.g., SARS-CoV-2), and public health concerns.
• Vaccine Development: Approaches to creating effective vaccines against viruses.

Summary of Differences:

Every Organelle in Detail

1. Nucleus

Location: Central region of eukaryotic cells. Function:

• Houses the cell's genetic material (DNA).
• Regulates gene expression and cell cycle activities (including replication, transcription, and RNA processing).
• Site of DNA replication and RNA transcription.
• Contains the nucleolus, where ribosomal RNA (rRNA) synthesis and ribosome assembly take place.

Involved in Cycles:

• Cell Cycle (Interphase, Mitosis/Meiosis): Nucleus controls DNA replication (S phase) and chromosome segregation during mitosis and meiosis.
• RNA Processing: Pre-mRNA splicing, addition of the 5' cap, and polyadenylation.

2. Mitochondria

Location: Scattered throughout the cytoplasm. Function:

• Powerhouse of the cell, responsible for ATP production via oxidative phosphorylation.
• Site of the tricarboxylic acid (TCA) cycle (Krebs cycle) and the electron transport chain (ETC).
• Plays a role in apoptosis (programmed cell death).
• Contains its own DNA, which encodes some mitochondrial proteins.

Involved in Cycles:

• Cellular Respiration (Glycolysis, Krebs Cycle, Oxidative Phosphorylation): Central role in energy production through ATP.
• Apoptosis: Initiates cell death via cytochrome c release.

3. Endoplasmic Reticulum (ER)

Location: Connected to the nuclear envelope, extending throughout the cytoplasm. Types: Rough ER (RER) and Smooth ER (SER).

Rough ER:

• Studded with ribosomes.
• Synthesizes and processes proteins destined for secretion or for the plasma membrane.

Smooth ER:

• Lacks ribosomes.
• Involved in lipid synthesis, detoxification of drugs and poisons, and calcium ion storage.

Involved in Cycles:

• Protein Synthesis: RER is the site of protein translation and folding.
• Lipid Metabolism: SER synthesizes lipids and steroid hormones.
• Detoxification: In liver cells, SER detoxifies harmful substances.

4. Golgi Apparatus

Location: Near the ER, in the cytoplasm. Function:

• Modifies, sorts, and packages proteins and lipids from the ER for transport to their final destinations (lysosomes, plasma membrane, or for secretion).
• Glycosylates proteins and lipids (adds carbohydrate groups).

Involved in Cycles:

• Protein and Lipid Transport: Proteins and lipids synthesized in the ER are processed and sorted for transport.

5. Lysosomes

Location: Scattered throughout the cytoplasm. Function:

• Contains hydrolytic enzymes responsible for degrading macromolecules (proteins, lipids, nucleic acids, carbohydrates) into their building blocks.
• Plays a role in autophagy (the process of recycling cellular waste).

Involved in Cycles:

• Autophagy: Lysosomes break down damaged organelles and proteins.
• Phagocytosis: Lysosomes degrade ingested material (e.g., bacteria) in immune cells.

6. Peroxisomes

Location: Scattered throughout the cytoplasm. Function:

• Contains enzymes for fatty acid β-oxidation and detoxification of hydrogen peroxide (H2O2) through the action of catalase.
• Important in lipid metabolism and detoxification processes.

Involved in Cycles:

• Fatty Acid Metabolism: Peroxisomes are involved in the breakdown of long-chain fatty acids via β-oxidation.

7. Ribosomes

Location: Bound to the rough ER or free-floating in the cytoplasm. Function:

• Site of protein synthesis. Ribosomes translate messenger RNA (mRNA) into polypeptide chains.
• Ribosomes on the rough ER synthesize membrane-bound or secretory proteins, while free ribosomes synthesize cytoplasmic proteins.

Involved in Cycles:

• Translation: Ribosomes are key components of the translation phase of protein synthesis, following transcription.

8. Cytoskeleton

Location: Distributed throughout the cytoplasm. Components:

• Microfilaments: Made of actin, involved in muscle contraction and cell division.
• Microtubules: Provide structural support and are tracks for motor proteins; involved in cell division and intracellular transport.
• Intermediate Filaments: Provide mechanical strength to cells.

Function:

• Maintains cell shape, facilitates intracellular transport, and assists in cell division.

Involved in Cycles:

• Cell Division (Mitosis/Meiosis): Microtubules form the spindle apparatus for chromosome separation.
• Intracellular Transport: Motor proteins like kinesin and dynein move vesicles along microtubules.

9. Plasma Membrane

Location: Surrounds the cell, separating the internal environment from the external environment. Function:

• Regulates the passage of substances in and out of the cell via passive and active transport mechanisms.
• Composed of a lipid bilayer with embedded proteins for signaling, transport, and cell recognition.

Involved in Cycles:

• Transport Cycles (Endocytosis, Exocytosis): Facilitates the uptake and secretion of substances.
• Signal Transduction: Contains receptors that mediate cellular responses to external signals.

10. Vesicles

Location: Cytoplasm, often near the ER and Golgi apparatus. Function:

• Small, membrane-bound sacs used for transport of materials within the cell.
• Includes transport vesicles, lysosomes, and secretory vesicles.

Involved in Cycles:

• Exocytosis and Endocytosis: Vesicles mediate the transport of molecules to and from the plasma membrane.

11. Centrosomes and Centrioles

Location: Near the nucleus, in the cytoplasm. Function:

• Centrosomes organize microtubules and play a crucial role in the formation of the mitotic spindle during cell division.
• Centrioles, found within the centrosome, are involved in organizing microtubules.

Involved in Cycles:

• Cell Division (Mitosis and Meiosis): Centrosomes help in the assembly of the spindle apparatus, which is essential for chromosome segregation.

12. Chloroplasts (only in plant cells and some algae)

Location: Found in the cytoplasm of plant cells. Function:

• Site of photosynthesis, converting light energy into chemical energy (glucose).
• Contains chlorophyll and other pigments for capturing light energy.

Involved in Cycles:

• Photosynthesis (Light and Dark Reactions): Chloroplasts perform light-dependent and light-independent (Calvin cycle) reactions to produce glucose.

13. Vacuoles

Location: Prominent in plant cells, smaller in animal cells. Function:

• Store nutrients, waste products, and help maintain turgor pressure in plant cells.
• Involved in intracellular digestion and release of waste products in animal cells.

Involved in Cycles:

• Storage and Homeostasis: Maintain osmotic balance and store substances in plant and animal cells.

Comprehensive Table of Organelles:

• Few of the microbes are pathogenic in nature

A pathogen is an organism, typically a microorganism such as bacteria, viruses, fungi, protozoa, or parasites, that can cause disease in its host by invading tissues, evading immune responses, and disrupting normal physiological functions. Pathogenicity refers to the specific mechanisms by which the pathogen causes harm, including its ability to adhere, colonize, multiply, produce toxins, and manipulate host cellular processes to its advantage. The severity of the disease caused depends on both the pathogen's virulence factors and the host's immune defenses.

• Decomposes organic Waste
• Generate Oxygen by photosynthesis
• Produce Chemicals products such as ethanol, acetone and vitamins.
• Produce fermented food such as vinegar, cheese and bread
• Produce products used in manufacturing (eg. cellulase) and disease treatment which is insulin

The Microbiome

The human microbiome is the collection of all the microbes - bacteria, fungi, protozoa and viruses that live on the human body. Microbes normally present in a defined enviroment are called normal Microbiota

• Normal Microbiota prevents growth of pathogens
• Normal Microbiota produce factors such as vitamins B and K

The Human microbiome project was carried out in united states to undedersatnd microbiome project in depth. Launched in 2007, the first phase focuesed on identifying and characterizing human microbial flora

History

Robert hook first reported the living things are composed of little boxes called cell. Antonie van Leeuwenhoek (late 1600s - 1700x) begain making use of simple microscope to visualize the microorganism, he started visualizing by examining the bacteria fungi and tinny organism found in water

• 1861: Louis Pasteur demonstrated that microorganisms are present in the air and living organism does not arise from the non living matter.
• 1876: Robert Koch discovered that a bacterium causes anthrax and provided the experimental steps, Koch's postulates, to demonstrate that a specific microbe causes a specific disease
• 1796: Edward Jenner inoculated a person with cowpox virus, who was then immune from smallpox, Vaccination is derived from the Latin word vacca, meaning cow, the protection is called immunity.