Microbiology Study Guide PDF

Microbiology Study Guide: Exam 1 Chapter 1: Introduction to Microbiology Definition of Microbiology and Microbes Microbiology - Study of organisms too small to be seen with the naked eye (mi Microbes - Includes bacteria, archaea, fungi, protozoa, algae, and viruses Taxonomic Classificat...

Microbiology Study Guide: Exam 1 Chapter 1: Introduction to Microbiology Definition of Microbiology and Microbes Microbiology - Study of organisms too small to be seen with the naked eye (mi Microbes - Includes bacteria, archaea, fungi, protozoa, algae, and viruses Taxonomic Classification of Microbes Three Domains of Life: determined by rRNA o Bacteria: Prokaryotic, single-celled, no nucleus o Archaea: Prokaryotic, single-celled, extreme environments o Eukarya: Eukaryotic, nucleus, membrane-bound organelles Eukaryotic Kingdoms: o Animalia o Plantae o Fungi o Protista (subdivided into algae and protozoa) Viruses (Obligate parasites): Non-living, require host cells to replicate which determines weather it is inactive or active, contain DNA or RNA Size Comparisons (smallest to largest): o Macromolecules (Proteins, DNA, Lipids, Carbohydrates): Typically range from 1–10 nm. o Viruses: 20–300 nm (smaller than bacteria but larger than macromolecules). o Bacteria & Archaea: 0.1–5 µm (micrometers). o Eukaryotic Cells: 10–100 µm (much larger than bacteria). Taxonomy o Genus and species are used to name organisms Roles of Microbes in Different Ecosystems Photosynthesis: Conversion of CO2 into organic material, producing oxygen Decomposition: Breakdown of organic matter into simpler compounds Symbiosis: Interactions between microbes and other organisms (mutualism, commensalism, parasitism) Nutrient Cycling: Microbes play a role in nitrogen and carbon cycling Key Scientists and Their Contributions Robert Hooke (1665): First description of microorganisms Antonie van Leeuwenhoek (1675): Discovered bacteria using a microscope Edward Jenner (1796): Developed the first vaccine (smallpox) Oliver Wendell Holmes (1843): Suggested doctors spread puerperal fever. Ignaz Semmelweis (1847): Advocated handwashing to reduce infections Louis Pasteur (1864): Disproved spontaneous generation, developed pasteurization Robert Koch (1876): Developed Koch’s postulates, proving specific microbes specific cause disease o Koch’s Four Postulates ▪ The microorganism must be present in all cases of the disease but absent in healthy organisms. ▪ The microorganism must be isolated from the diseased host and grown in pure culture. ▪ The cultured microorganism must cause the same disease when introduced into a healthy host. ▪ The microorganism must be re-isolated from the newly infected host and shown to be the same as the original. o Does not work for everything but does work for majority and is still used today Alexander Fleming (1928): Discovered penicillin, the first antibiotic Abiogenesis VS. Biogenesis Abiogenesis (Spontaneous Generation) o The theory that life arises from non-living matter. Biogenesis o The theory that life arises from pre-existing life. o Supported by scientific evidence. Key experiments: o Francesco Redi (1668) – Showed that maggots come from flies, not rotting meat. o Louis Pasteur (1861) – Used a swan-neck flask experiment to prove that microbes come from existing microbes, not spontaneously. Types of Symbiotic Relationships 1. Mutualism o Both organisms benefit from the relationship. ▪ Example: E. coli in the human gut – It helps digest food and produces vitamin K while getting nutrients and a stable environment. 2. Parasitism o One organism benefits (parasite), while the other is harmed (host). ▪ Example: Tapeworms in humans – The tapeworm absorbs nutrients from the intestines, weakening the host. 3. Commensalism o One organism benefits, while the other is unaffected. ▪ Example: Staphylococcus on human skin – The bacteria get shelter and nutrients, but the host is neither helped nor harmed. Use of Microbes in Industry Food Production: Fermentation for yogurt, cheese, beer, and bread Biotechnology: Genetic engineering, production of insulin using bacteria Bioremediation: Use of microbes to clean pollutants (oil spills, wastewater treatment) Medical Microbiology: Development of vaccines, antibiotics, and probiotics Bioremediation Definition: o Bioremediation is the use of microorganisms (bacteria, fungi, or plants) to break down and remove pollutants from the environment. Types of Bioremediation: o In Situ Bioremediation – Treatment occurs at the contamination site (e.g., oil spills in soil). o Ex Situ Bioremediation – Contaminated material is removed and treated elsewhere (e.g., in bioreactors). Examples: o Oil Spill Cleanup – Pseudomonas bacteria break down hydrocarbons in oil. o Heavy Metal Removal – Certain bacteria absorb toxic metals like mercury and lead. o Wastewater Treatment – Microbes digest organic waste and pollutants in sewage. Benefits: o Environmentally friendly, Cost-effective, Reduces hazardous waste without producing toxic byproducts o Bioremediation is widely used in pollution control, industrial waste management, and environmental restoration. Chapter 2: Biomolecules Definition and Classification of Biomolecules Organic Molecules: Contain carbon and hydrogen (e.g., carbohydrates, lipids, proteins, nucleic acids) Inorganic Molecules: Do not contain both carbon and hydrogen (e.g., water, salts, acids, bases) Definition Biomolecules and Macromolecules Biomolecules: Organic Molecules essential for life, including carbohydrates, lipids, proteins, and nucleic acids. Macromolecules: Large molecules made of smaller building blocks (monomers), such as proteins, DNA, and starch. Outer Electron Shell (Valence Shell): Importance o Determines chemical reactivity of an atom. o Atoms are most stable when the outer shell is full (octet rule: 8 electrons, except for hydrogen and helium, which need 2). o Involved in bond formation (e.g., covalent, ionic bonds). Electron Shells and Electron Count: o 1st shell: 2 electrons o 2nd shell: 8 electrons o 3rd shell: 18 electrons o 4th shell and beyond: 32 electrons Characteristics and Functions of the Four Major Biomolecules 1. Carbohydrates (Monosaccharides): o Energy storage and structural functions o Examples ▪ Glucose – Simple sugar (monosaccharide), main energy source for cells. ▪ Ribose – Five-carbon sugar in RNA & ATP. ▪ Deoxyribose – Five-carbon sugar in DNA (missing one oxygen compared to ribose). ▪ Lactose – Disaccharide (glucose + galactose), found in milk. ▪ Sucrose – Disaccharide (glucose + fructose), common table sugar. ▪ Cellulose – Polysaccharide in plant cell walls, provides structure, not digestible by humans.  2. Lipids (No monomers): o Hydrophobic molecules, play role in membrane structure (phospholipids and steroids) and as energy reserves (triglycerides) o Examples ▪ Triglycerides – Three fatty acids + glycerol, store energy in fat cells. ▪ Phospholipids – Two fatty acids + glycerol + phosphate, make up cell membranes. ▪ Cholesterol – Steroid, stabilizes cell membranes in animals and mycoplasmas, precursor for hormones. ▪ Ergosterol – part of membranes of fungi 3. Proteins (Amino Acids): o Made of amino acids, perform structural and enzymatic functions o Examples ▪ Amino Acids – Building blocks of proteins, 20 types. ▪ Proteins – Made of amino acids, function as enzymes, transporters, and structural components. 4. Nucleic Acids (Nucleotides): o Store and transfer genetic information o Examples ▪ DNA (Deoxyribonucleic Acid) – Stores genetic instructions, double- stranded. ▪ RNA (Ribonucleic Acid) – Helps in protein synthesis, single-stranded. Chapter 4: Prokaryotic Microorganisms Components of a Prokaryotic Cell External Structures: o Flagella: Provide motility, respond to stimuli (chemotaxis, phototaxis) o Fimbriae: Enable attachment to surface o Pili: Facilitate genetic exchange through conjugation Cell Envelope: o Gram-Positive Bacteria: Thick peptidoglycan layer, stains purple in Gram staining o Gram-Negative Bacteria: Thin peptidoglycan layer, outer membrane, stains pink Internal Structures: o Ribosomes: Site of protein synthesis o Plasmids: Small, circular DNA, carry antibiotic resistance genes o Endospores: Dormant structures resistant to extreme conditions o No Nucleus External Appendaged Present in Prokaryotes Flagella o Structure: ▪ Composed of three main parts: 1. Filament: A long, helical structure made of flagellin protein. 2. Hook: A curved structure connecting the filament to the basal body. 3. Basal Body: Anchors the flagellum to the cell membrane and acts as a motor powered by the proton motive force (PMF). o Function: ▪ Motility (Locomotion): Bacteria use flagella to move toward or away from stimuli (taxis), such as: Chemotaxis Phototaxis Fimbriae o Structure: ▪ Short, hair-like structures made of protein (pilin). ▪ Found in large numbers covering the bacterial surface. o Function: ▪ Attachment: Help bacteria adhere to surfaces, host cells, and each other. ▪ Biofilm Formation: Play a key role in forming bacterial biofilms, which protect bacteria from antibiotics and the immune system. Example: Escherichia coli uses fimbriae to attach to the urinary tract, leading to infections. Pili (Singular: Pilus) o Structure: ▪ Like fimbriae but longer and fewer in number. ▪ Composed of pilin proteins. o Function: ▪ Conjugation (Sex Pilus): The F pilus allows bacteria to exchange genetic material (plasmids) through horizontal gene transfer, spreading traits like antibiotic resistance. Nanowires o Structure: ▪ Very thin, long, tubular extensions of the cytoplasmic membrane that bacteria use as channels o Function: ▪ Allow direct transfer of amino acids, electrons, ATP, and food between bacterial cells. ▪ Transfers: Amino acids (food) Electrons Bacterial Classification Shapes: o Coccus (spherical/round) – Example: Streptococcus o Bacillus (rod-shaped) – Example: Escherichia coli o Vibrio (curved/comma-shaped) – Example: Vibrio cholerae o Spirillum (rigid spiral-shaped) – Example: Spirillum minus o Spirochete (flexible spiral-shaped) – Example: Treponema pallidum Pleomorphism: Different shapes in the same types of Bacteria (change in shape based on environmental conditions) Arrangements: o Cocci Arrangements: ▪ Single – Micrococcus ▪ Diplococci (pairs) – Neisseria gonorrhoeae ▪ Streptococci (chains) – Streptococcus pyogenes ▪ Staphylococci (grape-like clusters) – Staphylococcus aureus ▪ Tetrads (groups of four) – Micrococcus luteus ▪ Sarcinae (cube-like groups of eight) – Sarcina ventriculi o Bacilli Arrangements: ▪ Single – Escherichia coli ▪ Diplobacilli (pairs) – Moraxella ▪ Streptobacilli (chains) – Streptobacillus moniliformis ▪ Palisades (side-by-side arrangement) – Corynebacterium diphtheriae (insert photo of arrangements) Based on Flagella o Monotrichous – A single flagellum at one end (e.g., Vibrio cholerae). o Lophotrichous – A cluster of flagella at one or both ends (e.g., Pseudomonas species). o Amphitrichous – One flagellum at each end of the cell (e.g., Spirillum species). o Peritrichous – Flagella distributed all over the surface (e.g., Escherichia coli). o Atrichous – No flagella, non-motile bacteria (e.g., Lactobacillus). Stimulus of Movement Chemotaxis: movement in response to chemical signals o Positive Chemotaxis: movement of a cell in the direction of a favorable chemical stimulus o Negative Chemotaxis: Movement of a cell away from a potentially harmful compound Phototaxis: Movement toward light o Exhibited by some photosynthetic bacteria Flagellar movement Run: counterclockwise movement of the flagella o Cell swims in a smooth linear direction toward a stimulus Tumble: Flagellum reverse direction, causing the cell to stop and change course o Repellants cause numerous tumbles External Surface Layers Glycocalyx (Capsule and Slime Layer) o Structure: The glycocalyx is a gel-like layer made of polysaccharides (sometimes with proteins). It exists in two forms: ▪ Capsule: A well-organized, tightly bound structure surrounding the cell. ▪ Slime Layer: A loose, unorganized layer that is more easily washed off. o Function: ▪ Protects bacteria from desiccation (drying out). ▪ Helps bacteria evade the immune system by preventing phagocytosis by white blood cells. ▪ Facilitates adherence to surfaces, aiding in biofilm formation (e.g., dental plaque). S-Layer (Surface Layer) o Structure: A crystalline layer made of proteins or glycoproteins, found outside the cell wall in some bacteria. o Function: ▪ Provides structural support and protection against environmental stress. ▪ Acts as a permeability barrier, preventing toxic molecules from entering. ▪ Plays a role in pathogenicity by helping bacteria evade the host immune system. Fimbriae (Pili) o Structure: Short, hair-like appendages composed of protein subunits (mainly pilin). o Function: ▪ Fimbriae: Help bacteria adhere to surfaces, host tissues, and other bacteria, which is crucial for colonization (e.g., Escherichia coli attaching to the urinary tract). ▪ Pili (Singular: Pilus): Longer than fimbriae and can serve different functions: Sex Pilus: Involved in bacterial conjugation, a process where genetic material is transferred between bacteria. Type IV Pili: Assist in twitching motility, a form of movement using pili extension and retraction. Flagella o Structure: Long, whip-like appendages made of the protein flagellin and anchored to the bacterial cell by a basal body, hook, and filament. o Function: ▪ Enable motility through liquid environments. ▪ Help bacteria respond to environmental stimuli via taxis (e.g., chemotaxis toward nutrients). ▪ Can contribute to pathogenicity, allowing bacteria to reach specific host tissues. Gram-positive and Gram-negative Bacteria Gram Staining (Differential stains) Overview o Developed by: Hans Christian Gram o Purpose: Differentiates bacteria into two major groups based on their cell envelope structure: ▪ Gram-positive bacteria: Stain purple ▪ Gram-negative bacteria: Stain red (pink) Cell Envelope Differences: Gram-Positive vs. Gram-Negative Bacteria o Gram-Positive Bacteria ▪ Envelope Structure: Cell membrane (phospholipid bilayer) Thick peptidoglycan layer (20–80 nm) ▪ Peptidoglycan Layer: Provides structure and protection Flexible but rigid enough to maintain shape Contains teichoic and lipoteichoic acids, which: ▪ Help maintain cell wall stability ▪ Aid in cell division and growth ▪ Contribute to the acidic charge on the bacterial surface ▪ More resistant to lysis due to thick peptidoglycan ▪ Gram Staining Color: Purple (Retains crystal violet stain) o Gram-Negative Bacteria ▪ Envelope Structure: Outer membrane (phospholipid bilayer) with lipopolysaccharides (LPS) Thin peptidoglycan layer (1–3 nm) Inner membrane (phospholipid bilayer) ▪ Peptidoglycan Layer: Much thinner than in Gram-positive bacteria Located between two membranes Provides less structural rigidity ▪ Outer Membrane: Contains lipopolysaccharides (LPS), which: ▪ Contribute to toxicity (endotoxins) ▪ Help bacteria evade the immune system Acts as an additional barrier against antibiotics and harmful substances ▪ More sensitive to lysis due to the thin peptidoglycan layer ▪ Gram Staining Color: Pink/Red (Crystal violet washes out, absorbs safranin) Organization of genetic Material in Bacteria No nucleus – Bacteria have a nucleoid region where genetic material is located. Single, circular chromosome – Contains most of the bacterial DNA. No histones – Unlike eukaryotes, bacterial DNA is not wrapped around histone proteins (except in archaea). Plasmids – Small, circular pieces of extrachromosomal DNA that: o Carry non-essential genes (e.g., antibiotic resistance, virulence factors). o Can be transferred between bacteria via conjugation (horizontal gene transfer). Supercoiling – Helps compact the large chromosome into the small bacterial cell. Operons – Groups of genes that are transcribed together as a single unit (e.g., lac operon for lactose metabolism). Structure and Function of Bacterial Ribosomes Structure: o Composed of ribosomal RNA (rRNA) and proteins. o Smaller than eukaryotic ribosomes – 70S ribosomes, made of: ▪ Large subunit ▪ Catalyzes peptide bond formation (joins amino acids) ▪ Contains peptidyl transferase activity ▪ Small subunit ▪ Binds to mRNA and reads the genetic code ▪ Aligns mRNA and tRNA for translation o Where they are found: ▪ Prokaryotes: Free-floating in the cytoplasm. ▪ Found in the cytoplasm (free or attached to rough ER) and inside mitochondria & chloroplasts (which have their own ribosomes similar to prokaryotic ones). Function: o Protein synthesis – Translate mRNA into proteins. o Target for antibiotics – Some antibiotics (e.g., tetracyclines, macrolides) inhibit bacterial ribosomes without affecting eukaryotic ribosomes. Pleomorphism in Bacteria Definition: The ability of some bacteria to vary in shape and size rather than having a single, uniform shape. Causes: o Lack of a rigid cell wall (e.g., Mycoplasma species). o Environmental conditions (e.g., nutrient availability, temperature). o Genetic variations. Examples: o Mycoplasma pneumoniae – Lacks a cell wall, allowing it to change shape. o Corynebacterium diphtheriae – Shows variable shapes, from rods to club-like forms. Significance: o Can help bacteria evade the immune system. o Affects bacterial classification and identification in laboratory settings. Germination and Sporulation in Bacteria Sporulation (Endospore Formation) o Definition: The process by which some bacteria (e.g., Bacillus, Clostridium) form highly resistant endospores to survive harsh conditions. o Steps: ▪ DNA Replication – The bacterial chromosome is duplicated. ▪ Septum Formation – The cell membrane forms a small compartment for the developing spore. ▪ Forespore Development – The smaller compartment becomes the forespore, which will mature into an endospore. ▪ Protective Layers Form – The forespore is surrounded by multiple protective layers (cortex, spore coat). ▪ Dehydration & Dormancy – The endospore loses water and enters a dormant state, making it highly resistant. ▪ Mother Cell Lysis – The bacterial cell disintegrates, releasing the mature endospore. o Function: ▪ Allows bacteria to survive extreme conditions (heat, radiation, desiccation, chemicals). ▪ Endospores remain dormant until favorable conditions return. Germination (Endospore Reactivation) o Definition: The process by which a dormant endospore returns to its active, vegetative state. o Triggers: ▪ Presence of water and nutrients. ▪ Suitable temperature and environmental conditions. o Steps: ▪ Activation – Endospore senses favorable conditions. ▪ Germination Proper – Spore coat breaks down, water uptake begins, metabolic activity resumes. ▪ Outgrowth – Bacterium fully returns to a vegetative (active) state and begins cell division. o Function: ▪ Allows bacteria to resume growth and reproduction once conditions improve. Importance of Bacterial Endospores and Their Medical Implications Importance of Endospores o Survival Mechanism – Endospores help bacteria survive extreme conditions such as heat, desiccation, radiation, and chemicals. o Dormancy – They remain inactive for long periods but can germinate when conditions become favorable. o Resistant to Antibiotics and Disinfectants – Many common antibiotics and chemical disinfectants cannot penetrate endospore layers. o Widespread in Nature – Found in soil, water, and even inside the human body under specific conditions.  Medical Implications of Endospores o Disease Transmission – Endospores can persist in the environment and cause infections when ingested or inhaled. o Difficult to Kill – Require special sterilization methods (autoclaving at 121°C, strong disinfectants, UV radiation). o Major Endospore-Forming Pathogens: ▪ Bacillus anthracis – Causes anthrax, a deadly disease affecting humans and animals. ▪ Clostridium tetani – Causes tetanus (lockjaw) through toxin production. ▪ Clostridium botulinum – Produces botulinum toxin, leading to botulism (paralysis). ▪ Clostridium difficile – Causes severe antibiotic-associated diarrhea and colitis. Chapter 5: Eukaryotic Microorganisms Important Components of a Eukaryotic Cell Nucleus – Contains DNA, controls cell activities and gene expression. Endoplasmic Reticulum (ER): o Rough ER – Studded with ribosomes; involved in protein synthesis. o Smooth ER – Synthesizes lipids and detoxifies chemicals. Golgi Apparatus – Modifies, sorts, and packages proteins for transport. Mitochondria – Powerhouse of the cell; generates ATP through cellular respiration. Lysosomes – Contain digestive enzymes to break down waste and cellular debris. Peroxisomes – Detoxify harmful substances and break down fatty acids. Cytoskeleton: o Microtubules – Provide structure, help in cell division and intracellular transport. o Microfilaments – Aid in movement and shape maintenance. o Intermediate filaments – Provide mechanical support. Centrioles (in animal cells) – Involved in cell division (mitotic spindle formation). Vacuoles: o Large central vacuole (in plants) – Stores water, nutrients, and waste. o Small vacuoles (in animals) – Store and transport substances. Chloroplasts (in plant cells) – Site of photosynthesis, contains chlorophyll. Locomotor Appendages in Eukaryotic Microorganisms Flagella o Structure: ▪ Thicker than bacterial flagella. ▪ Covered by an extension of the cell membrane. ▪ Made of microtubules with a 9+2 arrangement (9 pairs around 2 central microtubules). ▪ Composed of long protein filaments called microtubules.  o Function: ▪ Provides movement with a whip-like motion. ▪ Used for propulsion in some protozoa, algae, and sperm cells. Cilia o Structure: ▪ Like flagella but shorter and more numerous. ▪ Found in rows, often numbering in the thousands. ▪ Made of microtubules (like flagella). o Function: ▪ Move in a coordinated back-and-forth motion. ▪ Can help with feeding and filtering in addition to movement. ▪ Common in ciliated protozoa (e.g., Paramecium) and human respiratory cells. Cell Membrane (Cytoplasmic Membrane) Function: o Serves as a selectively permeable barrier that regulates what enters and exits the cell. Structure: o Like prokaryotic cell membranes, consisting of a phospholipid bilayer with protein molecules embedded in it. o Protein Channels: Allow substances that cannot pass through the lipid bilayer to enter and exit the cell. o Integral Proteins: Span the membrane completely, involved in transport and cell communication. o Glycoproteins: Serve as signal molecules for communication with the external environment. o Steroids (e.g., Cholesterol, Ergosterol): ▪ Cholesterol is found in most animal cell membranes, making the membrane more rigid. ▪ Ergosterol is found in fungal and protozoan cell membranes, also contributing to membrane rigidity. o Glycocalyx ▪ Definition: A highly hydrated meshwork of carbohydrates that extends from the outer surface of the plasma membrane. ▪ Structure: Composed of polysaccharides, resembling the bacterial glycocalyx. Found in animal cells as the extracellular matrix, which provides structural support and aids in cell-cell communication. ▪ Function: Protects the cell and helps in adhesion to surfaces, like its role in bacteria. Cell Envelope in Eukaryotic Microorganisms All eukaryotic microorganisms contain a cell membrane in their cell envelope, but the additional layers vary across different groups: o Algae: ▪ Rigid cell wall made of cellulose fibers (like plants), which provides support and structure. ▪ The cell wall is not as flexible as the plasma membrane. o Fungi: ▪ Multilayered cell wall consisting of an inner layer of polysaccharide fibers (either chitin or cellulose). Chitin is a tough material, like the substance found in exoskeletons of insects like cockroaches. ▪ The outer layer is made of glycoproteins. ▪ The cell wall provides protection, rigidity, and shape. o Protozoa: ▪ On the inner side of the membrane, there is a thin protein layer called the pellicle. The pellicle provides elasticity to the cell envelope, allowing it to be more flexible and move. ▪ Protozoan Cyst A dormant, protective form found in eukaryotic protozoa that helps them survive harsh conditions and is not present in bacteria or prokaryotes. Membrane-Bound Organelles Nucleus o Structure: ▪ Surrounded by a nuclear envelope with pores for molecular exchange. ▪ Contains the nucleolus (site of ribosome production) and chromatin (DNA + proteins). o Function: ▪ Stores genetic material (DNA). ▪ Directs cell activities such as growth, metabolism, and reproduction through gene expression. Rough Endoplasmic Reticulum (Rough ER) o Structure: ▪ Network of membrane-bound sacs and ribosomes attached to the surface. o Function: ▪ Protein synthesis (ribosomes make proteins). ▪ Modification and folding of proteins before they are sent to the Golgi apparatus. ▪ Important in secretory proteins production (e.g., hormones). Smooth Endoplasmic Reticulum (Smooth ER) o Structure: ▪ Network of membrane-bound tubes without ribosomes.  o Function: ▪ Synthesis of lipids (e.g., phospholipids, steroids). ▪ Detoxifies harmful substances. ▪ Stores calcium ions in muscle cells. Golgi Apparatus (Golgi Body) o Structure: ▪ Stack of flattened membrane sacs. o Function: ▪ Modifies, sorts, and packages proteins and lipids for transport. ▪ Forms vesicles that transport materials to other parts of the cell or outside the cell. ▪ Secretion of hormones and other substances. Lysosomes o Structure: ▪ Membrane-bound sacs filled with digestive enzymes. o Function: ▪ Break down waste products (old organelles, food particles, and foreign substances). ▪ Involved in autophagy (cell recycling) and apoptosis (programmed cell death). Vacuoles o Structure: ▪ Membrane-bound sacs filled with water, nutrients, or waste. o Function: ▪ In plant cells, the central vacuole stores water and maintains turgor pressure. ▪ In animal cells, smaller vacuoles are used for storage and transport of substances. Mitochondria o Structure: ▪ Double-membrane organelles with their own DNA and ribosomes. ▪ Inner membrane folds into cristae, increasing surface area for energy production. o Function: ▪ Powerhouse of the cell—produces ATP (cell's energy currency) via cellular respiration. ▪ Regulates cell metabolism and apoptosis. Chloroplasts (in plant cells) o Structure: ▪ Double-membrane organelles containing chlorophyll. ▪ Inside, contains thylakoid membranes stacked into grana and the stroma. o Function: ▪ Site of photosynthesis—converts sunlight into chemical energy (glucose). ▪ Responsible for producing oxygen as a by-product. Additional Structures Chromosomes o Structure: ▪ Composed of DNA wrapped around histone proteins. ▪ Found in the nucleus during cell division. o Function: ▪ Carry the cell's genetic information. ▪ Directs cell functions by controlling gene expression. Ribosomes o Structure: ▪ Made of rRNA and protein. ▪ Found either free in the cytoplasm or attached to the rough ER. o Function: ▪ Protein synthesis by translating mRNA into polypeptides. Cytoskeleton o Structure: ▪ Made of three types of protein filaments: Microtubules (provide structure and transport pathways). Microfilaments (involved in cell movement and shape). Intermediate filaments (provide mechanical strength). o Function: ▪ Provides structural support for the cell. ▪ Involved in cell division, cell movement, and intracellular transport. Differences Between Yeasts and Molds Yeasts o Structure: ▪ Unicellular fungi, typically with an oval or round shape. ▪ Yeasts digest food externally by releasing enzymes that break down complex molecules outside their cells. Then, they absorb the smaller nutrients. Unlike most eukaryotes which digest internally o Function & Roles: ▪ Used in baking (bread rising) and alcoholic fermentation (beer, wine). ▪ In the absence of oxygen, yeasts produce ethanol as a by-product of fermentation (anaerobic). ▪ Carbon dioxide produced by yeast causes bread dough to rise. o Reproduction: ▪ Asexual reproduction: Yeasts mainly reproduce by budding, where a small part of the cell pinches off to form a new yeast cell. ▪ Sexual reproduction: Can occur through the formation of haploid sexual spores (conidia or ascospores). o Industrial Importance: ▪ Yeasts are essential in the food industry for baking and brewing, making them crucial for the production of bread, beer, and wine.  Molds oStructure: ▪ Molds are filamentous fungi made up of long, branching cells called hyphae. ▪ Hyphae types: Nonseptate hyphae: These are multinucleate cells without dividers. Septate hyphae: These hyphae have dividers (septa) that separate individual cells, but the cells remain connected through small pores in the septa. o Function & Roles: ▪ Molds secrete digestive enzymes outside their cells to break down complex food sources, then absorb the nutrients through the cell membrane. ▪ Carbohydrates are their main food source. o Reproduction: ▪ Molds grow and spread through their mycelium (the mass of hyphae), which can spread out in search of food. ▪ They can also reproduce asexually through the production of spores. Summary of Differences: o Cell Structure: ▪ Yeasts: Unicellular, oval shape. ▪ Molds: Multicellular, filamentous (made of hyphae). o Reproduction: ▪ Yeasts: Mainly reproduce asexually through budding; can reproduce sexually with haploid spores. ▪ Molds: Reproduce by forming spores; grow through mycelium. o Metabolism: ▪ Yeasts: Can ferment sugars to produce ethanol and CO2. ▪ Molds: Absorb nutrients through external digestion (secreting enzymes). o Function in Industry: ▪ Yeasts: Important in baking and brewing (alcoholic fermentation). ▪ Molds: Used in decomposing organic matter and can be involved in antibiotic production (e.g., penicillin). Fungi Overview Kingdom: Fungi (Miceteae) Estimated 5 million species of fungi. Macroscopic fungi: Large, visible fungi such as mushrooms and bread molds. Microscopic fungi: Fungi that are not visible to the naked eye, with two main morphological forms: o Yeasts (unicellular) o Molds (multicellular) Fungal Classification Kingdom: Fungi (Miceteae) Phyla (Major groups of fungi): o Microsporidia o Chytridiomycota o Blastocladiomycota o Neocallimastigomycota o Glomeromycota o Ascomycota o Basidiomycota Criteria for Classification: o Fungi are primarily classified based on their sexual reproductive structures. These structures help identify different phyla. o Asexual spore-forming structures and the types of spores produced are also used to classify fungi down to the genus and species level. Fungal Nutrition Heterotrophic organisms: Fungi acquire their nutrients from organic substrates. o Saprobes: Obtain nutrients from dead plants and animals (decomposers). o Parasites: Obtain nutrients from living organisms, often harming the host in the process (e.g., mycoses, fungal infections in animals). o Symbiotic mutualists: Fungi form mutualistic relationships with other organisms. ▪ Example: Lichens—a combination of fungus and algae. The fungus provides structure, while the algae perform photosynthesis. Challenges in treating fungal infections: o Fungi are eukaryotic cells, making them more difficult to treat (because our cells are also eukaryotic). o Fungi have their own detoxification system, which can make them resistant to some treatments. o Fungal infections can be particularly harmful to kidneys and liver in the host. Reproduction in Fungi Fungi can reproduce sexually or asexually, depending on environmental conditions. 1. Vegetative Reproduction o Involves the outward growth of hyphae (filamentous cells) or the fragmentation of hyphae/mycelium. o The fragments can grow into new individuals. o This is a clonal form of reproduction, meaning the offspring are genetically identical to the parent. 2. Sporulation (Main Mode of Reproduction) o Fungi commonly reproduce by spores. o Spore functions: ▪ Multiplication: Increase the number of fungi. ▪ Survival: Spores can survive in harsh conditions. ▪ Genetic variability (via sexual spores). ▪ Dissemination: Spread the fungus to new environments. Types of Spores 1. Asexual Spores o Produced by mitotic divisions (no genetic recombination). o Sporangiospores: Spores are enclosed in a sac-like structure called a sporangium. o Conidiospores: Spores are not enclosed—free spores released into the environment. o Roles: Rapid propagation of the fungus under favorable conditions. 2. Sexual Spores o Produced by the fusion of specialized male and female structures or fertile hyphae. o Genetic variability is introduced during sexual reproduction, making these spores important for evolutionand adaptation. o Majority of fungi form sexual spores, contributing to genetic diversity. Key Notes for Comparison Asexual vs. Sexual Spores: o Asexual spores are clonal (genetically identical to the parent). o Sexual spores contribute to genetic variability, which is crucial for evolution. Fungal Spores vs. Bacterial Endospores: o Fungal spores are reproductive and involved in growth and spread. o Bacterial endospores are highly resistant structures formed for survival under extreme conditions. Importance of Fungi in Natural Ecosystems 1. Decomposition of Organic Matter o Fungi play a vital role in breaking down dead plant and animal material, recycling nutrients back into the environment. o Without fungi, organic material would accumulate, and essential nutrients would be locked up, disrupting ecosystems. 2. Symbiotic Relationships o Fungi can form mutualistic partnerships with plants (e.g., mycorrhizal fungi), helping plants absorb water and nutrients, while receiving sugars from the plants in return. Importance of Fungi for Human Society 1. Food Industry o Fungi are used in food production (e.g., yeasts in baking and brewing, molds in cheese making). o Certain fungi like mushrooms are also harvested for consumption. 2. Biotechnology o Fungi are involved in the production of antibiotics (e.g., Penicillium species) and other pharmaceuticals. o They are also used in bioremediation, helping to clean up environmental pollutants.  3. Pathogenic Fungi o 300 fungal species are known to cause diseases in humans, often leading to community-acquired infections, hospital-associated infections, or opportunistic infections. ▪ Opportunistic infections are caused by fungi that are typically non- pathogenic but can cause disease in people with weakened immune systems. o Examples of human fungal diseases include athlete's foot, ringworm, and more serious conditions like aspergillosis. Subkingdom: Algae (for comparison) Characteristics of Algae: o No true roots, stems, or leaves—their structure is simpler than plants. o Photosynthetic organisms—primary producers of organic matter in ecosystems. o Algae produce a significant amount of oxygen through photosynthesis, contributing to the atmosphere. Types of Algae: o Algae can be unicellular, colonial, or multicellular (e.g., kelp). o Different pigments in algae give them varying colors, such as green, yellow, red, and brown. Ecological Roles: o Algae are an important part of the food chain, particularly in aquatic ecosystems, where they are consumed by organisms like zooplankton and fish. o Phytoplankton, which includes algae, are key producers in aquatic food webs. Algal Blooms: o Excessive growth of algae, known as algal blooms, can result in harmful environmental impacts, such as red tides (discoloration of water due to algae). o Some algal blooms produce toxins that can poison fish, marine animals, and humans. ▪ Example: Pfiesteria piscicida causes fish poisoning and human illness through exposure. Subkingdom: Protozoa General Characteristics o The term "protozoa" means "first animals", reflecting their early evolutionary origins. o Approximately 65,000 species have been identified. o Unicellular or colonial heterotrophic organisms (lack chlorophyll and cannot produce their own food). o Found in aquatic environments (freshwater & marine), moist soil, and as parasites in host organisms.  Feeding Habits: o Free-living protozoa: Feed on plant or animal debris, bacteria, or algae. o Parasitic protozoa: Feed on fluids or tissues of their hosts, often causing disease. Cell Structure & Cytoplasm Organization o Protozoa have a differentiated cytoplasm, divided into: ▪ Ectoplasm (Outer Layer) Clear, gel-like, and involved in: o Locomotion (movement). o Feeding (engulfing food particles). o Protection (structural support). ▪ Endoplasm (Inner Layer) Granular and houses organelles, including: o Nucleus – Controls cell functions. o Mitochondria – Produces ATP for energy. o Food vacuoles – Digest engulfed food. o Contractile vacuoles – Regulate water balance, preventing the protozoan from bursting due to osmosis. Reproduction and Life Cycle Asexual reproduction: o Binary fission – One cell splits into two identical daughter cells. o Multiple fission (Schizogony) – Nucleus divides multiple times before the cell splits into several new cells. Sexual reproduction: o Some protozoa undergo conjugation, where two cells temporarily fuse and exchange micronuclei for genetic recombination (common in ciliates like Paramecium). Life Cycle Alternation: o Trophozoite Stage: Active, motile, feeding form. o Cyst Stage: Dormant, resistant form that survives harsh conditions. The process of cyst formation is called encystment. Classification of Protozoa (Based on Locomotion) 1. Flagellates (Mastigophora) – Move using flagella. o Trypanosoma brucei (African sleeping sickness). o Giardia lamblia (causes giardiasis). 2. Amoeboids (Sarcodina) – Move using pseudopodia ("false feet"). o Entamoeba histolytica (amoebic dysentery). o Amoeba proteus (free-living, non-pathogenic). 3. Ciliates (Ciliophora) – Move using cilia. o Paramecium (free-living). o Balantidium coli (intestinal parasite in humans).  4. Apicomplexans (Sporozoa) – Non-motile, obligate parasites. o Plasmodium spp. (causes malaria). o Toxoplasma gondii (causes toxoplasmosis). Key Takeaways Protozoa are unicellular heterotrophic eukaryotes, with free-living and parasitic species. Cytoplasm is divided into ectoplasm (for movement & feeding) and endoplasm (which houses organelles). Reproduce asexually (binary fission, multiple fission) and sexually (conjugation in ciliates). Classified based on locomotion: flagella, pseudopodia, cilia, or no movement (apicomplexans).