Ch 4-11 Microbiology PDF

Ch 4 - All living things are composed of cells with basic characteristics: - Spherical, cubical, or cylindrical shapes - cytoplasm surrounded by membrane - DNA chromosomes and ribosomes - Metabolic capabilities - Two main cell types: prokaryotic (bacteria and archaea) and eukaryotic (animals...

Ch 4 - All living things are composed of cells with basic characteristics: - Spherical, cubical, or cylindrical shapes - cytoplasm surrounded by membrane - DNA chromosomes and ribosomes - Metabolic capabilities - Two main cell types: prokaryotic (bacteria and archaea) and eukaryotic (animals, plants, fungi, protists) External Cell Structures Flagella - Three-part structure: - Filament made of flagellin protein - Hook (curved sheath) - Basal body anchored in cell wall - Arrangements: - Monotrichous: single flagellum at one end - Lophotrichous: bunches at same site - Amphitrichous: flagella at both ends - Peritrichous: flagella across surface - Movement: - Clockwise rotation causes tumbling - Counterclockwise rotation enables smooth linear motion - Responds to chemical stimuli (chemotaxis) and light (phototaxis) Fimbriae and Pili - Fimbriae: Fine protein bristles for cell adhesion - Pili: Rigid tubes found only in gram-negative bacteria, enable DNA transfer through conjugation Glycocalyx - External coating made of sugars/proteins - Types: - Slime layer: loosely organized - Capsule: tightly organized - Functions: - Protection from dehydration - Inhibits phagocytosis - Enables biofilm formation Cell Envelope and Wall Structure Gram-Positive Bacteria - Thick peptidoglycan layer (20-80 nm) - Contains teichoic and lipoteichoic acids - More permeable to molecules Gram-Negative Bacteria - Thinner peptidoglycan layer - Double membrane structure - Contains lipopolysaccharides (LPS) - Porin proteins regulate molecular transport - Less permeable to molecules Internal Cell Structures Nucleoid and Plasmids - Single circular DNA chromosome - Plasmids: small circular DNA, not essential for growth Ribosomes - 70S type - Made of 60% RNA, 40% protein - Site of protein synthesis Storage Structures - Inclusions and granules for nutrient storage - Endospores: - Formed by certain gram-positive bacteria - Highly resistant to environmental stress - Can survive extreme conditions - Not a reproductive structure Bacterial Classification Basic Shapes - Coccus (spherical) - Bacillus (rod) - Spirillum (helical) - Vibrio (curved) - Spirochete (spiral) Major Taxonomic Groups - Domain Archaea: - Adapted to extreme environments - Unique membrane lipids and cell walls - Three main phyla: Crenarchaeota, Nanoarchaeota, Euryarchaeota - Domain Bacteria: - Proteobacteria (gram-negative) - Firmicutes (mainly gram-positive, low G+C) - Actinobacteria (gram-positive, high G+C) Medical Classification - Based on: - Cell wall structure - Shape and arrangement - Physiological traits - Important pathogenic families include: - Staphylococcaceae (skin infections) - Streptococcaceae (strep throat)  - Bacillaceae (anthrax, tetanus) - Mycobacteriaceae (tuberculosis) Special Groups Unusual Bacteria - Obligate intracellular parasites: - Rickettsias (Rocky Mountain spotted fever) - Chlamydias (eye infections, STDs) - Photosynthetic bacteria: - Cyanobacteria - Green and purple sulfur bacteria Archaea Characteristics - More related to Eukarya than Bacteria - Lack peptidoglycan in cell walls - Unique membrane lipids - Adapted to extreme environments (extremophiles) - Include methanogens, halophiles, and thermophiles Ch 6 Historical Context and Basic Properties - Louis Pasteur first postulated in 1884 that rabies was caused by something smaller than bacteria - Dmitri Ivanoski and Beijerinck identified the first virus in tobacco plants in the 1890s - Viruses are the most abundant microbes on Earth and played a key role in evolution - They are obligate intracellular parasites that cannot reproduce outside host cells Fundamental Characteristics - Size ranges from 20 to 450 nanometers in diameter - Lack cellular structure and protein-synthesizing machinery - Basic structure consists of: - Protein shell (capsid) - Nucleic acid core (DNA or RNA, never both) - Some viruses have an envelope - Multiply by taking control of host cell's genetic machinery - Highly specific in their attachment to host cells Viral Structure Capsids - Two main types: 1. Helical: forms cylindrical nucleocapsid 2. Icosahedral: 20-sided structure with 12 evenly spaced corners - Made of identical protein subunits called capsomers - Protects viral nucleic acid and assists in host cell entry Envelopes - Present in many animal viruses - Acquired when virus leaves host cell - Contains spike proteins essential for cell attachment - Viruses without envelopes are called naked viruses Complex Viruses - Some viruses have unique structures - Examples: - Poxviruses: covered by lipoprotein layer - Bacteriophages: have polyhedral head and helical tail Viral Multiplication General Phases 1. Adsorption: virus binds to host cell 2. Penetration: viral genome enters cell 3. Uncoating: nucleic acid release 4. Synthesis: viral component production 5. Assembly: new virus construction 6. Release: through budding or cell lysis Host Cell Effects - Cytopathic effects include: - Cell shape changes - Formation of inclusion bodies - Cell fusion (syncytium) - Some viruses cause persistent infections - Certain viruses can cause cancer (oncoviruses) Bacteriophages - Viruses that infect bacteria - Follow similar multiplication steps as animal viruses - Two main cycles: 1. Lytic cycle: immediate virus production and cell death 2. Lysogenic cycle: viral DNA integrates into host genome Medical Significance - Most common cause of acute infections - Several billion infections annually - Detection methods include: - Cell culture observation - Viral component screening - Antibody detection - Treatment challenges due to side effects of antiviral drugs Other Infectious Particles Prions - Misfolded proteins without nucleic acid - Cause fatal neurodegenerative diseases - Examples: - Scrapie in sheep - Mad cow disease - Creutzfeldt-Jakob Syndrome in humans Other Agents - Satellite viruses: depend on helper viruses - Viroids: naked RNA strands affecting plants - Both lack complete viral structure Ch 8 Basic Concepts of Metabolism - Metabolism encompasses all chemical and physical processes in cells - Two main types of reactions: - Catabolism: Breaking down larger molecules into smaller ones, releasing energy - Anabolism: Building larger molecules from smaller ones, requiring energy input Enzyme Structure and Function - Enzymes are biological catalysts that lower activation energy - Types: - Simple enzymes: Protein only - Conjugated enzymes (holoenzymes): Protein plus nonprotein components - Apoenzyme: Protein portion - Cofactors: Nonprotein portion (metal ions or organic molecules) Enzyme Characteristics - Have specific active sites for substrate binding - Show induced fit when substrates bind - Can be classified as: - Exoenzymes: Function outside cells - Endoenzymes: Function inside cells - Constitutive enzymes: Always present - Regulated enzymes: Production controlled by cellular needs Enzyme Regulation - Direct controls: - Competitive inhibition - Allosteric inhibition - Noncompetitive inhibition - Genetic controls: - Enzyme repression - Enzyme induction Energy and Cellular Metabolism ATP and Energy Transfer - ATP serves as cellular energy currency - Three phosphate groups with high-energy bonds - ATP synthesis occurs through: - Substrate-level phosphorylation - Oxidative phosphorylation - Photophosphorylation Major Metabolic Pathways Aerobic Respiration 1. Glycolysis - Converts glucose to pyruvate - Generates NADH and ATP 2. Krebs Cycle - Processes pyruvate - Produces CO2, NADH, and FADH2 3. Electron Transport Chain - Generates ATP through oxidative phosphorylation - Uses oxygen as final electron acceptor Alternative Metabolic Strategies - Anaerobic respiration: Uses alternative electron acceptors instead of oxygen - Fermentation: Incomplete oxidation without oxygen - Examples: Alcohol production by yeasts, acid production by bacteria Photosynthesis - Primary energy source for life on Earth - Two main stages: 1. Light-dependent reactions - Capture light energy - Split water - Produce ATP and NADPH 2. Light-independent reactions (Calvin Cycle) - Fix CO2 - Produce glucose Metabolic Integration - Pathways are often bidirectional (amphibolic) - Intermediates can be diverted between anabolic and catabolic processes - Key processes include: - Amination - Deamination - Transamination Environmental Factors - Enzyme activity affected by: - Temperature - pH - Osmotic pressure - Changes can lead to enzyme denaturation This comprehensive overview represents the major concepts covered in the text, organized in a logical flow from basic principles through complex metabolic processes. Ch 9 Basic Concepts Genetics is the study of heredity, exploring how biological traits are transmitted from parent to offspring, their expression and variation, and the structure and function of genetic material. The genome represents the total genetic material (DNA) in a cell, primarily existing in chromosomes but also found in mitochondria, chloroplasts, and plasmids. Chromosomes and DNA Structure - Chromosomes are discrete cellular structures containing packaged DNA - Eukaryotic chromosomes: multiple and linear, located in nucleus - Bacterial chromosomes: single circular loop - DNA structure consists of: - Nucleotides containing deoxyribose sugar, phosphate group, and nitrogenous base - Double helix formation with complementary base pairing (A-T, G-C) - Antiparallel arrangement (5' to 3' direction) DNA Replication The process occurs semi-conservatively: 1. Parent DNA molecule uncoils 2. Strands separate to serve as templates 3. New complementary strands synthesized Key enzymes involved: - Helicase: unwinds DNA - Primase: synthesizes RNA primer - DNA polymerase III: adds nucleotides - DNA polymerase I: removes RNA primers - Ligase: links DNA fragments ## Gene Expression ### Transcription - RNA synthesized using DNA template - Three stages: initiation, elongation, termination - RNA types: - Messenger RNA (mRNA): carries genetic code - Transfer RNA (tRNA): translates genetic code - Ribosomal RNA (rRNA): forms ribosomes ### Translation - Process occurs on ribosomes - Five stages: initiation, elongation, termination, protein folding and processing - Uses genetic code where three-base codons specify amino acids - Multiple ribosomes can work simultaneously (polyribosomal complex) ## Gene Regulation ### Operons Two types: 1. Inducible operons (e.g., lac operon) - Turned ON by substrate - Controls catabolic processes 2. Repressible operons (e.g., arginine operon) - Turned OFF by end product - Controls anabolic processes ## Mutations and DNA Changes Types of mutations: - Point mutations - Missense mutations - Nonsense mutations - Frameshift mutations - Silent mutations Repair mechanisms: - DNA polymerase proofreading - Mismatch repair - Light repair - Excision repair ## Genetic Recombination Three main mechanisms in bacteria: 1. Conjugation - Direct cell-to-cell contact - Transfer via fertility plasmid (F factor) 2. Transformation - Uptake of DNA fragments from environment - Recipient cell must be competent 3. Transduction - DNA transfer via bacteriophages - Can be generalized or specialized ## Viral Genetics - Viral genome contains minimal genes needed for reproduction - May be DNA or RNA based - Requires host cell machinery - Replication varies by virus type: - DNA viruses typically replicate in nucleus - RNA viruses typically replicate in cytoplasm Ch 11 ## Overview of Microbial Control Controlling microorganisms is essential for preventing infections and spoilage. Methods target various microorganisms including: - Vegetative bacterial cells and endospores - Fungal hyphae, spores, and yeasts - Protozoan trophozoites and cysts - Worms, viruses, and prions ## Physical Control Methods ### Heat-Based Methods #### Moist Heat - Autoclave: 121°C at 15 psi for 10-40 minutes - Tyndallization: Intermittent sterilization using free-flowing steam - Pasteurization: Flash method (71.6°C for 15 seconds) or UHT (134°C for 2-5 seconds) - Boiling water: 100°C for 30 minutes #### Dry Heat - Hot air ovens: 150-180°C for 2-4 hours - Incineration: Direct flame or infrared methods ### Radiation #### Ionizing Radiation - Gamma rays, X-rays, and cathode rays - Used for sterilizing medical supplies and food products - Deep penetrating power, breaks DNA #### Non-ionizing Radiation - Ultraviolet (UV) radiation - Creates pyrimidine dimers - Limited penetration power - Used for air and surface disinfection ### Filtration - Physical removal of microbes - Used for heat-sensitive liquids and air purification - Common in hospital isolation units and clean rooms ## Chemical Control Methods ### Halogens - Chlorine: Used in water treatment and bleach products - Iodine: Found in antiseptics like Betadine ### Alcohols - Ethyl and isopropyl alcohol - Most effective at 70% concentration - Used for skin antisepsis and surface disinfection ### Phenols and Derivatives - Examples include Lysol and Triclosan - Low to intermediate level disinfectants - Effective against bacteria, fungi, and some viruses ### Aldehydes - Glutaraldehyde (Cidex): 2% solution for instrument sterilization - Formaldehyde: Used as preservative and disinfectant ### Other Chemical Agents - Hydrogen peroxide: Produces toxic hydroxyl radicals - Heavy metals: Silver and mercury compounds - Quaternary ammonium compounds (quats) - Soaps and detergents ## Levels of Resistance ### Highest Resistance - Prions - Bacterial endospores (Bacillus, Clostridium) ### Moderate Resistance - Protozoan cysts - Naked viruses - Mycobacterium - Pseudomonas - Staphylococcus ### Lowest Resistance - Most vegetative bacterial cells - Fungal spores and hyphae - Yeasts - Enveloped viruses - Protozoan trophozoites ## Factors Affecting Microbial Control - Nature of material being treated - Degree of contamination - Exposure time - Agent concentration - Environmental conditions (temperature, pH) - Presence of organic matter or inhibitors ## Selection Criteria for Control Methods - Sterilization requirements - Material compatibility - Cost effectiveness - Safety considerations - Penetration ability - Reusability needs