Bacterial Cell Structure, Physiology, Metabolism, and Genetics (Chapter 1) PDF

Chapter 1  One of the main roles of a diagnostic or clinical microbiologist is to isolate, identify, and analyze the bacteria that cause disease in humans. Knowledge of microbial structure and physiology is extremely important to clinical microbiologists in three areas: 1. Culture of...

Chapter 1  One of the main roles of a diagnostic or clinical microbiologist is to isolate, identify, and analyze the bacteria that cause disease in humans. Knowledge of microbial structure and physiology is extremely important to clinical microbiologists in three areas: 1. Culture of organisms from patient specimens 2. Classification and identification of organisms after they have been isolated 3. Prediction and interpretation of antimicrobial susceptibility patterns Anton van Leeuwenhoek Dutch biologist/lens maker Discovered beasties in a water droplet in his homemade microscope First to study microorganisms “Father of protozoology and bacteriology” ✓Bacteria ✓Parasites ✓Fungi ✓Viruses  Unicellular organisms that lack a nuclear membrane and true nucleus Classified as Prokaryotes, having no mitochondria, ER, or Golgi bodies Absence of these structures differentiates them from Eukaryotes See Table 1-1 and Figure 1-1  Eukaryotic parasites exist as unicellular organisms of microscopic size, whereas others are multicellular. Protozoa are unicellular organisms within the kingdom Protista, which obtain their nutrition through ingestion. Motile or nonmotile  Categorized by their locomotive structures: – Flagella (whiplike) – Pseudopodia (false feet) – Cilia (eyelash) Multicellular parasites (e.g. tapeworm) may be as long as 7 to 10 meters – Flagella (whiplike) – Pseudopodia (false feet) – Cilia (eyelash) – Tapeworm  Heterotrophic eukaryotes that obtain nutrients through absorption Yeasts: group of unicellular fungi that reproduce asexually “True” yeasts do not form hyphae or mycelia  Most are multicellular and can reproduce sexually and asexually Bodies of multicellular fungi are composed of filaments called hyphae, which interweave to form mats called mycelia.  Molds: filamentous forms that can reproduce sexually and asexually Certain fungi can assume both morphologies (yeast and hyphae/mycelial forms) Yeast at incubator or human temperature Filamentous form at room temperature Dimorphic fungi: produce systemic diseases  Smallest infectious particles (virions) Cannot be seen under ordinary light microscopy Neither prokaryotic nor eukaryotic Effects can be seen as inclusions, rounding up of cells, and syncytium (cell fusion of host cells into multinucleated infected forms)  Distinguished from living cells by the following characteristics: Viruses consist of DNA or RNA but not both ✓ dsDNA ✓ ssDNA ✓ dsRNA ✓ ssRNA  They are acellular (not composed of cells), lack cytoplasmic membranes, and are surrounded by a protein coat. They are obligate intracellular parasites that require host cells for replication and metabolism. Growth does not occur in viruses. Viruses are mostly host and/or host cell specific. A virus that infects and possibly destroy bacterial cells is known as a bacteriophage. Taxonomy The orderly classification and grouping of organisms into taxa (categories) Involves three structured, interrelated categories: 1. Classification/Taxonomy 2. Nomenclature 3. Identification Taxonomy It is based on similarities and differences in genotype (genetic makeup of an organism) and phenotype (readily observable physical and functional features of an organism expressed by its genotype.)  Formal levels of bacterial classification ✓ Domain ✓ Kingdom ✓ Division (Phylum in kingdom Animalia) ✓ Class ✓ Order (not useful for bacteria) ✓ Family ✓ Tribe (not useful for bacteria) ✓ Genus ✓ Species ✓ Subspecies Naming of bacterial species into three categories: Family – similar to human “clan” Genus (pl. genera) – human last name Species (epithet) – human first name Strains Example: Staphylococcus aureus Micrococcaceae Penicillin resistant S. aureus Penicillin susceptible S. aureus  Naming assignments for each organism Standard rules: Family name is capitalized and ends in –aceae e.g. Micrococcaceae Genus name is capitalized and followed by species name in lowercase Both should be italicized in print or underlined in script e.g. Staphylococcus aureus By Phenotypic and Genotypic characteristics Species may be subdivided into: Subspecies (subsp.) – phenotypic differences Serovarieties (serovar.) – serologic differences Biovarieties (biovar.) – biochemical test result differences Phage typing: based on susceptibility to specific bacterial phages By Cellular Type Classifying organisms by cell organization Three distinct groups: Prokaryotes Eukaryotes Archaeobacteria Three domains: Bacteria Archaea Eukarya Prokaryotic Cell Structure Cytoplasmic Structures Cell Envelope Structures Surface Polymers Prokaryotic Cell Structure Cytoplasmic Structures Cell Envelope Structures Surface Polymers Prokaryotic Cell Structure Cytoplasmic Structures 1. Circular chromosome 2. Mesosome 3. Ribosomes 4. Cytoplasmic granules 5. Endospores Prokaryotic Cell Structure Cell Envelope Structures 1. Plasma Membrane 2. Cell Wall a) Gram-Positive b) Gram-Negative Prokaryotic Cell Structure Cell Envelope Structures 1. Plasma Membrane 2. Cell Wall a) Gram-Positive b) Gram-Negative c) Acid-Fast Prokaryotic Cell Structure Cell Envelope Structures 1. Plasma Membrane 2. Cell Wall a) Gram-Positive b) Gram-Negative c) Acid-Fast d) No Cell Wall Prokaryotic Cell Structure Surface Polymers 1. Capsule 2. Slime layers 3. Cell Appendages a) Flagella b) Pili c) Fimbriae Eukaryotic Cell Structure 1. Cytoplasmic structures 2. Cell Envelope structures Eukaryotic Cell Structure 1. Cytoplasmic structures a) Nucleus b) Nucleolus c) Nuclear membrane d) ER e) Golgi apparatus f) Ribosomes g) Mitochondria h) Lysosomes i) Peroxisomes j) Chloroplasts Eukaryotic Cell Structure 2. Cell Envelope structures a) Plasma Membrane b) Cell Wall c) Motility Organelles Cilia Flagella Microscopic Shapes Common Stains Used for Microscopic Visualization Gram stain Acid-Fast stains Acridine Orange Calcofluor White Methylene Blue Lactophenol Cotton Blue India Ink Endospore Stain Common Stains Used for Microscopic Visualization Gram stain (VIAS) Common Stains Used for Microscopic Visualization Acid-Fast stains (CAM) Common Stains Used for Microscopic Visualization Acridine Orange Common Stains Used for Microscopic Visualization Calcofluor White Common Stains Used for Microscopic Visualization Methylene Blue Common Stains Used for Microscopic Visualization Lactophenol Cotton Blue Common Stains Used for Microscopic Visualization India Ink Common Stains Used for Microscopic Visualization Endospore Stain Three major nutritional needs for growth: Carbon Nitrogen ATP ▪ Phosphate ▪ Phospholipids ▪ Sulfur ▪ Mineral ions (Na+, K+, Cl-, Ca2+) Nutritional Requirements for Growth Two basic groups of bacteria: I. Autotrophs(Lithotrophs) a. Phototrophs b. Chemolithotrophs II. Heterotrophs Nutritional Requirements for Growth Types of Growth Media: 1. Minimal medium 2. Nutrient media – NB, TSB 3. Enriched media – BAP, CAP 4. Selective media – MAC, CNA 5. Differential media – MAC, BAP 6. Transport medium – Stuart broth, Amies, Cary-Blair Nutrient Broth Trypticase Soy Broth Chocolate Agar MacConkey Agar Colistin-Nalidixic Acid Agar Transport Media Environmental Factors Influencing Growth 1. pH 2. Temperature 3. Gaseous composition of the atmosphere Environmental Factors Influencing Growth 1. pH Neutral pH (7.0-7.5) Environmental Factors Influencing Growth 2. Temperature Psychrophiles – cold (10°- 20°C) Mesophiles – moderate (20°- 40°C) – most common to humans Thermophiles - high (50°- 60°C) Environmental Factors Influencing Growth 3. Gaseous composition of the atmosphere Obligate aerobes Aerotolerant anaerobes Obligate anaerobes Facultative anaerobes Capnophilic Microaerophilic Bacterial Growth Generation Time Time required for one cell to divide into two cells Doubling Time Bacteria replicate by binary fission Bacterial Growth Growth Curve Bacterial Growth Determination of Cell Numbers Direct microscopic count Direct Plate Count Density measurement Metabolism Diagnostic schemes analyze each unknown microorganism for: 1. Utilization of a variety of substrates as a carbon source 2. Production of specific end products from various substrates 3. Production of an acid or alkaline pH in the test medium Fermentation and Respiration Fermentation Anaerobic Obligate and facultative anaerobes Electron acceptor: organic compound Mixture of end products (lactate, butyrate, ethanol and acetoin) Fermentation and Respiration Respiration Aerobic Obligate aerobes and facultative anaerobes Electron acceptor: oxygen Biochemical Pathways from Glucose to Pyruvic Acid 1. Embden-Meyerhof-Parnas (EMP) Glycolytic Pathway 2. Pentose Phosphate Pathway 3. Entner-Doudoroff Pathway Anaerobic Utilization of Pyruvic Acid (Fermentation) 1. Alcoholic fermentation 2. Homolactic fermentation 3. Heterolactic fermentation 4. Propionic acid fermentation 5. Mixed acid fermentation 6. Butanediol fermentation 7. Butyric acid fermentation Aerobic Utilization of Pyruvic Acid (Oxidation) Krebs or TCA cycle Carbohydrate Utilization and Lactose Fermentation Enterobacteriaceae family Two steps: 1. Entry of lactose into bacterial cytoplasm ▪ Enzyme: β-galactosidase permease 2. Break galactoside bond releasing glucose ▪ Enzyme: β-galactosidase Anatomy of DNA and RNA Terminology Genotype Phenotype Protein synthesis: Replication Transcription Translation Codon Genetic Elements and Alterations Bacterial Genome Genetic Elements and Alterations Extrachromosomal Elements Genetic Elements and Alterations Mobile Genetic Elements Genetic Elements and Alterations Mutations Genetic Recombination Mechanisms of Gene Transfer 1. Transformation 2. Transduction 3. Conjugation