1. Cell Structure and Taxonomy Hani Masaadeh, MD, Ph.D

3. Structure and Taxonomy Compound light microscope role. Compound light microscope role. Electron Microscope role. Electron Microscope role. Cell. (The fundamental unit of any living organism). Cell. (The fundamental unit of any living organism). Metabolism. Metabolism. DNA. DNA. Species. Species. Procaryotes and Eucaryotes. Procaryotes and Eucaryotes. Viruses, viroides (Kuru disease) and virions (Creutzfeldt–Jakob disease). Viruses, viroides (Kuru disease) and virions (Creutzfeldt–Jakob disease). Selective toxicity. Selective toxicity. Cytology. Cytology.

5. All living cells can be classified into two groups: Prokaryotes and Eukaryotes. All living cells can be classified into two groups: Prokaryotes and Eukaryotes. Prokaryote comes from the Greek words for prenucleus. Prokaryote comes from the Greek words for prenucleus. Eukaryote comes from the Greek words for true nucleus. Eukaryote comes from the Greek words for true nucleus. Plants and animals are entirely composed of eukaryotic cells. Plants and animals are entirely composed of eukaryotic cells. In microbial world, bacteria and archaea are prokaryotes. In microbial world, bacteria and archaea are prokaryotes. Other cellular microbes – fungi (yeasts and molds), protozoa, and algae ( Sea weeds) are eukaryotes. Other cellular microbes – fungi (yeasts and molds), protozoa, and algae ( Sea weeds) are eukaryotes. Viruses are noncellular elements. Viruses are noncellular elements. Types of Living Cells

6. Eucaryotes Cell structure Cell membrane. Both eucaryotic and procaryotic cells possess a cell membrane. Cell membranes have selective permeability, allowing only certain substances to pass through them. Cell membrane. Both eucaryotic and procaryotic cells possess a cell membrane. Cell membranes have selective permeability, allowing only certain substances to pass through them. proteins and phospholipids. proteins and phospholipids. True nucleus. True nucleus. Motile eucaryotic cells possess either cilia or flagella. Motile eucaryotic cells possess either cilia or flagella.

8. Cell Structure Cytoplasm. Cytoplasm. Endoplasmic reticulum. Endoplasmic reticulum. Rough. Rough. Smooth. Smooth. Ribosomes. Ribosomes. Golgi apparatus. Golgi apparatus. Lysosomes and Peroxisomes. Lysosomes and Peroxisomes. Mitochondria. Mitochondria. Plastids. Plastids. Cytoskeleton. Cytoskeleton. Cell wall. Cell wall. Flagella and Cilia. Flagella and Cilia.

9. Nucleus Command center. Command center. Nucleoplasm. Nucleoplasm. Chromosome. Chromosome. Nuclear membrane. Nuclear membrane. Genes. Genes. RNA. RNA. Genotype. Genotype. Nucleolus. Nucleolus.

12. 1 µm wide and 2 to 3 µm long. 1 µm wide and 2 to 3 µm long. Basic shapes: 1. Spherical coccus2. rod-shaped bacillus3. Spiral : have one or more twists, called vibrios when they look like curved rods, and spirilla when they look like a corckscew, spirochetes if helical and flexible. Basic shapes: 1. Spherical coccus2. rod-shaped bacillus3. Spiral : have one or more twists, called vibrios when they look like curved rods, and spirilla when they look like a corckscew, spirochetes if helical and flexible. Figures 4.1a, 4.2a, 4.2d, 4.4b, 4.4c The Prokaryotic Cell: Size, Shape

13. Figure 4.5 Unusual shapes Unusual shapes Star-shaped (rectangular) Stella Star-shaped (rectangular) Stella Square Haloarcula Square Haloarcula Most bacteria are monomorphic (maintain a single shape) Most bacteria are monomorphic (maintain a single shape) A few are pleomorphic (have many shapes, not just one) A few are pleomorphic (have many shapes, not just one) The Prokaryotic Cell: Size, Shape

14. Cocci and bacilli Cocci and bacilli Pairs: Diplococci, diplobacilli Pairs: Diplococci, diplobacilli Chains: Streptococci, streptobacilli Chains: Streptococci, streptobacilli Tetrads: division in 2 planes and remain in groups of four. Tetrads: division in 2 planes and remain in groups of four. Sarcinae: division in 3 planes and remain attached in cubelike groups of eight. Sarcinae: division in 3 planes and remain attached in cubelike groups of eight. Clusters: division in multiple planes forming clusters called Staphylococci Clusters: division in multiple planes forming clusters called Staphylococci Figures 4.1a, 4.1d, 4.2c The Prokaryotic Cell: Arrangements

19. Plasma Membrane Selective permeability allows passage of some molecules. Selective permeability allows passage of some molecules. Permeability depends on: Permeability depends on: Size: large molecules (Proteins) can not pass while small molecules (H 2 0, O 2, C0 2, simple sugars) pass easily. Size: large molecules (Proteins) can not pass while small molecules (H 2 0, O 2, C0 2, simple sugars) pass easily. Solubility: Lipid soluble molecules (0 2, CO 2, nonpolar organic molecules) pass easily. Solubility: Lipid soluble molecules (0 2, CO 2, nonpolar organic molecules) pass easily. Presence of transporter proteins. Presence of transporter proteins. Enzymes for ATP production Enzymes for ATP production Photosynthetic pigments on foldings called chromatophores or thylakoids Photosynthetic pigments on foldings called chromatophores or thylakoids Damage to the membrane by alcohols, quaternary ammonium (detergents), and polymyxin antibiotics causes leakage of cell contents Damage to the membrane by alcohols, quaternary ammonium (detergents), and polymyxin antibiotics causes leakage of cell contents

20. Cytoplasm: Composition and Functions Cytoplasm is the substance of the cell inside the plasma membrane. Cytoplasm is the substance of the cell inside the plasma membrane. 80% water and contains proteins (enzymes), carbohydrates, lipids, and inorganic ions. 80% water and contains proteins (enzymes), carbohydrates, lipids, and inorganic ions. It is thick, aqueous, semitransparent, and elastic. It is thick, aqueous, semitransparent, and elastic. Major structures: Nucleoid, ribosomes, inclusion bodies, protein filaments Major structures: Nucleoid, ribosomes, inclusion bodies, protein filaments Nucleoid, the nuclear area, contains a single long, continuous, circular thread of double stranded DNA called the bacteria chromosome which carries the genetic information rquired for the cell’s sturctures and functions. Nucleoid, the nuclear area, contains a single long, continuous, circular thread of double stranded DNA called the bacteria chromosome which carries the genetic information rquired for the cell’s sturctures and functions. Moreover, bacteria often contain an extrachromosomal, small circular, double stranded DNA molecules called Plasmids. Moreover, bacteria often contain an extrachromosomal, small circular, double stranded DNA molecules called Plasmids. Plasmids usually contain 5 to 100 genes responsible for antibiotic resistance, production of toxins, and synthesis of enzymes. Plasmids usually contain 5 to 100 genes responsible for antibiotic resistance, production of toxins, and synthesis of enzymes.

21. Figure 4.19 Cytoplasm: Ribosomes Ribosomes Ribosomes The sites of protein synthesis. The sites of protein synthesis. Composed of two subunits, each consists of protein and ribosomal RNA. Composed of two subunits, each consists of protein and ribosomal RNA. Prokaryotic ribosomes differ from eukaryotic ribosomes Prokaryotic ribosomes differ from eukaryotic ribosomes in number of proteins and rRNA molecules. in number of proteins and rRNA molecules. Smaller and less dense Smaller and less dense 70S ribosomes in prokaryotes and 80S ribosomes in eukaryotes. 70S ribosomes in prokaryotes and 80S ribosomes in eukaryotes. Several antibiotics work by inhibiting protein synthesis on prokaryotic ribosomes Several antibiotics work by inhibiting protein synthesis on prokaryotic ribosomes

22. Metachromatic granules (volutin) Metachromatic granules (volutin) Polysaccharide granules Polysaccharide granules Lipid inclusions Lipid inclusions Sulfur granules Sulfur granules Carboxysomes Carboxysomes Phosphate reserves Phosphate reserves Energy reserves Energy reserves Ribulose 1,5-diphosphate carboxylase for CO 2 fixation Ribulose 1,5-diphosphate carboxylase for CO 2 fixation Cytoplasm: Inclusions (Reserve deposites)

24. The Cell Wall A complex, semirigid structure responsible for the shape of the cell, surrounding the plasma membrane. A complex, semirigid structure responsible for the shape of the cell, surrounding the plasma membrane. CW prevents osmotic lysis of bacteria. CW prevents osmotic lysis of bacteria. CW maintain the shape of a bacterium and anchors the flagella. CW maintain the shape of a bacterium and anchors the flagella. Clinically, CW increases the ability of some bacteria to cause disease and it is the site of action of some antibiotics. Clinically, CW increases the ability of some bacteria to cause disease and it is the site of action of some antibiotics. CW is used to differentiate major types of bacteria. CW is used to differentiate major types of bacteria. Made of peptidoglycan (in bacteria) Made of peptidoglycan (in bacteria) Figure 4.6a–b

27. Figure 4.13b Gram-Positive Cell Walls Teichoic acids Teichoic acids Lipoteichoic acid links to plasma membrane Lipoteichoic acid links to plasma membrane Wall teichoic acid links to peptidoglycan Wall teichoic acid links to peptidoglycan Negatively charged, may regulate movement of cations. Negatively charged, may regulate movement of cations. Polysaccharides provide antigenic variation. Polysaccharides provide antigenic variation.

28. Figure 4.13b–c CW of Gram +ve and Gram –ve bacteria

29. Gram-Negative Outer Membrane Figure 4.13c

30. Gram-Negative Outer Membrane Lipopolysaccharides (LPS), lipoproteins, phospholipids Lipopolysaccharides (LPS), lipoproteins, phospholipids Forms the periplasm between the outer membrane and the plasma membrane. Forms the periplasm between the outer membrane and the plasma membrane. Protection from phagocytes and complement. Protection from phagocytes and complement. Porins (proteins) form channels through membrane permit the passage of molecules (nutrients) Porins (proteins) form channels through membrane permit the passage of molecules (nutrients) O polysaccharide antigen, e.g., E. coli O157:H7 O polysaccharide antigen, e.g., E. coli O157:H7 Lipid A is an endotoxin and is toxic in the host’s bloodstream or gastrointestinal tract. Lipid A is an endotoxin and is toxic in the host’s bloodstream or gastrointestinal tract.

31. Gram +ve CW Gram –ve CW Gram +ve CW Gram –ve CW Thick peptidoglycan composed of many layers. Thick peptidoglycan composed of many layers. Contains teichoic acids Contains teichoic acids In acid-fast cells, contains mycolic acid In acid-fast cells, contains mycolic acid Thin layer of peptidoglycan Thin layer of peptidoglycan No teichoic acids No teichoic acids Surrounded by outer membrane Surrounded by outer membrane Peptidoglycan layer is connected to the outer membrane via lipoproteins. Peptidoglycan layer is connected to the outer membrane via lipoproteins. A periplasm (gel like fluid) is found between the outer membrane and plasma membrane. A periplasm (gel like fluid) is found between the outer membrane and plasma membrane. CW of Gram +ve and Gram –ve bacteria

32. Atypical Cell Walls Mycoplasmas Mycoplasmas Lack cell walls Lack cell walls Sterols in plasma membrane to protect them from lysis. Sterols in plasma membrane to protect them from lysis. Archaea Archaea May lack walls, or unusual walls composed of polysaccharides and proteins but not peptidoglycan. May lack walls, or unusual walls composed of polysaccharides and proteins but not peptidoglycan. Archaea can not be Gram stained. Archaea can not be Gram stained.

33. External Structures: Glycocalyx Located outside cell wall Located outside cell wall Viscous (sticky), consists of gelatinous polysaccharide, polypeptide, or both. Viscous (sticky), consists of gelatinous polysaccharide, polypeptide, or both. It is made inside the cell and secreted to the cell surface. It is made inside the cell and secreted to the cell surface. If it is organized and firmly attached to the cell wall, it is called Capsule. If it is organized and firmly attached to the cell wall, it is called Capsule. Capsules increase bacterial virulence by preventing phagocytosis Capsules increase bacterial virulence by preventing phagocytosis Extracellular polysaccharide (EPS) allows cell to attach to various surfaces Extracellular polysaccharide (EPS) allows cell to attach to various surfaces Some bacteria use its capsule as a source of nutrition to produce energy. Some bacteria use its capsule as a source of nutrition to produce energy. A glycocalyx can protect a cell against dehydration. A glycocalyx can protect a cell against dehydration. Figure 4.6a–b

35. External Structures: Flagella Located outside cell wall Located outside cell wall Long filamentous appendages that propel bacteria. Long filamentous appendages that propel bacteria. It has 3 basic parts: It has 3 basic parts: 1. The filament: made of chains of flagellin 2. The hook: consisting of different protein 3. The basal body: Anchors the flagellum to the cell wall and plasma membrane. Flagellum moves the cell by rotating from the basal body. Flagellum moves the cell by rotating from the basal body. Figure 4.8a

36. Axial Filaments and Fimbriae Endoflagella Endoflagella In spirochetes In spirochetes Anchored at one end of a cell Anchored at one end of a cell Rotation causes cell to move Rotation causes cell to move Fimbriae allow attachment Fimbriae allow attachment Pili are used to transfer DNA Pili are used to transfer DNA from one cell to another from one cell to another

40. Cytoplasm: Endospores Resting cells formed when essential nutrients are depleted. Resting cells formed when essential nutrients are depleted. Bacillus (anthrax and food poisoning), Clostridium (gangarene, tetanus, botulism, and food poisoning) Bacillus (anthrax and food poisoning), Clostridium (gangarene, tetanus, botulism, and food poisoning) Highly durable dehydrated cells with thick walls and additional layers, formed internal to the bacterial cell membrane. Highly durable dehydrated cells with thick walls and additional layers, formed internal to the bacterial cell membrane. Resistant to desiccation, heat, Resistant to desiccation, heat, chemicals, radiation. chemicals, radiation. Sporulation: Endospore formation Sporulation: Endospore formation Germination: Return to vegetative Germination: Return to vegetative state state Figure 4.21b