1. Lecture BIOD 4: Prokaryotic Cell Structure &Function Morphology of Bacteria: - Prokaryotic cells are generally much smaller than Eukaryotic cells. - Although similar in morphology, bacteria remarkably vary in size, shape & arrangement. - Most bacteria come in one of three basic shapes: coccus, rod or bacillus, and spiral. Coccus: - The cocci are spherical or oval bacteria having one of several distinct arrangements: - Diplococcus: pair of cocci - Streptococcus: chain of cocci - Tetrad: square of 4 cocci - Sarcina: cube of 8 cocci - Staphylococcus: cocci in irregular, often grape- like clusters

2. Bacillus: - Bacilli are rod-shaped bacteria. They divide in one plane producing one of the following: Bacillus: a single bacillus Coccobacillus: oval and similar to a coccus Streptobacillus: a chain of bacilli Spiral: - A helical or corkscrew-shaped bacterium. Spirals come in 1 of 3 forms: Vibrio: curved or comma-shaped rod Spirillum: thick, rigid spiral Spirochete: thin, flexible spiral

3. Pleomorphic: - Bacteria that are variable in shape & lack a single characteristic form. Prokaryotic Cell Organization: - Bacteria are prokaryotic, single-celled, microscopic microorganisms; - Generally much smaller than eukaryotic cells; - Very complex despite their small size. - Structurally, a typical bacterium usually consists of: a cytoplasmic membrane surrounded by a peptidoglycan cell wall & maybe an outer membrane; a fluid cytoplasm containing a nuclear region (nucleoid) and numerous ribosomes; and often various external structures like a glycocalyx, flagella, and pili.

4. Nucleoid: - The most striking difference between procaryotes and eucaryotes is the packaging of the genetic material. - Eucaryotes have 2 or more chromosomes contained within a membrane-delimited organelle, the nucleus. - Procaryotes chromosome, single circle dsDNA, is located in irregular shaped region called nucleoid (also called nuclear body, chromatin body, nuclear region). - DNA (deoxyribonucleic acid): the nucleic acid that constitutes the genetic material of all cellular organisms. Polymer of nucleotides connected via a phosphate- deoxyribose sugar backbone.

5. - Many bacteria contain Plamids in addition to their chromosome. - Plasmids are circular dsDNA molecules, replicate independently of chromosome and may integrated in it; not required for cell growth and reproduction. - Plasmids carry extra genes that render bacteria drug-resistant, give them new metabolic activities, make them pathogenic!!!!, etc. Cytoplasmic Matrix, Ribosome and Inclusion Bodies: - Cytoplasmic Matrix is the substance lying between the plasma membrane and the nucleoid; - It is a relatively featureless fluid; about 70% water; packed with Ribosomes and inclusion bodies. - Inclusion Bodies are granules of organic or inorganic material that are stockpiled for future use (starch, fat, sulphur, gas vacuoles, etc.). - Ribosomes: structures made of protein and RNA; responsible for synthesis of cellular proteins. Mesosomes: - Invaginations of plasma membrane in the shape of vesicles, tubules and lamellae. - Play a role in cell wall formation during division; - Involved in chromosome replication and distribution to daughter cells.

6. Plasma Membrane: - Membranes are absolute requirement for all living organisms; interact in a selective fashion with environment. - Plasma Membrane is made of a phospholipid bilayer with integral and peripheral proteins embedded. - Imbedded in the membrane are proteins. Some stick completely through the membrane, while some are planted so that they only protrude through one surface. - These proteins are held in the membrane by virtue of hydrophobic and hydrophilic regions on the protein. Functions of PM: - Separates the cell from its environment. - Serves as a selective permeable barrier. - Transport systems used for nutrient uptake,waste excretion, protein secretion.

7. - PM is the location of a variety of metabolic processes such as respiration, photosynthesis, lipid synthesis and cell wall constituents synthesis. - Contains special receptor molecules that may help bacteria detect and respond to environmental changes. Cell Wall: - One of the most important parts of the prokaryotic cell. - Give shape, protect from osmotic lysis, protect from toxic substances. - Cell Wall is made of peptidoglycan; polymer of peptides (typically 4 amino acids long, cross-linked to other chains) and glycans (made of alternating amino sugars). - Sugars found in peptidoglycan: - N-acetylglucosamine (NAG). - N-acetylmuramic acid (NAM).

8. Gram Negative vs Gram Positive: - Christian Gram developed the Gram stain (1884); bacteria divided in 2 major groups: Gram(+) & Gram(-).

9. Gram Positive: - Thick homogeneous peptidoglycan layer. - Large amount of teichoic acids; not in Gram(-). - Inner plasma membrane.

10. Gram Negative: - More complex than Gram positive. - Thick outer membrane; contains lipids, lipopolysaccharides and lipoproteins. - Thin peptidoglycan layer. - Periplasmic space. - Plasma membrane.

11. Mechanism of Gram Staining: - Difference between Gram(+) & Gram(-) is due to the physical nature of their cell walls. - Gram(+) becomes Gram(-) when cell wall removed. - Peptidoglycan acts as a permeability barrier preventing loss of crystal violet. - Ethanol is thought to shrink pores of the thick peptidoglycan  dye-iodine complex retained  bacteria remain purple. - Gram(-) have very thin peptidoglycan. - Ethanol treatment extract enough lipid from wall and make more porous  purple crystal violet- iodine complex is more readily removed. - When counterstained with safranin  Gram(-) bacteria turn pink.

12. Flagella and Motility: - Need to be stained to be viewed under bright field microscopy. - The ultrastructure consists of flagellin, hook and basal body. - Flagellin: hollow rigid cylinder constructed of a single protein. - Hook: short curved segment that links flagellin to the basal body. - Basal body: Series of rings that drive the flagella.

13. Flagellar arrangements: 1. Monotrichous: a single flagellum, usually at one pole. 2. Amphitrichous: a single flagellum at both ends of the organism. 3. Lophotrichous: two or more flagella at one or both poles. 4. Peritrichous: flagella over the entire surface. Flagellar synthesis: - Complex process involving at least 20 to 30 genes, and 10 or more genes that encode proteins for hook and basal body. Flagellar movement: - Bacterium moves when the filament (in the shape of rigid helix) rotates. - Flagella act like propellers on a boat. - The E. coli motor rotates 270 rpm. - Vibrio alginolyticus rotates 1100rpm.

15. Capsules, Slime Layers & S Layers: - Layers of material outside the cell wall, vary in thickness and rigidity. - Protects bacteria from phagocytosis, viral infections, pH fluctuation, osmotic stress,... - Help bacteria to attach to surfaces of solid objects in aquatic environment and tissue surfaces in plants and animals. Pili & Fimbriae: - Tubular protein (short hair-like) structures extending from a bacterial surface used for attachment to environmental surfaces or cells. - Sex pili attach to surface of other bacteria during sexual mating.

16. - Chemotaxis is a response to a chemical gradient of attractant or a repellent molecules in the bacterium's environment. - Bacteria are attracted nutrients such as sugars and amino acids. - Taxis is a motile response to an environmental stimulus. - Chemotaxis is regulated by chemoreceptors located in the cytoplasmic membrane or periplasm of the bacterium bind chemical attractants or repellents. Chemotaxis: Bacterial Endospore: - An endospore is not a reproductive structure but rather a resistant, dormant survival form of the organism, enable bacteria to resist harsh environment. - Endospores are quite resistant to high temperatures (including boiling), most disinfectants, low energy radiation, drying, etc. - The endospore can survive possibly thousands of years until a variety of environmental stimuli trigger germination, allowing outgrowth of a single vegetative bacterium. - Spore formation follows a very complex multistage process.

18. - Under conditions of starvation, especially the lack of carbon and nitrogen sources, a single endospores form within some of the bacteria. The process is called sporulation. -Transformation of dormant spores into active vegetative cells is done in 3 stages: (1) Activation. (2)Germination. (3) Outgrowth.