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LEC 1 The Science of Microbiology & Cell Structure Organisms: 1. Viruses 2. Prions 3. Prokaryotes 4. Protists VIRUS 1. Virions Newly synthesized virus after a bout of replication 2. Characteristics: nucleic acid, protein coat, envelope (brought about by virions when moving out of host) 3. Replication a. Acc to nucleic acid o DNA: goes to nucleus -> converted to mRNA -> go to ribosomes -> undergo translation -> virions (goes out of host) (+) RNA Same template Goes to ribosome & starts translating itself (-) RNA Not infectious unless converted to (+) by base pairing Needs polymerase to change from (-) to (+) Strand homologue goes to ribosomes and starts translating Retrovirus Not infectious until they become DNA DNA binds to nucleus in host cell and converts to RNA -> goes to ribosome -> protein synthesis Drugs w/c destroy the virus are directed towards destroying the reverse transcriptase b. Replication products (only virus, not host because the host eventually dies) o Early mRNA: enzymes o Late mRNA: structural proteins Assembly into virions o Naked = cell death (bursting) o Enveloped = no cell death (budding off; carrying part of their host cell membrane) Ex. HIV: does not destroy CD4 lymphocyte 3. c. d. e. propensity to aggregate partial resistance to proteolysis induces PrPc to fold and refold into prion form

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Diseases associated w/ Prions: a. Kuru b. Creutzfeldt-Jakob Disease(CJD) c. Gerstmann-Straussler-Scheinker Dse d. Fatal familial insomia e. Scrapie= sheep f. Bovine spongiform encephalopathy Manifestations: sporadic, genetic and infectious

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PROKARYOTES 1. Characteristics a. Small size, absence of nuclear membrane b. DNA: circular, 1 chromosome c. Nucleoid: folded parts of DNA d. Organelles: chromatophores, ribosomes 2. Prokaryotic Diversity: a. gene size b. generation of metabolic energy: o purple bacteria: lightmetabolic energy o blue green(cyano): produce energy in the absence of light o aerobic o anaerobic: electron acceptors, fermentation

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Prokaryotic communities 1. Types o Consortia: different organisms w/in a physiologically interconnected community o Clone: derived from one cell 2. Communication: Quorum Sensing (through release of pheromone) o Regulates transcription of genes for the following activities: Bioluminescence Plasmid conjugal transfer (drug resistance) Production of virulence determinants Survival strategies o Symbiosis: gut bacteria o Parasitism: rickettsiae & chlamydiae Classification: structural, physiologic, biochemical, genetic

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N Delta agent: Hep D; too small to code for a single capsid protein; needs Hep B virus When it combines with Hep B, there will be fulminant hepatitis

PRIONS (look like nucleic acids) 1. Nature: infectious, resistant to nucleases & proteases 2. Normal counterpart: PrPc a. sialoprotein b. high content of alpha-helical 2 structures c. sensitive to proteases d. soluble in detergent e. expressed in the surface of neurons Abnormal isoform: PrPres a. high beta sheet content b. insoluble to detergents

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PROTISTS 1. 2. 3. 4. 5. Algae -

Features: true nucleus, membrane bound organelles, microtubules, microfilaments Gene expression: nucleus -> E.R Reproduction: haploid gametes -> diploid Taxonomy: morphologic properties Members: algae, protozoa, fungi, slime molds

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Produce O2 as product of photosynthesis Chlorophyll in chloroplasts

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Protozoa Fungi Non-photosynthetic Mycelia or yeasts (dimorphic;usually pathogenic) Subdivisions: Chytridiomycota Zygomycota Ascomycota Basidiomycota Deuteromycetes (Imperfect Fungi) Mainly unicellular May form multicellular structures (kelps) *If L forms are actively dividing, this can cause chronic inflammation (not all streptococcus will die & some may exist as protoplasts, actively divide -> inflammation) Capsule and Glycocalyx (for adhesion) o Made of polysaccharide o In bacillus: not polysaccharide (-) charge of surface will prevent phagocytosis; making it virulence factors Flagella: flagellin: H antigen (can cause Ab production) Pili: also antigenic, pilins, adhesions, cause antigenic variation o Minor proteins found at surface of bacteria o Bacteria can rearrange the minor proteins into something that the antibodies cannot recognize anymore -> bacteria is not neutralized Endospores (bacilli & clostridium can form spores)

Unicellular, non-photosynthetic Heterotrophs

Slime Molds Life cycle: has a fruiting body that releases spores -> germinates -> becomes myxamoebae -> plasmodium (consortia of amoeba) -> fruiting body Plasmodia = analogous to mycelium Differentiates into stalked body that can produce individual motile cells (flagellated or ameboid) OPTICAL METHODS 1. Light Microscope A. Bright field Microscope B. Phase Contrast Microscope C. Dark Field Microscope D. Fluorescence Microscope E. Differential Interference Contrast 2. Electron Microscope 3. Confocal Scanning Laser Microscope 4. Scanning Probe Microscope

Function of Capsule: 1. Protection 2. Identification 3. Vaccine preparation (activate cell-mediated immunity) 4. Tissue attachment (similar to glycocalyx if capsule becomes very complex) 5. Antibiotic barrier Capsulated organisms: Streptococci Meningococcus Haemophilus influenza Klebsiella pneumonia Some coliforms Yersinia Bacillus **Capsulated organisms tend to be more pathogenic Note: it is possible for bacteria to have more than 1 nucleoid (when it is actively dividing) Streptococci Not true cocci Has thylakoids (mitochondria) w/c can produce ATP in cell membrane Carboxysome: inclusion bodies with carbon **Polysaccharide found in gram (-) as part of lipopolysaccharide; also found in gram +! Exotoxin Bacteria has protein secretion channels (type I-IV) Type II= gram negative bacteria( elastase, phospholipase C, exotoxin A in P. aeruginosa) TypeV= IgA protease of N. gonorrheae, cytotoxin of Helibacter pylori. Type I= alpha hemolysin of E. coli, adenylyl cyclase of Bordetella pertussis

EUKARYOTIC CELL STRUCTURE Nucleus Cytoplasmic structures: E.R, mitochondria, chloroplasts, lysosomes, peroxisome, cytoskeleton *mitochondria & chloroplasts = plastids (not in prokaryotes) *cytoskeleton = microfilaments, microtubules, intermediate filaments (not in prokaryotes) Surface layers: cytoplasmic membrane & cell wall (chitin, cellulose) Motility organelles: flagella (directed movement), cilia (microtubules), pili (move through twitching) PROKARYOTIC CELL STRUCTURE Nucleoid: chromosome & plasmids (extrachromosomal DNA) Cytoplasmic structures Cell envelope (well developed, compared to Eukaryotes, w/o plastids): 1. Cell membrane 2. Cell wall (protoplast, spheroplast, L forms cause chronic infection) - peptidoglycan (very thick in gram + very thin in gram -) Protoplast: gram + bacteria w/o peptidoglycan layer *may have been destroyed by penicillin Spheroplast: gram -, w/ remnant of outer wall w/o peptidoglycan

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Staining Gram Stain Acid Fast Negative Staining Flagella Stain=tannic acid, basic fuchsin Capsule Stain=negative; Welch method Staining of Nucleoids=Feulgen stain Spore Stain=Malachite green; carbolfuchsin Morphologic Changes during Growth 1. Cell division: binary fission 2. Cell groupings: cocci may form chains, pairs, bundles or flat plates REMEMBER! Prokaryotic cell is SIMPLER than eukaryotic but its CELL ENVELOPE is more complex.

*Teichoic acid: found in cytoplasmic cell membrane & capsule (gram +) *Gram (-) bacteria: has an outer membrane that is asymmetrical - outer leaflet has the endotoxin *Lipopolysaccharide: the bacteria needs to be destroyed to release this - Lipid A - Core antigen - O antigen Cell Wall -

Diaminopimelic acid=unique to bacterial cell wall AFB= peptidoglycan and mycolic acid PCN, lysozymes, autolysins destroy cell wall Mycoplasma has no cell wall

Endospore Formation Bacillus and Clostridium Sporulation=depletion of carbon, nitrogen or phosphorous Germination: 1. Activation=heat, abrasion, acid 2. Initiation=water, release of calcium dipicolinate, degradation of enzymes 3. outgrowth ENDOSPORE Core=chromosome, protein synthesizing apparatus, energy generating system based on glycolysis; calcium dipicolinate Spore wall=innermost; peptidoglycan Cortex=thickest; unusual type of petidoglycan Coat=keratin like protein Exosporium=lipoprotein Spore forming Pathogens Clostridium botulinum Clostridium tetani Clostridium perfringens Bacillus anthracis Coxiella burnetii