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Microbiology: Chapter 4

Cellular Anatomy
Shapes / Arrangements: Coccus (cocci)
Usually round, can be oval, elongated or flatened on one side.

- Diplococci: remain in pairs (2) after dividing
- Streptococi: remain attached in chainlike patterns
- Tetrad: remain in groups of 4 after dividing
- Sarcinae: remain attached in cubelike groups of eight
- Staphylococci: Form grapelike clusters
Shapes / Arrangements: Bacillus (bacilli)
Most appear as single rods.

- Diplobacilli: appear in pairs after division
- Streptobacilli: occur in chains
- Coccobaccilli: look somewhat like cocci, more marshmallow shaped
Shapes / Arrangements: Spirals
Spiral bacteria have one or more twists, never straight.

- Vibrio: Curved rods / bent bacillus
- Spirillum: helical / corkscrew shape, stiff / rigid, move via external flagela
- Spirochetes: helical / spiral , flexible, move via endoflagellum / axial filaments
Shape / Arrangements: Other
- Star-shaped / stella
- Rectangular, flat (halophilic archaea)
- Triangular
Shape / Arrangements
Bacteria shape is determined by heredity. Cell wall gives bacterium its shape.

1. Monomorphic: Most bacteria are monomorphic. Maintain a single shape.

2. Pleomorphic: (genetically) they can have many shapes / change shape. (No cell wall - Mycoplasmas (type of bacteria) or cell wall was destroyed)
Bacterial Cell Parts (4.6): Cell Envelope
Cell envelope = membrane + cell wall + (some) glycocallyx
Bacterial cell parts: Cell envelope (Membrane)
Membrane: 4.14

- Biphospholipid layer that is self-sealing / self-assembling, fluid mosaic model, semi-permeable, selective.
- Peripheral proteins lie at inner or outer surface. Integral proteins inside membrane (transmembrane & channels with pores).
- Some membrane proteins are for transport (eg. receptor) and some are enzymes involved in chemical reactions occurring just inside or outside membrane.
- Glycoproteins (proteins attached to carbohydrates) & glycolipids (lipids attached to carbohydrates).

- Serve as selective barrier (selective permeability). Allow H2O, O2, CO2 & some simple sugars in / out. Ions penetrate membrane slowly. Large molecules (proteins) cannot pass through PM.
- NB to breakdown of nutrients and production of energy - pm contains enzymes that catalyze reactions for breakdown of nutrients & ATP production.
- Site of cell wall formation.
- Point of attachment for bacterial genome / chromosome & site of genome replication
Bacterial cell parts: Cell envelope (Cell wall)
Cell Wall: (4.13, T4.1)

Structure & Functions:
- Cell envelope is semirigid structure responsible for shape of cell, which provides means of identification.
- Surrounds underlying plasma membrane and protects it and interior of cell from adverse changes in environment.
- Almost all proKs have cell walls.
- Major function is to prevent bacterial cells from rupturing when water pressure inside cell is greater than outside the cell (osmotic lysis - hypotonic environment eg. distilled water). Most bacteria like 1% or less salt solution. Exceptions: Staph aureus & Staph epidermides (like 5 - 7% salt)
- Point of anchorage for external structures such as flagella.
- Contributes to ability of some species to cause disease and is site of some antibiotics.
- Chemical composition of cell walls used to differentiate major types of bacteria.
- EuKs with cell walls: plants, algae, fungi. Chemically different from proKs, simpler in structure and less rigid.
Bacterial cell parts: Cell envelope (Gram-positive cell walls) t4.1
- Many layers of peptidoglycan forming thick rigid structure
- Peptidoglycan: Two sugars make up the carbohydrate backbone: N-acetylglucosamine (NAG) & N-acetylmuramic acid (NAM). Also have amino acids intertwined bound with peptide bonds.
- Contain teichoic acids that reinforces the thick wall
- No extra outer membrane
- Susceptible to (cell wall destroyers) eg. penicillin, sulfonamide & lysozyme (natural antibiotic found in tears, sweat, syliva, mucus). (Penicillin, lysozyme etc. destroy peptidoglycan cell walls)
Bacterial cell parts: Cell envelope (Gram-negative cell walls) t4.1
- One or few layers of peptidoglycan (thin) which makes them more susceptible to mechanical breakage
- Extra outer membrane
- No teichoic acids
- Lipid A: (in outer membrane) Released when gram-negative bacteria die (endotoxin). Causes adverse symptoms such as fever, vommiting, diahreah, dilation of bvs, shock, blood clotting. Patient might get sicker before getting better.
- Polysaccharide O: (in outer membrane) Functions as an antigen (Ag)
- Resistant to penicillin, sulfonamide & lysozyme (natural antibiotic found in tears, sweat, saliva, mucus)
Bacterial cell parts: Atypical cell walls
- Mycoplasmas (genus) (eg. M. pneumoniae) have no cell wall and are ploemorphic. Smallest known bacteria that can grow and reproduce outside living host cells. Their plasma membranes have sterols (lipids) that help protect them from lysis.

- Mycobacterium (genus): (eg. M. tuberculosis & M. leprae) (identified through acid-fast staining). Have an acid-fast wall: hydrophobic waxy lipid (mycolic acid) in their cell wall. If the mycolic acid layer is removed from the cell wall they appear gram+ (attraction between cells and simple stains)
Bacterial cell parts: Glycocalyx
- Glycocalyx (sugar coat).
- ProKs make glycocalyx inside cell and secreted on surface of cell.
- Bacterial glycocalyx is viscous (sticky), gelatinous polymer that is external to the cell wall.
- Can protect cell against dehydration, and its viscocity may inhibit the movement of nutrients out of the cell.
- 3 types of glycocalyx: Capsule, Slime layer, EPS (extracellular polymeric substance)
Bacterial cell parts: Glycocalyx: Capsule
If glycocalyx is organized and firmly attached to cell wall (tight-fitting) = capsule
- polypeptides & polysaccharides
- delicate structure
- only seen with negative staining (look like halo around bacteria)
- Virulence factor: (bacterial virulence: degree to which a pathogen causes diseas) Something they have (eg. capsule) that other bacteria don't have that allow them to survive. Can stick / adheare and cause disease. Also, provides resistance to phagocytocis. (only encapuslated B. anthracis causes anthrax; only encapsulated Streptococcus pneumoniae)
- prevents food and water loss
- In some cases if there aren't any nutrients available, they can "eat" their glycocalyx
Bacterial cell parts: Glycocalyx: Slime layer
If glycocalyx is unorganized and only loosely attached to the cell wall = slime layer.
In some cases, slime layer makes phagocytosis even harder.
Bacterial cell parts: Glycocalyx: EPS (extracellular polymeric substance)
(sugar only - not good antigens)
- Type of glycocalyx that helps cells in a biofilm attach to their taget environment and to each other.
(Biofilm: microbial community that usually forms a slimy layer on a surface eg. rocks, plant roots, human teeth, medical implants, water pipes & other bacteria)
External appendages: Flagella
(4.7, 4.8, 4.9)
- Long filamentous appendages that propel bacteria. Allow for motility: ability of org to move by itself
- Some proKs have flagella
- Atrichous: no flagella
- Monotrichous: one flagella
- Amphitrochous: one flagella at each end
- Lophotrichous: tuft of flagella at one end
- Peritrichous: flagella around perimeter / distributed over entire cel) Moves via swarming and "runs & tumbles"
- Taxis: movement of bacterium toward or away from particular stimulus. Phototaxis: move towards light. Chemotaxis: attracted to / repelled by chemical (receptors in cell wall and passes info to flagella)
External appendages: Endoflagella / Axial filament
- Spirochetes move via endoflagella / axial filaments
- eg. [Treponema pallidum (syphilis), Borrelia burgdorferi (lyme diseas)] often hidden so use indirect ELISA to test for it
- bundles of fibrils at end of cell and spiral around it
- spiral movement / corkscrew
External appendages: Pili
- Usually longer than fimbriae
- One pilus or two pili per cell
- Sex pilus: allow for transfer of DNA/genetic material from one cell to another (conjugation). Can be same or different species.
- Occur when bacteria are in threatened environment
- Often involves exchange of specialized genes (located in plasmids) that add a new function to the recipient cell (eg. antibiotic resistance or ability to digest its medium more efficiently)
External appendages: Fimbriae
- Can be at ends of cell or evenly distributed over entire cell surface.
- Vary from few to several hundred per cell (usually more)

Virulence factor:
- Have tendency to adhere to each other and to surfaces. Involved in forming biofilms on surfaces like liquids, glass & rocks.

- Can also help bacteria to stick to epithelial surfaces in body (eg. fimbriae on N. gonorrrhoeae (gonorrhea) help microbe to colonize mucous membranes) (eg. N. meningitis) (eg. fimbriae of E. coli O157 enable bacteria to stick to lining of small intestine causing diarrhea)
Cell structures: 1. Nucleus
No nuclear membrane or nucleoli (nucleoid is region of genetic material)

True nucleus, consisting of nuclear membrane / nuclear envelope with pores (semi-permeable) and nucleoli (nucleolus)
Cell structures: 2. Genome
- Circular double-stranded DNA.
- May have plasmids containing "resistant" genes that was picked up along the way.
- Typically no histones (archaea have histones)

- Multiple linear chromosomes
- Diploid (2N) number of chromosomes (46 in humans)
- Histones / histone proteins attached to DNA
Cell structures: 3. Cell Wall
Prokaryotic: (see #8)
- Usually present; chemically complex (typically include peptidoglycan)

- When present, chemically simple
- Simpler in structure & less rigid (than ProKs)
- Algae & plants = cell wall consists of cellulose
- Fungi = cell wall made of chitin (polymer of NAG units)
- Protists = pellicle: not a typical cell wall but a flexible outer protein covering
Cell structures: 4. Ribosomes
- Functions as sites of protein synthesis
- Composed of two subunits (small + large)
- Each subunit made of protein + type of rRNA (ribosomal RNA)
- S = Svedberg / sedimentation rate (how quickly they settle to the bottom)

- Have 70S ribosomes
- smaller & less dense than ribosomes of EuKs
- Small subunit (30S) + Larger subunit (50s)

- Have 80S ribosomes found on surface of RER (rough endoplasmic reticulum) and nuclear membrane (membrane-bound ribosomes) & free in cytoplasm (free ribosomes)
- Larger & denser than ProKs ribosomes
- Small subunit (40S) + Larger subunit (60S)
- Subunits made in nucleolus - exit nucleus - join together in cytosol
- Mitochondria and chloroplasts have 70S ribosomes like ProKs
Cell structures: 5. Organelles
No membrane-bound organelles

1. Golgi complex: Consists of curved cisterns. Modifies & packages proteins synthesized by ribosomes on RER. Vesicles either transported out of cell, into cell membrane or remain in cytoplasm as storage vesicle (lysosome)

2. Lysosome: formed from Golgi. Contain as many as 40 different kinds of powerful digestive enzymes capable of breaking down various molecules (can digest bacteria)

3. Endoplasmic Reticulum: Extensive network of flattened membranous cisterns. RER (studded with ribosomes) is continuous with the nuclear envelope for processing and sorting of proteins synthesized by ribosomes. SER have unique enzymes. Synthesizes fats and steroids (estrogens / testosterone). In liver, SER help release glucose into bloodstream & inactivate or detoxify drugs or alcohol. In muscle, SER releases Ca that triggers contraction.

4. Mitochondria: Vary depending on type of cell. Double membrane (smooth outer membrane + inner membrane arranged in folds / cristae). Cristae increases surface area for chemical reactions. Inside is semifluid substance - matrix. Have 70S ribosomes and some of their own DNA. Can reproduce on own by growing and dividing in two. [Basis of theory of endosymbiosis]. Enzyme that makes ATP on cristae of inner membrane & many metabolic steps in cellular respiration occur in matrix.

5. Chloroplasts: Found in algae and green plants. Membrane enclosed with chlorophyll (pigment) and enzymes required for the light-gathering phases of photosynthesis. Chlorophyll inside thylakoids (sacs) which form stacks (grana). Have 70S ribosomes, DNA & enzymes for protein synthesis. Can multiply on own within cell, by increasing in size and dividing in two (resemblent of bacterial multiplication)
Cell structures: 6. Cytoplasm (organelles + cytosol)
Prokaryotic: Only cytosol. No cytoskeleton or cytoplasmic streaming. Enzymes found in cytosol. (recall: cell wall give cell its structure)

- Cytoskeleton: microfilamens, intermediate filaments (rods) & microtubules (cylinders). Provides support and shape / structure, and assist in transporting substances through cell & movement (phagocytosis)
- Cytoplasmic streaming: cytoplasm flows in and out of ER & among cell parts, help distribute nutrients & move cell over a surface
- Enzymes mostly found in organelles.
Cell structures: 7. Endospores
Prokaryotic: Endospores (time capsule / seed) are "resting cells" formed internal to the bacterial cell membrane, by some bacteria (mostly gram+) when they are environmentally threatened & essential nutrients are depleted. Highly durable dehydrated cells with thick walls and additional layers. When released into environment, can survive extreme heat, lack of water, and exposure to many toxic chemicals and radiation. Contain DNA, some RNA, ribosomes & enzymes. Allow bacteria to "survive" / repopulate. When endospore matures, the cell wall ruptures / lyses, killing bacterial cell and endospore is freed. Can remain dormant for many years.

Germination: endospore returns to vegetative / resting state, triggered by physical or chemical damage to its coat. Bacteria "grows back"

Endospore formation = sporulation / sporogenesis (not means of reproduction - does not increase number of cells) occurs in threatened env.

Eukaryotic: None
Cell structures: 8. Inclusions
Inclusions are reserve deposits containing nutrients for use when environment is deficient (pockets of food / astonaut food) (#1, 2, 3, 4, 7) stored food for germination later on)

1. Metachromatic Granules: Contain a reserve of inorganic phosphate (polyphosphate) that can be used in ATP production

2. Magnetosomes: inclusions of iron oxide (Fe3O4). Attracted to food source (magnets) & can decompose / breakdown hydrogen peroxide (H2O2)

3. Lipid inclusions: lipid storage for energy reserve

4. Polysaccharide Granules: Glycogen & starch

5. Carboxysomes: contain enzymes that help fix (stick) CO2 that is used by organism. Bacteria that photosynthesis (cyanobacteria) (not food source)

6. Gas vacules: allow organism (eg. cyanobacteria) to float (eg. in water) to receive appropriate oxygen, light & nutrients (not source of food)

7. Sulfur granules: energy reserve for sulfur bacteria that derive energy by oxidizing sulfur
Cell structures: 9. Glycocalyx
Prokaryotic: Present as a capsule, slime layer or EPS (polypeptides & polysaccharides) (see #13, 14, 15)

Eukaryotic: (animal cells) Plasma membrane is covered by glycocalyx containing sticky carbohydrates. It strengthens the cell surface, helps attach cells together, attract water & may contribute to cell-cell recognition.
Cell structures: 10. Flagella & Cilia
Prokaryotic: Some have flagella for motility - allow bacteria to move by it self. Rotate like a helicopter.
Bacteria do not have cilia.

Eukaryotic: Some have flagella for cellular locomotion and moving substances accross cell surface. Contain cytoplasm and enclosed by plasma membrane. Consist of microtubules.
- Flagella: few & long. Ambulate / wag
- Cilia: numerous & short. Help move materials accross surface of cells.
Cell structures: 11. Size
Prokaryotic: typically 0.2 - 2.0 micrometers in diameter

Eukaryotic: typically 10 - 100 micrometers in diameter
Cell structures: 12. Membrane
Prokaryotic: Does not have carbohydrates or sterols (except mycoplasmas - no cell wall, have stiffer cell membrane with sterols)

Eukaryotic: Have carbohydrates (bacterial attachement) & sterols (complex lipids eg. cholesterol). Sterols associated with ability of membrane to resist lysis resulting from increased osmotic pressure (in dilute environment)
Cell structures: 13. Division
- Cell division: binary fission
- Sexual recombination: none, transfer of DNA only - conjugation (sex pilus)

- Cell division: animal cells: mitosis
- Sexual recombination: meiosis (production of gametes)
Yeast divides through budding - unequal division. Still becomes full sized eukaryotic yeast cell.
Transport: 1. Passive: Simple & facilitated diffusion
Materials move accross plasma membranes of proKs & EuKs by passive and active transport.

Passive transport: substances move through semi-permeable membrane from area of high concentraion to area of low concentration (move down its conc. gradient), without using ATP / energy

1. Simple diffusion: Net movement of molecules or ions from area of high conc. to area of low conc. Movement continues until equilibrium (eg. O2 & CO2, stain/dye)

2. Facilitated diffusion: integral membrane proteins (transporters) function as channels / pores or carriers that facilitate the movement of ions or large molecules (eg. glucose, fructose, galactose) accross the pm. Still considered passive since materials move from high to low and no energy is used. In prokaryotes mostly nonspecific transporter proteins and in eukaryotes mostly specific transporter proteins.
Transport: 1. Passive: Osmosis (tonicity)
3. Osmosis: Net movement of solvent (eg. water) across a selectively permeable mebrane from area of high concentration to area of low concentration of solvent molecules (opposite solute).

(Tonicity) cells are subjected to three kinds of osmotic solutions:

1. Isotonic solution: water leaves and enters cell at same rate (no net movement) & cell's contents are in equilibrium with solution outside the cell wall.

2. Hypotonic solution: outside environment has lower concentration of solutes than inside cell. Most bacteria prefer environment with 1% or less salt content, but are protected by their cell walls. If cell wall is weak (eg. gram-) or damaged (caused by lysozyme and antibiotics like penicillin), water moves in and causes cell to undergo osmotic lysis.

3. Hypertonic solution: Environment with higher concentration of solutes outside than inside cell. Bacterial cells shrink and plasmolyze (collapse) because water leave cell through osmosis. Cell wall does not protect against this. Some bacteria (eg. S. epidermis found on skin, S. aureus) & halophiles (archae) can live in more salty environment.
Transport: Active processes
In active processes the cell must use ATP to move substances from areas of low concentration to areas of high concentraions (against conc. gradient). Substances move from high to low or low to high depending on molecule (eg. if molecule is too large if it can't get in by itself)

1. Active transport: Uses transporter proteins to move substances from low to high (usually from outside into cell) (eg. ions, amino acids, simple sugars). Allow movement of substances at a constant rate, even in short supply.

2. Group translocation: special type of active transport used by proKs where substance is chemically altered during transport accross membrane. Molecule is changed (by adding something and making it bigger) so it cannot leak out of cell. (Euks does this too but its called something else).

Eukaryotes also use pinocytosis & phagocytosis that are considered active processes.
Evolution: Endosymbiosis
(Fig 10.2)
Endosymbiotic theory: larger bacterial cells lost cell wall and engulfed smaller bacterial cells. Nucleus developed from invagination / folding of plasma membrane around chromosome. Theory based on membrane bound organelles found in eukaryotes & invagination of plasma membrane. Eukaryotes developed from prokaryotes. Prokaryotes: antibiotic sensitivity, bacteria are sensitive to certain antibiotics, so are mitochondria and chloroplasts.

Endosymbiosis: relationship in which one org. lives whithin another (living together)