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Microbiology

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					                                     Cell Theory

1. All organisms consist of one or more cells
2. Basic unit of life
3. Can only come from other cells


                                     Microbiology
                       (Bacteria, Viruses, Protistans, and Fungi)

I.     Kingdom Monera
       A. Bacteria
          1. All prokaryotic and unicellular
          2. Most abundant and widespread organisms
          3. Many pathogenic
             a. many cause disease
             b. many are beneficial
          4. Size
             a. smallest of all organisms
                 1.) 0.2 – 10 um (micrometer 1/1,000,000th of a meter)
          5. Shapes
             a. coccus (sphere)
                 1.) variety of arrangements
             b. bacillus (rod)
             c. spirillum (spiral)
       B. Some bacterial disease
          1. Plague
             a. transmitted by rodents (fleas from rodents)
             b. very sensitive to antibiotics
          2. Anthrax
             a. found in cattle and soil
             b. forms spores (resistant cells)
             c. can lay dormant until it finds a host
          3. Tetanus
             a. lives in soil
             b. 2 forms
                 1.) adsorbed and fluid
             c. produces neurotoxin affecting nervous system
             d. “lockjaw”
             e. vaccine
          4. Botulism
             a. Botox
             b. Food poisoning (canned foods)
             c. Most potent toxin on the planet
             d. Can be waterborne
   5. E. Coli
      a. lives in gut
      b. prevents pathogenic organisms from establishing themselves
      c. produces vitamins (k)
      d. mostly beneficial unless it enters bloodstream or urine
   6. Strep Throat
      a. particular strain of streptococcus
      b. one strain responsible
      c. occurs normally in 25% of population
      d. very sensitive to penicillin
      e. can cause rheumatic fever or scarlett fever
      f. menengitis – general term applies to inflammation of menegis
C. Some beneficial bacteria
   1. Cyanobacteria
      a. blue-green
      b. pond scum
      c. photosynthesizing bacteria
          1.) produce oxygen
          2.) early atmosphere didn’t have oxygen
          3.) made all of the oxygen in early atmosphere
      d. might produce up to 70% of earth’s oxygen
      e. can buy it as a food (spirulina)
   2. Normal oral and gut flora
      a. establish themselves
      b. out compete pathogenic organisms
      c. disrupting them causes problems
          1.) Yeast infections from antibiotics
   3. Nitrogen-fixing bacteria
      a. immodium nitrate, etc.
      b. in fertilizer
      c. N2 in air – plants cannot use it, but bacteria can. Bacteria live in soil,
          roots of plant absorb it from soil, then use it to produce protein for
          consumption.
   4. Decaying bacteria
      a. recycle nutrients of dead organisms so other organisms can use it.
      b. Compost is the result
   5. Fermenting Bacteria
      a. anaerobic process of food products
      b. produce cheese/yogurt
D. Viruses
   1. Noncellular obligate parasites
      a. obligate = has to be parasitic
      b. noncellular = not made up of cells
      c. not a living organism
      d. reside in cells of a host
      e. extremely small (18-350 nanometers)
                1.) need electron microscope to see
            f. consist of
                1.) strand of nucleic acid (DNA or RNA)
                2.) surrounded by outer protein coat
            g. Replicates inside a host cell
                1.) pirates host’s metabolic mechanisms
                2.) trick cells into DNA replication of the virus
                3.) have to wait for immune system to stop it – antibiotics can’t do
                    anything to help
                4.) antibodies destroy protein coating of the virus
      E. Some Viral Diseases
         1. Rabies
            a. transmitted through bite of infected animals
            b. affects Central Nervous System (CNS)
         2. AIDS
            a. infects a particular type of our white blood cells (immune system cells)
            b. renders immune system ineffective
            c. don’t die from the virus itself
         3. Ebola
            a. appears in isolated villages in Africa every few years
            b. high mortality rate (60%-70%)
            c. short incubation
            d. appears/disappears very rapidly
            e. highly contagious
         4. Hepatitis
            a. condition – inflammation of the liver
            b. caused by injury or alcoholism
            c. routes of transmission vary
                1.) water transmission (sewage) (Hepatitis A)
                2.) blood borne (Hepatitis B)
                3.) blood borne (Hepatitis C)
         5. Smallpox
            a. completely irradicated by vaccination
            b. high mortality rate
            c. retained by countries as biological weapons
         6. West Nile Virus
         7. Colds
         8. Influenza
II.   Kingdom Protista
      A. Unicellular organisms (eukaryotic)
         1. Some simple multicellular organisms
         2. Many pathogenic
         3. Many free living (non-pathogenic)
         4. Many closely related to other kingdoms
            a. fungi
            b. plantae
               c. animalia
       B. Fungus-like protistans
          1. Saprophytic or parasitic heterotrophs
               a. feed on decay
          2. e.g.; water and slime molds
       C. Animal-like protistans
          1. protozoans (“first animals”)
          2. Unicellular
          3. Heterotrophic
          4. Examples;
               a. amoeba
                   1.) characterized by pseudopodia (false feet), used for locomotion
                   2.) some are free living
                   3.) some are parasitic
                       a.) e.g.; amoebic dysentery
               b. Flagellates
                   1.) locomotion by flagella (whip-like structures)
                   2.) many free living
                   3.) many parasitic
                       a.) e.g.; giardia
                            1. ] in local water (streams, lakes)
                            2. ] intestinal parasite
       D. Intracellular parasites
          1. Live part of their life inside cells of host
               a. e.g.; malaria
                   1.) transmitted by Anopheles Mosquito
                   2.) Infects human liver and red blood cells
                   3.) Results in anemia
       E. Ciliates
          1. Locomotion by cilia
          2. Most free living
          3. Few parasitic
               a. e.g.; Balantidium coli
III.   Plant-like protistans
       A. Algae
          1. photosynthetic autotrophs (most)
          2. free living
          3. unicellular or multicellular
          4. Examples:
               a. Diatoms
                   1.) unicellular
                   2.) silica shells
                   3.) fresh water and marine
                   4.) mined for abrasives and filters
                       a.) toothpaste and polishes
       B. Dinoflagellates (dino = terrible)
         1. unicellular
         2. flagella for locomotion
         3. marine
         4. some bio-illuminate
         5. produce toxin (neurotoxin)
         6. cause red tide
      C. Red Algae
         1. multicellular (most)
         2. marine (most)
         3. seaweed
         4. Uses:
            a. agar (gelatin like substance)
                 1.) used for DNA tests
            b. nori (sushi) wrap
      D. Brown algae
         1. brown algae
         2. multicellular
         3. marine (most)
            a. giant kelp
         4. Uses;
            a. extracts used in ice cream, beer, etc. as a thickening agent. (Keragenin)
      E. Green Algae
         1. unicellular, colonial, multicellular
         2. most freshwater
         3. closest relatives of plants
IV.   Kingdom Fungi
      A. Molds, mushrooms, yeasts
         1. most cellular eukaryotes
         2. few unicellular
            a. yeasts
         3. all heterotrophic (sets it apart from plants)
            a. absorption – release digestive chemicals to break down food, then
                 absorb it.
            b. Not photosynthetic
            c. Most saprophytic (eat decay)
            d. Few pathogenic (disease causing parasites)
         4. composed of mycelium (hyphae)
            a. hyphae is the name for the fuzzy material you can see with your eyes.
            Individual strands are hyphae. Many hyphae = mycelium.
      B. Some Fungal Disease
         1. Valley fever
            a. caused by spores released by mycelium in soil kicked up when farmers
                 turn the soil
            b. can manifest into pulmonary condition
            c. can become systemic
         2. Athlete’s foot
      a. spreads in wet areas
      b. fungal disease infects surface of skin
      c. related to ringworm
   3. Ergotism (ergot poisoning)
      a. results from ingesting infested grains (wheat, and especially rye)
      b. fungus produces chemical which is just like LSD
      c. basis for Salem witch hunts (?)
      d. mushroom poisoning
          1.) toxic to the liver
C. Some benefits of fungi
   1. decomposers
   2. fermentation products (cheeses, etc.)
   3. antibiotics (penicillin)
   4. food (mushrooms)
                                  Plants and Animals
                                    Kingdom Plantae

I.     Kingdom Plantae
       A. multicellular
       B. photosynthetic autotrophs
       C. approximately 300,000 species
       D. most terrestrial
       E. a few aquatic
II.    Nonvascular plants
       A. Bryophytes
          1. Mosses and liverworts
       B. lack vascular tissue (veins, etc.)
          1. for transporting water and nutrients through the plant
          2. restricts size of plant (usually 1-2 in., always less than 8 in.)
          3. use diffusion
          4. lack roots
          5. water transports gametes
          6. restricted to moist areas
III.   Seedless vascular plants
       A. Ferns, horsetails and relatives
       B. Have vascular tissue (2 types)
          1. Xylem
              a. transport water from roots up to leafy material for photosynthesis
          2. Phloem
              a. transport food materials like sugars downward to stem and root
          3. Intermediate size
          4. Water transports gametes
          5. Restricted to moist habitats
IV.    Seed Plants
       A. Pollen is vehicle of dispersal of sperm (male gametes)
          1. transported to eggs by wind or animals
       B. Fertilization results in seed
          1. plant embryo, nutritional material, protective coat
       C. Allows freedom from aquatic environments
       D. Includes gymnosperms and angiosperms
          1. gymnosperms (naked seed)
              a. conifers and relatives
              b. seeds are exposed (naked)
              c. conifers = come bearing (pine trees)
                  1.) pines, firs, cedars, junipers, sequoia, etc.
                  2.) seeds are exposed
                  3.) leaves are needle like or scale like
                  4.) most are evergreen
                  5.) produce an antifreeze to keep leaves from freezing and falling off
          2. angiosperms
             a. flowering plants
             b. seeds enclosed in an ovary
                 1.) seeds not exposed
             c. most numerous and diverse group of plants
       E. Fruit
          1. mature ovary (ovum)
          2. protects the seeds
          3. aids in dispersal of seeds
             a. Animals eat the fruit, walk away and deposit the seeds elsewhere in
                 their feces.

                                    Flower Anatomy




The Flower:
The flower is the reproductive unit of some plants (angiosperms). Parts of the flower
include petals, sepals, one or more carpels (the female reproductive organs), and stamens
(the male reproductive organs).

The Female Reproductive Organs:
The pistil is the collective term for the carpel(s). Each carpel includes an ovary (where
the ovules are produced; ovules are the female reproductive cells, the eggs), a style (a
tube on top of the ovary), and a stigma (which receives the pollen during fertilization).

The Male Reproductive Organs:
Stamens are the male reproductive parts of flowers. A stamen consists of an anther
(which produces pollen) and a filament. The pollen consists of the male reproductive
cells; they fertilize ovules.

Fertilization:
Pollen must fertilize an ovule to produce a viable seed. This process is called pollination,
and is often aided by animals like bees, which fly from flower to flower collecting sweet
nectar. As they visit flowers, they spread pollen around, depositing it on some stigmas.
After a male's pollen grains have landed on the stigma during fertilization, pollen tubes
develop within the style, burrowing down to the ovary, where the sperm fertilizes an
ovum (an egg cell), in the ovule. After fertilization, the ovule develops into a seed in the
ovary.

Types of Flowers:
Some flowers (called perfect flowers) have both male and female reproductive organs;
some flowers (called imperfect flowers) have only male reproductive organs or only
female reproductive organs. Some plants have both male and female flowers, while other
have males on one plant and females on another. Complete flowers have stamens, a pistil,
petals, and sepals. Incomplete flowers lack one of these parts.


                                   Plants and Animals
                                     Kingdom Animalia

I.     Kingdom Animalia
       A. Multicellular
          1. most have tissues, organs and organ systems
          2. all are heterotrophic (eat food)
          3. all aerobic (require oxygen)
          4. most are motile (have the ability to move around – mobile)
          5. over 2 million species
II.    Phylum Porifera
       A. Sponges
          1. asymmetric (no symmetry whatsoever)
          2. lack true tissue (specific tissues)
III.   Phylum Ctenophora
       A. Comb jellies
       B. Similar to jellyfish except:
          1. lack nematocysts (stinging cells)
          2. have 8 rows of comb-like structures
       C. Some bioluminescent
IV.    Phylum Platyholmenthes
       A. Flatworms
          1. bilateral symmetry
              a. single line of symmetry
                  1.) front, back, left, right, top, bottom
          2. no body cavity
           3. many are free living
               a. planaria
           4. many parasitic
               a. flukes
               b. tapeworms
V.      Phylum Nematoda
        A. Roundworms (i.e.; heartworm)
           1. unlined body cavity
           2. many parasitic
               a. Trichinella
               b. Elephantiasis
VI.     Phylum Mollusca
        A. Clams, snails, octopus, squid
           1. lined body cavity (mesentery)
               a. allows for connection of organs within body cavity
           2. some with well developed shells
           3. well developed senses
           4. primitive invertebrates
VII.    Phylum Annelida
        A. Earthworms and relatives
           1. segmented
           2. few parasitic
               a. leeches
VIII.   Phylum Arthropoda
        A. Spiders, insects, crustaceans, and relatives
           1. jointed appendages
               a. increased locomotion
           2. Exoskeleton of chitin
               a. structural carbohydrate
           3. many beneficial
           4. many pathogenic or harmful
               a. mosquitoes
               b. flies
               c. ants
IX.     Phylum Echinodermata
        A. Starfish and relatives
           1. secondary radial symmetry (reverted to radial symmetry)
           2. water vascular system with tube feet (hydraulic feet)
X.      Phylum Chordata
        A. Vertebrates and relatives
           1. notochord
               a. long flexible rod that runs the length of the body and provides support
           2. dorsal hollow nerve chord
               a. nerve chord running along the length of the noto chord
               b. collection of nerve tissue
           3. pharyngeal gill slits
      a. opening from inside to outside
      b. near pharynx
      c. developed into respiratory organs
   4. post anal tail
   5. All four characteristics present at some time during development
B. Vertebrates
   1. chordates with:
      a. a notochord that develops into a vertebral column (backbone)
      b. the anterior (front end) nerve chord (dorsal hollow nerve chord)
          expanded to form a brain
   2. Seven living classes of vertebrates
      a. Class Agnatha
          1.) jawless fishes
              a.) lampreys and hagfishes
          2.) skeleton made of cartilage
          3.) lack jaws
          4.) many parasitic
      b. Class Chordrichthyes
          1.) cartilaginous fishes
              a.) sharks and rays
          2.) skeleton of cartilage
          3.) formidable jaws
          4.) have a tongue
      c. Class Osteichthyes
          1.) bony fishes
              a.) trout, salmon, tuna, etc.
          2.) skeleton of bone
              a.) more protection in head area
              b.) most diverse and numerous group of vertebrates
      d. Class Amphibia
          1.) amphibians
              a.) salamanders, frogs, toads
          2.) first terrestrial vertebrates
          3.) still dependent on water in some way
              a.) permeable skin (will dry out)
              b.) permeable eggs
      e. Class Reptilia
          1.) reptiles
              a.) crocodiles, turtles, lizards, snakes
              b.) much less dependent on water
              c.) scales
              d.) amniotic egg (sac inside shell)
      f. Class Aves
          1.) birds
              a.) feathers
                   1.] homeothermic (warm-blooded)
                         2.] waterproof
             g. Class Mammalia
                1.) mammals
                2.) hair
                3.) homeothermic
                4.) mammary glands
                    a.) modified sweat glands containing modified fatty sweat to feed
                         the young

                                      Ecology
I.    Ecology
      A. Oikos = home
      B. Ology = study of
      C. Study of the interactions of organisms
         1. with one another
         2. with the physical environment
II.   Levels of organization studied in Ecology
      A. Populations
         1. group of individuals of the same species occupying a particular area
         2. examines how individuals of the same species interact with one another
         3. population size
             a. number of individuals in a particular area
                 1.) e.g.; number of mule deer in Yosemite National Park
         4. Population Density
             a. number of individuals per unit acre within a particular area
                 1.) e.g.; number of mule deer per acre in Yosemite National Park
         5. Carrying capacity
             a. maximum number of individuals an area can support
             b. changes as environment changes
      B. Community Ecology
         1. Community
             a. all populations that occur in a particular area
             b. examine how various populations interact with one another
         2. Habitat
             a. description of the environment in which an organism lives
             b. often defined by dominant plants present
                 1.) e.g.; oak woodland, desert scrub, valley grassland, marshland,
                      riparian
         3. Niche
             a. the role or the occupation that an organism has within the Community
             b. often described by feeding behavior, period of activity, and habitat
                 1.) e.g.; diurnal predator, nocturnal aerial insectivore, terrestrial
                       scavenger, fossorial herbivore
         4. Symbiosis
             a. “living together”
             b. Interactive relationship between two different species
                  1.) commensalism
                      a.) one species benefits, other is unaffected
                      b.) e.g.; burrowing owls and prairie dogs/ground squirrels, lichens
                          and pine trees.
                  2.) mutualism
                      a.) both benefit
                      b.) e.g.; flowering plants and pollinators, lichens, fruit producing
                          plants and frugivores
                  3.) Predation/Parasitism
                      a.) one species benefits, other is harmed
                      b.) e.g.; mountain lion and mule deer, deer and buckbrush,
                          tapeworms and humans, fleas and dogs
                  4.) Competition
                      a.) both species harmed in some way
                      b.) due to similar requirements for limited resources
                      c.) e.g.; mountain lions and wolves, bats and nighthawks
III.   Food Chain
       A. linear depiction of feeding relationships
          1. producers (autotrophs)
          2. primary consumers (herbivores)
          3. secondary consumers (predators that feed on primary consumers)
          4. tertiary consumers (predators that feed on secondary consumers)
          5. decomposers (feeds on dead material)
IV.    Food Web
       A. Complex three dimensional model depicting feeding relationships
V.     Morphological Adaptations
       A. Mimicry
          1. Resemblance of one organism to another organism to one’s benefit.
          2. E.g.; stick bug
       B. Crypsis
          1. Aspect of appearance that prevents detection
          2. E.g.; chameleon, stick bug
       C. Aposematism
          1. conspicuous appearance to provide warning
          2. e.g.; bright colors, rattle on rattlesnake
VI.    Ecosystem ecology
       A. Ecosystem
          1. Interaction of various species in communities with each other and physical
              environment
          2. Physical environment includes;
              a. water
              b. sunlight
              c. soil
              d. fire
              e. wind
              f. rocks

				
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