FUNDAMENTALS OF BIOLOGY
MICROBIOLOGY

I. Classification of organisms

A. Taxonomy

  1. Def: the science of classifying organisms
  2. Developed by Linnaeus in 1750

B. Classification hierarchy

  1. Kingdom
  2. Phylum
  3. Class
  4. Order
  5. Family
  6. Genus
  7. Species

C. Major kingdoms

  1. Monera: example: bacteria, blue-green algae
  2. Protist: example: protozoans, algae
  3. Fungi: example: mushrooms, mold, yeast
  4. Plantae: example: plants, trees
  5. Animalia: example: worms, insects, vertebrates

D. Taxonomic names

  1. Binomial nomenclature
    1. Two-name name
    2. Genus-species
      1. Homo sapien: modern man
      2. Equus caballus: horse
      3. Canis familiaris: dog
  2. Many species contain several varieties

KINGDOM MONERA
II. Viruses

A. Basic properties

  1. Viruses don't have any of the following:
    1. Nucleus
    2. Cytoplasm
    3. Cellular organelles
    4. Plasma membrane
  2. Viruses do have the following:
    1. Genetic material (DNA or RNA)
    2. Proteins
  3. Viruses can reproduce only when in a living cell
  4. Viruses are extremely small (500 nm is the largest)
  5. Most viruses cause harmful diseases

B. Basic structure

  1. Genetic material is surrounded by protein (capsid)
  2. Common shapes:
    1. Icosahedron: 20 sided regular polygon
    2. Helix: Single twisted strand
  3. Bacteriophage
    1. Special viruses that attack bacteria
    2. Have a very unique structure                    
      1. Head: contains the genetic material
      2. Tail: rod-shaped middle section
      3. Tail fibers: six leg-like structures

C. Virulence

  1. Def: the ability of a virus to affect a cell
  2. The Lytic Cycle
    1. Attachment: virus attaches to the cell
    2. Entry: genetic material injected into the cell
    3. Replication: viral genes take control of the cell and start to make viral proteins and more genes
    4. Assembly: virus particles form within the cell
    5. Release: cell ruptures when full of viruses and the new viruses go on to infect more cells
  3. Latent virus
    1. Def: when a virus enters a cell but is inactive
    2. Lysogenic virus
      1. Viral genes attach to the bacterial DNA
      2. Bacterial DNA replicates making more viral DNA
      3. When some external stimulus (UV, chemicals, or heat) occurs, the virus enters the lytic cycle
      4. Ex: Herpes simplex
  4. Cells respond to viral infection by making interferon that helps to stop the virus from making proteins

III. Bacteria (Phylum Schizomycophyta)

A. Basic structure

  1. Procaryotic: no true nucleus or organelles
  2. Nuclear area: single circular strand of DNA
  3. Mesosomes
    1. Indentations in the plasma membrane with enzymes
    2. Enzymes do photosynthesis and/or respiration
  4. Ribosomes: make proteins
  5. Cell wall: rigid outer structure
  6. Capsule
    1. Layer of proteins and sugars outside cell wall
    2. Protects the cell from attack
  7. Flagella: long whiplike structures for movement
  8. Pili: short hairs used for attachment to things

B. Basic shapes

  1. Coccus: spherical (round) cells
  2. Bacillus: rod-shaped cells
  3. Spirillum: twisted (corkscrew) shaped cells
  4. Bacterial relationships
    1. Diplo- : two
    2. Strepto- : twisted in a chain
    3. Staphyl- : clusters of cells

C. Types of bacteria

  1. Class Eubacteria: true bacteria
  2. Class Rickettsiae
    1. All are parasites
    2. Cause diseases in humans (Ex. Typhus)
  3. Class Actinomycota
    1. Some cause diseases (Tuberculosis, leprosy)
    2. Many are used to make antibiotics (Tetracycline)
  4. Class Spirochetae
    1. Cause many human diseases
    2. Ex: syphilis

D. Bacterial nutrition

  1. Most are saprophytes: feed on dead things
    1. Secrete digestive juices outside of the cell
    2. Absorb digested nutrients through cell wall
  2. Some are parasites: feed on a living host
  3. Some are autotrophs
    1. Photosynthetic
      1. H2S is the hydrogen source
      2. Oxygen is not produced
    2. Chemosynthetic
      1. Make food out of inorganic chemicals
      2. Found in very dark places

E. Bacterial respiration

  1. Obligate aerobes (aerobic)
    1. Must have oxygen
    2. Ex. Diptheria, tuberculosis
  2. Obligate anaerobes (anaerobic)
    1. Cannot have oxygen or else they will die
    2. Ex. Tetanus (lockjaw)
  3. Facultative bacteria
    1. Can live in either state but prefer oxygen
    2. Ex. E. coli (inside human stomach)

F. Reproduction and Growth

  1. Bacteria reproduce by a special process of mitosis called binary fission
  2. Bacteria grow rapidly and reproduce quickly if all the right conditions are met
  3. If unfavorable conditions exist, they will form a hard covering (endospore) around the DNA
  4. When favorable conditions return, the endospores develop into bacterial cells

G. Importance of bacteria

  1. Nitrogen Cycle
    1. Plants need nitrogen in order to grow
    2. Bacteria living in the roots take nitrogen fromthe air and give it to the plants
    3. This is called nitrogen fixation
  2. Food preparation
    1. All dairy products use bacteria
      1. Cottage cheese
      2. Yogurt
      3. Butter
    2. Hard cheeses use several types of bacteria
    3. Vinegar in a product of bacteria

H. Controlling Bacteria

  1. Bacteria compete with humans for food
  2. Several ways are used to keep food from spoiling
    1. Refrigeration and freezing
    2. Boiling and sealing (canning)
    3. Drying
    4. Pasteurization
    5. Chemical preservatives
  3. Bacteria also cause diseases
  4. Drugs are used to kill bacteria (antibiotics)

IV. Blue-green algae (Phylum Cyanophyta)

A. Basic characteristics

  1. Procaryotic
  2. Contain chlorophyll spread throughout the cytoplasm
  3. Do normal photosynthesis (produce oxygen)

KINGDOM PROTISTA

V. General Characteristics

A. Single celled organisms (unicellular)

B. Some are heterotrophic

  1. Phylum Sarcodina
  2. Phylum Ciliophora
  3. Phylum Mastigophora
  4. Phylum Sporozoa
  5. Phylum Myxomycophyta

C. Some are autotrophic (algae)

  1. Phylum Chlorophyta
  2. Phylum Phaeophyta
  3. Phylum Rhodophyta
  4. Phylum Chrysophyta
  5. Phylum Pyrrophyta
  6. Phylum Euglenophyta

D. Most live in water

E. Some are parasitic

VI. Heterotrophic Protists (protozoans)

A. Phylum Sarcodina

  1. Basic characteristics
    1. Constantly changing body shape
    2. Move by amoeboid movement
      1. Bulge forms in the plasma membrane
      2. Cytoplasm flows into the bulge
      3. This forms a pseudopod "false foot"
    3. Show taxes: movement in response to stimulus
  2. Example: Amoeba proteus
    1. Structure
      1. Ectoplasm: watery cytoplasm near membrane
      2. Endoplasm: denser inner cytoplasm
      3. Nucleus
      4. Contractile vacuole: removes water
      5. Food vacuole: formed when pseudopods get food
    2. Reproduction
      1. Asexual mitosis (binary fission)
      2. Cyst: hard covering to withstand bad condition
  3. Other Sarcodines
    1. Entamoeba gingivalis: helps in tooth decay
    2. Entamoeba histolytica: dysentery
    3. Foraminifera: hard shells of limestone (chalk)

B. Phylum Ciliophora

  1. Basic characteristics
    1. Covered with cilia
    2. Move & get food by rhythmic beating of the cilia
  2. Example: Paramecium
    1. Structure
      1. Pellicle: outer covering
      2. Macronucleus: large kidney-shaped structure
      3. Micronucleus: reproductive nucleus
      4. Oral groove: sweeps food into mouth
      5. Gullet: blind pocket which forms food vacuole
      6. Contractile vacuoles: remove water
    2. Movement
      1. Moves in a zig-zag path by beating cilia
      2. Taxes away from light, heat, & chemicals
    3. Reproduction
      1. Asexual: binary fission
      2. Sexual: Conjugation
        1. Two cells join at the oral groove
        2. Exchange genetic material
  3. Other Ciliates
    1. Stentor: giant protozoan (2.5 mm)
    2. Vorticella: non-moving with cilia on the top
    3. Didinium: protozoan predator (sucks cytoplasm)

C. Phylum Mastigophora

  1. Basic characteristics
    1. Have flagella
    2. Move by whipping flagella like a propeller
    3. Some are photosynthetic
  2. Examples
    1. Trypanosoma: causing African sleeping sickness
    2. Tryconympha: live in termites & digest cellulose

D. Phylum Sporozoa

  1. Basic characteristics
    1. Adult forms have no movement (non-motile)
    2. All form spores some time in their lifetime
    3. All are parasitic
  2. Example: Plasmodium: responsible for malaria

E. Phylum Myxomycophyta (Slime molds)

  1. Basic characteristics
    1. No cell wall or plasma membrane
    2. Flowing mass of cytoplasm with many nuclei
    3. Ooze over things digesting dead material
    4. During reproduction, it forms a fruiting body

VII. Autotrophic protists (Algae)

A. Basic structure

  1. Cell wall: made of cellulose
  2. Chloroplasts: contain chlorophyll
  3. Pyrenoids: starch storage bags
  4. Algae relationships
    1. Filament: thin, chain-like column of cells
    2. Thallus: complex body made of many cells

B. Phylum Chlorophyta (Green algae)

  1. Characteristics: mostly freshwater, some terrestrial
  2. Examples:
    1. Chlamydomonas: have two flagella
    2. Spirogyra: spiral-shaped chloroplasts

C. Phylum Phaeophyta (Brown algae)

  1. Characteristics
    1. Marine (salt water)
    2. Extensive thallus
      1. Blades: leaf-like structures
      2. Holdfast: root-like structure (to rocks)
      3. Air bladder: hold blades near surface
    3. Produces algin
      1. Jelly-like coating on the leaves
      2. Used as a thickener in foods (ice cream)
      3. Used as a base for cosmetics
  2. Example: Macrocystis (Kelp)

D. Phylum Rhodophyta (Red algae)

  1. Characteristics
    1. Marine
    2. Thin ribbon-like thallus
    3. Live with animals that live in tropical waters
      1. Secrete calcium carbonate skeleton
      2. Help to build up reefs
  2. Example: Chondrus

E. Phylum Chrysophyta (Golden algae)

  1. Characteristics
    1. Cell walls of silica (sand)
    2. Store food as oil drops
    3. Both marine and freshwater
    4. They are the phytoplankton
      1. Most important photosynthetic organism
      2. Produce most of the oxygen in the world
      3. Provide food for the larger marine animals
  2. Example: Diatoms

F. Phylum Pyrrophyta (Dinoflagellates)

  1. Characteristics
    1. Contain two flagella
    2. Many are bioluminescent: produce light
    3. Sometimes they bloom and die releasing toxins into the water (red tide)
  2. Examples
    1. Noctiluca: bioluminescent
    2. Gonyaulax: produce red tides

G. Phylum Euglenophyta

  1. Characteristics
    1. Can be autotrophic or heterotrophic
    2. Live in freshwater
  2. Example: Euglena
    1. Structure
      1. Pellicle: maintains shape
      2. Flagella: for locomotion (movement)
      3. Eyespot: light sensitive area
      4. Contractile vacuole: removes water

KINGDOM FUNGI

VIII. General characteristics

A. All are heterotrophic

  1. Parasites: feed on living things
  2. Saprophytes: feed on dead things

B. All are decomposer organisms (reducers)

C. Produce root-like anchoring structures

D. Lack specialized structures for digestion

E. Require oxygen and moisture

IX. Phylum Eumycophyta (true fungi)

A. Basic structures

  1. Cell walls made of chitin
  2. Form filaments called hyphae
    1. Hyphae grow in and on food
    2. Release digestive enzymes which dissolves food
    3. Nutrients are absorbed by the hyphae

B. Types of hyphae

  1. Rhizoids
    1. Imbedded in the material the fungus is living on
    2. Serve as "roots" and help to digest food
  2. Aerial hyphae
    1. Absorb O2, produce spores, & spread fungus
    2. Stolon: form new filaments
    3. Sporophore: produce spores
  3. Haustoria
    1. Produces by parasitic fungi
    2. Enter cell & obtain food directly from cytoplasm
  4. Mycelia
    1. Masses of intertwined hyphae
    2. Usually white in color

C. Fungal reproduction

  1. Fragmentation: breaks in pieces
  2. Stolons: fungus sends out "runners"
  3. Spores: seed-like structures

D. Types of fungi

  1. Class Zygomycota
    1. Produce spores in special cases (sporangium)
    2. Have many nuclei
    3. Most common molds belong to this class
    4. Example: Rhizopus
  2. Class Basidiomycota (Club fungi)
    1. Produce spores in club-shaped structures
    2. Contain hyphae which spread through the soil
    3. Eventually, a club-shaped mushroom is formed
      1. Parts of the mushroom
        1. Stipe: body portion (stalk)
        2. Gills: thin flaps underneath
        3. Cap: hard covering on the top
      2. Gills contain spores which are released
    4. Examples:
      1. Mushrooms
      2. Puffballs
      3. Bracket (shelf) fungi: generally only on wood
  3. Class Ascomycota (Sac fungi)
    1. Produce spores in sac-like structures
    2. Some are used to make medicines: Penicillium
    3. Examples:
      1. Mildews
      2. Yeasts
      3. Morel
  4. Class Deuteromycota
    1. Do not have a means of sexual reproduction
    2. Many are parasitic
    3. Examples: Ringworm, Athlete's foot

X. Lichens

A. Def: a combination of an algae and a fungus

B. Lichens show mutualism

  1. Algae provides food (photosynthesis)
  2. Fungus provides a place to live

C. Grow mostly on rocks

D. Type of lichens

  1. Crustose: crust-like patches
  2. Foliose: leaf-like structures
  3. Fruticose: shrub-like structures
E. Reproduction
  1. Lichens release soredia (spores)
  2. Soredia are particles with both an algae & a fungus
  3. Soredia land somewhere and grow into a new lichen