Chapter 2


The Chemistry of Biology



Fundamental Building Blocks

  Atom the smallest particle of an element

  Proton positive charge

  Neutron no charge

  Electron negative charge

  Water and the pH Scale

  measures the degree of acidity of a solution

  measured on a log  scale of 0 to 14

  Compares concentration of H+ (acidic) to OH- (basic)

  most microorganisms live in neutral range (pH 7)

  Inorganic chemicals - do not contain both carbon and hydrogen

  Organic chemicals - more complex and contain both carbon and hydrogen





  Important energy source

  Monosaccharides simple sugar (glucose)

  Disaccharides - 2 monosaccharides (lactose, sucrose)

  Polysaccharides 5 or more monosaccharides in linear or branched patterns (cellulose,  chitin)


  hydrophobic - do not dissolve in water

  Important for membrane structure

  storage lipids (ex. triglycerides)

  membrane lipids (ex. phospholipids)

  steroids (ex. cholesterol)

  Proteins (Polypeptides)

  Catalyze all reactions required for life

  Combinations of 20 basic amino acids held together by peptide bonds

  Must have proper shape to function

  High temperature or high/low pH can denature protein

  Nucleic Acids

  Deoxyribonucleic acid (DNA) - contains nucleotide genetic code

  Ribonucleic acid (RNA) - decodes information in DNA to form amino acids in protein




Chapter 3



Tools of the Laboratory



Culturing Microorganisms: The Five Is


  A tiny sample of microorganism (inoculum) is introduced to a growth medium using sterile technique

  Observable growth = culture

  Sample may come from many sources depending on the researchers goals (i.e. blood, infected tissue, soil, air, food, etc.)

  Culture medium may be contained in a test tube, flask, or Petri dish and may be inoculated with sterile loops, needles, pipettes, or swabs

  Some microorganisms require live cell cultures or an animal host to grow


  Primarily occurs between 20 and 40 degrees Celsius

  Usually within 24-48 hours growth can be seen with the naked eye


  Separation of individual bacterial cells from other cells

  Colony a discrete mound of cells that formed from a single bacterial cell

  Can use Streak Plate or Pour Plate Method


  Pure culture- contains one known species

  Mixed culture - contains two or more known species

  Contaminated culture - contains unwanted microbes of uncertain identity


  The microorganism can be transferred to a slide and viewed microscopically

  A variety of staining techniques and special media can be used to identify the organism




Classification of Media

  Physical state

  Liquid  - growth appears as a turbidity (cloudiness) or precipitate formation

Broths, milks, infusions

  Semisolid has a clot-like consistency at room temperature

Used to determine the motility of bacteria

  Solid has a firm surface at room temperature on which microorganisms can form discrete colonies (agar)

  Chemical Content

  Synthetic media- composed of precise amounts of  pure chemicals

  Complex media - include items which are not specifically known, usually animal or plant extracts

  Functional Type

  General purpose media - designed to grow a broad spectrum of microbes

Ex. Trypticase soy agar (TSA)

  Enriched media - preferentially enhances the growth of one particular species in a mixed culture

Ex. Blood agar

  Selective media - allows growth of certain groups of microbes and inhibits the growth of others

  Ex. Mannitol salt agar

  Differential media - allows the growth of many microorganisms and displays differences among them

  Ex. MacConkey agar


Miscellaneous Media

  Biochemical tests determine the presence of metabolic reactions 

  catalase test

  urease test

  sugar fermentation tests




The Microscope

  Microscopy the study of objects using a microscope

  Simple microscopes - have only one lens

  Compound microscopes - have more than one lens



Principles of Light Microscopy


  Light passes through the specimen and objective lens where it is magnified forming the real image

  The real image is then projected through the ocular lens and further magnified resulting in the virtual image (1000X)

  Resolution - the capacity of an optical system to distinguish two adjacent objects from one another

  Oil is used on high power lens to prevent refraction of light rays

  Contrast the degree of bending that light undergoes as it passes from one medium to another (refractive index)

  iris diaphragm controls the amount of light entering the condenser



Variations on the Light Microscope

  Bright-Field microscope

  Forms an image when light is transmitted through the specimen

  The specimen appears darker than the surrounding area

  Dark-Field microscope

  A stop disc blocks all light from entering the objective lens

  Organisms stand out as bright objects against a dark background

  Phase-Contrast microscope

  Light is refracted differently in cells than their surroundings so denser material appears darker

  Good for viewing the organelles within cells

  Fluorescent microscope

  Uses fluorescent dyes and UV light to produce the image

  Fluorescent cells stand out as illuminated objects against a dark background

  Transmission electron microscope

  Forms an image by transmitting electrons through the specimen

  Used to observe the detailed structures of cells and viruses



Microscopic Examination

  Wet Mount - a drop of culture is placed on a slide and overlaid with a coverslip

  Used to observe live, moving microorganisms

  Fixed, stained smears

  Smear a thin layer of specimen dried on a slide

  Heat fixation the slide is gently heated simultaneously killing the specimen and fixing it to the slide

  Staining procedure that applies colored chemicals (dyes) to the specimen

  Positive stain dye sticks to the specimen giving it color

  Negative stain dye does not stick to the specimen but rather the area around it forming a negative image



Positive Stains

  Simple stains - require only one dye

  Ex. Crystal violet and methylene blue

  Differential stains - use two dyes; one primary stain and one counterstain

  can distinguish between different cell types or parts

  Ex. Gram stain and acid-fast stain

  Special stains - emphasize certain cell parts not seen with the other types of stains

  Ex. Capsule and flagella staining