Review Sheet for Test #1         Biology 2212         Dr. James K. Adams

Biology - Scientific study of life
    Characteristics of life B Composed of cells/Maintenance of boundaries (cell membranes/sheets of cells),
        metabolism, reproduction, growth/development/maintenance, movement in response to stimuli
    Maintenance of Homeostasis
Hierarchical Organization of Life: Atoms/Molecules, Organelles/Cells, Tissues, Organs, Org. Systems,
        Organism, Population, Community, Ecosystem, Biosphere/Ecosphere

Chemistry - Life processes dependent on Chemistry; study of Matter and Energy
    Energy -- Cell Energetics -- Energy Transformations
        Energy - capacity to do work
            States: kinetic (in action) or potential (stored)
            Types - radiant (light), electrical, mechanical, chemical, thermal (heat)
        Laws of Thermodynamics:
            First: Energy Finite (can't be created or destroyed) but convertible
            Second: Every conversion increases entropy (some energy lost as heat)

MATTER -- Atoms: made up of subatomic particles:
                electrons (negative), protons (positive), neutrons (neutral)
           Atomic number (proton #)
           Atomic mass/weight (protons + neutrons)
       Electrons - move; have energy
          orbitals (can hold a pair of electrons)
          electron shells
          valence electrons - # of e-'s in outer shell; determine chemical properties of atoms
Chemical bonds - "shared" pair of electrons -- formation of molecules/compounds
        electronegativity - strength of attraction of an atom for electrons
    Covalent bonds:
        non-polar - e-'s shared equally (atoms involved equally electronegative); strongest bonds in
             solution
        polar - e-'s shared unequally, charge difference across bond (atoms involved not equally 
             electronegative)

    Polar does not equal Charged (see ions, below; to be charged atoms/molecules must have 
                different numbers of electrons and protons, not simply an uneven distribution)
    
    Ionic bonds - involves ions
         one strongly electronegative atom "takes" electrons from weakly electronegative atoms; results
              in ions negative anions and positive cations
          charges attract each other (hold ions together); strongly polar bonds

Important concept in understanding polarity: "Like dissolves like" - polar substances (eg., water)
    dissolve other polar substances, non-polar substances (eg., lipids) dissolve other non-polar 
    substances

    Hydrogen bonds - weak; unequally "shared" proton; though weak, still important in protein/NA 
        structure; also important in keeping water liquid

Biologically important inorganic molecules -

Although presented here as inorganic, there are organic salts and organic acids and bases

Classes of organic molecules - contain carbon (C)/rich in energy (lots of bonds)
         All have hydrogen (H), most also have oxygen (O) and nitrogen (N)

Hydrocarbons: Understand the concept of isomers (same chemical formula, different chemical 
    structure)
Carbon-Carbon bonding - single, double, triple; ring structures
Saturation
Functional groups: (Others also important (phosphate, sulfhydryl) but must be able to draw the following):

Dehydration syntheses (condensation) / Hydrolysis
     used in synthesizing/breaking down polysaccharides, neutral/phospholipids, proteins, nucleic acids

I. Carbohydrates - (C(H2O))n; end in -ose and/or begin with glyc-; KNOW FUNCTIONS

II. Lipids - fats and oils; essentially non-polar; KNOW FUNCTIONS

III. Proteins - structurally and functionally most varied group of organic molecules
        Amino Acids (A.A.'s) - basic building blocks of proteins; 20 different types
        Peptide bonds (formed by dehydration synthesis) -- Proteins are essentially polypeptides

Structural levels of proteins - primary, secondary, tertiary, quaternary
        primary -- Amino acid sequence
        secondary and tertiary structure in essence determined by primary (A.A.sequence); secondary
                structure due to hydrogen bonding between carboxyl/amine groups
        tertiary structure due to covalent/hydrogen bonding, charge differences, size differences, between
                different R groups
        quaternary -- more than one polypeptide chain "stuck together" to form functional protein; same
                interactions as at tertiary level (but between R-groups of different chains)

structure determines function; may include additional extra components (co-factors, coenzymes, etc.)

Functions of proteins:
    Structural proteins - typically secondary structural complexity only; form fibers or sheets; can have
            secondary and quaternary structure with no tertiary structure (for example, collagen)
    Functional proteins - tertiary or quaternary complexity; often soluble (in cytoplasm); includes
            antibodies, clotting, some hormones, transport (eg., hemoglobin), and . . .

     Enzymes - organic catalysts for biochemical reactions
            Chemical Reactions: all reactions require some initial input of energy
            Types: synthesis - requires a net input of energy
                    degradation - liberates energy
                    exchange - energy balance depends on reactants (substrates) and products
                Endergonic/Exergonic reactions - Coupling of
                Free energy of the reaction
         Enzymes and Enzyme function: Virtually all reactions in the body require enzymes
            Do not change equilibrium of reactants (substrates) and products, or the free energy
            Do speed the rate of reactions (catalysts) by reducing the Ea (energy of activation)
            Active site   Activators and Inhibitors (competitive/non-competitive)

IV. Nucleic Acids

Functions: from DNA you make RNA, from RNA you make proteins, and the proteins make you

    Nucleic acids are composed of nucleotide units - phosphate/5 carbon sugar/nitrogenous base
           phosphates and 5 carbon sugars make up the backbone
   Nitrogenous bases:
         purines (double-ringed): adenine and guanine
         pyrimidines (single-ringed): cytosine, thymine (DNA), and uracil (RNA)


    DNA - double helix; backbone with deoxyribose sugar
         cytosine . . . guanine; adenine . . thymine (. . . and . . represent # of hydrogen bonds)
     RNA - single stranded; ribose sugar; uracil instead of thymine
        ATP - (adenosine triphosphate) - (RNA) adenine nucleotide with two more phosphates
               high energy phosphate-phosphate bonds = body's ready source of energy

MIXTURES:   Solutions; Colloids (Sols and Gels); Suspensions

CELL STRUCTURE - cells are the fundamental units of life; cells are small because . . .?
    Cell membrane - fluid mosaic model  
        Components:    Phospholipid bilayer, with cholesterol
              Extrinsic/intrinsic proteins
             Glycocalyx in animal cells (cell-cell recognition) -- "fuzzy coat" of glycolipids/
                      glycoproteins; each cell type unique
          Cell membrane is sempermeable (selectively/differentially permeable)
                    regulates movement of molecules into and out of cells
          hypo-/iso-/hypertonic solutions
        Junctions: Tight, Gap, Desmosomes
    Transport across the cell membrane:
         Passive processes: No energy expenditure required
                 Diffusion -- Osmosis is a special case of a solvent (water) diffusing through a 
                    semipermeable membrane
                 Facilitated diffusion -- uses carrier proteins
         Active processes: Energy (ATP) required
                 Active transport -- also uses carrier proteins; example: Na+ - K+ pump
                 Endocytosis - bulk transport into the cell
                     Phagocytosis
                     Pinocytosis
                     Receptor-mediated pinocytosis
                 Exocytosis - Bulk transport out of the cell

Cytoplasm/Cytosol -- with inclusions

Cellular organelles - in the cytoplasm; KNOW STRUCTURES/FUNCTIONS of each