Physiology 1, Fall 2008, LPC

Chapter 2- Molecular Interactions

I – Chemistry Review

Subatomic particles – protons, electrons, neutrons
# protons determines element
electrons can be lost, gained or shared -> chemical bonds
isotopes of an element contain different numbers of neutrons

II - Molecular Bonds and Shapes

Ionic – electrons gained or lost
Covalent – electrons shared
            Can -> polar or nonpolar molecules
                        Polar – unequal charge on molecule – hydrophilic
                        Nonpolar – symmetrical molecule – hydrophobic
Hydrogen – weak attraction between H and nearby O, N or Fl
Van der Waals Forces – weak, nonspecific attractions between atoms. Help hold shape of proteins

Bonds determine shape of molecule, therefore function

III – Biomolecules

Intro

Biomolecules – organic molecules in/from living organisms
Organic molecules – contain C

Carbohydrates, lipids, proteins – energy or building blocks
Nucleotides – genetic material (DNA, RNA), energy carrying (ATP), regulate metabolism (cAMP)

Functional groups – hang together, transferred together

Carbohydrates

(CH2O)n
organized as:
mono –, di (-ose) –, poly –  saccharides
Polysaccharides  Animal storage – glycogen. Plant storage– starch. Plant structure – cellulose.

Lipids

Fats or oils
Lipids & Phospholipids
3-C molecule (glycerol) with fatty acid tails (long C chains) -> hydrophobic
Phospholipid also has –H2PO4 group

Steroids, Eicosanoids – regulate bodily functions (hormones)

Proteins

Made of amino acids (aas). 20 different aas possible in proteins
Amino acids = central C linked to H, NH2, COOH, variable R groups.
Amino acids linked together by peptide bond (remove H2O between NH2 & COOH groups)
Names = oligopeptides, polypeptides, proteins – according to number of aas present
Structure

Primary – linear sequence of aas
Secondary – shape, stabilized by H bonds. Alpha-helix & beta-pleated sheets common.
Tertiary – 3D. Fibrous, wound together long chains of helices or pleated sheets, water insoluble. Globular, chains fold back on themselves.. S-S, other forces.
Quaternary – several protein chains together -> functional protein

Nucleotides

3 part molecule = PO4, 5-C sugar, nitrogenous base
PO4 = PO4
Sugar = deoxyribose (DNA) or ribose (RNA)
Base = G, C, A, T (DNA) or U (RNA)

Store energy - ATP, NAD, FAD

Transmit Information

from outside to inside cell – cAMP
reproduction – DNA
transcription & translation (& regulate transcription) - RNA

IV – Aqueous Solutions, Acids, Bases, and Buffers

Terminology

Solute = dissolved substance
Solvent = dissolving medium (usually water)
Solution = combination of solute and solvent(s)
Concentration = amount of solute/unit volume of solvent

Mass of one mole = mass of individual particles.  Molecular mass – number of atoms X atomic mass of element in molecule. Ex: H2 = 2 atoms X 1 (mass of H) = 2

Concentration

Molarity = number of moles of solute/liter

Equivalent = molarity X number of charges/ion. Ex: 3M Na+ = 3 eq/L. 3M Ca++ = 6 eq/L. 

% solution = weight/volume (10g solute/100 ml final solution = 10% solution) OR volume/volume (1ml concentration solution/ 100 ml final solution = 1% solution)

pH

Concentration of H+ in a solution. Range = 0-14. 
pH 7 = neutral =  H2O = equal H+ and OH-
pH less than 7 = acid. Acidic chemical adds H+ to solution
pH more than 7 = base. Basic chemical takes H+ from solution

Buffer – resists change in pH of solution.

V – Protein Interactions
Proteins in body provide structure and regulate bodily processes.

Soluble proteins

1. Enzymes – Speed reactions. Presence or absence determines whether or not chemical reaction can happen in normal body conditions.
2. Membrane transporters – bring substances into or out of cells
3. Signal molecules – coordinate processes among cells
4. Receptor proteins - bind signal molecules
5. Binding proteins – bind molecules for transport. Ex: Thyroid binding protein
6. Regulatory proteins – allow or stop cells processes
7. Immunoglobulins = antibodies – help protect body from harmful cells and substances

Protein binding is extremely specific. Depends on shapes and molecular interactions.

Molecule that binds to protein of interest = ligand.

Affinity = attraction between protein and ligand

P + L = PL (P = protein, L = ligand, PL = bound complex)
Because process reversible, concentrations reach equilibrium (some always bound, some always unbound)
                        [P] [L]
Keq = Kd =     [PL]

Small Kd = lower dissociation constant = high affinity between protein & ligand

Factors affecting binding

Isoforms – nearly same molecule with slight variation -> different affinity

Activation – protein needs modification to become active

Cofactor – necessary for binding

Inhibitors
            Competitive – competes with ligand by binding reversibly to active site
            Irreversible – bind to binding site, cannot be displaced

Allosteric modulator – binds to protein, not at active site. Changes activity of protein
            Allosteric activator
            Allosteric inhibitor

pH & temperature – change shape -> change ability to bind

Body regulates amount of proteins to regulate function

Efficient
Effective
more enzyme - > faster production

Reaction rate can reach a maximum

Each protein has bound as much ligand as possible = saturation