Quick Review of Subatomic Particles and Bonds PDF

3 Subatomic Particles • Protons • Neutrons • together with p+ determine atomic mass • Electrons • 4 important roles in physiology: 2 Covalent Bonds • …create molecules • Strong bonds require energy to make or break • Share pairs of electrons • Single, double, and triple bonds • Polar and non...

3 Subatomic Particles • Protons • Neutrons • together with p+ determine atomic mass • Electrons • 4 important roles in physiology: 2 Covalent Bonds • …create molecules • Strong bonds require energy to make or break • Share pairs of electrons • Single, double, and triple bonds • Polar and nonpolar molecules 3 Noncovalent Bonds • Ions are charged atoms • Cations • Lost electrons • Positively charged (+) • Anions • Gained electrons • Negatively charged (–) • Hydrogen bonds • dependent on polar covalent bonds • Van der Waals forces 4 Noncovalent Interactions • Hydrophilic interactions create biological solutions What determines solubility? • 6 Expressions of Solution Concentration • Percent solutions • 5% glucose solution • 5 g in 100 mL • 50 g in 1 L • 20 mg/dL • Molarity • mol/L • more common in biological solutions: mmol/L or mM 7 Hydrophilic Interactions 8 Hydrophobic Interactions 9 Large Molecule Shape • 10 Can be affected by free [H+] pH • • • • • 11 What does pH measure? How is it calculated? What determines if something is acidic or basic (alkaline)? What does an acid do in solution? What does a base do? A Diversity of Proteins • Jobs proteins can have: • Enzymes • Membrane transporters • Signal molecules • Receptors • Binding proteins • Immunoglobulins • Regulatory proteins • What they all have in common: 14 • all bind other molecules through noncovalent interactions Protein Interactions • Binding sites • specificity to a ligand • other sites may bind cofactors • Ligand or substrate? 15 Protein-Binding Reactions are Reversible • Affinity: the degree to which a protein (P) is attached to its ligand (L) • Because this binding is reversible this interaction between proteins and their ligands they tend towards a state of equilibrium • equilibrium: rate of binding… P + L → PL • is equal to the rate of unbinding (called dissociation)… P + L ← PL • or, combining the two… P + L ⇌ PL 16 Protein-Binding Reactions are Reversible • Equilibrium Constant • for any reversible reaction, we can look at the concentrations of the products and reactants and compare the ratio of products to reactants to see how close to equilibrium it is: [PL] [P][L] • if there are equal concentrations of products (protein bound to ligand) as there are reactants (separate protein and ligands) then the expression above equals 1 • this ratio is known as the equilibrium constant or Keq: [PL] Keq = [P][L] 17 Protein-Binding Reactions are Reversible • Dissociation Constant • if the equilibrium constant shows the ratio of products to reactants, the inverse shows the ratio of unbound reactants over the bound products: [P][L] Kd = [PL] • when Kd < 1 the bound products are favored (indicating high protein-ligand binding affinity) • when Kd > 1 the unbound reactants are favored (low protein-ligand binding affinity) • Competitors: similar ligands that can compete for the binding site of a protein • Agonists: competitors that mimic each other 18 Application • A researcher is designing a drug that binds a particular cell receptor protein. Several agonists have been identified, but two in particular show the most promise: • Candidate A: Kd = 4.9 • Candidate B: Kd = 0.3 • Which candidate molecule has the most potential for success? 19 Factors That Alter (Modulate) Protein Binding 20 Antagonists 21 Physical Factors • pH and temperature • each cell can modulate its own response by increasing or decreasing the amount of a particular protein • up-regulation • programmed production of new proteins • increase or enhance a cell’s response to a ligand • down-regulation • programmed removal of proteins 22 • decrease a cell’s response to a ligand Functionally: • 3 Fluid-Filled Spaces • Extracellular fluid (ECF) • Plasma • Interstitial fluid • Intracellular fluid (ICF) 25 Membranes • Maintain the boundaries • Regulate passage across boundaries 26 2 Types of Biological Membranes 1. Tissue that lines a cavity or separates spaces 28 2 Types of Biological Membranes 2. Cell membrane • separates a cell from the ECF • regulates exchange with ECF • communication between ICF and ECF 29 Basic Cell Membrane Structure • Lipids • phospholipids • cholesterol • Proteins • Carbohydrates • glycoproteins • glycolipids • glycocalyx 30 Individual Cells Show Compartmentation 32 Organelles Create Compartments • Specialization of functions 33 Protein Synthesis • …demonstrates how subcellular compartmentation allows for specialization 34