By: Debbie Schwagerman January 31, 2005

1. Chapter 2: Chemical Foundations By: Debbie Schwagerman January 31, 2005

2. Atomic Bonds and Molecular Interactions Each atom has a defined number and geometry of covalent bonds.

3. Atomic Bonds and Molecular Interactions Electrons are shared unequally in polar covalent bonds. Atoms with higher electronegativity values have a greater attraction for electrons.

4. Atomic Bonds and Molecular Interactions Covalent bonds are much stronger and more stable than noncovalent bonds.

5. Atomic Bonds and Molecular Interactions • Ionic bonds result from the attraction of a positively charged ion (cation) for a negatively charged ion (anion). • The atoms that form the bond have very different electronegativity values and the electron is completely transferred to the more electronegative atom. • Ions in aqueous solutions are surrounded by water molecules, which interact via the end of the water dipole carrying the opposite charge of the ion.

6. Atomic Bonds and Molecular Interactions Van der waals interactions are caused by transient dipoles.

7. Atomic Bonds and Molecular Interactions The hydrophobic effect causes nonpolar molecules to adhere to one another.

8. Atomic Bonds and Molecular Interactions Molecular complementarity permits tight, highly specific binding of biomolecules.

9. Chemical Building Blocks of Cells • Proteins • Amino Acids • Nucleic Acids • Nucleotides • Polysaccharides • Monosaccharides

10. Chemical Building Blocks of Cells Common structure of amino acids.

11. Chemical Building Blocks of Cells • 20 amino acids. • All amino acids in nature are L form. • Structure consists of Ca, to which an amino group, a carboxyl group, a hydrogen atom, and a variable group. • Amino acids are classed according to their R group.

12. Chemical Building Blocks of Cells Common structure of nucleotides.

13. Chemical Building Blocks of Cells • Common structure: phosphate group, base, and a five-carbon sugar. • Sugar is either DNA or RNA. • Bases are adenine, guanine, cytosine, thymine (DNA), and uracil (RNA). • Nucleotides link together to build nucleic acids.

14. Chemical Building Blocks of Cells • Monosaccharides are carbohydrates of combinations of carbon and water in a one-to-one ratio. • Except for fructose, all sugars are in nature are D form. • D-Glucose (C6H12O6) is primary energy source.

15. Chemical Building Blocks of Cells • Polysaccharides: • Disaccharides are simplest polysaccharides. • Anomeric carbon of one sugar molecule is linked to hydroxyl oxygen of another sugar molecule. • Polysaccharides can contain dozens to hundreds of monosaccharides.

16. Chemical Equilibrium • The extent to which a reaction can proceed and the rate at which the reaction takes place determines which reactions occur in a cell. • Reactions in which the rates of the forward and backward reactions are equal, so that the concentrations of reactants and products stop changing, are said to be in chemical equilibrium. • At equilibrium, the ratio of products to reactants is a fixed value termed the equilibrium constant (Keq) and is independent of reaction rate.

17. Chemical Equilibrium • Keq depends on the nature of the reactants and products, the temperature, and the pressure. • The Keq is always the same for a reaction, whether a catalyst is present or not. • Keq equals the ratio of the forward and reverse rate constants (Keq = kf/kr). • The concentrations of complexes can be estimated from equilibrium constants for binding reactions.

18. Biochemical Energetics • The change in free energy ∆G is the most useful measure for predicting the direction of chemical reactions in biological systems. Chemical reactions tend to proceed in the direction for which ∆G is negative. • A chemical reaction having a positive ∆G can proceed if it is coupled with a reaction having a negative ∆G of larger magnitude. • The chemical free energy change ∆G equals -2.3RT log keq. Thus the value of ∆G can be calculated from the experimentally determined concentrations of reactants and products at equilibrium.