Chemistry of Life

Structure of Atoms:

• Consist of protons, neutrons and electrons.


• Atomic nuclei have protons and neutrons (each 1 amu).


• Each element has a different number of protons, e.g. hydrogen has 1 proton, carbon 14.


• The number of protons equals the atomic number of an element.


• Atoms with the same number of protons but different numbers of neutrons are isotopes.


• Cells of living organisms consist of organic and inorganic molecules which are made up of atoms.

Electrons

• The number of electrons (e-) equals the number of protons in the nucleus.


• Electrons move at near light speed, have both wave and matter properties, when their energy level is raised they are said to be in an �excited state�, emission spectra is when this excited electron drops back to its ground state.


• Electrons orbit the nucleus at specific levels called shells.  The shell closes to the nucleus is the innermost shell and has up to 2 electrons.  Second and third shells (L and M) have a maximum of 8 electrons.  If an element has another shell that is filled it is chemically inert.



Chemical Bonds

• Bonds are formed by gaining, loosing or sharing electrons.


• The formation of ionic or covalent bonds depends on the differences between electronegativity in the atoms involved.


• Covalent bonds: formed when atoms share electrons and are very strong.  They are polar if they are between different types of atoms e.g. oxygen and hydrogen as in H2O. 


• Ionic Bonds: atoms become ions when they gain or lose electrons and are weaker than covalent and dissociate in water. 


• Hydrogen Bond: are weak intra or inter molecular attractions between molecules with a net dipole.  Dipoles are created when there is unequal sharing of electrons between H and an electronegative atom like oxygen or nitrogen.



Organic Molecules

• Molecular formulas describe the composition of a substance.


• Structural formulas describe how atoms are arranged in a molecule.


• Nomenclature is the naming procedure for organic molecules.


• Stereochemistry are isomers that have the same molecular formula but different structural formulas.



Nomenclature

• Single bond share one pair of electrons and name ends in (�ane).


• Double bonds share two pairs of electrons, name ends in (-ene).


• Triple bonds share three pairs of electrons, name ends in (-yne).



Biological Macromolecules

• Carbohydrates: made up of monosaccharides (e.g. glucose), stores energy, and modifies other macromolecules (glycolipids, glycoproteins).


• Lipids fat triglycerides (glycerol), phospholipids, stores energy, makes up cell membranes and steroid hormones.


• Proteins: single amino acids join forming peptides, functions as structural proteins and enzymes.


• Nucleic Acids: individual nucleotides link to form genetic material, RNA, DNA. 



Acids, Bases and Buffers

• Electrolytes are substances that release ions in water.


• Acids release H+ in water.


• Bases release OH- in water.


• Strong acids and bases completely dissociate in H2O.


• pH is the concentration of hydrogen ions [H+] in solution.  At pH 7 hydrogen ion concentration equals hydroxyl concentration, [H+] = [OH-].


• Buffers provide pH stability by resisting changes to pH when small amounts of acid or base are added.


• Buffers are weak acids or weak bases and their salts.


Biochemical Reactions
Thermodynamics:
• First Law: Energy is always concerned and cannot be created or destroyed.


• Second Law: Systems tend to become disordered. 


• Entropy (S): describes the degree of disorder in a system. 


• ΔG Gibbs Free Energy is the amount of energy available to do work. 


• ΔG= ΔH - T ΔS (ΔH is enthalpy change), ΔS entropy change, T=temperature (K)


• If ΔG<0 spontaneous reaction, If ΔG>0 non-spontaneous reaction, If ΔG=0 reaction is at equilibrium.


• Enzymes in biochemical reactions lower the activation energy.  Activation energy is the energy required to begin a reaction. 


• Types of enzyme reactions: oxidoreductase, transferase, hydrolase, ligase, isomerase and ligase.