AUGUST 29TH Earth s Unique Atmosphere The cause of Earth s unique atmosphere is photosynthesis and other biological processes that keep earth in disequilibrium Biochemistry reveals how the collection of inanimate molecules that constitute living organisms interact to maintain and perpetuate life How the little things come together to make living big things Water The Solvent of Life Most organisms are about 70 or more water by weight In order to understand biochemistry we must understand water Water is polar weakens electrostatic interactions due to its high dielectric constant has two lone pairs of electrons and forms hydrogen bonds Water is both a hydrogen bond donor and a hydrogen bond acceptor Properties of Water Water binds strongly to itself and can form as many as 4 hydrogen bonds at one time Hydrogen bonds are dynamic they are constantly changing Realistically this means that water is actually only participating in about 3 4 hydrogen bonds on average Water has a high melting point boiling point and heat of vaporization because of its hydrogen bonds They bonds are mostly electrostatic with only about 10 of them being covalent Hydrogen bonds are highly directional with linear bonds being the strongest Water Forms Hydrogen Bonds with Other Polar Molecules Any molecule with a hydrogen attached to a nitrogen oxygen or sulfur can participate in hydrogen bonding Hydrogen bonds are important concerning interactions between alcohol and water and between peptide groups in polypeptides The Hydrophobic Effect Water binds strongly to itself and when faced with a nonpolar surface it will attempt to maximize its hydrogen bonding by forming a partially ordered structure This partially ordered structure decreases entropy which is unfavorable formation of micelles Partially ordered structures are like cages around nonpolar molecules Amphipathic compounds contain both polar or charged and nonpolar regions Some examples include detergents and fatty acids lipids The strength of hydrophobic interactions comes from the thermodynamic stability of minimizing the number of ordered water molecules required to surround the hydrophobic portions of solute molecules The hydrophobic effect is important in protein folding and lipid lipid interactions cell membranes The pH Scale Kw is the ionization constant of water and equals the concentration of H multiplied by the concentration of OH This equals 1 x 10 4 M2 pH log H Strong Acids and Bases Strong acids and bases are those that ionize completely in aqueous solution Most mineral acids are strong acids like HCl HNO3 and H2SO4 Lye NaOH KOH and similar compounds are strong bases The pH of a 1 M solution of HCl is 0 The pH of a 0 1 M solution of NaOH is 13 Examples of Simple Acid Base Problems How much NaOH must be added to 1 L water to reach pH11 A pH of 11 implies that the concentration of H equals 10 11 M This means that the concentration of OH is 10 3 M For 1 L of pure water we need 10 3 moles of NaOH The molecular weight of NaOH is 40 g mole so we need 0 04 g or 40 mg NaOH 10 mg of HCl is added to 1 L of pure water what is the final pH 10 mg 36 5 g mole 2 74 x 10 4 moles in 1 L Thus the concentration of H is 2 74 x 10 4 M The pH is then 3 56 Weak Acids and Bases Weak acids and bases don t ionize completely in solution The conjugate acid and the conjugate base will be present in measurable amounts The equilibrium between them is described by the equilibrium constant Ka which equals the concentration of H multiplied by the concentration of the base divided by the concentration of the acid The larger the Ka is the stronger the acid is The stronger the acid the weaker pKa log Ka so the smaller the pKa the stronger the acid the base Titration Curves A buffer is a solution of a conjugate acid base pair at a pH where both species are present in significant amounts This solution resists changes in the pH The maximal buffering capacity is near the pKa the pH where HA A At some point as you add base to a solution the concentration of OH stops increasing because you start deprotonating Eventually you ll deprotonate all of the acid and the pH will begin to rise again Henderson Hasselbach equation When the concentration of the base equals the concentration of the acid the pH is the same as the pKa A good buffer is 1 pH unit from the pKa Buffer Example What is the pH of a buffer prepared from 0 1 M sodium acetate and 0 04 M acetic acid Use the Henderson Hasselbach equation Answer 5 16 AUGUST 31ST Amino Acids The Basics Amino acids are the building blocks of proteins Their general structure is a central carbon atom alpha carbon with four substituents including a primary amino group a carboxylic acid a hydrogen atom and a side chain or R group that gives the amino acid its identity There are only 1 or 2 exceptions to this general structure Amino acids are chiral with the ones in proteins being the L isomers They are NOT flat the alpha carbons are tetrahedral At neutral pH amino acids are zwitterions molecules bearing groups with opposite charge Nonpolar Aliphatic Side Chains Glycine Alanine Proline Valine Leucine Isoleucine Methionine Glycine is the only achiral amino acid and is unusually flexible in conformation within a protein because its R group is so small Proline is an exception to the general structure of an amino acid and is unusually rigid in conformation Alanine Valine Isoleucine and Phenylalanine tend to cluster together in the center of proteins because of hydrophobic effects Methionine is one of two amino acids containing sulfur Isoleucine is an isomer of leucine Aromatic Side Chains Phenylalanine Tyrosine and Tryptophan Phenylalnine is the most hydrophobic of the three Tyrosine and Tryptophan can participate in hydrogen bonding Both rings of Tryptophan are aromatic and it is a good hydrogen bond donor but not a good hydrogen bond acceptor because of its aromaticity Tryptophan and Tyrosine strongly absorb UV light at 280 nm This can be used to calculate the concentration of a purified protein Absorbance equals epsilon l c Polar Uncharged Side Chains Serine Threonine Cysteine Asparagine and Glutamine Asparagine and Glutamine are amides of other amino acids Cysteine can form disulfide bonds Disulfide Bonds Two Cysteine residues can form a covalent cross link or disulfide bond within a protein structure The disulfide bond is the difference between the oxidized and the reduced form of Cysteine Acidic Negatively Charged Side Chains Aspartate and Glutamate