Biochemistry Notes (Week One) I.

Water -Chemical Bonds -Types of molecules: polar, nonpolar, ionic -Properties of Solvents -Electro negativity: the tendency of an atom to attract electrons towards itself -Ionization: the process of converting an atom or molecule into an ion by adding or removing charged particles A. Water and Hydrogen Bonds 1. The water molecule and its ionization products H+ and OH- profoundly influence structure. 2. Hydrogen bonds between water molecules provide the cohesive forces that make water a liquid at room temperature a. Q: What is a hydrogen bond? Hydrogen bears a partial positive charge and oxygen has a partial negative charge. b. As a result, there is an electrostatic attraction b/w oxygen atom of one water molecule and hydrogen of another. c. Hydrogen bonds, ionic, hydrophobic, and van der waals interactions are individually weak, but collectively have significant influence on 3-D structures of proteins. 3. Polar biomolecules can dissolve readily in water because they replace water-water interactions with energetically favorable water-solute interactions. In contrast, non-polar biomolecules interfere with water-water interactions and unable to form water-solute interactions. a. Why? Nonpolar molecules are poorly soluble in water. 4. In aqueous solutions, non polar molecules tend to cluster together. 5. Water as a solvent-water dissolves many crystalline salts by hydrating their component ions. The NaCl crystal lattices are disrupted as water molecules cluster about the Cl- and Na+ ions stabilizing the ions, weakening the electrostatic interactions, breaking the lattice B. Dispersion of Lipids in Water 1. Hydrophobic effect: accounts for why nonpolar regions of molecules cluster together in water. 2. It takes more energy for polar water to surround each individual non polar end, so it clusters which is more energetically favorable. 3. Micelles: all hydrophobic groups are sequestered (secluded) from water; ordered shell of H2o is minimized, and entropy is further increased. a. Michelles are characteristic of amphipatic cells, in which there is a polar head and nonpolar tail, and all the nonpolar ends cluster together to minimize exposure to water. C. Water in Liquid and Ice Form 1. In water @ liquid, water molecules are disorganized and in a continuous motion, so each molecule forms hydrogen bonds with 3.4 other molecules. 2. In ice, each water molecule is fixed in space and forms hydrogen bonds with 4 other water molecules to yield a regular lattice structure. a. Breaking hydrogen bonds to destabilize crystal lattice requires high thermal energy, so theres a high melting point b. Ice crystal lattice structure makes ice less dense than liquid water, thus ice floats in water

BUT! Hydrogen Bonds are not unique to water. They readily form between an electronegative atom and hydrogen atom covalently bonded to another electronegative atom.

D. 1. Four Types of Weak Non Covalent bond Interactions Among Biomolecules in Aqueous Solut. a. Hydrogen Bonds: between neutral groups and between peptide bonds b. Ionic interactions c. Hydrophobic d. Van der waals 2. Hydrogen bonding doesnt work for CH (hydrogen covalently bonded to carbon) because carbon is only a little bit more electronegative then H. So CH bonds is barely, very weakly polar. E. If its polar, there is hydrogen bonding! 1. Uncharged, but polar biomolecules such as sugars dissolve readily in water b/c of stabilizing effect of hydrogen bonds b/w hydroxyl groups or carbonyl groups of sugar and polar H2o in water. 2. Alcohols, aldehydes, ketones, and compounds containing NH bonds all form hydrogen bonds with water molecules and are soluble. F. Van Der Waals/London Dispersion Forces 1. Are weak intermolecular forces that arise from interactive forces between instantaneous dipole in molecules without permanent dipole moments. II. Ionization of Water, Acids, and Bases Q: Which of the following is true about acids and bases? A: Strong acids and bases are completely ionized in dilute aqueous solutions A. Acids are proton donors and bases are proton acceptors 1. The greater the acidity of a solution, the lower its pH. a. weak acids partially ionize to release H ion, thus lowering the pH, weak bases accept H ion, increasing pH. b. the stronger the acid, the lower its pKa; stronger base, higher pKa 2. The Henderson-Hasselbalch relates pH, pKa, and buffers