580.221 BME Molecules and Cells L02 Molecular Forces p1 Lecture Two Molecular forces: Chemical basis of specificity and affinity Outline: chemical foundations (covalent, noncovalent) 4 weak forces importance of pH, pKa, Henderson-Hasselbach equation Molecular Binding The &quot;lock and key&quot; explanation (unique matching, rigid shapes fit each other) is overly simplistic polymer chain of repeated subunits that are covalently attached. Examples proteins, DNA, RNA (see below). The subunits are called monomers and need not all be identical (e.g. amino acids in a protein) chirality specific 3D arrangement of an atom's shared bonds (more when considering protein structure) Water-Related Reactions condensation reaction in which the release of a water molecule results in the formation of a covalent bond (i.e., making a polymer). Repeated condensation of amino acids results in a chain (polypeptide). hydrolysis reaction in which a water molecule joins another molecule, sometimes breaking up a pre-existing covalent bond (i.e., breaking a polymer). Non-covalent Bonds These are weak forces in cells why? Because in water (cells are mostly water), these forces are weaker than covalent bonds. This is not necessarily true in a different environment. You should nderstand what changes the strength of these bonds in water. 1. hydrogen bonds bonds where a proton (hydrogen) is shared between two electronegative atoms oxygen and nitrogen being the most common. In aqueous solutions, water molecules (55M) do most hydrogen bonding. Note the directionality (called polarity; not to be confused with solvent polarity!) of the hydrogen bonding. There are hydrogen `donors' and `acceptors', and they have to pair up in the right direction. In addition, the three atoms are co-linear. 580.221 BME Molecules and Cells L02 Molecular Forces p2 2. ionic bonds interactions between molecular species of opposite polarity, in order to neutralize charge (i.e., Na + Cl -) These bonds are usually weak in cells because of salt shielding (hence, too many ions could interfere with a specific ionic bond). Polarity (see above meaning) is obvious. 3. van der Waal's forces dipole-dipole interactions because of statistical jiggling of atoms that create instantaneous dipoles. This attractive force only acts at a very short range (energy decays with r-6). In addition, it is the only repulsive force (energy decays with r-12) on the list, and provides the `hard' surface required for lock-and-key analogy to be relevant. These two parts of the <a href="/keyword/van-der-waals/" >van <a href="/keyword/der-waals/" >der waals</a> </a> interactions are NOT specific for the atoms involved. Rather, these forces are only important when many molecules from one surface can simultaneously be very close to many molecules on the binding surface. In other words, <a href="/keyword/van-der-waals/" >van <a href="/keyword/der-waals/" >der waals</a> </a> are important when the 3D shapes of the surfaces match well. This force is very weak so many interaction are required. 4. hydrophobicity (water-repulsive) not really a force, a hydrophobic reaction is a repulsion of non-like things (i.e., water and oil don't mix). Molecules that are NOT polar (no dipole, internal charge separation) are usually hydrophobic, since water is polar (oxygen has a slightly more negative charge, and the hydrogens have a slightly positive charge). Water has a great attraction for itself, and prefers to solvate (i.e. contact) as little non-polar material as possible, so it `pushes' hydrophobic molecules together. This strength of hydrophobic attraction increases with temperature (see Free Energy later) Non-covalent mediated interactions between molecules `recognition' Two molecules encounter each other randomly. If they match correctly, non-covalent bonds will begin to form. As the molecules come closer and closer together, hydrophobic and van der Waal's forces will become more significant. If there is no good matching between the two molecules, they will go their separate ways. pH, Henderson-Hasselbach Equation pH: measure of the amount of hydrogen ions present. p is defined to be p = - log10 , so pH=- log10[H+] For an acid: HA H + A + - K acid [H ][A ] (at equilibrium); = + - [HA] by taking the operator p = - log10 all the way through : A- pK acid = pH - log10 , or [HA] [ ] - pH = pK acid + log10 [HA] [A ] which is the Henderson-Hasselbach equation. Ionization An ion is simply a molecule with that is either positively or negatively charged (not neutral) amount charged Fractional _ Ionization = total amount 580.221 BME Molecules and Cells L02 Molecular Forces p3 for an acid, Fractional _ Ionization = [A ] [HA] + [A ] - - By rearranging the Henderson-Hasselbach equation, it's easy to express the ratio [A-]/[HA] in terms of pH and pKacid. If we let R=[A-]/[HA], then it's just as easy to express the Fractional_Ionization in terms of R.