BIOL 302 1st Edition Lecture 2 Outline of Last Lecture I. SyllabusOutline of Current Lecture II. Chapter IA. Functional GroupsB. StereochemistryC. Bonding – Covalent and noncovalentD. Free Energy and pKaCurrent Lecture III. At the biochemical level all organisms have many common featuresIV. Some common functional groups of biochemical moleculesThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.V. Molecular asymmetry: chiral and achiral moleculesA. Achiral can be superimposed on its mirror imageB. Chiral molecule cannot be super imposed on its mirror imageVI. Assigning Stereochemistry: Priority RulesA. 1.) Identify the four different atoms or groups attached to the stereogenic center.B. 2.) Rank the atoms or groups through highest atomic numbers, degree of substitution.C. 3.) Orient a projection of the molecule in space so that the group or atom of lowest rank is eclipsed by the stereogenic center.D. 4.) Determine the ranking of the remaining visible atoms or groupsE. If the ranking declines in a clockwise direction, the configuration is R; if the ranking declines in a counterclockwise direction, the configuration is S.VII. Biochemists indicate stereochemistry with D/L systemA. Represented this way the R-group is always below the central carbon.B. If the amino group is on the left side, the amino acid is LVIII. Stereoisomers can have different effects in humansS,S S,RIX. Bonding in biological systemsA. Covalent and non-covalent bonds are important for the structure and stability of macromoleculesB. Covalent Bonds1. The strongest bonds 2. A typical C-C bond has a bond length of 1.54 Å and 85 kcal/mol3. Double bonds, C=C are even stronger, and are somewhat shorter (175 kcal/mol, 1.34 Å)4. Adenine can be written in two equivalent ways called resonance structures. The composite structure shows intermediate bond length and strengthC. Non covelent bonds1. Weaker than covelent bonds but crucial to biochemical processes2. Four fundamental noncovelent bonds types area. Electrostaticb. H-bondsc. Van der waalsd. HydrophobicD. Ionic/Electrostatic Interactions1. Attractive or repulsive forces between charged groups3. The energy of a electrostatic interaction is given by Coulombs law (left)4. D is the dielectric constant. As D decreases, the strength of electrostatic interactions increase5. Strength varies. In biological systems -3 to -8 kcal/mol6. By convention attractive forces have negative energy�=��_1 �_2/��7. Low dielectric constants (nonpolar environment) increase the strength of electrostatic interactions8. Weak acids / Weak basesE. H-bonding1. Attractive forces between two electronegative atoms through sharing of a hydrogen atom2. The H-bond donor is the group that includes both the atom to which the H is more tightly linked and H itself3. The H-bond acceptor is the atom less tightly linked to the H4. Directionality of the H-bondi. Strongest H-bonds have 3 atoms in a straight lineii. Strength -1 to -5 kcal/molF. van Der Waals2. Attractive or repulsive forces between any molecule, but mostly attributed to interactions involving molecules that are uncharged3. Weakest non-covalent interaction, but the strength scales with contact area4. Strength -0.5to -1 kcal/molG. Hydrophobic interactions/effect1. Water being a polar, H-bonding molecule is unable to interact favorably with non-polar molecules2. Water molecules form ordered “cages” or “ice-burgs” around these nonpolar moleculesH. Hydrophobic interactions stabilize micelles and membranesX. Water can act as a hydrogen bond donor and a hydrogen bond acceptorXI. The double helix reveals multiple non-covalent interactionsElectrostatic repulsionBase stackingXII. Summary: Non-covalent bonding in biological systemsXIII. The first and second law of thermodynamicsA. First law: the total energy of a system and its surroundings is constantB. Second law: The total entropy of a system and its surroundings always increases.∆G= ∆H system – T ∆S system < 0 ∆G Gibbs free energy change∆H Enthalpy changeT Temperature∆S Entropy changeXIV.Clicker question :Which of the following is allowed according to the first and second law of thermodynamics?A. For a reaction to occur spontaneously, ∆G has to be greater than 0.B. A positive change of the enthalpy and a decrease of the entropy result in a spontaneousreaction.C. A negative change of enthalpy and an increase of entropy always results in a spontaneous reaction.D. A negative change of enthalpy and a negative change of entropy always results in a spontaneous reaction.XV. pH effects in biological systemsXVI. Weak acids / Weak basesA. Buffering in biological systems make use of acids that do not completely dissociate inwater – these are the weak acids/bases1. Each acid has a characteristic tendency to lose a proton in aqueous solution2. The stronger the acid the greater the tendency to lose a proton3. Equilibrium constants for proton dissociation are usually called ionization constantsXVII. Henderson Hasselbach equationXVIII. pKa values provide a convenient measure of acid strengthA. The pKa expresses on a logarithmic scale, the relative strength of a weak acid or weak baseB. The stronger the acid, the lower the pKa; the stronger the base the higher the pKaXIX. pKa values can be determined experimentallyA. At the inflection point, pH = pKaB. Shown in the boxes are the predominant ionic forms at the indicated pHC. “Buffering range”, where the pH changes the least on addition of H+ or OH-D. Spans 1 pH unit above to1 pH unit below the pKaXX. Some common buffers in biological systemsA. Titration curves for acetic acid (pKa 4.76), dihydrogen phosphate (pKa 6.86), and ammonium ion (pKa 9.25).XXI. Clicker question: Which is the strongest acid? Strongest base?A. strongest acid ammonium ion, strongest base acetic acidB. strongest acid acetic acid, strongest base ammonium ion.XXII. Clicker questionA. The pH of the blood plasma of most individuals is 7.4, but in a severely diabetic person, this value can fall to pH 6.8. The blood plasma [H+] in a diabetic person will be ______ than the blood plasma [H+] in a normal person.a. Lower by about 10 X b. Lower by about 4 Xc. About the samed. Higher by about 4 Xe. Higher by about 10 XXXIII. Configurations of geometric isomersXXIV. Typical ranges of bond