Slide 1Slide 2Slide 3Properties of Covalent BondsAromatic RingsDelocalized Electrons in Aromatic RingsA related idea: conjugated double bondsAbsorption of Lightb - caroteneSlide 10Slide 11Slide 12High Energy BondsWeak chemical interactions that are important in biologySlide 15Slide 16Clicker QuestionBiology Happens in WaterHydrogen BondsHydrogen BondsSlide 21Ionic Bonds = Electrostatic Interactionsvan der Waals ForcesSlide 24van der Waals Forces in Protein StructureStacking of Aromatic RingsHydrophobic InteractionsFatty acids are examples of hydrophobic biomoleculesSlide 29Slide 30Slide 31Slide 32Importance of Weak Interactions in BiologyMany biological molecules are charged.pH: a measure of H+ concentrationpH ScaleSlide 37Looking for Clinical Experience?Join Carle Foundation Hospital as a volunteer!As a volunteer you will: Gain vital experience needed for any healthcare related field. Interact with patients and nursing staff.Become an important aspect of the area’s leading provider for healthcare and trauma services.Carle strives to serve people through high quality care, medical research and education including: The area’s only Level I Trauma Center A Level III Neonatal Intensive Care Unit 300 Physicians in 50 specialtiesApply now online at:http://www.carle.org/volunteering Application Deadline: Fall Semester—August 29Spring Semester—November 15Summer—April 15Questions? Contact Dorian Bradford at [email protected] or at 383-3362MCB 250 - Lecture 2Some Chemical Fundamentals•Strong Bonds–Covalent bonds –Cis/trans isomerism (Lecture 1)–Resonance and aromaticity, UV absorbance–Stereoisomerism (D,L)•Weak Bonds–Ionic bonds–Hydrogen bonds–Van der Waals interactions–Hydrophobic “bonds”Chemical Fundamentals: Chemical BondsProperties of Covalent Bonds•Rotation about some bonds but not others•Resonance and aromaticity•Steroisomerism•Some bonds have a high transfer potential: the concept of a “high energy bond”Aromatic RingsCCCCCCHHH HHHBenzeneCCCCCCHHH HHH=2 “resonance” structures with alternation or “conjugated” double bondsThe true structure cannot be represented by a single valence-bond structure but can be thought of as a hybrid of the two. The two forms are NOT in equilibrium.Delocalized Electrons in Aromatic RingsA related idea: conjugated double bondsCHCHHCHHCHButadiene“Conjugated” Double BondsAlternating double and single bondsElectrons delocalizedAbsorption of LightAbsorbanceWavelength•Electrons move in “quantized” orbitals.•Light of the appropriate energycan kick electrons into a higher energy orbital.•The “absorption spectrum” providesinformation about molecular structure.•All molecules absorb radiation.•Aromatics and compounds with conjugated double bonds absorb light in the UV or visible range.An absorption spectrumb - caroteneMore conjugated double bonds means that light of lower energy will be absorbed.b-carotene absorbs in the visible and is intensely colored.The bases of DNA and RNA absorb light at 260 nm, while the aromatic amino acid tryptophan absorbs light at 280 nm.StereoisomerismNineteen of the 20 amino acids can exist as distinct L- or D- stereoisomers. Life evolved to use L-amino acids in proteins.Why only one stereoisomer in biological systems? Most biological interactions depend on precise interactions between chiral molecules. Only one form will fit, the other won’tThis one fits. This one doesn’t.High Energy BondsThis does not refer to bonds that are “strong”, but rather those that release significant energy when hydrolyzed. ATP hydrolysis is a perfect example.ΔG ~ -7 kcal/molWeak chemical interactions that are important in biology•Hydrogen bonds•Ionic bonds•van der Waals interactions•Hydrophobic interactionsWater is a polar molecule: it has a dipole moment as a result of unequal sharing of electrons.Hydrogen Bonds Account for the Properties of Water, which forms a Lattice StructureClicker QuestionDespite its lattice structure, water can flow because ...A. hydrogen bonds break and re-form rapidly. B. many water molecules have no hydrogen bonds. C. hydrogen ions can move between molecules. D. hydrogen bonds are too weak to affect movements. E. None of the above.Biology Happens in Water•H2O is a polar solvent.•H2O is a protic solvent: it makes hydrogen bonds. It is both a H-bond donor and an H-bond acceptor.•These two properties make the interactions that underlie biological processes possible.Hydrogen BondsStrength of the Hydrogen Bond is Affected by OrientationStraight is BetterTwo WaterMoleculesTwo Parts of One Large MoleculeHydrogen Bonds•Hydrogen covalently bonded to electronegative elements (O and N in biological systems), the H-bond donor, can interact with another electronegative element (O or N), the H-bond acceptor.•H-bonds are directional: stronger interaction if linear (see next slide).• Not all H-bonds are equally strong but generally DG approximately 3-7 kcal/mole.All things being equal, they’ll line up to maximize (straighten) the hydrogen bondCCNNOHExample: hydrogen bond between two peptide backbones.Orientation MattersStrongerWeakerIonic Bonds = Electrostatic InteractionsOpposite Charges AttractCH2-CH2-CH2-CH2-NH3+ - OOC-CH2 Lysine AspartateDG approximately 5 kcal/mole in water but stronger interactions are possible inside protein molecules.These interactions are not directional.Note also that like charges repel.van der Waals Forces•The electron clouds of all molecules attract each other very weakly. (The attraction is weaker than ionic or H-bonds).•The effect is very dependent on the distance between the two molecules (1/r6) but if the molecules are too close the electron clouds repel.•Individual van der Waals interactions are weak but the sum of a number of van der Waals interactions can result in a significant force.•van der Walls forces are therefore most significant when two large surfaces fit together.van der Waals Forces in Protein StructureStacking of Aromatic RingsStacking interactions – van der WaalsOverlapping p-bonds stabilize interaction of stacked aromaticsVery important in stabilizing DNA structureHydrophobic Interactions•Hydrophobic – water hating•Hydrophilic – water loving -H2O H-bonds very well with itself•Molecules without a dipole moment do not interact well with H2O•These hydrophobic molecules are excluded by H2O•“Oil and