BISC 330L Biochemistry Spring 2015 USC Lecture 2 Wednesday Jan 14 2015 1 Continue Chapter 1 material The complex and diverse biological world can be unified at biochemical level Proteins performing similar biochemical activities have similar structures Fundamental metabolic processes are conserved across different species Genes encoding similar functions are found in diverse organisms The biochemical processes underlie the physical basis of biological heredity Formation a double helix DNA Two complementary DNA strands Double helix Denatured strands Annealed strands Cooling Heating Chapter 1 Biochemistry An Evolving Science Diverse yet similar Structure function analysis of DNA General chemistry review Properties of water Acid base reactions in biochemical processes Review of Chemistry Covalent Bonds sharing electrons stability is the key polar v nonpolar molecules water is polar C H are nonpolar Non covalent bonds opposites attract Ionic bonds Na Cl Hydrogen bonds weak Hydrophobic interaction van der Waals force Covalent bonds require sharing of electrons Review of Chemistry Covalent Bonds sharing electrons stability is the key polar v nonpolar molecules water is polar C H are nonpolar Non covalent bonds electrostatic interactions hydrogen bonds van der Waals interactions hydrophobic interactions opposites attract Coulomb s law E kq1q2 Dr Ionic bonds Na Cl Hydrogen bonds weak van der Waals interactions Hydrophobic interactions What is wrong with this picture Common noncovalent H bond in DNA RNA and proteins C What is wrong with this picture Hint 1 Hint 2 Hydrogen Bonds Electrostatic interactions Weaker than covalent bonds Energies range from 4 20kJ mol Longer than covalent bonds Usually exist on a straight Line van der Waals Interactions Asymmetric charge distribution Attraction increases as two atoms come closer to each other Optimum van der Waals contact distance Closer than contact distance leads to repulsion 2 4kJ mol Even nonpolar groups can weakly attract by induced dipole van der Waals interaction van der Waals forces are stronger if they act as a team Protein protein Interactions interaction energy increases with total contact surface area Chapter 1 Biochemistry An Evolving Science Diverse yet similar Structure function analysis of DNA General chemistry review Properties of water Acid base reactions in biochemical processes Water H2O is a polar molecule 0 8 0 4 0 4 Oxygen draws electrons away from two hydrogens H bonding between H2O molecules in ice Hydrophobic Interactions Hydrophobicity of nonpolar surfaces promotes aggregation by releasing H2O molecules in contact with the surfaces enabling released H2O to form more H bonds with bulk H2O Electrostatic repulsions between negatively charged phosphate groups anions in DNA Reduced by water s high dielectric constant 80 and by addition of salt cations e g Mg2 DNA is stabilized by van der Waals contacts between stacked base pairs Double helix formation and entropy 1st law total energy of a system and its surroundings is constant 2nd law total entropy of a system plus its surroundings always increases G Hsystem T Ssystem describes the energetics of biochemical reactions 25oC pH 7 0 1M NaCl 250 kJ mol A loss of entropy in the system must be met with the release of heat to the surroundings Chapter 1 Biochemistry An Evolving Science Diverse yet similar Structure function analysis of DNA General chemistry review Properties of water Acid base reactions in biochemical processes DNA denaturation dissociation of double helix by addition of base H acceptor DNA denaturation by the addition of base Addition of base H acceptor to DNA causes denaturation above pH 9 by deprotonating G Why pH 9 7 Start with substance HA Ka H A HA pKa log Ka pH pKa log H log H A HA H H A HA 1 A HA A HA When pH pKa deprotonated form is equal to protonated form Note Addition of acid H donor to DNA also causes denaturation below pH 5 by protonating Adenine and Cytosine H H Na Ac H Cl Na Cl HAc Na Ac of 1M HCl Na Ac H Cl Na Cl HAc Read p 14 17 for derivation of Henderson Hasselbalch Equation of 1 M HCl End of Lecture 2 How about these two pictures