Fundamentals of Biochemistry Third Edition Donald Voet • Judith G. Voet • Charlotte W. Pratt Chapter 1 Introduction to the Chemistry of Life Copyright © 2008 by John Wiley & Sons, Inc. What is Biochemistry? • Biochemistry is more like – chemical biology • Has aspects of many different disciplines – Cell biology, genetics, immunology, microbiology, pharmacology, and physiology • Study of how chemicals interact and influence biological systems Central Questions • What are the chemical and 3-D structures of biological molecules? • How do biological molecules interact? • Who do living organisms use biological molecules? • How is energy made and used by living organisms? • What are the mechanisms for organizing biological molecules and regulating their activities? • How is genetic information stored, transmitted, and expressed? Section 1 - Origins of life • Only a few elements make up living organisms. – Other elements may include • B, F, Al, SI, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I, and W • Two theories of origins of life – Miller & Urey, electric discharge to a “primordial” atmosphere – Hydrothermal conditions in seawater • Generation of functional groups Interactions between functional groups replication Section 2 – Cellular Architecture • Formation of cells – From vesicles • Compartmentation – Protection from environment – Higher concentration of reactants leads to more reactions – Different composition from environment • Problems – Run out of precursor molecules • Appearance of mechanisms to generate new ones (catalysis) – Need energy to make molecules • Appearance of photosynthesis – Survive in an oxygen rich environment • Appearance of aerobic respiration • Adaptation – Diversification – Differentiation of cells generated multicellular organisms Types of Cells • Prokaryotes – – – – Lack a nucleus Various sizes Individual cells Suited to environment • Eukaryotic – Contain a nucleus • Stores DNA – Much larger – Contains organelles Relationship of Organisms Evolution • Natural Selection – Mutation in genetic material arise by chemical damage or inherent errors • Positive mutations are passed to future generations • Negative mutations usually are eliminated • Principles of Evolution – – – – Evolution is not directed toward a particular goal Individuals are varied The past determines the future Evolution is ongoing Section 3 - Thermodynamics • First Law of Thermodynamics – energy is conserved • The study of energy (U) – System, surroundings, heat (q) and work (w), enthalpy (H) • ΔU = Ufinal – Uinitial = q – w • w = PΔV (for a system a constant pressure) • H = U + PV – ΔH = ΔU + PΔV = qP – w + PΔV • ΔH = qP • In biological systems there is no volume change (PΔV = 0) and ΔH = ΔU • Spontaneous Processes – First Law of Thermodynamics cannot alone explain • Second Law of Thermodynamics – a spontaneous process is defined as the conversion of order to disorder • Disorder is defined as the number of energetically equivalent arrangement (W) • Entropy (S) is a measure of randomness • S = kB ln W • For a spontaneous process such as the exchange of gas, overall energy (U) and enthalpy (H) change is zero • The change in entropy (S) must be greater than zero – ΔSsystem + ΔSsurroundings = ΔSuniverse > 0 • In biological systems, we cannot measure W – ΔS ≥ (q/T) • 2H2 + O2 → 2H2O • At constant pressure (with spark) Spontaneous qP H S H T S 0 T T • Gibbs free energy (G) • G = H – TS • ΔG = ΔH – TΔS – Exergonic (spontaneous) – Endergonic (not spontaneous) – Equilibrium (ΔG = 0) • Entropy depends on volume, and therefore, concentration • The free energy of substance A is: C c D d G G RT ln Aa B b G RT ln K eq – GA = G°A + RT ln [A] • For the general reaction: C D G eq eq RT K eq e a b Aeq B eq c – aA +bB ↔ cC + dD van‘t Hoff d H 1 S ln Keq R T R y mx b • Convention: T = 25°C; P = 1 atm; activity = 1 • New definition of standard state – Activity of water is 1 even though concentration is 55.5 M – [H+] is 1 at pH = 7 NOT pH = 0 – Acid-base reactions are defined as the naturally occurring ion at pH = 7 NOT pH = 0. • Therefore, define new ΔG – Biochemists use ΔG°’ instead of ΔG° to distinguish between the different standard conditions • Organisms obey thermodynamics • Organisms are open systems and never reach equilibrium • Organisms are at a steady state (the system does not change with time) • Biological catalysts (enzymes) provide a better pathway for reactions to occur – This allows for reasonable reaction rates Practice – You should be able to complete all of the problems at the end of the chapter. Exam questions will require the understanding of all topics covered.