1. Fundamentals of Biochemistry Third Edition Fundamentals of Biochemistry Third Edition Chapter 1 Introduction to the Chemistry of Life Chapter 1 Introduction to the Chemistry of Life Copyright © 2008 by John Wiley & Sons, Inc. Donald Voet Judith G. Voet Charlotte W. Pratt

2. 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

3. 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?

4. 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

5. Interactions between functional groups replication

8. 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

9. 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

10. Types of Cells Prokaryotes –Lack a nucleus –Various sizes –Individual cells –Suited to environment

11. Eukaryotic –Contain a nucleus Stores DNA –Much larger –Contains organelles

12. Relationship of Organisms

13. 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

14. 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 = U final – U initial = q – w w = PΔV (for a system a constant pressure) H = U + PV –ΔH = ΔU + PΔV = q P – w + PΔV ΔH = q P In biological systems there is no volume change (PΔV = 0) and ΔH = ΔU Spontaneous Processes –First Law of Thermodynamics cannot alone explain

15. 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 = k B ln W

16. 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 –ΔS system + ΔS surroundings = ΔS universe > 0 In biological systems, we cannot measure W –ΔS ≥ (q/T)

17. 2H 2 + O 2 → 2H 2 O (with spark) Spontaneous At constant pressure Gibbs free energy (G) G = H – TS ΔG = ΔH – TΔS –Exergonic (spontaneous) –Endergonic (not spontaneous) –Equilibrium ( ΔG = 0)

18. Entropy depends on volume, and therefore, concentration The free energy of substance A is: –G A = G° A + RT ln [A] For the general reaction: –aA +bB ↔ cC + dD van‘t Hoff

19. 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

20. 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.