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Biochemistry : Chemistry in biological systems Slide 2 Biochemistry is the study of the chemical processes and transformations in living organisms Key metabolic processes are common to many organisms. Most of biochemical reactions are done by enzymes, the catalysts of biological systems Slide 3 Biochemistry Berg Tymoczko Stryer Part 1. The molecular design of life Part 2. Transducing and sorting energy : degradation of molecules (CH, FA, Pr) Part 3. Synthesizing the molecules of life : AA, NT (DNA, RNA), Lipids, Pr Slide 4 Part 1. The molecular design of life Chapter 1. Prelude: Biochemistry and the genomic revolution Chapter 2. Biochemical evolution Chapter 3. Protein structure and function Chapter 4. Exploring proteins Chapter 5. The flow of genetic information Chapter 6. Exploring genes Chapter 7. Exploring genes Chapter 8. Enzymes: Basic concepts and kinetics Slide 5 Chapter 1: Prelude: Biochemistry Slide 6 Geological and biochemical findings support a time line for the evolutionary path Slide 7 Cystic fibrosis DNA: The storage of genetic information Slide 8 The tree of life. A possible evolutionary path from a common ancestor cell to the diverse species present in the modern world can be deduced from DNA sequence analysis. Slide 9 Base: A, C, G, T DNA is constructed from four building blocks Slide 10 Covalent structure of DNA Slide 11 Two single strands of DNA combine to form a double helix Slide 12 Double Helix: Watson AND Click propsosed in 1953 Slide 13 Watson-Crick base pairs: A-T & G-C Slide 14 DNA structure explains heredity and storage of information 1.The structure is compatible with any sequence of bases. 2. Because of base pairing, the sequence of base along one strand completely determines the sequence along the other strand. Slide 15 * RNA is an intermediate in the flow of genetic information Ribose instead of Deoxyribose Uracil instead of Thymine * Proteins, encoded by nucleic acids, perform most of functions Slide 16 Concept from Chemistry 1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry Slide 17 Slide 18 Covalent Bonds Slide 19 Resonance Structures A molecule that can be written as several resonance structures has greater stability than does a molecules without multiple resonance structures. Slide 20 Non-covalent Bonds 1.Electrostatic interactions: E=kq 1 q 2 /Dr 2 2.Hydrogen bonds 3.van der Waals interactions r q1q1 q2q2 Slide 21 Properties of water 1.Water is a polar molecule 2.Water is highly cohesive Slide 22 Structure of water molecule Distribution of charge is asymetric Slide 23 Structure of ice Highly ordered and open structure Slide 24 at pH 7 Polar and non polar biomolecules Slide 25 Hydrogen bonds are highly directional and capable of holding two hydrogen bonded molecules or groups in a specific geometric arrangement. Slide 26 The strength of hydrophobic interactions results from the systems achieving greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules. The hydrophobic Effect Slide 27 DNA double helix: Expression of the rules of chemistry Slide 28 1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry Slide 29 Heat is released in the formation of the double helix Slide 30 Energy coupling links reaction in Biology Slide 31 1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry Slide 32 The movement of hydrinium and hydroxide ions in the electric field is anomalously fast Slide 33 Neutral pH The ionization of water (K w ) is expressed by an equilibrium constant Slide 34 Acid-Base reactions can disrupt the double helix The pK a for the proton on N-1 of guanine is 9.7 ; When pH equals the pKa, the concentration of the deprotonated form is equal to the concentration of the protonated form. Slide 35 Henderson-Hasselbalch equation The tendency of any acid (HA) to lose a proton and form its conjugated base (A-). Slide 36 pKa Buffer action Biological systems need a solution system to resist a signficant change in pH Slide 37 At pH 9, the ratio of acetate ion and acetic acid is very high (18000). At pH 3, the ratio is about 0.03. pKa = 4.75 Conclusion: Buffers function best close to the pKa values of their acid component. Slide 38