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Biochemistry

Biochemistry. : Chemistry in bio logical systems. Biochemistry is the study of the chemical processes and transformations in living organisms. Most of biochemical reactions are done by enzymes , the catalysts of biological systems.

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Biochemistry

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  1. Biochemistry : Chemistry in biological systems

  2. Biochemistry is the study of the chemical processes and transformations in living organisms Most of biochemical reactions are done by enzymes, the catalysts of biological systems Key metabolic processes are common to many organisms.

  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

  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

  5. Chapter 1: Prelude: Biochemistry

  6. Geological and biochemical findings support a time line for the evolutionary path

  7. Cystic fibrosis DNA: The storage of genetic information

  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.

  9. DNA is constructed from four building blocks Base: A, C, G, T

  10. Covalent structure of DNA

  11. Two single strands of DNA combine to form a double helix

  12. Double Helix: Watson AND Click propsosed in 1953

  13. Watson-Crick base pairs: A-T & G-C

  14. DNA structure explains heredity and storage of information • 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.

  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

  16. Concept from Chemistry • Types of chemical bonds • Thermodynamics • The principle of Acid-base chemistry

  17. Covalent Bonds

  18. Resonance Structures A molecule that can be written as several resonance structures has greater stability than does a molecules without multiple resonance structures.

  19. Non-covalent Bonds q1 q2 • Electrostatic interactions: E=kq1q2/Dr2 • Hydrogen bonds • van der Waals interactions r

  20. Properties of water • Water is a polar molecule • Water is highly cohesive

  21. Structure of water molecule Distribution of charge is asymetric

  22. Structure of ice Highly ordered and open structure

  23. Polar and non polar biomolecules at pH 7

  24. Hydrogen bonds are highly directional and capable of holding two hydrogen bonded molecules or groups in a specific geometric arrangement.

  25. The hydrophobic Effect The strength of hydrophobic interactions results from the system’s achieving greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules.

  26. DNA double helix: Expression of the rules of chemistry

  27. Types of chemical bonds • Thermodynamics • The principle of Acid-base chemistry

  28. Heat is released in the formation of the double helix

  29. Energy coupling links reaction in Biology

  30. Types of chemical bonds • Thermodynamics • The principle of Acid-base chemistry

  31. The movement of hydrinium and hydroxide ions in the electric field is anomalously fast

  32. The ionization of water (Kw) is expressed by an equilibrium constant Neutral pH

  33. Acid-Base reactions can disrupt the double helix The pKa 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.

  34. Henderson-Hasselbalch equation The tendency of any acid (HA) to lose a proton and form its conjugated base (A-).

  35. Buffer action Biological systems need a solution system to resist a signficant change in pH pKa

  36. At pH 9, the ratio of acetate ion and acetic acid is very high (18000). At pH 3, the ratio is about 0.03. Conclusion: Buffers function best close to the pKa values of their acid component. pKa = 4.75

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