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lehninger(sixth edition) Ch 01: The foundations of biochemistry


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The foundations of biochemistry are the first chapter of lehninger's biochemistry.

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lehninger(sixth edition) Ch 01: The foundations of biochemistry

  1. 1. CHAPTER-1 Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)
  2. 2. Learning Objectives • Prokaryotic and eukaryotic cell structure and functions of each structure. • Organic chemical bonds and functional groups. • Stereoisomers and cis-trans conformations. • Basics of Thermodynamics and Chemical Kinetics. • Basics of Catabolism and Anabolism. • Biochemical hierarchy from monomerspolymerscell structure. • Evolution of cells: endosymbiosis; vertical and horizontal gene transfer. • Evolution of proteins: orthologs and paralogs.
  3. 3. Prokaryote and Eukaryote Cells what size you see in a microscope? what’s its volume and how much actin and mitochondria could it hold? how many molecules?
  4. 4. Prokaryotic Cell calculate the length of DNA in a bacterial cell… here it is all folded up!
  5. 5. Bacterial Cytoplasm Is Full of Molecules
  6. 6. Prokaryotic Cell Envelope
  7. 7. Eukaryotic Cell
  8. 8. Muscle Cells
  9. 9. Eukaryotic Cytoskeleton: Actin (red), Microtubules (green) Surround the Nucleus (blue). Fluorescence Microscopy.
  10. 10. Cytoskeleton Elements Bacteria also have filaments (actin like) and microtubules to organize their cytoplasm.
  11. 11. Biological Monomers What to Look For = What’s Important: Functional Groups: amino, carboxyl, carbonyls (both), alcohol, methyl, phosphate, sulfhydryl, and others. Covalent Bonds – single, double, triple. Ionization state, or not. Solubility How Monomers are Polymerized Weak Bonds = H-bonds, Ionic bonds, hydrophobic interactions, van der Waals forces.
  12. 12. The Monomers
  13. 13. Structure to Molecular Hierarchy
  14. 14. Periodic Chart
  15. 15. Carbon Bonding
  16. 16. Carbon Bonding
  17. 17. Geometry of carbon bonding
  18. 18. Common Functional Groups of Biological Molecules
  19. 19. several functional groups in single biomolecule.
  20. 20. Molecular Weight or Mass Biochemistry uses both Molecular Weight (Mr) or Molecular Mass (m) in “Daltons” Carbon has Mr = 12 or m = 12D Very Small Proteins have a mass of 10,000D = 10kD Very Large ones have mass of >1million D = 1,000kD (Titin a muscle protein ~3 million D)
  21. 21. Representation of molecules Ball-and-stick model Space-filling model Structural formula in perspective form
  22. 22. Cis and Trans (Configurations of geometric isomers)
  23. 23. Cis and Trans – Conformational Change
  24. 24. Chirality Problem 11 is about two pharmacological drugs and fits right in here with chirality and drug dosage.
  25. 25. This is Pasteur Looking at Dried Rabbit Spinal Chord….used as a Rabies Vaccine Tartaric acid precipitates out of aging wine into two types of crystals that Pastuer separated with tweezers and determined the optical rotation of polarized light.
  26. 26. Chiral Rotation Rectus (right) Sinister (left)
  27. 27. Rotation by Priorities Priorities of Some Biochemical Functional Groups -OCH2 > -OH > -NH2 > -COOH > -CHO > -CH2OH > -CH3 > -H
  28. 28. Interactions between biomolecules are specific
  29. 29. Stereoisomers Have Different Biological Effects
  30. 30. ATP
  31. 31. Thermodynamics You Already Know Endothermic vs Exothermic ΔG = ΔH – T ΔS ΔG is related to the Equilibrium Constant ΔG = G products – G reactants Reactants = Substrates ΔGo = standard free energy change (we will change this later) for aA + bB  cC + dD ΔG = ΔGo + RT ln K eq
  32. 32. AAA : Hexokinase Rxn
  33. 33. How to speed reactions up Higher temperatures Stability of macromolecules is limiting Higher concentration of reactants Costly as more valuable starting material is needed Change the reaction by coupling to a fast one Universally used by living organisms Lower activation barrier by catalysis Universally used by living organisms
  34. 34. Metabolic Pathway • produces energy or valuable materials Signal Transduction Pathway • transmits information Series of related enzymatically catalyzed reactions forms a pathway
  35. 35. Example of a negative regulation: Product of enzyme 5 inhibits enzyme 1 Pathways are controlled in order to regulate levels of metabolites
  36. 36. Anabolism and Catabolism
  37. 37. Metabolic Diversity
  38. 38. Information Codes Prism of Sennacherib Bacterial DNA ~700 BC, Assyrian
  39. 39. DNA Replication
  40. 40. Central Dogma DNA code Transcription  Translation  Protein
  41. 41. A
  42. 42. Miller and Urey Experiment in a Garage, 1953
  43. 43. RNA World to DNA/RNA/Protein World
  44. 44. Current Year
  45. 45. Endosymbiotic Origin of Mitochondria and Chloroplasts
  46. 46. From Darwin to Orthologous and Paralogous Genes
  47. 47. Paralogous Selection Required Gene Duplication
  48. 48. Things You must have to know • To understand what defines living organisms and how biochemists isolate cell structures • To know cell structures and their functions • To know the organic structure of biomolecule’s functional groups and bonds • To grasp principles of bioenergetics and chemical kinetics • To know basics of catabolism and anabolism and biochemical hierarchy • To review the forces driving evolution and know the difference between orthologous and paralogous evolution of proteins. • To be able to do Problems 1, 3, 5, 8, 11, 12