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Cell Structure, Thermodynamics, and Biochemical Pathways

Explore the structure and function of prokaryotic and eukaryotic cells, learn about organic chemical bonds and functional groups, and understand the basics of thermodynamics and biochemical pathways. Discover the evolution of cells and proteins, and delve into the intricate world of biomolecular interactions. Gain insights into the principles of biochemistry from Nilsen and Cox's Lehninger Principles of Biochemistry.

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Cell Structure, Thermodynamics, and Biochemical Pathways

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  1. CHAPTER-1 Adopted from Nilsen and cox – Lehninger principles of biochemistry (sixth edition)

  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. 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. Prokaryotic Cell calculate the length of DNA in a bacterial cell…here it is all folded up!

  5. Bacterial Cytoplasm Is Full of Molecules

  6. Prokaryotic Cell Envelope

  7. Eukaryotic Cell

  8. Muscle Cells

  9. Eukaryotic Cytoskeleton: Actin (red), Microtubules (green) Surround the Nucleus (blue). Fluorescence Microscopy.

  10. Cytoskeleton Elements Bacteria also have filaments (actin like) and microtubules to organize their cytoplasm.

  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. The Monomers

  13. Structure to Molecular Hierarchy

  14. Periodic Chart

  15. Carbon Bonding

  16. Geometry of carbon bonding

  17. Common Functional Groups of Biological Molecules

  18. several functional groups in single biomolecule.

  19. 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)

  20. Representation of molecules Structural formula in perspective form Ball-and-stick model Space-filling model

  21. Cis and Trans(Configurations of geometric isomers)

  22. Cis and Trans – Conformational Change

  23. Chirality Problem 11 is about two pharmacological drugs and fits right in here with chirality and drug dosage.

  24. 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.

  25. Chiral Rotation Rectus (right) Sinister (left)

  26. Rotation by Priorities Priorities of Some Biochemical Functional Groups -OCH2 > -OH > -NH2 > -COOH > -CHO > -CH2OH > -CH3 > -H

  27. Interactions between biomolecules are specific

  28. Stereoisomers Have Different Biological Effects

  29. ATP

  30. Thermodynamics You Already Know Endothermic vs Exothermic ΔG = ΔH – T ΔS ΔG is related to the Equilibrium Constant ΔG = G products – G reactantsReactants = Substrates ΔGo = standard free energy change (we will change this later) for aA + bB  cC + dD ΔG = ΔGo + RT ln K eq

  31. AAA : Hexokinase Rxn

  32. 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

  33. Series of related enzymatically catalyzed reactions forms a pathway • Metabolic Pathway • produces energy or valuable materials • Signal Transduction Pathway • transmits information

  34. Pathways are controlled in order to regulate levels of metabolites Example of a negative regulation: Product of enzyme 5 inhibits enzyme 1

  35. Anabolism and Catabolism

  36. Metabolic Diversity

  37. Information Codes Prism of Sennacherib Bacterial DNA ~700 BC, Assyrian

  38. DNA Replication

  39. Central DogmaDNA code Transcription  Translation  Protein

  40. A

  41. Miller and Urey Experimentin a Garage, 1953

  42. RNA World to DNA/RNA/Protein World

  43. Current Year

  44. Endosymbiotic Origin of Mitochondria and Chloroplasts

  45. From Darwin to Orthologous and Paralogous Genes

  46. Paralogous Selection Required Gene Duplication

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