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Biomolecules and water

stucture of biomolecules, properties of water, cell and compsition

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Biomolecules and water

  1. 1. Biological Molecules and Water Prof.Dr. Kaya EMERK
  2. 2. Aim of the Lectures • Scope of Biochemistry • Get acquainted with life processes • Know about living organisms • Learn about biomolecules • Know the composition of living organisms • Learn about the characteristics of water
  3. 3. The Earliest Fossils Schopf et al.(2002) 3.45 Byr From Joyce, 2002
  4. 4. Two Big Questions 1. What is the manner in which the ancestor emerged from materials available then? Can we reconstruct it? 2. How did all extant living organisms evolve from the common ancestor?
  5. 5. The Origin of Life – a Fact and an Assumption • Unity of life – all extant living organisms are constructed of the same materials, and function according to the same principles . • All organisms are descendants of a single ancestral form of life. De duve ,chap1
  6. 6. A Problematic Issue in Creating RNA • It’s not likely that RNA molecule was created in prebiotic conditions mainly because of the difficulty in attaching pyrimidines (C, U) to ribose to form pyrimidines nucleosides. A period of time when environment enabled RNA to be created Primitive clay self-replicating system, from which an RNA system evolved A simpler RNA-like molecule, maybe only with purines (A, G) and from which an RNA system evolved Joyce, 1989
  7. 7. Creating Life in the “Warm little Pond” Creating the Monomers Making Polymers Making Systems
  8. 8. 1. Buildup of building blocks in solution. 2. Formation of Coacervates. 3. Heterotrophic. Problems. 1. Low concentration of building blocks. 2. Hydrolysis favoured. 3. No reasonable pathway to the nucleotides. 4. Chirality. Oparin-Haldane (late 20s) (from Fenchel, 1998)
  9. 9. From Schopf,2002 The Building Blocks – The first experiment Urey, Miller 1953 – from Schopf, 2002 & Smith, Szathmary,1995
  10. 10. Schopf, 2002 1. Early atmosphere probably didn’t contain hydrogen H2. This reduces the production of organics. 2. Most polymers are unstable at high temperature. Does not replicate by themselves reliably, when longer than 40-60 units. 3. A non chiral system cannot select among mirrored versions of the same molecule. Problems
  11. 11. Heterotrophic theory •A primordial soup of simple molecules arose first •Driven by non biological energy like radiation or heat •Assembled in complex molecules and •Led to primitive life forms
  12. 12. Reducing atmosphere Biomolecules synthesis Prebiotic soup Complex molecules A heterotrophic origin of life? Claudia Crestini - WUTA08
  13. 13. Colloids and surfacesA: Physicochem Eng. Aspects 2003 219: 281-290. A comparison of micelle formation of ionic surfactants in formamide, in N-methylformamide and in N, N-dimethylformamide. M.Salim Akhter, Sadeq M. Alawi Langmuir. 2004 Jan 20;20(2):329-35. Solvation dynamics of formamide and N, N-dimethylformamide in aerosol OT reverse micelles. Shirota H, Segawa H. “Formamide has a high boiling point, without azeotropic effects, and a wide range of uses as a solvent. It has an efficient solubilizing effect on nucleobases, nucleosides, nucleotides, amino acids, proteins, sugars, metalsand salts” Becker, B. J. Chem. Eng. 1970 Formamide. Phisical and Chemical properties
  14. 14. HCN + H2O H2N H O Formamide + H2O - O H O Ammonium formate NH4 +t1/2= ca. 40 yr at 60°C and pH 6.0 t1/2 ca. 10 yr at 30°C and pH 6.0 radical conditions H H O Formaldehyde Sugars Thermal degradation > 210 °C HCN H2O NH3 CO Thermal degradation (Hofmann, Ber. 1882) HNCO H2 (Lin, Langmuir 1994) Hydrogen cyanide (A) (B) (C) (D) Elemental formamide chemistry
  15. 15. The mineral Honeycomb Role of minerals metals and metal oxides in prebiotic chemistry
  16. 16. The role of minerals and metal oxides on prebiotic processes. A general overview • Minerals can accumulate the prebiotic precursors (concentration effect) • Minerals can act as catalytic environments, reducing the activation energy for the formation of products • Minerals can tune the selectivity of prebiotic syntheses • Minerals may act as a template • Minerals are benign environments to degradation
  17. 17. Bioorganic Med. Chem. 9 (2001) 1249-1253 A Possible Prebiotic Synthesis of Purine, Adenine, Cytosine, and 4(3H)- Pyrimidinone From Formamide: Implications for the Origin of Life Raffaele Saladino,Claudia Crestini, Giovanna Costanzo, Rodolfo Negri and Ernesto Di Mauro
  18. 18. Outline • What Are the Distinctive Properties of Living Systems? • What Kinds of Molecules Are Biomolecules? • What Is the Structural Organization of Complex Biomolecules? • How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition? • What Is the Organization and Structure of Cells? • What Are Viruses?
  19. 19. Essential Question • Despite the spectacular diversity of life, the elaborate structure of biological molecules, and the complexity of vital mechanisms, are life functions ultimately interpretable in chemical terms?
  20. 20. Outline • 1.1 Distinctive Properties of Living Systems • 1.2 Biomolecules: Molecules of Life • 1.3 Biomolecular Hierarchy • 1.4 Properties of Biomolecules • 1.5 Organization and Structure of Cells • 1.6 Viruses as Cell Parasites
  21. 21. On Life and Chemistry... • “Living things are composed of lifeless molecules” (Albert Lehninger) • “Chemistry is the logic of biological phenomena” (Garrett and Grisham)
  22. 22. Chapter 3 Biomolecules pages 53-73 99% of the mass of most cells is H, O, N, and C These are the smallest elements that can form 1,2,3 and 4 bonds. Required in grams/day Required in milligrams or less/day
  23. 23. 1.1 Distinctive Properties of Living Systems • Organisms are complicated and highly organized • Biological structures serve functional purposes • Living systems are actively engaged in energy transformations • Living systems have a remarkable capacity for self-replication
  24. 24. 1.2 Biomolecules: The Molecules of Life H, O, C and N make up 99+% of atoms in the human body ELEMENT PERCENTAGE Oxygen 63 Hydrogen 25.2 Carbon 9.5 Nitrogen 1.4
  25. 25. 1.2 Biomolecules: The Molecules of Life • What property unites H, O, C and N that renders these atoms so appropriate to the chemistry of life? • Answer: Their ability to form covalent bonds by electron-pair sharing.This is possible due to their capacity to form sp3 hybrids
  26. 26. 34 Hierarchical structure of life • The biosphere - Global resource cycles • Biomes - Energy and material interchange • Ecosystems - Species interdependence • Animal populations - Competition and the food chain • Individual organisms - Physiological functioning • Limbs, physiological systems - Organism homeostasis • Tissues - Growth, maintenance, repair • Cells - Growth, specialisation, death • Organelles - Cell homeostasis • Macro Molecules - Folding, recognition, binding • Building Block Molecules - Combine to form polymers • Chemical elements - Chemical binding
  27. 27. 1.3 A Biomolecular Hierarchy Simple Molecules are the Units for Building Complex Structures • Metabolites and Macromolecules • Organelles • Membranes • The Unit of Life is the Cell
  28. 28. Biomolecules are complex, but are made up of simpler components
  29. 29. 1.4 Properties of Biomolecules Reflect Their Fitness to the Living Condition • Macromolecules and Their Building Blocks Have a “Sense” or Directionality • Macromolecules are Informational • Biomolecules Have Characteristic Three- Dimensional Architecture • Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions
  30. 30. 1.2 Biomolecules: The Molecules of Life What are the bond energies of covalent bonds? Bond Energy kJ/mol H-H 436 C-H 414 C-C 343 C-O 351
  31. 31. 1.4 Properties of Biomolecules Reflect Their Fitness to the Living Condition Important numbers! • van der Waals: 0.4-4.0 kJ/mole • Hydrogen bonds: 12-30 kJ/mole • Ionic bonds: 20 kJ/mole • Hydrophobic interactions: <40 kJ/mole
  32. 32. Two Important Points About Weak Forces • Biomolecular Recognition is Mediated by Weak Chemical Forces • Weak Forces Restrict Organisms to a Narrow Range of Environmental Conditions
  33. 33. Proteins, nucleic acids, polysaccharides and lipids are the most abundant biomolecules
  34. 34. Polymers (Joyce, 2002)
  35. 35. Biomolecules are compounds of carbon Carbon atoms form 4 tetrahedral single bonds. Two carbon atoms sharing a single bond can rotate around the single bond.
  36. 36. Two carbon atoms sharing a double bond are closer and cannot rotate about the double bond. The carbons and the atoms bound to them form a plane.
  37. 37. From Mason, 1990
  38. 38. Examples of functional groups
  39. 39. Functional groups can have chirality The central carbon (α-carbon) is a chiral center
  40. 40. Organization and Structure of Cells • Prokaryotic cells – A single (plasma) membrane – no nucleus or organelles • Eukaryotic cells – much larger in size than prokaryotes – 103 -104 times larger! – Nucleus plus many organelles – ER, Golgi, mitochondria, etc.
  41. 41. • The cell is the smallest unit of life. • All organisms are composed one or more cells. • New cells arise from previously existing cells.
  42. 42. Rough and Smooth ER
  43. 43. • Digest food • Autophagy • Autolysis
  44. 44. • Rid body of toxic substances • Contains enzymes that can oxidize various organic substances Liver cell
  45. 45. • Centriole pair • Assemble microtubules • Assist in cell division • 9 clusters of microtubule triplets
  46. 46. Water Around theWorld
  47. 47. One atom of oxygen Two atoms of hydrogen o HH Water Chemical Properties
  48. 48. The structure of water
  49. 49. Charge distribution in water
  50. 50. 104.5o
  51. 51. Physical and Chemical Properties of Water Physical and Chemical Properties of Water High – Boiling point, melting point, heat of evaporation, surface tension, viscosity, dielectric constant Density maximum at 4°C
  52. 52. Properties of Water
  53. 53. How to remove water: phase changes The phase diagram for water
  54. 54. Hydrogen bonding in water www.llnl.gov/str/October05
  55. 55. Properties of Water Hydrogen Bonding! 2 – 10% of the O-H bond strength
  56. 56. p.42
  57. 57. Water is a familiar solvent, but has many anomalous properties Ken A. Dill, et al. Modeling water, the hydrophobic effect, and ion solvation. Ann. Rev. Biophys. Biomol. Struct., 34 : 173-199 Simple models demonstrate how water can be more dense as a liquid than as ice
  58. 58. Water becomes highly organized around solutes to maximize the number of hydrogen bonds Dill et al., 2005
  59. 59. Clathrates - Water Reorganization Crystal structure of diethylamine hydrate Waters reorient to maintain full H-bonding, even in the presence of non- polar solutes, forming “cages”. Water molecules become highly organized. (Each water molecule loses up to 2 entropy units, ~0.6 kcal/mol)
  60. 60. Understanding The Hydrophobic Effect • By self-associating, hydrophobic molecules reduce the amount of non-polar surface exposed to solvent. • This explains the separation of oil and water. Restrict oil to one phase, water to another, and minimize the extent of water reorganization • Association of hydrophobes is the result of an increase in the disorder of water, not merely due to “sticking interactions” between the hydrophobes
  61. 61. Interaction between Non polar and Polar Substances and Water Hydrophilic (water-loving) substances (polar and ionic (electrolytes)) readily dissolve in H2O Hydrophobic (water-fearing) molecules are nonpolar Hydrophobic effect - the exclusion of nonpolar substances by water (critical for protein folding and self- assembly of biological membranes) Amphipathic molecules have hydrophobic chains and ionic or polar ends.
  62. 62. Fig. 2-4, p.37
  63. 63. Table 2-5, p.41
  64. 64. 2.8 The pH Scale • pH is defined as the negative logarithm of the concentration of H+
  65. 65. Titration curve for phosphoric acid (H3PO4)
  66. 66. The Henderson-Hasselbalch Equation
  67. 67. Buffered Solutions Resist Changes in pH WHY?
  68. 68. Acetic acid is a weak acid • Weak acids and bases do not dissociate completely in H2O
  69. 69. Carbonate buffering equilibria
  70. 70. Percentages of carbonic acid and its conjugate bases as a function of pH
  71. 71. Regulation of the pH of blood in mammals