Biomolecules and water
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stucture of biomolecules, properties of water, cell and compsition
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Biomolecules and water
- 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
- 4. The Earliest Fossils Schopf et al.(2002) 3.45 Byr From Joyce, 2002
- 5. 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?
- 6. The Origin of Life â a Fact and an Assumption ⢠Unity of life â 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
- 7. A Problematic Issue in Creating RNA ⢠Itâs 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
- 8. Creating Life in the âWarm little Pondâ Creating the Monomers Making Polymers Making Systems
- 9. 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)
- 10. From Schopf,2002 The Building Blocks â The first experiment Urey, Miller 1953 â from Schopf, 2002 & Smith, Szathmary,1995
- 11. Schopf, 2002 1. Early atmosphere probably didnât 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
- 12. Heterotrophic theory â˘A primordial soup of simple molecules arose first â˘Driven by non biological energy like radiation or heat â˘Assembled in complex molecules and â˘Led to primitive life forms
- 13. Reducing atmosphere Biomolecules synthesis Prebiotic soup Complex molecules A heterotrophic origin of life? Claudia Crestini - WUTA08
- 14. 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. âFormamide 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 saltsâ Becker, B. J. Chem. Eng. 1970 Formamide. Phisical and Chemical properties
- 15. 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
- 16. The mineral Honeycomb Role of minerals metals and metal oxides in prebiotic chemistry
- 17. 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
- 18. 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
- 19. 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?
- 20. 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?
- 21. 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
- 22. On Life and Chemistry... ⢠âLiving things are composed of lifeless moleculesâ (Albert Lehninger) ⢠âChemistry is the logic of biological phenomenaâ (Garrett and Grisham)
- 23. 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
- 26. 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
- 27. 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
- 28. 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
- 34. 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
- 35. 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
- 37. Biomolecules are complex, but are made up of simpler components
- 38. 1.4 Properties of Biomolecules Reflect Their Fitness to the Living Condition ⢠Macromolecules and Their Building Blocks Have a âSenseâ or Directionality ⢠Macromolecules are Informational ⢠Biomolecules Have Characteristic Three- Dimensional Architecture ⢠Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions
- 39. 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
- 48. 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
- 50. 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
- 63. Proteins, nucleic acids, polysaccharides and lipids are the most abundant biomolecules
- 65. 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.
- 66. 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.
- 68. From Mason, 1990
- 69. Examples of functional groups
- 70. Functional groups can have chirality The central carbon (Îą-carbon) is a chiral center
- 85. Organization and Structure of Cells ⢠Prokaryotic cells â A single (plasma) membrane â no nucleus or organelles ⢠Eukaryotic cells â much larger in size than prokaryotes â 103 -104 times larger! â Nucleus plus many organelles â ER, Golgi, mitochondria, etc.
- 87. ⢠The cell is the smallest unit of life. ⢠All organisms are composed one or more cells. ⢠New cells arise from previously existing cells.
- 101. ⢠Digest food ⢠Autophagy ⢠Autolysis
- 102. ⢠Rid body of toxic substances ⢠Contains enzymes that can oxidize various organic substances Liver cell
- 103. ⢠Centriole pair ⢠Assemble microtubules ⢠Assist in cell division ⢠9 clusters of microtubule triplets
- 107. ďąOne atom of oxygen ďąTwo atoms of hydrogen o HH Water Chemical Properties
- 108. The structure of water
- 109. Charge distribution in water
- 110. 104.5o
- 115. Physical and Chemical Properties of Water Physical and Chemical Properties of Water High â Boiling point, melting point, heat of evaporation, surface tension, viscosity, dielectric constant Density maximum at 4°C
- 116. Properties of Water
- 117. How to remove water: phase changes The phase diagram for water
- 124. Hydrogen bonding in water www.llnl.gov/str/October05
- 125. Properties of Water Hydrogen Bonding! 2 â 10% of the O-H bond strength
- 130. p.42
- 144. 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
- 145. Water becomes highly organized around solutes to maximize the number of hydrogen bonds Dill et al., 2005
- 146. Clathrates - Water Reorganization Crystal structure of diethylamine hydrate Waters reorient to maintain full H-bonding, even in the presence of non- polar solutes, forming âcagesâ. Water molecules become highly organized. (Each water molecule loses up to 2 entropy units, ~0.6 kcal/mol)
- 147. 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 âsticking interactionsâ between the hydrophobes
- 150. 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.
- 151. Fig. 2-4, p.37
- 152. Table 2-5, p.41
- 164. 2.8 The pH Scale ⢠pH is defined as the negative logarithm of the concentration of H+
- 170. Titration curve for phosphoric acid (H3PO4)
- 173. Buffered Solutions Resist Changes in pH WHY?
- 176. Acetic acid is a weak acid ⢠Weak acids and bases do not dissociate completely in H2O
- 178. Percentages of carbonic acid and its conjugate bases as a function of pH
- 179. Regulation of the pH of blood in mammals
Hinweis der Redaktion
- Heterotrophic theory tra le teorie piĂš studiate suggerita per la prima volta in the
- Precursori chimici elementari si formano mediante reazioni nellâatmosfera prebiotica si concentrano nella prebiotic soup dove avvengono trasformazioni piĂš complesse fino
- Formata da ossidi per scarica elettrica o da hcn idrolisi che è uno dei precursori chimici
- La reattività della formammide può essere tunata da metalli e ossidi metallici
- Sintetizzate contemporaneamente
- 2. Have Mars been checked for chirality? 3. How far away can chirality be observed?
- 2 centrioles, nine clusters of microtubule triplets
- FIGURE 2.1 The structure of water. Oxygen has a partial negative charge, and the hydrogens have a partial positive charge. The uneven distribution of charge gives rise to the large dipole moment of water. The dipole moment in this figure points in the direction from negative to positive, the convention used by physicists and physical chemists; organic chemists draw it pointing in the opposite direction.
- FIGURE 2.6 A comparison of linear and nonlinear hydrogen bonds. Nonlinear bonds are weaker than bonds in which all three atoms lie in a straight line.
- FIGURE 2.3 Ionâdipole and dipoleâdipole interactions help ionic and polar compounds dissolve in water. (a) Ionâdipole interactions with water. (b) Dipoleâdipole interactions of polar compounds with water. The examples shown here are an alcohol (ROH) and a ketone (R2CAO).
- FIGURE 2.2 Hydration shells surrounding ions in solution. Unlike charges attract. The partial negative charge of water is attracted to positively charged ions. Likewise, the partial positive charge on the other end of the water molecule is attracted to negatively charged ions.
- FIGURE 2.5 Micelle formation by amphipathic molecules in aqueous solution. When micelles form, the ionized polar groups are in contact with the water, and the nonpolar parts of the molecule are protected from contact with the water.
- FIGURE 2.4 An amphiphilic molecule: sodium palmitate. Amphiphilic molecules are frequently symbolized by a ball and zigzag line structure, where the ball represents the hydrophilic polar head and the zigzag line represents the nonpolar hydrophobic hydrocarbon tail.
- FIGURE 2.10 The ionization of water.
- FIGURE 2.12 pH versus enzymatic activity. Pepsin, trypsin, and lysozyme all have steep pH optimum curves. Pepsin has maximum activity under very acidic conditions, as would be expected for a digestive enzyme that is found in the stomach. Lysozyme has its maximum activity near pH 5, while trypsin is most active near pH 6.
- FIGURE 2.13 Titration curve for acetic acid. Note that there is a region near the pKa at which the titration curve is relatively flat. In other words, the pH changes very little as base is added in this region of the titration curve.
- FIGURE 2.14 Buffering. Acid is added to the two beakers on the left. The pH of unbuffered H2O drops dramatically while that of the buffer remains stable. Base is added to the two beakers on the right. The pH of the unbuffered water rises drastically while that of the buffer remains stable.
- FIGURE 2.15 The relationship between the titration curve and buffering action in H2PO4 -. (a) The titration curve of H2PO4 -, showing the buffer region for the H2PO4 -/HPO4 2- pair.
- FIGURE 2.16 Two ways of looking at buffers. In the titration curve, we see that the pH varies only slightly near the region in which [HA] = [A-]. In the circle of buffers, we see that adding OH- to the buffer converts HA to A-. Adding H+ converts A- to HA.
- FIGURE 2.16 Two ways of looking at buffers. In the titration curve, we see that the pH varies only slightly near the region in which [HA] = [A-]. In the circle of buffers, we see that adding OH- to the buffer converts HA to A-. Adding H+ converts A- to HA.