Introduccion

• Key elements that account for ~98% of the dry weight of most organisms

  • C
  • N
  • O
  • H
  • Ca
  • P
  • K
  • S
• These elements form a variety of reactive functional groups that participate in biological structure and biochemical reactions
• Current model for the origin of life

  Organisms arose from the polymerization of simple organic molecules to form more complex molecules, some of which were capable of self-replication
• Polymerization reactions

  Formation of water (condensation reaction)
• Complementary surfaces of molecules and macromolecules provide a template for biological specificity (e.g., macromolecular assembly, enzyme activity, and expression and replication of the genome)
• Prokaryotic and eukaryotic cells

  Eukaryotic cells are distinguished by a variety of membrane-bounded organelles and an extensive cytoskeleton
• Phylogenetic evidence based on comparisons of ribosomal RNA genes have been used by Woese and colleagues to group all organisms into three domains: archaea, bacteria, and eukarya
• Eukaryotes contain several membrane-bounded structures, such as mitochondria and chloroplasts, which may be descended from ancient symbionts
• Archaea

  Represent a third domain or branch of life in the three-domain system of classification, while they outwardly resemble bacteria, their genomes and the proteins encoded in them more closely resemble those of eukaryotes
• Biological evolution is not goal-directed, requires some built-in sloppiness, is constrained by its past, and is ongoing
• Natural selection directs the evolution of species
• First law of thermodynamics

  Energy (U) is conserved; it can neither be created nor destroyed
• Enthalpy (H)

  A thermodynamic function that is a sum of the energy of the system and the product of the pressure and the volume (PV)

  
• Since biochemical processes occur at constant pressure and have negligible changes in volume, the change of energy of the system is nearly equivalent to the change in enthalpy (ΔU ≈ ΔH)

  
• Second law of thermodynamics

  Spontaneous processes are characterized by an increase in the entropy of the universe, that is, by the conversion of order to disorder
• Spontaneity of a process

  Determined by its free energy change (ΔG = ΔH – TΔS). Spontaneous reactions have ΔG < 0 (exergonic) and nonspontaneous reactions have ΔG > 0 (endergonic)
• For any process at equilibrium, the rate of the forward reaction is equal to the rate of the reverse reaction, and ΔG = 0
• Energy, enthalpy, entropy, and free energy


  State functions; they depend only on the state of the system, not its history
• The entropy of a solute varies with concentration; therefore, so does its free energy. The free energy change of a chemical reaction depends on the concentration of both its reactants and its products
• Equilibrium constant of a chemical reaction

  Related to the standard free energy of the reaction when the reaction is at equilibrium (ΔG = 0) as follows: ΔG° = –RT ln Keq

  
• The equilibrium constant varies with temperature by the relationship: d(ln Keq)/dT = -ΔH°/RT^2, where ΔH° and ΔS° represent enthalpy and entropy in the standard state

  
• Biochemical standard state

  Temperature is 25°C, the pH is 7.0, and the pressure is 1 atm. The activities of reactants and products are taken to be the total activities of all their ionic species, except for water, which is assigned an activity of 1. [H+] is also assigned an activity of 1 at the physiologically relevant pH of 7
• Isolated system

  Cannot exchange matter or energy with its surroundings
• Closed system


  Can exchange only energy with its surroundings and inevitably reaches equilibrium
• Open systems

  Exchange both matter and energy with their surroundings and therefore cannot be at equilibrium. Living organisms must exchange both matter and energy with their surroundings and are thus open systems
• Living systems can respond to slight perturbations from the steady state to restore the system back to the steady state
• The recovery of free energy from a biochemical process is never total, and some energy is lost to the surroundings as heat. Hence, while the system becomes more ordered, the surroundings experience an increase in entropy
• Enzymes

  Accelerate the rate at which a biochemical process reaches equilibrium by interacting with reactants and products to provide a more energetically favorable pathway for the biochemical process to take place
• Water is essential to biochemistry because: (a) Biological macromolecules assume specific shapes in response to the chemical and physical properties of water, (b) Biological molecules undergo chemical reactions in an aqueous environment, (c) Water is a key reactant in many reactions, usually in the form of H+ and OH– ions, (d) Water is oxidized in photosynthesis to produce molecular oxygen, O2, as part of the process that converts the sun's energy into usable chemical form
• Structure of water

  Closely approximates a tetrahedron with its two hydrogen atoms and the two lone pairs of electrons of its oxygen atom "occupying" the vertices of the tetrahedron
• The high electronegativity of oxygen relative to hydrogen results in the establishment of a permanent dipole in water molecules
• Hydrogen bonds

  Represented as D—H···A, where D—H is a weakly acidic compound so that the hydrogen atom (H) has a partial positive charge, and A is a weakly basic group that bears lone pairs of electrons. A is often an oxygen atom or a nitrogen atom (occasionally sulfur)
• Water is strongly hydrogen bonded, with each water molecule participating in four hydrogen bonds with its neighbors; two in which it donates and two in which it accepts. Hydrogen bonds commonly form between water molecules and the polar functional groups of biomolecules, or between the polar functional groups themselves
• Characteristic properties of water due to strongly hydrogen bonded character

  • High heat of fusion, allowing water to act as a heat sink
  • High heat of vaporization, requiring relatively more heat input to vaporize
  • Ability to dissolve most polar compounds
  • Open structure makes ice less dense than liquid water, inhibiting total freezing of large bodies of water
• A variety of weak electrostatic interactions are critical to the structure and reactivity of biological molecules. These interactions include, in order of increasing strength, London dispersion forces, dipole–dipole interactions, hydrogen bonds, and ionic interactions
• Water as a solvent

  Excellent solvent of polar and ionic substances due to its property of surrounding polar molecules and ions with oriented shells of water, thereby attenuating the electrostatic forces between these molecules and ions
• Hydrophobic effect


  The tendency of water to minimize its contact with nonpolar (hydrophobic) molecules, largely driven by the increase in entropy caused by the necessity for water to order itself around nonpolar molecules
• Amphiphilic or amphipathic molecules

  Have both polar (or charged) and nonpolar functional groups and are therefore simultaneously hydrophilic and hydrophobic
• Osmosis


  The movement of solvent across a semipermeable membrane from a region of lower concentration of solute to a region of higher concentration of solute. Osmotic pressure of a solution is the pressure that must be applied to the solution to prevent an inflow of solvent
• Diffusion


  The random movement of molecules in solution (or in the gas phase), responsible for the movement of solutes from a region of high concentration to a region of low concentration