Biochem Basics

• Biochemistry


  The study of the chemical processes that occur in living organisms
• Biology


  The study of life and living organisms (structure, function, growth etc.)
• Chemistry


  The study of matter (solids, liquids and gases)
• Element


  Made up of one type of atom
• Molecule


  Made up of two or more atoms bonded together
• Compound


  Made up of two or more different elements bonded together
• Atomic structure


  Proton (+ve), Neutron (neutral), Electron (-ve), The nucleus
• Atomic number


  The number of protons determine the element
• Atomic mass


  Both protons and neutrons contribute to total mass
• Isotopes


  Variations of an element due to different number of neutrons
• Isotopes are usually radioactive as the nucleus is unstable and decays to release energy in the form of radiation (alpha, beta and gamma)
• Deuterium's nucleus is relatively stable, so is not radioactive. Tritium's nucleus is unstable and is therefore radioactive
• Ions


  Atoms with variations in their electrons, charged molecules
• Gain of electrons


  Gives an overall negative charge
• Loss of electrons


  Gives an overall positive charge
• Electron shells/energy levels


  Electrons exist outside the nucleus and form shells, each shell has a maximum number of electrons it can hold
• When each shell has its maximum load of electrons, the atom is said to be stable
• Valence electrons


  The electrons in the outermost shell determine reactivity
• Covalent bonding


  Electrons are shared between atoms to complete shells
• Ionic bonding


  Electrons are gained or lost, creating positive and negative charges that attract
• Hydrogen bond


  A weak electrostatic attraction between two polar groups
• Van der Waals interactions

  Weak interactions due to fluctuations in electron clouds
• Hydrophobic interactions


  Non-polar molecules force water molecules to organize around them
• Chemical bonds are held together by the way electrons are shared, donated, or distributed, and breaking these bonds releases the energy that was holding them together
• Non-polar molecules do not dissolve in water because they prefer to make hydrophobic interactions rather than ionic or hydrogen bonds
• Oxidation


  The loss of electrons from a molecule
• Reduction


  The gaining of electrons by a molecule
• Oxidation and reduction reactions are of central importance to metabolism, and one cannot happen without the other (redox reactions)
• The flow of electrons in redox reactions can be harnessed to produce chemical energy in the form of ATP
• If Iron (Fe2+) undergoes a reaction and becomes Fe

  Iron has been reduced
• During ATP production, glucose is oxidised and oxygen is reduced
• Components of matter

  • Elements
  • Molecules
  • Compounds
• Examples of matter

  • Atom Hydrogen
  • Molecule of Hydrogen (H2)
  • H2 + O = H2O (water) both a compound and a molecule
• Components of atomic structure

  • Proton (+ve)
  • Neutron (neutral)
  • Electron (-ve)
  • The nucleus
• Relative size of things: 10^-3 = milli, 10^-6 = micro, 10^-9 = nano, 10^-12 = pico, 10^-15 = femto, etc.
• Atomic number


  The number of protons determine the element
• Atomic mass


  Both protons and neutrons contribute to total mass
• Helium


  • Has 2 protons and 2 neutrons giving a mass of 4 or 4 g/mol
• Mole


  The amount of substance of a system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12
• Calculating the number of moles in 4g of a molecule of Oxygen

  1. Molecular mass of oxygen is 16 (therefore 16 g/mole)

  2. However, a molecule of oxygen is O2 (therefore 16 x 2 = 32 g/mole)

  3. To calculate the number of moles, use the formula: Moles = mass/relative formula mass

  4. Therefore, 4/32 = 0.125 moles

  
  

  What is the mass of 0.125 moles of O2? Therefore, 0.125 x 32 = 4g