Topic 2 - Molecular Biology

• The 4 ubiquitous elements in biological systems

  • Oxygen
  • Carbon
  • Hydrogen
  • Nitrogen
• Other trace elements found in organic compounds

  • bromine
  • calcium
  • chlorine
  • chromium
  • copper
  • iodine
  • iron
  • magnesium
  • manganese
  • molybdenum
  • phosphorus
  • potassium
  • selenium
  • silicon
  • sodium
• There are other trace elements found in certain phyla only e.g. strontium in certain corals (Cnidaria)
• Covalent compounds


  Electrons are shared between atoms to generate strong bonds within compounds
• Carbon forms millions of different covalently-bonded compounds, mainly with hydrogen and oxygen
• Oxygen is absorbed in elemental form but is quickly converted to its compounds during transportation and respiration
• Prosthetic groups


  Elements that form with larger organic molecules eg. magnesium in chlorophyll, iron in haemoglobin
• All of Biology can be explained at a molecular level
• The molecules in cells, and the elements that go to form them, are the basis of all events that occur in Nature
• Everything that is observed has a molecular explanation
• Frederick Wöhler, a German physician, was the first to synthesise a biological molecule, urea, from inorganic compounds

  
• Urea was thought to be synthesised only in living organisms

  
• Urea had been thought to be found only in living organisms

  
• The formation of urea from ammonium cyanate helped to disprove the theory of vitalism, which has been completely falsified by subsequent findings

  
• All of the observations of biology now have a molecular explanation, and that is now universally accepted
• Carbon


  • Four electrons in its outer (second) shell
  • Each atom can form four strong covalent bonds using these 4 electrons and therefore forms very stable, large molecules
  • Bonds to other carbon atoms, or other atoms such as hydrogen, nitrogen, oxygen, sulfur and the halogens
  • Forms long-chain and cyclic compounds that are stable, this allows a very high number of possible organic compounds to exist
  • Produce a tetrahedral structure, due to the four bonds, which allows the formation of varied carbon compounds which have different 3-D shapes and hence, different biological properties
  • Double and triple bonds can form with an adjacent carbon atom, allowing unsaturated compounds to form
  • Can form part of (and join onto) many different functional groups that give organic compounds their individual properties

  
• Key molecules required to build structures that enable organisms to function

  • Carbohydrates
  • Proteins
  • Lipids
  • Nucleic Acids
  • Water
• Monomers


  Small single subunits that bond with many repeating subunits to form large molecules (polymers) by a process called polymerisation
• Polymers


  Large molecules that contain 1000 or more atoms therefore having a high molecular mass
• Macromolecules


  Very large molecules that contain 1000 or more atoms therefore having a high molecular mass
• Polymers can be macromolecules, however not all macromolecules are polymers as the subunits of polymers have to be the same repeating units
• Metabolism


  A catch-all term used to describe all the chemical reactions that take place within cells and organisms
• Metabolites


  The molecules involved in metabolism
• Metabolic pathway


  A series of interlinked metabolic reactions
• Types of metabolic reactions

  • Anabolic
  • Catabolic
• Anabolic reactions


  Involved with the building of large molecules from smaller ones
• Examples of anabolic reactions

  • Photosynthesis, where CO2 and water are built up into complex sugars
  • Protein synthesis, where amino acids are joined together in sequence
  • The buildup of fat stores ahead of animal hibernation
• Anabolic reactions


  • Endergonic (they require an input of energy to take place)
  • Energy-storing products are the end result
• Catabolic reactions


  Involved with breaking down large molecules into smaller ones
• Examples of catabolic reactions


  • Respiration, where CO2 and water are produced from the breakdown of sugars
  • Deamination of proteins to release urea
  • The depletion of fat stores during animal hibernation
• Catabolic reactions


  Exergonic (free energy is released for cellular processes or as excess heat)
• Hydrogen bonding plays an important role between many biological molecules
• Key functions of hydrogen bonding

  • Dissolving of solutes in water
  • The cohesion and adhesion of water molecules
  • Base-pairing between the two strands of DNA
  • Forming part of the secondary and tertiary levels of structure in proteins
  • Giving tensile strength to cellulose and collagen
  • Interactions between mRNA and tRNA during protein synthesis
  • Surface effects on membranes between polar phosphate groups and water
• Hydrogen bonding in water

  • Water is composed of atoms of hydrogen and oxygen
  • One atom of oxygen combines with two atoms of hydrogen by sharing electrons (covalent bonding)
  • The oxygen atom attracts the electrons more strongly than the hydrogen atoms, resulting in a weak negatively charged region on the oxygen atom (δ-) and a weak positively charged region on the hydrogen atoms(δ+), this also results in the molecule's asymmetrical shape
  • This separation of charge due to the electrons in the covalent bonds being unevenly shared is called a dipole
  • Water is therefore a polar molecule

  
• Hydrogen bonds form between the positive and negatively charged regions of adjacent water molecules

  
• Properties of water caused by hydrogen bonding

  • Excellent solvent – many polar substances can dissolve in water
  • A relatively high specific heat capacity
  • A relatively high latent heat of vaporisation
  • Water is less dense when a solid (ice floats, allowing aquatic life to flourish beneath)
  • Water has high surface tension and cohesion
  • It acts as a reagent

  
• Covalent bonds


  Bonds that form when atoms share pairs of electrons
• Polar molecule


  A molecule with an uneven distribution of charge, with a slightly positive and slightly negative end
• Hydrogen bonds


  Weak bonds that form between a hydrogen atom attached to a highly electronegative atom (such as oxygen or nitrogen) and another highly electronegative atom

  
• Formation of hydrogen bonds in water

  1. Positive and negatively charged regions of adjacent water molecules attract

  2. Hydrogen bonds are constantly breaking and reforming

  3. When there are large numbers present they form a strong structure