Biochemistry

• Metabolism


  The total of all the enzyme-catalysed reactions in a cell or organism. It involves the breakdown of molecules with the release of energy and the synthesis of molecules that are required by the cell.
• Catabolism


  The breakdown of complex molecules into simpler molecules. Such processes release energy.
• Anabolism


  The synthesis of more complex molecules from simpler precursor molecules. Such processes require energy.
• Metabolic pathways


  Organized biochemical reactions, each step of which is catalysed by a specific enzyme in an aqueous environment
• Metabolic pathways


  • Linear
  • Cyclic
• Metabolites


  Compounds taking part in metabolism
• Respiration


  • A catabolic process by which cells generate energy through the breakdown of glucose
  • Common to the metabolism of all cell types, whether bacterial, fungal, plant or animal
• Photosynthesis


  • An anabolic process in which carbon dioxide from the atmosphere is taken in by plants and combined with water to form energy-rich molecules such as glucose
  • Water molecules are 'split' and oxygen is released as a by-product
  • A complex series of enzyme-controlled reactions occurring inside chloroplasts
• Photosynthesis


  6CO2(g) + 6H2O(l) → C6H12O6(aq) + 6O2(g)
• Photosynthesis is responsible for the origin and maintenance of oxygen in the atmosphere. It essentially 'fixes' carbon (in the form of carbon dioxide) into biomass.
• Photosynthesis and respiration are largely responsible for the global balance of carbon dioxide and oxygen in the atmosphere, though levels of carbon dioxide are increasing, largely due to emissions of carbon dioxide from the combustion of fossil fuels.
• The shape of a molecule determines the way it behaves inside cells and metabolic pathways. The chemical nature of a molecule is dependent upon the shape as well as the distribution of the electron density in its covalent bonds. The shape of a molecule and its polarity influence the physical and chemical properties of the elements involved.
• Aerobic respiration


  • Involves the breakdown of glucose in the presence of molecular oxygen to form carbon dioxide and water
  • A complex series of enzyme-controlled steps involving a large number of intermediates (in linear and cyclic metabolic cycles)
• Aerobic respiration

  C6H12O6(aq) + 6O2(g) → 6CO2(g) + 6H2O(l)
• Anaerobic respiration


  • Respiration that occurs in the absence of oxygen
  • In humans, lactic acid is formed, but in plants and yeast ethanol is formed
• Anaerobic respiration in yeast


  C6H12O6(aq) → 2CO2(g) + 2C2H5OH(l)
• The two processes of photosynthesis and respiration help to maintain the balance between carbon dioxide and oxygen in the atmosphere.
• In addition to carbohydrates, lipids and proteins can be used as energy sources for ATP synthesis. This happens during starvation. After hydrolysis, these large molecules form fatty acids plus glycerol and amino acids. These three types of molecule can also be catabolized to release energy and so produce ATP.
• Condensation reactions


  1. Involve the reaction between the functional groups of two smaller molecules to form one large molecule with the release of a water molecule

  2. An addition reaction followed by an elimination reaction
• Condensation polymerization


  • Each of the reacting molecules must possess at least two reactive functional groups
  • Examples include the condensation of amino acids to form proteins, the condensation of nucleotides to form DNA, the condensation of propane-1,2,3-triol (glycerol) and fatty acids to form lipids, and the condensation of glucose to form starch and cellulose
• Hydrolysis


  1. The reverse of condensation

  2. A molecule is hydrolysed when a water molecule reacts with a large molecule to break a specific bond (ester or amide) and form two smaller molecules
• Water behaves as a solvent and hydrates all biological molecules, as a reactant (during hydrolysis), and as a product (during condensation reactions). These all rely on its polar nature and its ability to form intermolecular hydrogen bonds.
• Maltotriose formation


  1. Three molecules of glucose react together

  2. Form water

  3. Write a balanced equation

  4. State the type of reaction
• Suggest how the trisaccharide can be hydrolysed to form glucose
• Proteins


  The most diverse of the biopolymers responsible for metabolism and structural integrity of living organisms
• Components of proteins


  • 2-amino acids
  • Amide links (peptide bonds)
• Amino acids


  Amphoteric, can exist as zwitterions, cations and anions
• Levels of protein structure


  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Protein's 3D shape


  Determines its role in structural components or in metabolic processes
• Enzymes


  Most are proteins that act as catalysts by binding specifically to a substrate at the active site
• Enzyme activity


  Depends on conformation, sensitive to changes in temperature, pH and presence of heavy metal ions
• Chromatography


  Separation based on different physical and chemical principles
• Amino acids


  Contain an amine and a carboxyl group bonded to a central common atom
• Types of amino acids


  • Non-polar/hydrophobic
  • Polar, uncharged
  • Basic (positively charged at pH 6.0-8.0)
  • Acidic (negatively charged at pH 6.0-8.0)
• Amino acids in solid state and neutral aqueous solution


  Exist as zwitterions
• Zwitterion formation leads to ionic bonding in crystalline amino acids, resulting in high melting points and good solubility in water
• Peptide bond formation


  1. Amino acids condense through amide link formation to form a polypeptide chain

  2. Polypeptide chain then folds to form a biologically active protein
• Peptide bonds experience restricted rotation due to resonance, giving rise to trans and cis conformations
• Primary structure is the specific sequence of amino acid residues in a protein
• Small changes in primary structure can result in large changes in biological function