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 pathway

  A sequence of enzyme-catalysed steps that achieve a chemical conversion
• Metabolic pathways may be linear or cyclic
• Metabolites

  Compounds taking part in metabolism
• Respiration

  • A process by which cells generate energy through the breakdown of glucose
  • A catabolic process
  • 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 can be summarized by the following overall chemical equation: 6CO2(g) + 6H2O(l) → C6H12O6(aq) + 6O2(g)
• Aerobic respiration involves the breakdown of glucose in the presence of molecular oxygen to form carbon dioxide and water
• The overall equation for aerobic respiration is: C6H12O6(aq) + 6O2(g) → 6CO2(g) + 6H2O(l)
• Anaerobic respiration in yeast is known as fermentation: C6H12O6(aq) → 2CO2(g) + 2C2H5OH(l)
• Buchner's experiment with cell-free yeast extract introduced the concept of an 'enzyme' and falsified the earlier idea that only cytoplasm could carry out metabolic processes
• Condensation reaction

  The reaction between the functional groups of two smaller molecules to form one large molecule with the release of a water molecule
• Hydrolysis

  The reverse of condensation, where a water molecule reacts with a large molecule to break a specific bond and form two smaller molecules
• Hydrolysis reactions can occur in the presence of acid without the presence of enzymes
• Biopolymers formed by condensation reactions

  • Proteins
  • Lipids
  • DNA
• Condensation polymerization requires each reacting molecule to possess at least two reactive functional groups
• Hydrolysis of proteins produces amino acids, and hydrolysis of starch and cellulose produces glucose
• Sucrose can be hydrolysed to form glucose and fructose
• Phobic

  Polar, uncharged
• Basic

  Positively charged at pH 6.0–8.0
• Acidic

  Negatively charged at pH 6.0–8.0
• R group contains

  • Hydrocarbon chain
  • Hydroxyl (–OH), sulfhydryl (–SH) or amide (–CONH2) groups
  • Amino group (–NH2)
  • Carboxyl group (–COOH)
• Amino acids are white crystalline solids under standard conditions
• Amino acids exist in the solid state and in neutral aqueous solution as zwitterions
• Zwitterion

  Internal acid–base reaction where a hydrogen ion is released from the carboxyl group and protonates the amine group
• The presence of zwitterions leads to ionic bonding in crystalline amino acids involving electrostatic forces of attraction between oppositely charged ends of the zwitterions
• This results in high melting (or decomposition) points and good solubility in water
• Protein synthesis in cells

  1. Amino acids condense (in the presence of enzymes) through the formation of the amide link (–CONH–), or peptide bond, to form a polypeptide chain

  2. Polypeptide chain then folds to form a biologically active protein
• Peptide formation between two amino acids

  CH3O HHO H2N C C + N C C HOH HHOH Ala Gly -H2O CH3OH H2N C C N C COOH HHH peptide Ala-Gly bond
• They are referred to as 2-amino acids as the amine group is attached to the first carbon after that of the carboxyl functional group in the chain
• Peptide bonds experience restricted rotation due to resonance (π delocalization), giving rise to two possible conformations: the trans conformation is generally more stable
• Each particular protein has a specific number of amino acid residues bonded in a specific sequence between an amine group and a carboxyl group. This is known as the primary structure
• A small change in a primary structure can result in a large change in biological function
• Ribonuclease A is a relatively short polypeptide of 124 amino acid residues and it illustrates the key features of the primary chain structure of polypeptides
• The sequence is written with the –NH2 group which has not been converted into a peptide link at the left-hand end. The unchanged –COOH group is written at the right-hand end
• Amino(N)-terminal end

  The end of the peptide chain with the –NH2 group
• Carboxyl(C)-terminal end

  The end of the peptide chain with the −COOH group
• In biological cells the synthesis of a protein is directional, with the protein chain being synthesized from the N-terminal end to the C-terminal end