biochemical pathways

• Biochemical reactions


  Reactant ---> product
• Biochemical pathway


  1. Initial reactant

  2. Product

  3. Product becomes reactant for next step

  4. Final product
• Reactants


  The starting molecules that are chemically changed to form products
• Substrates


  Reactant molecules in each step
• Types of biochemical pathways


  • Anabolic reactions
  • Catabolic reactions
• Anabolic reactions


  • Require activation energy (ATP)
  • Simple molecules to complex molecules
  • Endergonic reaction

  
• Catabolic reactions


  • Occur when large organic molecules are broken down into smaller, simpler ones, releasing energy in the process
  • Complex molecule to simple molecule
  • Exergonic reaction

  
• Catabolic


  Breakdown of molecule
• Anabolic


  Building of a complex molecule
• Require energy, so the energy level of the initial reactants is lower than that of the final products
• Produce a net release of energy as the energy level of the initial reactants is higher than that of the final
• Enzymes


  • Catalysts - speed up biological reactions + regulate cell metabolism
  • Are proteins
  • Has an active site - specific region where the substrate binds and where catalysis occurs
  • Substrate goes through modification at active site

  
• High specificity


  The enzyme will only bind with a single type of substrate

  
• Low specificity


  The enzyme will bind a range of related substrates, e.g. lipases hydrolyse any fatty acid chain (bond specific)

  
• Enzyme-substrate interaction models


  • Lock and key - The specific substrate fitting into the active site, reaction only occurs if the substrate fits
  • Induced fit - Change in shape (conformational change) in active site occurs when substrate binds, active site is flexible to achieve a tighter/better fit

  
• Reactions are often reversible and so can often be catalysed in both directions (substrate —> product, and product — > substrate)
• Different enzymes catalyse a reaction in each direction. For example, DNA polymerase builds DNA and DNAase breaks it down

  
• Enzymes can be reused over and over again
• Activation energy


  All reactions need an input of energy to start
• How enzymes reduce activation energy


  • Proximity and orientation - Enzymes bring the parts of the molecules involved in the reaction, closer to each other
  • The micro-environment - Most active sites are hydrophobic, the absence of water results in a non-polar environment, allowing stabilising interactions
  • Ion exchange - The amino acids in the active site can often take H+ ions from, or donate them to the substrate

  
• How enzymes regulate biochemical pathways


  • Sequences of enzymes catalysing reactions
  • Each substrate to specific to enzyme active site
  • Product of each reaction becomes the reactant for next reaction

  
• Types of enzymes


  • Follicular cells of the thyroid gland producing thyroxine
  • Liver cells converting toxic ammonia to urea
  • Chlorophyll-containing cells carrying out photosynthesis
• Enzymes involved in photosynthesis


  • Water-oxidising
  • ATP synthase
  • Rubisco

  
• Water-oxidising enzyme


  Splits water molecules, releases hydrogen ions and electrons that are recycled, oxygen is released as waste
• ATP synthase


  Generates ATP for second stage of photosynthesis

  
• Rubisco


  Main catalyst of photosynthesis, captures inorganic carbon dioxide and catalyses it to organic 3 carbon molecules that are then assembled into sugar molecules

  
• Enzymes required in cellular respiration


  • Phosphofructokinase (PFK)
  • Dehydrogenase

  
• Dehydrogenase


  Catalyse removal of hydrogen atoms from substrates, consuming one glucose molecule to produce six carbon dioxide molecules involved the removal of 12 hydrogen atoms
• Cofactors - inorganic


  • Magnesium (Mg2+)
  • Copper (Cu2+)
  • Manganese (Mn2+)
  • Calcium (Ca2+)
• Inorganic cofactors


  Do not contain carbon, form bonds at the active site of their enzyme and also bond with the substrate
• Coenzymes


  Organic non-protein compound that is loosely binded with an enzymes active site, additional non-protein groups that are needed for enzymes to function

  
• Cofactors - organic


  • Prosthetic groups - cofactors that are tightly bound to an enzyme and are essential for it to function as a catalyst
  • Coenzymes - cofactors that loosely bound to their enzymes only when the enzyme is acting on a substrate

  
• Major coenzymes in photosynthesis


  • NADP (nicotinamide adenine dinucleotide phosphate)
  • Coenzyme A (CoA)
  • ATP (adenosine triphosphate)

  
• Major coenzymes in cellular respiration


  • NAD (nicotinamide adenine dinucleotide)
  • FAD (flavin adenine dinucleotide)
  • ATP (adenosine triphosphate)

  
• Unloaded forms of coenzymes in photosynthesis


  • ADP
  • NADP+

  
• Loaded forms of coenzymes in photosynthesis


  • ATP
  • NADPH

  
• Unloaded forms of coenzymes in cellular respiration


  • ADP + Pi
  • NAD+
  • FAD
  • CoA
• Loaded forms of coenzymes in cellular respiration


  • ATP
  • NADH
  • FADH2
• Unloaded coenzymes


  Coenzymes accept a chemical group, proton or electron
• Loaded coenzymes


  Coenzymes donate a chemical group, proton or electron