biochem topic 2

• ALL cells and organisms require energy
• Energy


  Critical for biological processes like growth, development, mechanical work
• How cells obtain energy from energy rich compounds

  • Carbohydrates
  • Lipids
  • Proteins
• Bioenergetics

  Living organisms exist in a dynamic steady state - a balance between building up (anabolism) and breaking down (catabolism)

  
• Organisms appear to maintain a constant composition but the population of molecules is far from being static - biomolecules constantly being degraded and resynthesised
• Maintaining a steady state requires constant source of energy
• Organisms Perform Energy Transductions to Accomplish Work to Stay Alive

  • Synthesis of new biomolecules / chemical bonds
  • Transport molecules against concentration gradient
  • Mechanical work
  • Maintenance of body temperature

  
• Without energy, cells can't renew biomolecules and will decay to equilibrium with their surroundings, leading to death
• Endergonic

  Process that requires energy input, not spontaneous
• Exergonic

  Process that releases energy, occurs spontaneously
• Gibbs free energy (G)

  The amount of energy available during a reaction

  
• Gibbs free energy change (∆G)

  Determines whether reactions are spontaneous

  
• Types of reactions in cells

  • Energy-liberating reactions (exergonic, catabolic)
  • Energy-requiring reactions (endergonic, anabolic)

  
• Energy Coupling

  Endergonic reactions are coupled to exergonic reactions so the overall process has a negative free energy change and occurs spontaneously

  
• Standard Free Energy Change ∆G°

  Free energy change of a reaction under standard conditions (T=298K, P=1atm, [reactants/products]=1M)
• Biological standard free energy change (∆G'°)

  Same as ∆G° but with [H+]=10-7M (pH 7.0) and [H2O]=55.5M, and [Mg2+]=1mM
• Gibbs Free Energy

  A reacting system continues changing until equilibrium is reached, where the rates of forward and reverse reactions are the same

  
• Equilibrium constant (Keq)

  Defines the relationship between the [reactants] and [products] at equilibrium
• Both Keq and standard free energy change are constants for each reaction
• ∆G (actual free energy change)

  Determines reaction direction in cells, not ∆G° (standard free energy change)

  
• Energetics Within the Cell are Not Standard
• Metabolism

  • The sum of ALL biochemical reactions occurring within the cell
  • Classified as catabolic pathways (degradative, release energy) and anabolic pathways (synthetic, require energy input)

  
• Metabolic pathway

  Sequence of consecutive biochemical reactions where the product of one reaction becomes the reactant in the next

  
• Plants and humans are different and use different proteins, so each organism needs energy to synthesise their own specific macromolecules
• Reactions must proceed in a controlled way, with energy transfer rarely exceeding 60 kJ/mol, to allow multi-steps to be finely controlled
• Reciprocal regulation

  Activation of one metabolic pathway while suppressing the opposite pathway
• Mechanisms of metabolic control

  • Control of intracellular substrate concentration
  • Control of amount of enzymes
  • Control of allosteric enzymes by inhibitors and activators
  • Negative regulation (feedback inhibition)
• Reactions

  • Must proceed in a controlled way (so energy input or output can be controlled)
  • Energy transfer in cell reactions rarely exceed 60 kJ/mol
  • Energy released in glucose oxidation is 2800 kJ/mol

  
• Reactions

  • Allows multi-steps to be finely controlled
  • The more "checkpoints" in a reaction, the more the pathway can respond to stimulation or challenges from the environment
• Anabolic and catabolic pathways

  Need to be regulated
• Reciprocal regulation

  Activation of one pathway, while suppressing the opposite pathway
• Mechanisms of metabolism regulation

  • Control of intracellular substrate concentration
  • Control of amount of enzymes
  • Control of allosteric enzymes by inhibitors and activators
  • Negative regulation (feedback inhibition)
  • Reversible covalent modification through signalling substances (e.g. hormones)
• Metabolism is regulated to achieve balance and economy
• Common biochemical reactions

  • Cleavage and formation of C–C bonds
  • Hydrolysis and condensation reactions
  • Internal rearrangements, isomerisation
  • Eliminations (without cleavage)
  • Group transfers (H+, CH3+, PO32–)
  • Oxidations-reductions (e– transfers)

  
• Glucose oxidation

  C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy

  
• Combustion

  All of the energy is released as heat, which is not a useable form to the cell
• Cells

  Overcome this by oxidising glucose in many steps, and trapping the released energy in small, useable forms of energy – hence 10 reactions in glycolysis

  
• Adenosine Triphosphate (ATP)

  • Common chemical store of energy in cells
  • Useable energy stored in phosphoanhydride bonds

  
• Mg-ATP complex

  The active form of ATP in the cell
• Hydrolysis of ATP to ADP

  • Exergonic reaction: yields a lot of energy because the products are very stable compared to the reactants
  • Standard free energy for hydrolysis of ATP to ADP is -30.5 kJ/mol