Bioenergetics

• Spontaneous reactions can occur without added energy, they have -ΔG (free energy decreases).

  Nonspontaneous reactions require energy, they have +ΔG (free energy increases).

  A reaction is reversible if it has a free energy change of only 1 kcal/mol wherein it can readily go in either directions (Le Chatlier's Principle).

  Le Chatlier's Principle states that when stress is applies to a system in equilibrium, the system needs to react to minimize the effect of the stress.

  Only the endpoints of an irreversible reaction is irreversible.
• Formula for Gibbs free energy -> ΔG° = -RTnKeq

  Gibbs free energy indicates the thermodynamic favorability of a physical or chemical process.

  ΔG°' is used to denote the free energy in a modified standard state wherein there is a change in hydrogen-ion concentration from 1M to 1x10^-7 (pH 7).
• Oxidation-Reduction reactions are those in which electrons are transferred from a donor to an acceptor

  • oxidation: the loss of electrons; the substance that loses the electrons is called a reducing agent (LEORA)

  • reduction: the gain of electrons; the substance that gains the electrons is called an oxidizing agent (GEROA)

  examples of oxidizing agents -> NAD+ and FAD

  examples of reducing agents -> NADH and FADH
• Metabolism: the chemical reactions of biomolecules. It is the biochemical basis of life processes and is the sum total of the chemical reactions of biomolecules in an organism

  Catabolism: the breakdown of larger molecules into smaller ones; an oxidative process that releases energy

  Anabolism: the synthesis of larger molecules from smaller ones; a reductive process that requires energy
• All cells require energy to function

  Light from the sun is the ultimate source of energy for all life on earth

  photosynthetic organisms use light energy to drive the energy-requiring synthesis of carbohydrates

  non-photosynthetic organisms consume these carbohydrates and use them as energy sources
• Endergonic reactions require input of energy.

  Exergonic reactions release energy.
• Thermodynamics- branch of science that answers questions about processes that are energetically favorable
• Free Energy of a System

  ΔG < 0 spontaneous exergonic -> energy released

  ΔG = 0 Equilibrium

  ΔG > 0 Nonspontaneous endergonic -> energy required
• Life and Thermodynamics

  • ΔG=ΔH-TΔS• ΔH is heat of a reaction at constant pressure
  • ΔS is the change in entropy
  • ΔG is the change in free energy
  • T is the temperature
• Isolated system - no change of matter or energy
• Closed system - energy change may occur
• Open system - energy and/or matter exchange may occur
• Entropy: a thermodynamic quantity representing the unavailability of a system's thermal energy for conversion into mechanical work, often interpreted as the degree of disorder or randomness in the system
• Carbon in most reduced form: alkane
• Carbon in most oxidized form: CO2 (final product of catabolism
• • In catabolism, large molecules are broken down to smaller products, releasing energy and transferring electrons to acceptor molecules of various sorts. The overall process is one of oxidation.
• • In anabolism, small molecules react to give rise to larger ones; this process requires energy and involves acceptance of electrons from a variety of donors. The overall process is one of reduction
• formula for equilibrium constant:

  
• Equilibrium: Reversible chemical reaction in which no net change in the amounts of reactants and products occurs
• if Keq >> 1 : At equilibrium there is more products than reactants. The reaction is product favoured
• if keq = 1 : At equilibrium there is an equal amount of products and reactants
• if Keq << 1 : At equilibrium there is more reactants than products. The reaction is reactant favoured
• Conversion of ethanol to acetaldehyde is a two-electron oxidation
• Coenzyme: a non protein substance that takes part in an enzymatic reaction and is regenerated for further reaction

  • metal ions- can behave as coordination compounds. (Zn2+, Fe2+)

  • organic compounds, many of which are vitamins or are metabolically related to vitamins.
• • Nicotinamide adenine dinucleotide (NAD+) is an important coenzyme
  • Acts as a biological oxidizing agent
  • The structure of NADH is comprised of a nicotinamide portion. It is involved in the reaction. It is a derivative of nicotinic acid
  • NAD+ is a two-electron oxidizing agent, and is reduced to NADH
• • Flavin adenine dinucleotide (FAD) is also a biological oxidizing agent

  • Protons, as well as, electrons are accepted by FAD
• • Energy must be expended to put on additional negative charge on ADP
  • Also, entropy loss when ADP is phosphorylated because there is a potential loss of resonance hybridization of inorganic phosphate (Pi) upon phosphorylation of ADP to ATP
• 4 (-) charges on ATP and 3 on ADP, therefore ATP is less stable.
• • The coupling of energy-producing and energy-requiring reactions is a central theme in the metabolism of all organisms
  • Energy cannot be used directly, must by shuttled into easily accessible forms of chemical energy
  • “High Energy” bonds- bonds that require or release convenient amounts of energy, depending on the direction of the reaction
  • ATP is essential high energy bond-containing compound
  • Phosphorylation of ADP to ATP requires energy
  • Hydrolysis of ATP to ADP releases energy
• • Hydrolysis of ATP to ADP releases energy

  • In the coupling of biochemical reactions, the energy released by one reaction, such as ATP hydrolysis, provides energy for another
• Reactions in which metabolites are reduced are part of anabolism; they require reducing agents, such as NADH, NADPH, and FADH2, all of which are the reduced forms of coenzymes mentioned
• • activation: the formation of a more reactive substance

  • A metabolite is bonded to some other molecule and the free-energy change for breaking the new bond is negative.

  • Causes next reaction to be exergonic
• Coenzyme A (CoA-SH) contains units of 2-mercaptoethylamine, pantothenic acid, and 3’,5’-ADP
• NAD+, NADP+, FAD, and coenzyme A—share an important structural feature: all contain ADP. In NADP+, there is an additional phosphate group at the 2' position of the ribose group of ADP. In CoA, the additional phosphate group is at the 3' position.
• The metabolically active form of a carboxylic acid is the corresponding acyl-CoA thioester, in which the thioester linkage is a high-energy bond