Thermodynamics

• Thermodynamics involves energy in bonds and entropy.
• Entropy is less than energy in the bonds but still involves energy.

Role of Thermodynamics in Biology

• Reactions (anabolic and catabolic) are used for bodily function.
• Thermodynamics helps to determine different reactions.
• Spontaneous reactions occur naturally such as rusting.
• Non-spontaneous reactions need energy input like a "kick start".
• Gibbs Free Energy (ΔG) measures if a reaction occurs spontaneously.
• Reactions with a negative (–) ΔG are spontaneous.
• Reactions with a positive (+) ΔG are non-spontaneous.

Determining ΔG

• What is used to determine ΔG:
• If a reaction releases heat (ΔH).
• ΔH is the change in heat of a reaction and is a measurable parameter that can approximate enthalpy change.
• Enthalpy is the energy content of the bonds.
• If DH is negative (-ve), the reaction releases heat and an exothermic reaction occurs.
  • Negative ΔH favors spontaneity, but it is insufficient on its own.
• If DH is positive (+ve), the reaction requires/absorbs heat and an endothermic reaction occurs.
• Whether the reaction tends towards disorder (ΔS).
• Entropy (S) is how "spread out" or dispersed energy is in a system.
• The more dispersed energy means the more "disorder".
• If ΔS is negative (-ve), energy is less dispersed.
• If ΔS is positive (+ve), energy is more dispersed.
  • Positive ΔS favors spontaneity, though it is not sufficient on its own.

How Enthalpy and Entropy Determine ΔG

• Negative ΔG is needed for a reaction to occur spontaneously.
• ΔG = ΔH - TΔS
• Entropy determines if energy becomes more or less dispersed.
• Temperature is defined in Kelvin.
• Enthalpy determines if heat is absorbed or released.
• Release of heat in addition to spreading out corresponds to negative ΔG, which results in a spontaneous reaction.

Gibbs Free Energy (ΔG)

• Negative ΔG is spontaneous and exergonic.
• Positive ΔG is non-spontaneous and endergonic.
• If ΔG = 0, the reaction is at equilibrium.
• When at equilibrium, there is no net transfer of heat or energy.

Spontaneity of Reactions

• Assessing the spontaneity of reactions:
• Negative ΔH and Positive ΔS will always result in a spontaneous reaction.
• Positive ΔH and Positive ΔS will sometimes result in a spontaneous reaction if ΔS is large enough to overcome ΔH.
• Negative ΔH and Negative ΔS will sometimes result in a spontaneous reaction if ΔH is large enough to overcome ΔS.
• Positive ΔH and Negative ΔS will never result in a spontaneous reaction.
• Positive ΔS means disorder increases as size becomes larger.
• Negative ΔS means the size is smaller with ordered orientation.

AG°

• ΔG tables provide ΔG values under standard conditions for easy comparison.
• Standard Gibbs free energy change is represented as ΔG°.
• Calculation of ΔG° occurs under following conditions:
  • 298 K (room temperature).
  • pH = 7 which is neutral.
  • 1 M of each reactant and product.
• Some common biological reactions have a positive ΔG°. Since this is the case, these reactions need energy and are not spontaneous.
• Reactions with a positive ΔG° can still happen by adding energy by ATP addition and releasing energy in a phosphole bond. Trapping glucose in gluconeogenesis is an example.

Reaction Coupling

• Reactions with a positive ΔG° can still occur in our bodies by coupling them to a reaction with a very negative ΔG°.
• The energy released from the negative ΔG° runs the one with the positive ΔG°.
• A common coupled reaction is ATP hydrolysis.
• To overcome a positive ΔG°, ATP is included to allow the reaction to occur spontaneously.
• Alternatively, changing the concentrations of substrates and products helps a reaction with a positive ΔG° to occur.

Enzymes

• Enzymes are catalysts made of protein that speed up specific reactions and remain unchanged by the reactions.
• Enzymes lower the activation energy (Ea) of a reaction, and work without changing:
  • The free energy (ΔG) of the reaction.
  • Disturbing equilibrium.
  • Affecting the amount of product, but produce the product faster.

Activation Energy

• Activation energy (Ea) is the minimum amount of energy needed to make or break the bonds necessary for a reaction to occur.
• It can also be called the "Free Energy of Activation", or ΔG‡.
• Activation energy can be defined as the amount of energy needed to reach the transition state (TS).
  • The transition state is the highest energy configuration formed when reactants change to products.
  • It is transient and not isolated.
• Enzymes lower activation energy in the catalyzed reaction, though there’s no change in overall free energy of the reaction
• Enzymes
  • Enzymes bind substrates in their active site.
  • Only substrates with the correct size and shape enter into the active site.
  • Protein structure puts specific amino acids, often distant and based on the primary, into proximity.
• The enzyme active site:
  • Allows them to work together and catalyze reactions.
  • The substrate enters the active site and binds the enzyme to form an enzyme-substrate (ES) complex.
  • The enzyme-substrate complex's binding induces a conformational change in shape of the enzyme (Induced fit model).
  • Induced fit is a process where the enzyme active site changes to allow substrates to enter the active site, ES in the enzyme-substrate substrate complex forms.

Enzyme Classification

• Enzymes are classified by reaction type.
• Enzyme classes include:
  • Oxidoreductases (EC 1).
  • Transferases (EC 2).
  • Hydrolases (EC 3).
  • Lyases (EC 4).
  • Isomerases (EC 5).
  • Ligases (EC 6).

Oxidoreductases

• Oxidoreductases catalyze redox reactions.
• Redox involves reduction/oxidation reactions.
• The reactions occur in a lot of anabolic and catabolic processes.
• Anabolic and catabolic processes: - Anabolic reactions form molecules. - Catabolic reactions break down molecules.
• The mnemonic LEO GER helps with remembering the rules of a redox reaction
• LEO = Loss of Electrons is Oxidation.
• GER = Gain of Electrons is Reduction.
• Common oxidoreductases include:
• Oxidases which are specific to redox reactions where oxygen is the electron acceptor.
• Reductases.
• Dehydrogenases.
• The coenzyme B3 or B2 is typical to dehydrogenases.
• NAD+/NADH and FAD/FADH2 are examples of common coenzymes.

Transferases

• The transferases synthesize molecules by catalyzing the transfer of a group from one molecule to another.
• Transferases are common in creation/synthesis of polymers like:
  • Peptides/proteins from amino acids.
  • Di-/oligo-/poly- saccharides from monosaccharides.
  • Triglycerides from fatty acids.
  • DNA from nucleotides.
• Transferases often use a mechanism called "nucleophilic substitution".
• Common transferases include:
• Kinases: Transfer a phosphate group from ATP to another (non-water) molecule .
• Polymerases: Transfers a monomer to a polymer, especially with DNA and RNA. "X" transferases: Transfer "X" from one molecule to another. "X" = name of group being transferred, and the ending is then changed to "yl".

Example Name

• Example: if "X”= a peptide, then the enzyme is a peptidyl transferase.
• The coenzyme A, or CoA (aka CoASH): carries fatty acid chains in the form of fatty acyl CoA and transfers the chains to glycerol to make triglycerides.

Hydrolases

• Hydrolases catalyze hydrolysis reactions by using water (H2O) as a nucleophile to break molecules.
• Hydrolases break up polymers like:
  • Proteins → peptides, and peptides → amino acids.
  • Di-/oligo-/poly- saccharides → monosaccharides.
  • Triglycerides → fatty acids and glycerol.
  • DNA → nucleotides.
• Common hydrolases:
  • “X”-ases, "X" is the molecule broken apart.
  • Peptidases: Hydrolyze peptides to release smaller amino acid fragments.
  • Lipases: Hydrolyze lipids (triglycerides) to release fatty acids..
  • ATPases: Hydrolyze ATP to release P..
  • Phosphatases: Hydrolyze monophosphate esters (ex AMP, but not ATP) to release a phosphate group.
• The lipase speed up of a reaction by using acid/base hydrolysis. A hydrogen is removed from water by the enzyme base to create -OH. An -OH is now a better nucleophile than water and the enzyme remains unchanged at the course of a reaction.

Lyases

• Lyases play with water to create or remove bonds and include:
  • Hydratases: add water across a double bond via Addition or hydration.
  • Dehydratases: remove water across a double bond via Elimination or dehydration.
  • Decarboxylases: remove via Decarboxylation.

Practice

• Hydration is the process of adding water across a double bond, while hydrolysis is the process using water to break a molecule. Hydratase is the enyzme that adds water, while hydrolase is the enzyme that breaks molecules water. Dehydration is the process of removing water, while dehydratase is the enzyme that catalyst the removing water. Dehydrogenase is an enzyme that catalyzes the removal of hydrogen.

Isomerases

• Isomerases create isomers (molecules with the same molecular formula but different structural arrangements)
• Isomerization = is the rearrangement of a group{s} within a molecule with no net addition or elimination of atoms.
• Mutase is a common type of isomerase that transfers functional groups intramolecularly.

Ligases

• Ligases join 2 things together catalyzing reactions that join 2 molecules with the use of ATP for energy.
• Specific ligases include:
  • Carboxylases: joins CO2 to a molecule.
  • “X”-ligases and “X”-synthetases: X referrers to the molecules being joined/being created and synthase or synthetase.
• Example: glutamate-cysteine ligase, aka y-glutamylcysteine synthetase is part an antioxidant reaction, is an example of when DNA with a break in its strand, uses DNA ligase to be fixed.

Cofactors and Coenzymes

• Enzymes are helped from cofactors and coenzymes
• Cofactors are typically metal cations like Mg2+ and Zn2+.
• Mg2+ helps to:
  • Position the ATP in the active site
  • Stabilize the negative changes on the ATP and allows the nucleophile access to phosphate.
• Coenzymes are typically derived from vitamins.
  • An example is B3, or NAD, used for accepting and donating electrons in redox reactions.

Environmental Effects

• Enzymatic activity can be impacted by internal environmental changes like:
  • Temperature:
    • The optimal temperature for enzymes usually matches the organism's typical temperature.
    • Changes in temperature through fevers can also be a factor.
  • pH:
    • Changing pH effects protonation state of the enzyme or substrate disrupting bonds.
      • Hydrogen-bonds: Removal/ additions can effect bond.
      • Electrostatic interactions can turn COO- into COOH or removing and H can turn NH3+ into NH2.
• Lysosome environment considerations:
  • A main site of intracellular enzymatic degradation for molecules is impacted by what pH lysosomal enzymes are active at. Lysosomes at pH of 4-5 while cytosol is at pH7. This differential is critical for enzyme functionality.

Michaelis-Menten Kinetics

• Michaelis and Menten developed a kinetics equation for certain reactions.
• This equation allows for determination of enzyme health based on:
  • Maximum rate.
  • Affinity for the substrate, inhibitor, or coenzyme.
• Reactions need to be first order. - Rate is directly proportial to a concentration of a single substrate. - What about reactions that involved more than a single subtrate: - Pseudo first order is when there is at least two substrates or more, MM still applies. - Reaction diagrams - In a zero reaction rate, enzymes stop increasing rate even if subtrate increases.

Equation

• Formula used to measure the above factors:
• Vo = Vmax[S] / ([S]+KM)
• Vo: initial reaction rate.
• Vmax: maximum velocity. Km: measure of enzyme affinity:
  • Small Km = enzymes bind well giving high affinity. - Large Km = enzymes don't bind together creating low affinity.
• Graphing subtrate against reaction rate determines Vmax which allows for an idea of how much subtrate is needed in total.
• Lineweaver-Burk is the reciprocal of MM, and the formula can be used using a graph. 1/Vo = (1/Vmax) + (Км/ Vmax) (1 / [S]), using a Y axis of Vmax and a X axis of sub rate helps graph the enzyme reaction.

Explores thermodynamics, spontaneity, and enzymes. Covers Gibbs free energy, exergonic/endergonic reactions, temperature effects, ATP coupling, and redox reactions. Also covers enzyme kinetics, Km values, ligases, and hydratases.