Enzymes

The active site is a specific site on the enzyme surface where the enzyme binds a specific molecule called the substrate and catalyzes its transformation into the product.

1. Enzymes (proteins)
2. Ribozymes (ribonucleic acids)

Enzymes are the agents of metabolism, catalyzing every chemical step of a metabolic pathway, such as glycolysis, which requires specific enzymes for each step.

Catalytic power is the ratio of the rate of a catalyzed reaction to the rate of the uncatalyzed reaction. For example, urease has a catalytic power of 10^14, meaning it catalyzes the reaction 10^14 times faster than the uncatalyzed reaction.

Enzyme specificity refers to the ability of an enzyme to catalyze one particular reaction on a specific substrate to produce a specific product. Some enzymes are very specific, binding only one substrate, while others have broad specificity, binding a class of compounds to produce a new class of products.

Cofactors are nonprotein components required by many enzymes to carry out their catalytic functions. They can be inorganic ions like Fe2+, Mg2+, or Zn2+, and are essential for the enzyme's activity.

A holoenzyme is the active form of an enzyme that includes its coenzyme or cofactor bound to it, enabling the enzyme to perform its catalytic function effectively.

The six categories of enzymes are:

1. Oxidoreductases - catalyze oxidation-reduction reactions.
2. Transferases - transfer C, N, or P functional groups.
3. Hydrolases - cleave covalent bonds with water.
4. Lyases - add or remove groups to form double bonds.
5. Isomerases - catalyze isomerization changes.
6. Ligases - join two molecules with covalent bonds.

Coenzymes are organic molecules that assist enzymes in catalyzing reactions. Most coenzymes cannot be synthesized by animals and must be obtained from the diet, deriving from vitamins.

The traditional method for naming enzymes involves adding the suffix -ASE to the name of the substrate or to a descriptive term for the reaction the enzyme catalyzes, such as urease for the enzyme that acts on urea.

An apoenzyme is the enzyme form that exists without its prosthetic group or cofactor.

Ligases are enzymes that catalyze the formation of bonds using the energy derived from ATP hydrolysis. An example is pyruvate carboxylase, which converts pyruvate, bicarbonate, and ATP into oxaloacetate, ADP, and inorganic phosphate.

The noncovalent interactions involved in substrate binding include electrostatic interactions, hydrogen bonding, dipole-dipole interactions, hydrophobic interactions, and van der Waals interactions. These interactions are crucial for the specificity of substrate binding.

Isomerases catalyze isomerization reactions, which involve the conversion of one isomer into another. An example is phosphoglycerate mutase, which interconverts 3-Phosphoglycerate and 2-Phosphoglycerate.

The Lock and Key Hypothesis is a theory that describes enzyme specificity, where the enzyme is likened to a lock and the substrate to a key. This hypothesis suggests that the enzyme's active site is a perfect fit for the substrate, but it does not account for the flexibility of enzymes, which are not rigid like locks.

The induced fit hypothesis suggests that the shape of an enzyme's active site changes upon substrate binding, allowing for a precise fit between the enzyme and the substrate. This dynamic recognition process enables the enzyme to undergo conformational changes that facilitate the catalytic reaction.

Lyases are enzymes that catalyze the addition of groups to double bonds or the elimination of groups to form double bonds. An example of a lyase is aldolase.

Transition states are high-energy states that occur during the conversion of reactants to products, while reaction intermediates are stable species that form during the reaction and exist between the transition states of elementary steps.

Catalysts enhance reaction rates by lowering the activation energy required for a reaction. This allows a greater population of molecules to have sufficient energy to overcome the energy barrier, thus increasing the rate of reaction without altering the equilibrium constant.

A negative ΔG°' indicates that the reaction is spontaneous in the direction from substrate to product, reflecting that the product has a lower ground state energy than the substrate.

The term is prochiral.

They are designated as pro-S and pro-R.

The greater the activation energy, the slower the reaction. Activation energy is the energy required to reach the transition state, and it determines how quickly reactants can be converted to products.

The rate determining step is the slowest step in a reaction pathway, characterized by the highest activation energy. It dictates the overall rate of conversion from reactants to products, as the rate of the entire reaction cannot exceed the rate of this slowest step.

Catalysts do not affect the reaction equilibria or the corresponding standard free energy change. They facilitate the reaction without altering the overall free energy difference between reactants and products.

The activation energy is the energy barrier that must be overcome for a reaction to occur. A lower activation energy results in a higher reaction rate, as more molecules can achieve the necessary energy to reach the transition state.

The free energy of substrate binding lowers the activation energy by ensuring that the substrate binds tightest at the transition state. This relationship highlights how effective binding at the transition state can facilitate the reaction process.

The Eyring Equation states that the reaction rate (v) is related to the activation energy (∆G*) by the formula: v = k_B T e^(-∆G*/RT), where k_B is Boltzmann's constant, T is the temperature in Kelvin, and R is the universal gas constant.

The activation energy (∆G*) represents the energy barrier that must be overcome for a reaction to proceed, and it directly influences the rate of the reaction as described by the Eyring Equation.

The larger the difference between the free energy of the transition state and that of the ground state of the reactants, the less stable the transition state, resulting in a slower reaction rate.

The catalyst lowers the activation energy by the same amount for both the forward and reverse reactions, ensuring that the equilibrium constant remains unchanged despite the enhancement of the reaction rate.

The binding energy is a major source of energy used to lower the activation energy and contributes to the specificity of the enzyme for its substrate. It is optimized in the reaction transition state.

The transmission coefficient (κ) represents the probability that the breakdown of the activated complex will proceed to products rather than reverting back to reactants. It is generally assumed to be around 1.

Enzymes recognize specific substrates to form a specific ES complex through noncovalent interactions, which include hydrogen bonds, hydrophobic interactions, and electrostatic interactions.

Weak noncovalent interactions formed in the enzyme-substrate (ES) complex maximize binding energy when the substrate reaches the transition state. This lowers the activation energy by ensuring that the substrate binds tightest at the transition state, making these interactions a major driving force in enzymatic catalysis.

Enzymes lower the activation energy by utilizing the binding energy derived from noncovalent interactions with the substrate, which stabilizes the transition state and optimizes the binding energy in the reaction transition state.

The rate constant k' is influenced by the vibrational frequency (υ) of the bonds that break, the transmission coefficient (κ), and the activation energy of the transition state (ΔG‡).

Transition state analogs are stable molecules that resemble the transition state and bind tightly to the enzyme. This tight binding is significant because it supports the theory that enzymes preferentially bind their transition states, which can be utilized in rational drug design by understanding specific enzyme reaction mechanisms.

The relationship is given by the equation: ΔG‡ = -RTln K‡, where ΔG‡ is the free energy of activation, R is the gas constant, T is the temperature, and K‡ is the equilibrium constant for the transition state.

Enzymes do not alter the thermodynamic parameters such as equilibrium constants; thus, Keq remains the same regardless of the presence of the enzyme.

The diagram shows that the catalyzed reaction has a lower activation energy peak (41 kJ) compared to the non-catalyzed reaction (40 kJ), indicating that the enzyme facilitates the reaction by lowering the energy barrier.

Coenzymes are complex organic or organometallic molecules that assist enzymes in catalysis, often serving as intermediate carriers of functional groups. Unlike cofactors, which are typically inorganic, coenzymes can be loosely or tightly bound to the enzyme.

Substrate stereospecificity refers to the ability of enzymes to selectively bind and catalyze reactions involving chiral substrates. Enzymes, composed of L-amino acids, have asymmetric active sites that allow them to catalyze stereospecific reactions, ensuring that only specific stereoisomers are processed.

If an enzyme is completely complementary to the substrate, the ES complex becomes incredibly stable and low in energy, resulting in an increase in activation energy. This is because any change in the ES complex towards the transition state would disrupt the optimized binding interactions, thus stabilizing the substrate instead of the transition state.

1. The ability to self replicate
2. The ability to catalyze chemical reactions efficiently and selectively.