shaun Flashcards
(39 cards)
Enzyme
Biological catalyst
Are all enzymes proteins?
No, but mostly
Are enzymes reusable?
Yes
What is the reason why living organisms can exist at moderate temps?
Due to catalysts.
In the absence of an efficient catalyst, a reaction such as orotidine decarboxylation would require very high temperatures to proceed at a measurable rate.
Reaction kinetics and equilibrium constants
Reaction Rate and Substrate Concentration:
In uncatalyzed reactions, increasing the amount of substrate leads to a faster reaction rate.
Catalyzed reactions (with an enzyme):
The reaction goes faster even at lower substrate concentrations compared to an uncatalyzed reaction.
However, the reaction reaches a maximum rate (asymptote) where adding more substrate does not increase the reaction speed.
This is due to saturation of the enzyme: all active sites on the enzyme are occupied, so the rate cannot increase further despite the addition of more substrate.
Concept of Free Energy
Free energy: The energy available in a physical system that can be used to do work.
Gibbs Free Energy (G): Refers to the portion of energy in a system that can be converted into work, while maintaining constant temperature and pressure.
Free Energy Change (ΔG):
A negative ΔG indicates that a reaction can occur spontaneously, meaning the reaction releases energy and can proceed without external input.
Second Law of Thermodynamics
“There is a negative free energy change only when the overall entropy of the universe is increased.” This emphasizes that for a process to be spontaneous (favorable), the total entropy (disorder) of the universe must increase, even if the entropy of the system decreases.
Gibbs Free Energy (ΔG)
ΔG is always negative for a favorable (spontaneous) process. A negative Δ𝐺 (<0) indicates that the process can occur without the input of external energy.
This form connects the free energy change to the total entropy change of the universe, highlighting that a process is spontaneous when the entropy of the universe increases.
the difference between two important concepts in reaction thermodynamics
ΔG is the overall free energy change in a reaction. It represents the difference in Gibbs free energy between the products and the reactants. This value tells us whether a reaction is spontaneous (negative Δ𝐺) or non-spontaneous (positive Δ𝐺) under constant temperature and pressure.
ΔG ‡ is the activation energy required to initiate a reaction. This represents the energy barrier that must be overcome for the reaction to proceed. It’s not about whether the reaction is thermodynamically favorable but about how quickly the reaction can happen. A higher activation energy means a slower reaction, whereas a lower activation energy means a faster reaction.
Graph showing difference between a non-catalyzed and a catalyzed reaction in terms of Gibbs free energy (ΔG) and activation energy (ΔG ‡ )
High temp needs less kinetic energy and low temp needs more
ΔG‡ (non): This represents the activation energy for the non-catalyzed reaction, which is higher. Fewer molecules (indicated by the smaller shaded area under the curve) have sufficient kinetic energy to overcome this higher barrier, so fewer molecules can react without a catalyst.
ΔG‡ (cat): This is the activation energy for the catalyzed reaction, which is lower. More molecules (indicated by the larger shaded area under the curve) have sufficient kinetic energy to surpass this lower barrier, so more molecules can react when a catalyst is present.
Enzymes speed up the rate at which the equilibrium is reached: This means that enzymes increase the reaction rate by lowering the activation energy, allowing both the forward and reverse reactions to occur more quickly. As a result, the system reaches equilibrium faster than it would without an enzyme.
Enzymes do not change the position of the equilibrium: This means that while enzymes can speed up the rate of reaction, they do not alter the concentrations of the reactants and products at equilibrium. The equilibrium constant (Keq), which is determined by the ratio of products to reactants at equilibrium, remains the same with or without an enzyme. The enzyme only affects how quickly equilibrium is achieved.
Lock and key hypothesis
Induced fit
(happens after)
Conformational selection
(happens before)
Binding energy
Binding energy is the free energy that is released when weak, non-covalent bonds (such as hydrogen bonds, van der Waals forces, and ionic interactions) form between the substrate and the enzyme’s active site.
These weak interactions help to stabilize the enzyme-substrate complex, which is essential for lowering the activation energy and driving the reaction forward.
Maximization during the transition state: The binding interactions between the enzyme and substrate are strongest when the substrate is in its transition state, which is the most unstable and high-energy point along the reaction pathway. This stabilization of the transition state by the enzyme is a key mechanism by which enzymes lower the activation energy and increase the reaction rate.
Enzymes have evolved to recognize the transition state of the chemical reactions they catalyze. This means that the enzyme is specifically structured to bind to and stabilize the transition state of the substrate.
The transition state can be understood as the critical point in the reaction at which a bond “decides” whether it will break or reform. It is a high-energy, unstable configuration where the substrate is midway between the reactant and product forms.
Enzyme structure: The active site and the rest
The active site of an enzyme is the location where catalysis occurs. However, only a small number of amino acids in the enzyme, out of hundreds, are directly involved in catalysis.
What is the rest of the protein for?
Positioning the active site residues: The rest of the protein helps in positioning the active site residues correctly, even in cases where it may be energetically unfavourable.
Providing the correct micro-environment: The surrounding structure of the protein ensures the active site has the right conditions for catalysis, such as adjusting the pKa values of amino acid residues.
Additional sites for recognition and control: Other parts of the protein may serve roles in enzyme regulation, like allosteric sites, which modulate enzyme activity when bound by regulators.
Active site of the enzyme chymotrypsin
Key Elements:
Catalytic Triad:
D102 (Aspartic acid 102): This residue helps in stabilizing and orienting H57 to facilitate proton transfer.
H57 (Histidine 57): Histidine acts as a base, abstracting a proton from S195, making it a stronger nucleophile.
S195 (Serine 195): Serine is the nucleophilic residue that directly attacks the peptide bond of the substrate, initiating the catalytic process.
Oxyanion Hole:
This structure stabilizes the negatively charged oxygen (oxyanion) that forms during the transition state of the reaction. The oxyanion hole is crucial for lowering the activation energy and speeding up the reaction.
Proteolysis
Proteolysis is the process of breaking down proteins into smaller fragments, such as peptides or amino acids, by the action of enzymes known as proteases or peptidases.
Enzyme activity regulation
Proteolysis is catalyzed by enzymes called proteases, which cleave the peptide bonds between amino acids in a protein.
Functions of Proteolysis:
Protein degradation: Proteolysis helps in breaking down proteins that are damaged, misfolded, or no longer needed by the cell. This prevents the accumulation of defective proteins and allows the recycling of amino acids for the synthesis of new proteins.
Activation of zymogens (pro-enzymes): Many enzymes are synthesized in an inactive form (zymogens) and are activated by proteolytic cleavage. For example, digestive enzymes such as pepsin and trypsin are produced as inactive precursors (pepsinogen and trypsinogen) and are activated by proteolysis in the digestive tract.
Regulation of biological processes: Proteolysis plays a key role in processes like blood clotting (through the cleavage of clotting factors), apoptosis (programmed cell death), and immune responses (through the activation of complement proteins).
Processing of polypeptides: Some proteins, such as hormones and growth factors, are initially synthesized as longer precursors and undergo proteolysis to become fully functional.
Proteolytic breakdown of enzymes:
This serves as a one-way “off” switch, where enzymes are irreversibly inactivated by proteolytic degradation. This is a common mechanism to terminate enzyme activity and maintain regulation in biological systems.
Transient (temporary) covalent modification
Phosphorylation is an example of this type of regulation, where a covalent attachment of a phosphate group to an enzyme can act as a two-way “on-off” switch.
Phosphorylation can either activate or deactivate enzymes depending on the enzyme and the site of phosphorylation, and this process is reversible, making it a key regulatory mechanism in many cellular processes.