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Question 1

Enzyme

Answer 1

Biological catalyst

Question 2

Are all enzymes proteins?

Answer 2

No, but mostly

Question 3

Are enzymes reusable?

Answer 3

Yes

Question 4

What is the reason why living organisms can exist at moderate temps?

Answer 4

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.

Question 5

Reaction kinetics and equilibrium constants

Answer 5

Question 6

Reaction Rate and Substrate Concentration:

Answer 6

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.

Question 7

Concept of Free Energy

Answer 7

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.

Question 8

Second Law of Thermodynamics

Answer 8

“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.

Question 9

Gibbs Free Energy (ΔG)

Answer 9

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.

Question 10

the difference between two important concepts in reaction thermodynamics

Answer 10

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.

Question 11

Graph showing difference between a non-catalyzed and a catalyzed reaction in terms of Gibbs free energy (ΔG) and activation energy (ΔG ‡ )

Answer 11

Question 12

High temp needs less kinetic energy and low temp needs more

Answer 12

Question 13

Answer 13

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.

Question 14

Answer 14

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.

Question 15

Lock and key hypothesis

Answer 15

Question 16

Induced fit

Answer 16

(happens after)

Question 17

Conformational selection

Answer 17

(happens before)

Question 18

Binding energy

Answer 18

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.

Question 19

Answer 19

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.

Question 20

Enzyme structure: The active site and the rest

Answer 20

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.

Question 21

Active site of the enzyme chymotrypsin

Answer 21

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.

Question 22

Proteolysis

Answer 22

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.

Question 23

Enzyme activity regulation

Answer 23

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.

Question 24

Transient (temporary) covalent modification

Answer 24

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.

Question 25

Allostery

Answer 25

Allosteric regulation involves a graded response where substrates or other regulatory molecules bind to sites on the enzyme (allosteric sites) that are not the active site. These molecules can either enhance or inhibit enzyme activity in a non-covalent manner.
Allosteric regulation provides a way for enzymes to be fine-tuned based on cellular needs, allowing enzymes to respond to changes in the concentrations of substrates or other regulators.

Question 26

Co-factors

Answer 26

Many enzymes are active as proteins alone, meaning they do not need any additional components to function.

Other enzymes require co-factors for activity. These are non-protein molecules or ions that are necessary for the enzyme’s catalytic function.

Metal ions are frequent co-factors. Many enzymes rely on metal ions like magnesium (Mg²⁺), zinc (Zn²⁺), or iron (Fe²⁺) to assist in catalysis by stabilizing charges or facilitating electron transfers.

Organic co-factors are referred to as co-enzymes. These organic molecules help enzymes carry out their reactions and are often derived from vitamins.

Tightly bound co-enzymes that remain permanently attached to the enzyme are known as prosthetic groups. These co-factors are integral to the enzyme’s structure and function and do not dissociate from the enzyme after the reaction.

Question 27

Apo-enzyme + co-factor = holo-enzyme

Answer 27

Apo-enzyme: This is the inactive form of an enzyme that lacks its necessary co-factor. The apo-enzyme is the protein part of the enzyme but without the non-protein co-factor that it needs for full activity.

Co-factor: This is the non-protein component (which could be a metal ion, a co-enzyme, or a prosthetic group) that is required for the enzyme’s catalytic activity.

Holo-enzyme: This is the active form of the enzyme, which includes both the apo-enzyme (protein part) and the co-factor. Once the apo-enzyme binds with its co-factor, the enzyme becomes fully functional and capable of catalyzing reactions.

Question 28

Specificity and Promiscuity in Enzymes

Answer 28

Enzymes can display a range of specificities:

Some enzymes are highly specific, catalyzing only a single type of reaction with a particular substrate.
Others may be less specific and can act on a range of similar substrates.
Highly specific enzymes:

These enzymes are exquisitely specific to one reaction and often act on only one particular substrate. This high specificity ensures precise biochemical control over metabolic pathways.
Enzymes that accept many similar substrates:

Some enzymes have broader specificity and can catalyze reactions for many similar substrates, which allows for more flexibility in biological systems.
Enzyme promiscuity (also called “moonlighting”):

Promiscuous enzymes are capable of catalyzing multiple reactions, often involving structurally diverse substrates. This enzymatic promiscuity can contribute to the redundancy, resilience, and adaptability of biological systems, allowing organisms to survive changes in their environment by making use of alternative substrates or pathways.

Question 29

Protein-Ligand Binding Equilibrium

Answer 29

Protein + Ligand ⇌ Protein-Ligand Complex
Ka represents the strength of binding (the higher, the stronger the binding).

Kd represents how easily the complex dissociates (the lower, the stronger the binding).

Question 30

fraction of protein occupied by ligand (𝜃 also denoted as
𝑓) in a binding interaction

Answer 30

Question 31

Answer 31

Question 32

Michaelis-Menten Model

Answer 32

Question 33

Key assumptions in deriving the Michaelis-Menten model for enzyme kinetics

Answer 33

Question 34

Equation of the michaelis-mentren model

Answer 34

Question 35

Reaction rate or velocity

Answer 35

Question 36

Answer 36

Question 37

The steady state assumption

Answer 37

The rate of formation of the enzyme-substrate complex (ES) is equal to the rate of its breakdown. This means that the concentration of the enzyme-substrate complex (ES) remains constant over time, even as the substrate concentration (S) changes.

Question 38

The steady state assumption equation

Answer 38