MOL100 Chemical reactions, equilibrium and enzyme catalysis

This set of flashcards covers key concepts from the lecture on chemical reactions, equilibrium, and enzyme catalysis, including definitions of reaction rates, equilibrium, energy forms, activation energy, and detailed aspects of enzyme function like active sites, Km, and ATP/NADPH roles.

What is the primary function of enzymes in cells?

Enzymes are proteins that facilitate chemical reactions.

Why are chemical reactions and enzymes important for cells?

Chemical reactions occur permanently in all cells, and enzymes facilitate these reactions, such as amino acids forming peptides or glucose synthesizing glycogen.

Do enzymes catalyze anabolic or catabolic pathways?

Enzymes catalyze both catabolic (breaking down food molecules for energy/building blocks) and anabolic (synthesizing cell molecules) pathways.

What two factors determine the reaction rate?

The reaction rate depends on the rate constant and the concentration of the molecules.

What does a higher rate constant indicate about a reaction?

A higher rate constant means that the reaction is energetically favorable.

When is chemical equilibrium reached for a reaction?

Chemical equilibrium is reached when the forward and reverse reaction rates are equal.

How do catalysts (like enzymes) affect reaction rates and equilibrium?

Catalysts affect the rate constant and thus the reaction rate of both the forward and reverse reactions, speeding up the time to equilibrium without changing its position.

What is the difference between chemical equilibrium and steady state in a cell?

In chemical equilibrium, reaction rates are the same and concentrations become constant. In a cell, a chemical equilibrium for a reaction may not be reached because a product can be consumed for a coupled reaction, leading to a steady state where concentrations remain constant due to coupled reactions.

What is the dissociation constant (Kd) used to describe for noncovalent binding reactions?

The dissociation constant (Kd) describes the binding reaction equilibrium, indicating the affinity of one molecule for another.

How does a lower Kd value relate to binding affinity?

The lower the Kd, the higher the affinity (tighter binding) of one molecule for another.

What is pH a measure of?

pH is the negative logarithm of the proton concentration in a solution.

What characterizes an acid?

Acids are molecules that tend to release protons.

What characterizes a base?

Bases are molecules that tend to take up protons.

What are zwitterions?

Zwitterions are biomolecules (like amino acids) that have groups that can both release and take up protons, meaning their net charge depends on the pH.

Why is pH important for molecular interactions?

Many molecular interactions depend on differences in charge, so changes in pH affect the binding properties of proteins and other macromolecules.

What do buffers do in cells?

Buffers can take up protons and hydroxyl ions, thereby avoiding fluctuations of the pH in cells.

What are the two principal types of energy?

The two principal types of energy are kinetic energy (energy of movement) and potential energy.

What is Gibbs free energy (G)?

Gibbs free energy (G) is the energy that can be used to do work, and ΔG describes the change in free energy of a reaction.

What defines an exergonic reaction?

In exergonic reactions, products contain less free energy than reactants (ΔG < 0), meaning they are energetically favorable and can occur spontaneously.

What defines an endergonic reaction?

In endergonic reactions, products contain more free energy than reactants (ΔG > 0), meaning they only occur when external energy is added.

What is activation energy?

Activation energy is the energy required to reach the transition state of a reaction, even for exergonic reactions.

How do catalysts (like enzymes) reduce activation energy?

Catalysts reduce the required activation energy by lowering the free energy of the transition state.

What effect does lowering activation energy have on reaction rate?

Lower activation energy makes the reaction faster in both directions by increasing the rate constant.

How do cells make endergonic reactions possible?

Cells make endergonic reactions possible by coupling them to exergonic reactions.

What is ATP's role as an energy currency in cells?

ATP is a key energy currency; breaking its phosphoanhydride bonds releases energy, which cells use to power endergonic reactions after generating ATP from light or nutrients.

What is the function of NAD+ and NADP+ in cells?

NAD+ and NADP+ (and FAD) are electron carrier molecules that can accept electrons from one molecule and transfer them to another, storing energy in their reduced forms (NADH, NADPH).

What is a ligand in the context of proteins?

A ligand is any molecule that binds to a protein.

What is a substrate in the context of enzymes?

A substrate is a ligand of an enzyme that can be chemically modified by the enzyme.

What are the two essential parts of an enzyme's active site?

The active site consists of a substrate binding site and a catalytic site.

What two properties are determined by non-covalent interactions between the substrate and the substrate binding site?

Non-covalent interactions determine the specificity (how many different ligands an enzyme can bind) and affinity (how strong the ligand is bound) of the enzyme.

What happens to an enzyme after it processes a substrate?

After processing, enzymes remain functional and repeat the processing with new substrate molecules.

What factors influence the rate of an enzymatic reaction?

The rate of an enzymatic reaction depends on the concentration of substrate and enzyme, and on the affinity of the binding.

What is the Michaelis constant (Km)?

Km is the substrate concentration at which the enzymatic reaction rate is half-maximal.

How does a smaller Km relate to substrate affinity?

A smaller Km indicates a higher affinity of the enzyme for its substrate.

What is described by the Michaelis-Menten equation?

The Michaelis-Menten equation describes the rate of product formation (V0) at a given substrate concentration [S], determined by the maximal reaction rate (Vmax) and the affinity (Km).

How does lysozyme cleave polysaccharides?

Lysozyme cleaves polysaccharides in bacterial cell walls by hydrolyzing the glycosidic bonds between monosaccharides, involving deformation of a sugar unit and specific amino acid residues (Glu35, Asp52) in its active site.