Cell Metabolism: Energy and Enzymes

In living systems, mass/matter and energy cannot be created or destroyed; they are only transformed into different forms.
In a chemical reaction with 7 carbon atoms in the reactants, there will be 7 carbon atoms in the products, as atoms are conserved.

To understand chemical reactions inside the cell, it is important to figure out:
- Can the reaction occur on its own (spontaneous) or does it require energy to occur?
- Which reactions will proceed quickly (frequently) vs. slowly (not frequently)?
- How the cell makes reactions speed up?

Energy is the capacity to do work or cause change.
Kinetic energy: associated with motion.
- Heat: During every energy transfer, some energy is lost as heat.
Potential energy: energy matter has due to its location or structure.
- Gradients on opposite sides of the membrane.
- Chemical energy: molecules possess energy due to the arrangement of electrons in bonds between their atoms.
Free energy (G) is the amount of energy in a system that is available to do work at constant temperature and pressure.

For analyzing a chemical reaction, you can calculate the change in G (called ”delta G” or $"\Delta G"$ ). Ex. Imagine you have a toy car at the top of a slide. Free energy is like how much push that car has to go down the slide all by itself! It's the energy that's ready to make things happen without needing extra help, like you pushing the car.
$ΔG = G<em>{products} – G</em>{reactants}$
$ΔG$ only depends on the energy of the products and reactants.
If $"\Delta G"$ is negative, the reaction releases energy.

Exergonic:
- $"\Delta G"$ is negative.
- Reaction gives off energy.
- Reaction is spontaneous (can happen by itself).
Endergonic:
- $"\Delta G"$ is positive.
- Reaction absorbs energy.
- Reaction is not spontaneous (won’t happen without putting in outside energy).
Processes that increase the entropy of the universe can occur spontaneously.
Spontaneous processes occur without energy input; they can happen quickly or slowly.
Examples of exergonic reactions:
- Ice melting at room temperature.
- Breaking down carbohydrates into water and carbon dioxide.
- Ions going down their concentration gradients.
Examples of exergonic reactions: ATP hydrolysis.
- ATP -> ADP + Phosphate ion.
- Excess energy released by breaking the phosphate-phosphate bond can be used to drive other reactions.

If you pair an exergonic reaction with an endergonic reaction, the exergonic reaction can power the endergonic one.
Main exergonic reaction that powers others in the cell: ATP -> ADP + Phosphate. (ATP (Adenosine Triphosphate) is the main source of energy for cells. ( ATP is used, it loses one phosphate group and becomes ADP (Adenosine Diphosphate), releasing energy in the process. This energy is then used to power other reactions in the cell.)
$ΔG_{ATP} = -7.3 kcal/mol$ (just tells you how much energy you get from using that one battery.)

The initial energy needed to start a chemical reaction is called the activation energy ( $E_A$ ).
The lower the activation energy, the more likely it is to proceed, so overall the reaction will happen more quickly.
Activation energy generally comes from heat from the environment.
- Heat makes molecules move randomly, which can give them enough energy to break bonds (overcome the activation energy).

Enzymes are proteins or RNA that are catalysts: they speed reactions by lowering the activation energy.
Each reaction in your cells requires an enzyme!
Enzymes do not affect $"\Delta G"$ . $"\Delta G"$ just has to do with the energies of the products and reactants, and enzymes are not products or reactants.
Activation energy is independent of $"\Delta G"$ .
Enzymes are specific for catalyzing a particular reaction. They have an active site where reactants bind.
- The reactants that bind to the enzyme are called the enzyme’s substrates.
- Enzyme names often end with –ase.
Most enzymes are proteins. Their side-chains have different jobs:
- Most hold the tertiary or quaternary structure together
- At the active site, they interact with the substrate

Orienting Substrates Correctly
- The active site can hold substrates in a precise orientation, making it easier for them to interact and form new bonds.
- By bringing the reacting parts of the molecules closer and correctly aligned, the enzyme reduces the energy needed for the reaction to occur.
Straining Substrate Bonds
- The enzyme can stretch or bend key bonds in the substrate molecules, weakening them and making them easier to break.
- This 'straining' reduces the amount of energy required to break those bonds, facilitating the reaction.
Providing a Favorable Microenvironment
- The active site can create a specific microenvironment that is more conducive (easy) to the reaction.
- For example, it might provide an acidic or basic environment that facilitates the transfer of hydrogen ions (H+) or other charged species, which can be critical for certain reactions.
Covalently Bonding to the Substrate
- In some cases, the enzyme may temporarily and covalently bind to the substrate.
- This forms a short-lived intermediate that makes it easier for a subsequent reaction to occur. Importantly, the enzyme's structure is always restored to its original state after the reaction is complete.

Optimal Conditions
- Enzymes generally have the highest activity under the specific conditions in which they evolved. This ensures they function efficiently within the organism's typical environment.