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Metabolism and Enzymes

Cells are constantly carrying out thousands of chemical reactions needed to keep the cell, and your body as a whole, alive and healthy. All of the chemical reactions that take place inside of a cell are called the cell’s metabolism.
  • Metabolism is very complex.
  • In this diagram you will see the core metabolic pathways in a eukaryotic cell, such as the cells that make up the human body.
  • Each line is a reaction, and each circle is a reactant or product.
In the metabolic web of the cell, some of the chemical reactions release energy and can happen spontaneously (without energy input). However, others need added energy in order to take place. 
  • Metabolism has 2 different processes.
  1. The process of breaking down of things
  2. The process to rebuild them in different ways that we will find useful
Metabolic pathways can be broadly divided into two categories based on their effects
The process of breaking down is called the catabolic pathway.
The process of building up is called the anabolic pathway.

Catabolic pathways involve the breakdown of complex molecules into simpler ones and typically release energy. Energy stored in the bonds of complex molecules, such as glucose and fats, is released in catabolic pathways. 
Anabolic pathways build complex molecules from simpler ones and typically need an input of energy. Building glucose from carbon dioxide is one example. 

Forms of Energy
For metabolism to occur one will need to acquire energy.
  • Energy is the capacity to cause change.
  • Is the ability to rearrange a collection of matter
  • It exists in various forms, and life depends on the ability of cells to transform energy from one type into another.
Energy can be associated with the relative motion of objects which is called kinetic energy.
  • Ex: Heat or thermal energy due to the random movements of atoms or molecules

Energy that us not kinetic is called potential energy, an object that is not moving possess energy.
  • Ex: Water behind a dam stores energy because of its altitude above sea level.

Chemical Energy is a term used by biologists to refer to the potential energy available for release energy by breaking down complex molecules.
  • These complex molecules such as glucose are known to have high chemical energy.
  • During a catabolic reaction, atoms are rearranged and energy is released, resulting in lower-energy breakdown products
The Laws of Energy Transformation
The study of the energy transformations that occur in a collection of matter is called thermodynamics. Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter.

According to the first law of thermodynamics, the energy of the universe is constant. 
  • Energy can transferred and transformed, but it cannot be created or destroyed
  • It is known as the principle of conservation of energy
A logical consequence of the loss of usable energy during energy transfer or transformation  is that each such event makes the universe more disordered. Scientists use a quantity called entropy as a measure of disorder. The more randomly arranged a collection of matter is, the greater its entropy.
The second law of thermodynamics states:
  • every energy transfer or transformation increases the entropy of the universe. 
  • For a process to occur spontaneously, it must increase the entropy of the universe.
Free Energy
In 1878, J. Willard Gibbs defined a very useful function called Gibbs free energy of a system symbolized by the letter G. Free energy measures the portion of a system's energy that can preform work when temperature and pressure are uniform throughout the system.
The change in free energy can be calculated for any specific chemical reaction with the following formula:
H symbolizes the change in the system's enthalpy, S is the change in the system's entropy, and T is the absolute temperature in Kelvin (K) units.
Once we know the value of G for a process, we can use it to predict whether the process will be spontaneous.
  • G must be less than ZERO, a negative number, so the process would be spontaneous.
  • If G is greater or equal to ZERO then it is never spontaneous
 Another term for a state of maximum stability is equilibrium which there is an important relationship between free energy and equilibrium. As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases. Free energy increases when a reaction is somehow pushed away from equilibrium.

Free Energy and Metabolism (Exergonic and Endergonic Reactions in Metabolism)
Based on their free-energy changes, chemical reactions can be classified as either exergonic or endergonic. An exergonic reaction proceeds with a net release of free energy or heat. An endergonic reaction reaction absorbs work energy. 
ATP and Reaction Coupling
ATP can be thought of as the main energy currency of cells. The energy released by hydrolysis (breakdown) of ATP is used to power many energy-requiring cellular reactions. An appreciable amount of energy is released when one of these bonds is broken in a hydrolysis (water-mediated breakdown) reaction. ATP is hydrolyzed to ADP in the following reaction:
In most cases, cells use a strategy called reaction coupling, in which an energetically favorable reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction. When reaction coupling involves ATP, the shared intermediate is often a phosphorylated molecule (a molecule to which one of the phosphate groups of ATP has been attached).

A substance that speeds up a chemical reaction—without being a reactant—is called a catalyst. The catalysts for biochemical reactions that happen in living organisms are called enzymes. Enzymes are usually proteins, though some RNA molecules act as enzymes too.
  • Enzymes lower a reaction's activation energy.
  • Enzymes work by binding to reactant molecules and holding them in such a way that the chemical bond-breaking and bond-forming processes take place more readily.
  • enzymes don’t change a reaction’s ∆G value
  • enzymes don’t affect the free energy of the reactants or products.
  • enzymes lower the energy of the transition state, an unstable state that products must pass through in order to become reactants. 
Active Sites
To catalyze a reaction, an enzyme will grab on (bind) to one or more reactant molecules. These molecules are the enzyme's substrates.
In some reactions, one substrate is broken down into multiple products. In others, two substrates come together to create one larger molecule or to swap pieces.The part of the enzyme where the substrate binds is called the active site.

Environmental effects on enzyme function

  • Temperature. A higher temperature generally makes for higher rates of reaction, enzyme-catalyzed or otherwise.
  • pH. pH can also affect enzyme function. Active site amino acid residues often have acidic or basic properties that are important for catalysis.
Enzyme Regulation
Because enzymes guide and regulate the metabolism of a cell, they tend to be carefully controlled.
  • Regulatory molecules. Enzyme activity may be turned "up" or "down" by activator and inhibitor molecules that bind specifically to the enzyme.
  • Cofactors. Many enzymes are only active when bound to non-protein helper molecules known as cofactors.
  • Compartmentalization. Storing enzymes in specific compartments can keep them from doing damage or provide the right conditions for activity.
  • Feedback inhibition. Key metabolic enzymes are often inhibited by the end product of the pathway they control (feedback inhibition).
Reversible inhibitors are divided into groups based on their binding behavior. 
  • An inhibitor may bind to an enzyme and block binding of the substrate, for example, by attaching to the active site. This is called competitive inhibition, because the inhibitor “competes” with the substrate for the enzyme.
  • In noncompetitive inhibition, the inhibitor doesn't block the substrate from binding to the active site. Instead, it attaches at another site and blocks the enzyme from doing its job. This inhibition is said to be "noncompetitive" because the inhibitor and substrate can both be bound at the same time.

Allosteric Regulation

Allosteric regulation, broadly speaking, is just any form of regulation where the regulatory molecule (an activator or inhibitor) binds to an enzyme someplace other than the active site. The place where the regulator binds is called the allosteric site

Feedback Inhibition of Metabolic Pathways

  • In feedback inhibition, a metabolic pathway is switched off by the inhibitory binding of its end product to a n enzyme that acts early in the pathway.
  • Prevents the cell from wasting chemical resources by synthesizing more insoleucine than necessary.