Cellular Energy and Enzyme Function: Biochemistry Fundamentals
Cellular Life and Open Systems
Living cells function as open systems, constantly exchanging matter and energy with their environment.
Key System Definitions
- Open System: A system that continuously exchanges matter and energy with its surroundings, transforming and storing energy to perform biological activities.
- Equilibrium System: A system where the values of certain predefined variables are maintained over time within a range of tolerance.
- Dynamic Balance of Flows: The typical state of living organisms, often referred to as an open system in balance.
Energy Storage: ATP and Other Nucleotides
Cells possess mechanisms to transform, store energy, and synthesize molecules necessary for replication. All cells utilize the ATP (Adenosine Triphosphate) molecule as a source of useful chemical energy, as it contains two energy-rich phosphate bonds.
Other nucleotides, such as Cytosine Triphosphate (CTP), Guanine Triphosphate (GTP), or Uracil Triphosphate (UTP), are also involved in metabolic processes, performing similar energy functions.
Enzymes: Catalysts of Life
Enzymes are proteins that specifically catalyze certain biochemical reactions by binding to the substrate (the molecule or metabolite undergoing transformation). Ribozymes are ribonucleoprotein enzymes.
The substrate is accommodated in the active site. The bond between the enzyme and substrate involves steric recognition. Enzymes are highly specific to each substrate and biochemical reaction.
Enzymatic Catalysis Properties
Enzymes behave like any other catalyst in that:
- They decrease the activation energy.
- They only accelerate spontaneous processes.
- They do not change the equilibrium of a reaction, but rather speed up its arrival.
- They are free and unchanged at the end of the reaction.
Factors Affecting Enzyme Activity
Effect of pH and Temperature
Temperature variations induce conformational changes in the tertiary or quaternary structure of enzymes, altering their active sites and consequently their biological activity.
Variations in the pH of the medium cause a change in the surface electrical charges of the enzymes, affecting their structure and function.
Enzyme Structure and Cofactors
- Holoenzymes
- Enzymes associated with a non-protein molecule (cofactor) upon which their activity depends.
- Apoenzyme
- The protein component of the enzyme.
- Cofactors
- Molecules associated with the holoenzyme. Cofactors are diverse in nature and may include metal cations or complex organic molecules (coenzymes that bind weakly to the apoenzyme).
Classification of Enzymes
Enzymes are often associated with the suffix -ase (e.g., amylase, hydrolases, or isomerases). Currently, enzymes are classified primarily based on the type of reaction they catalyze (e.g., oxidoreductases, transferases, hydrolases, etc.).
The Enzymatic Reaction Cycle
The enzymatic reaction proceeds through the binding of the substrate (S) to the enzyme (E), forming the enzyme-substrate complex (ES). The general reaction equation is:
E + S → ES → E + P
(Where P is the product.)
Enzyme Specificity and Binding Models
Enzymes are highly specific to the reactions they catalyze. The enzyme structure is complementary to the substrate molecule to which it attaches.
Binding Models
- Key-Lock Model: Describes the complementarity between the enzyme and substrate as being analogous to a lock and key (rigid fit).
- Induced Fit Model: Proposes that the union is not rigid; the active site undergoes a conformational change upon substrate binding to achieve optimal fit.
Regulation: Inhibition of Enzyme Activity
Enzyme activity can be suppressed through different inhibitory mechanisms:
- Reversible Inhibitors: Temporarily bind to the enzyme. These include competitive inhibitors.
- Irreversible Inhibitors (Poisons): Bind permanently to the active site, completely suppressing enzyme activity (leading to permanent inactivation).
Allosterism
Allosterism is a crucial regulatory mechanism involving molecules called ligands or effectors. These molecules bind specifically to the enzyme at sites other than the active site, known as regulatory centers, causing a conformational change.
This binding often results in the transformation between the active and inactive forms of the enzyme. Enzymes regulated this way are called allosteric enzymes.
- Substrates often act as ligand activators.
- Reaction products often behave as ligand inhibitors, preventing the binding of substrate molecules to the enzyme.
Kinetics of the Enzymatic Reaction
The reaction rate increases until it reaches a maximum velocity ($V_{max}$), which occurs when the enzyme is fully saturated with substrate.
- Turnover Number ($k_{cat}$) or Catalytic Constant
- The maximum number of substrate molecules that one enzyme molecule can transform per unit time.
- Michaelis Constant ($K_M$)
- A measure of the affinity of the enzyme for its substrate. A small $K_M$ value indicates a very strong bond between the enzyme and substrate.