Proteins and Enzymes: Structure, Function, and Regulation

Proteins: Structure and Function

Functions of Proteins

Proteins are essential macromolecules that perform a wide variety of functions in biological systems.

• Enzymatic activity: Many proteins act as enzymes, catalyzing biochemical reactions.

• Structural support: Proteins such as collagen and keratin provide structural integrity to cells and tissues.

• Transport: Hemoglobin and other proteins transport molecules throughout the body.

• Signaling: Hormones and receptor proteins are involved in cellular communication.

• Defense: Antibodies are proteins that help defend against pathogens.

Amino Acids: Structures and Properties

Amino acids are the building blocks of proteins, each containing an amino group, a carboxyl group, and a unique side chain (R group).

• General structure: $\mathrm{NH_2{-}CHR{-}COOH}$

• Classification: Amino acids are classified as nonpolar, polar, acidic, or basic based on their side chains.

• Peptide bonds: Amino acids are linked by peptide bonds formed via condensation reactions.

Conformations of Proteins

Proteins have four levels of structural organization:

• Primary structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary structure: Regular folding patterns such as alpha helices and beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: The overall three-dimensional shape of a single polypeptide, stabilized by interactions among side chains.

• Quaternary structure: The arrangement of multiple polypeptide subunits in a protein complex.

Denaturing Proteins

Denaturation refers to the loss of a protein's native structure due to external stress, such as heat, pH changes, or chemicals.

• Effects: Denatured proteins lose their biological activity.

• Reversibility: Some denaturation processes are reversible, while others are not.

Enzymes: Structure, Mechanism, and Regulation

Nomenclature of Enzymes

Enzymes are named based on the reactions they catalyze, often ending with the suffix "-ase." The International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into six major classes.

• Oxidoreductases: Catalyze oxidation-reduction reactions.

• Transferases: Transfer functional groups between molecules.

• Hydrolases: Catalyze hydrolysis reactions.

• Lyases: Add or remove groups to form double bonds.

• Isomerases: Catalyze isomerization changes within a molecule.

• Ligases: Join two molecules together using ATP.

Lock & Key and Induced Fit Models

Enzyme specificity is explained by two models:

• Lock & Key Model: The enzyme's active site is a perfect fit for the substrate, like a key in a lock.

• Induced Fit Model: The enzyme's active site molds itself around the substrate upon binding, enhancing specificity and catalytic efficiency.

Enzyme Inhibition

Enzyme activity can be regulated by inhibitors, which decrease or prevent enzyme function.

• Competitive inhibitors: Bind to the active site, competing with the substrate.

• Noncompetitive inhibitors: Bind to a site other than the active site, altering enzyme conformation.

• Reversible inhibitors: Can dissociate from the enzyme, allowing activity to resume.

• Irreversible inhibitors: Bind permanently, inactivating the enzyme.

Factors Influencing Enzyme Activity

Several factors affect the rate of enzyme-catalyzed reactions:

• Temperature: Higher temperatures generally increase activity up to an optimum, after which denaturation occurs.

• pH: Each enzyme has an optimal pH range for activity.

• Substrate concentration: Increasing substrate concentration increases reaction rate until saturation.

Enzyme Activity and Kinetics

Enzyme kinetics describes how reaction rates change with varying conditions.

• Michaelis-Menten equation: Describes the relationship between substrate concentration and reaction rate:

$v = \frac{V_{max}[S]}{K_m + [S]}$

• $V_{max}$: Maximum reaction rate

• $K_m$: Substrate concentration at half-maximal velocity

Regulation of Enzyme Activity

Enzyme activity is regulated through various mechanisms:

• Feedback inhibition: End products inhibit an earlier step in the pathway.

• Allosteric enzymes: Enzyme activity is modulated by molecules binding to sites other than the active site.

• Proenzymes (zymogens): Inactive enzyme precursors activated by specific modifications.

• Protein modification: Covalent modifications such as phosphorylation can activate or deactivate enzymes.

Example: Allosteric Regulation

Phosphofructokinase, a key enzyme in glycolysis, is allosterically inhibited by ATP, preventing excessive glucose breakdown when energy is abundant.