🧬Biochemistry Unit 3 – Protein Function and Enzymes

Introduction to Proteins

• Proteins are essential macromolecules that play crucial roles in virtually all biological processes
• Consist of one or more polypeptide chains folded into specific three-dimensional structures
• Polypeptide chains are composed of amino acids linked together by peptide bonds
• The sequence of amino acids in a protein is determined by the genetic code
• Proteins can be classified based on their functions (enzymes, structural proteins, transport proteins, signaling proteins, and more)
• The structure and function of proteins are intimately linked
• Proteins are synthesized through the process of translation on ribosomes

Protein Structure and Folding

• Protein structure is hierarchical and can be described at four levels: primary, secondary, tertiary, and quaternary
• Primary structure refers to the linear sequence of amino acids in a polypeptide chain
• Secondary structure involves local folding of the polypeptide chain into α-helices and β-sheets stabilized by hydrogen bonds
• Tertiary structure is the three-dimensional arrangement of a single polypeptide chain
  • Stabilized by various interactions, including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges
• Quaternary structure is the arrangement of multiple polypeptide chains into a multi-subunit complex
• Protein folding is the process by which a polypeptide chain acquires its native three-dimensional structure
  • Driven by the minimization of free energy and the burial of hydrophobic residues in the protein core
• Chaperones are proteins that assist in the proper folding of other proteins
• Misfolded proteins can lead to various diseases (Alzheimer's, Parkinson's, and Huntington's)

Protein Functions in the Body

• Proteins serve a wide range of functions in living organisms
• Enzymes catalyze biochemical reactions by lowering activation energy and increasing reaction rates
• Structural proteins provide mechanical support and maintain cell shape (collagen, elastin, and keratin)
• Transport proteins move molecules across membranes or throughout the body (hemoglobin and ion channels)
• Signaling proteins are involved in cell communication and signal transduction (hormones and receptors)
• Antibodies are specialized proteins produced by the immune system to recognize and neutralize foreign substances
• Contractile proteins (actin and myosin) are responsible for muscle contraction and movement
• Storage proteins (ferritin and casein) store and supply essential nutrients

Enzymes: Nature's Catalysts

• Enzymes are highly specific and efficient biological catalysts that accelerate chemical reactions
• Most enzymes are proteins, although some RNA molecules (ribozymes) also possess catalytic activity
• Enzymes lower the activation energy ($E_a$) of reactions, allowing them to proceed at physiological conditions
• The active site is the region of an enzyme where substrate binding and catalysis occur
• Enzymes are highly specific for their substrates due to the complementary shape and chemical properties of the active site
• Cofactors are non-protein components (metal ions or organic molecules) that are required for enzyme activity
  • Coenzymes are organic cofactors that are loosely bound to the enzyme (NAD+, FAD, and coenzyme A)
• Enzymes can be classified based on the type of reaction they catalyze (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases)

Enzyme Kinetics and Mechanisms

• Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions
• The Michaelis-Menten equation describes the relationship between reaction velocity ($v$), maximum velocity ($V_{max}$), substrate concentration ($[S]$), and the Michaelis constant ($K_m$)
  • $v = \frac{V_{max}[S]}{K_m + [S]}$
• $K_m$ is the substrate concentration at which the reaction velocity is half of $V_{max}$ and indicates the enzyme's affinity for the substrate
• $V_{max}$ is the maximum reaction velocity achieved when the enzyme is saturated with substrate
• The catalytic efficiency of an enzyme is measured by the ratio $k_{cat}/K_m$, where $k_{cat}$ is the turnover number
• Enzymes can follow different catalytic mechanisms, such as the lock-and-key model, induced fit model, and the proximity and orientation effects

Factors Affecting Enzyme Activity

• Temperature influences enzyme activity by affecting the kinetic energy of molecules and the stability of the enzyme
  • Enzymes have an optimal temperature at which their activity is highest
  • High temperatures can denature enzymes, leading to a loss of activity
• pH affects enzyme activity by altering the ionization state of amino acid residues in the active site
  • Each enzyme has an optimal pH range where its activity is maximal
• Substrate concentration affects reaction velocity, as described by the Michaelis-Menten equation
• Product accumulation can inhibit enzyme activity through feedback inhibition
• Enzyme concentration directly influences reaction velocity, with higher concentrations leading to faster rates until substrate becomes limiting
• Activators are molecules that enhance enzyme activity by binding to allosteric sites or stabilizing the active conformation
• Inhibitors are molecules that decrease enzyme activity through various mechanisms (competitive, non-competitive, or uncompetitive inhibition)

Enzyme Regulation and Inhibition

• Enzyme activity is tightly regulated to maintain homeostasis and respond to cellular needs
• Allosteric regulation involves the binding of effector molecules to sites other than the active site, causing conformational changes that alter enzyme activity
  • Allosteric activators increase enzyme activity, while allosteric inhibitors decrease it
• Feedback inhibition is a regulatory mechanism in which the end product of a metabolic pathway inhibits the activity of an earlier enzyme in the pathway
• Competitive inhibition occurs when an inhibitor molecule competes with the substrate for binding to the active site
  • Competitive inhibitors increase the apparent $K_m$ but do not affect $V_{max}$
• Non-competitive inhibition occurs when an inhibitor binds to a site other than the active site, reducing the enzyme's catalytic efficiency
  • Non-competitive inhibitors decrease $V_{max}$ but do not affect $K_m$
• Uncompetitive inhibition occurs when an inhibitor binds only to the enzyme-substrate complex, reducing both $V_{max}$ and $K_m$
• Irreversible inhibition involves the formation of a covalent bond between the inhibitor and the enzyme, permanently inactivating it

Applications in Medicine and Biotechnology

• Enzymes are valuable tools in medicine and biotechnology due to their specificity and efficiency
• Diagnostic enzymes are used to detect the presence of specific substances in biological samples (glucose oxidase for measuring blood glucose)
• Therapeutic enzymes are used to treat various diseases by replacing deficient enzymes or targeting specific molecules (DNase for cystic fibrosis and thrombolytics for dissolving blood clots)
• Industrial enzymes are used in the production of food, beverages, textiles, and pharmaceuticals (amylases in brewing and proteases in leather processing)
• Recombinant DNA technology allows the production of enzymes in large quantities by cloning and expressing the genes in suitable host organisms (insulin production in bacteria)
• Enzyme immobilization techniques enable the reuse of enzymes and improve their stability in industrial processes
• Directed evolution is a method for improving enzyme properties (stability, activity, or specificity) through iterative rounds of mutagenesis and selection
• Enzymes are used in bioremediation to degrade pollutants and clean up environmental contaminants (petroleum-degrading bacteria)