Proteins and Enzymes: Structure, Function, and Regulation

Chapter 19: Amino Acids and Proteins

Functions of Proteins

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

• Structural proteins: Provide support and shape to cells and tissues (e.g., collagen in connective tissue).

• Enzymatic proteins: Catalyze biochemical reactions (e.g., amylase, lactase).

• Transport proteins: Carry molecules across cell membranes or through the bloodstream (e.g., hemoglobin).

• Defensive proteins: Involved in immune responses (e.g., antibodies).

• Regulatory proteins: Control cellular processes (e.g., insulin regulates blood glucose).

• Contractile proteins: Enable movement (e.g., actin and myosin in muscles).

Amino Acids: Structures and Properties

Amino acids are the building blocks of proteins. Each amino acid contains an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a unique side chain (R group) attached to a central carbon atom (the alpha carbon).

• General structure: $\mathrm{H_2N{-}CHR{-}COOH}$

• Classification: Based on the properties of the R group (e.g., nonpolar, polar, acidic, basic).

• Chirality: Most amino acids (except glycine) are chiral and exist as L- and D-isomers; only L-amino acids are found in proteins.

Conformations of Proteins

Proteins have four levels of structure that determine their shape and function:

• Primary structure: The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.

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

• Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, stabilized by interactions among R groups (hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges).

• Quaternary structure: The arrangement of multiple polypeptide subunits in a functional protein (e.g., hemoglobin has four subunits).

Denaturing Proteins

Denaturation is the process by which a protein loses its native structure and, therefore, its function. This can be caused by changes in temperature, pH, or exposure to chemicals.

• Effects: Disruption of secondary, tertiary, and quaternary structures without breaking peptide bonds (primary structure remains intact).

• Examples: Cooking an egg (heat denatures egg white proteins), adding acid to milk (causes curdling).

Chapter 20: Enzymes and Vitamins

Nomenclature of Enzymes

Enzymes are biological catalysts that speed up chemical reactions. They are usually named by adding the suffix -ase to the name of the substrate or the type of reaction they catalyze.

• Examples: Lactase (breaks down lactose), DNA polymerase (synthesizes DNA).

• Classification: Enzymes are classified into six major classes based on the type of reaction catalyzed (e.g., oxidoreductases, transferases, hydrolases).

Lock & Key and Induced Fit Models

These models describe how enzymes interact with their substrates:

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

• Induced Fit Model: The enzyme's active site is flexible and molds itself around the substrate upon binding, enhancing the fit and catalytic activity.

Enzyme Inhibitors

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

• Competitive inhibitors: Compete with the substrate for binding to the active site; inhibition can be overcome by increasing substrate concentration.

• Noncompetitive inhibitors: Bind to a site other than the active site, changing the enzyme's shape and reducing activity; cannot be overcome by increasing substrate concentration.

• Reversible inhibitors: Bind non-covalently and can dissociate from the enzyme.

• Irreversible inhibitors: Bind covalently and permanently inactivate the enzyme.

Factors Influencing Enzyme Activity

Several factors affect the rate at which enzymes catalyze reactions:

• Temperature: Enzyme activity increases with temperature up to an optimum point, then decreases due to denaturation.

• pH: Each enzyme has an optimal pH; deviations can reduce activity or denature the enzyme.

• Substrate concentration: Increasing substrate concentration increases reaction rate until the enzyme is saturated.

Enzyme Activity and Kinetics

Enzyme kinetics describes how the rate of enzyme-catalyzed reactions depends on substrate concentration and other factors.

• Michaelis-Menten equation:

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

• V: Reaction rate

• Vmax: Maximum rate

• [S]: Substrate concentration

• Km: Michaelis constant (substrate concentration at half-maximal velocity)

Regulation of Enzyme Activity

Cells regulate enzyme activity to control metabolic pathways and maintain homeostasis.

• Feedback inhibition: The end product of a pathway inhibits an enzyme involved earlier in the pathway, preventing overproduction.

• Allosteric enzymes: Enzymes with regulatory sites; binding of effectors changes enzyme activity.

• Proenzymes (zymogens): Inactive enzyme precursors activated by specific cleavage (e.g., pepsinogen to pepsin).

• Protein modification: Covalent modification (e.g., phosphorylation) can activate or deactivate enzymes.

Type of Regulation	Description	Example
Feedback Inhibition	End product inhibits an early enzyme in the pathway	ATP inhibits phosphofructokinase in glycolysis
Allosteric Regulation	Effector binds to regulatory site, altering enzyme activity	Phosphofructokinase regulation by ATP/AMP
Proenzyme Activation	Inactive precursor activated by cleavage	Trypsinogen to trypsin
Protein Modification	Covalent addition/removal of groups	Phosphorylation of glycogen phosphorylase

Additional info: Academic context and examples have been added to expand on the brief points in the original file and ensure the notes are self-contained and suitable for exam preparation.