Biology - Enzymes and Their Functions PDF

Thursday, September 5, 2024 10:16 Amino Acids and the Role of pH: Amino Acids Basics Amino acids are the building blocks of proteins. Each amino acid has an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a unique side chain (R group) attached to a central...

Thursday, September 5, 2024 10:16 Amino Acids and the Role of pH: Amino Acids Basics Amino acids are the building blocks of proteins. Each amino acid has an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a unique side chain (R group) attached to a central alpha carbon. The side chain (R group) determines the unique properties of each amino acid (e.g., polar, nonpolar, acidic, or basic). Classification of Amino Acids Amino acids are categorized based on the properties of their side chains: ○ Nonpolar (hydrophobic): Tend to repel water (e.g., glycine, alanine). ○ Polar (hydrophilic): Attract water (e.g., serine, threonine). ○ Acidic: Contain additional carboxyl groups (e.g., aspartic acid, glutamic acid). ○ Basic: Contain additional amino groups (e.g., lysine, arginine). Ionization and the Role of pH Amino acids can exist in different ionization states depending on the pH of their environment. At low pH (acidic), amino acids are fully protonated (positive charge on the amino group). At high pH (basic), amino acids lose protons (negative charge on the carboxyl group). At neutral pH (around 7), amino acids exist as zwitterions (both positively and negatively charged, but overall neutral). pKa and Buffering Capacity Each amino acid has a characteristic pKa, which is the pH at which 50% of the molecule is ionized. The buffering capacity of an amino acid refers to its ability to resist changes in pH. This is important in maintaining the proper pH balance in the body. The body's pH is tightly regulated because even small changes in pH can affect protein structure and function. Isoelectric Point (pI) The isoelectric point (pI) is the pH at which the amino acid has no net charge (neutral). This is important in protein purification techniques, as proteins will behave differently depending on their charge at different pH levels. Protiens Page 1 Thursday, September 5, 2024 10:20 Protein Structure Proteins are large biomolecules made of long chains of amino acids. Their function is closely related to their structure, which is organized into four levels: Primary Structure: The linear sequence of amino acids, determined by genetic information. This sequence dictates how the protein will fold and function. Secondary Structure: Local folding patterns within a protein chain, stabilized by hydrogen bonds. The most common types are: ○ Alpha helices: Right-handed coils. ○ Beta sheets: Sheet-like structures, which can be parallel or antiparallel. Tertiary Structure: The three-dimensional conformation of the protein, driven by interactions between side chains (hydrophobic interactions, ionic bonds, disulfide bonds, and hydrogen bonds). This structure determines the protein’s biological activity. Quaternary Structure: Some proteins consist of multiple polypeptide chains (subunits) that come together to form a functional protein. Hemoglobin is an example of a protein with quaternary structure. Fibrous and Globular Proteins Proteins are generally classified into two types based on their shape and function: Fibrous proteins: These are long, insoluble proteins that play structural roles (e.g., collagen, keratin). Globular proteins: These are compact, soluble proteins with dynamic functions, such as enzymes (e.g., hemoglobin, myoglobin). Protein Folding and Stability Protein folding is a highly regulated process that ensures the correct three-dimensional structure is achieved. Chaperone proteins assist in folding by preventing misfolding or aggregation. Denaturation: Proteins can lose their structure (and thus their function) when exposed to factors like heat, pH changes, or chemicals. This process is often irreversible. The proper folding of proteins is crucial because misfolding can lead to diseases like Alzheimer’s and Parkinson’s. Post-translational Modifications After translation, proteins often undergo modifications that affect their function: Phosphorylation: Addition of a phosphate group, which can regulate enzyme activity. Glycosylation: Addition of carbohydrate groups, important for protein stability and recognition. Proteolysis: Cleavage of a protein, often to activate or deactivate it. Protein Function Proteins have a wide range of functions in the body, including: Enzymes: Catalyze biochemical reactions. Structural proteins: Provide support and shape to cells (e.g., collagen in connective tissue). Transport proteins: Move molecules across membranes or through the body (e.g., hemoglobin transporting oxygen). Hormonal proteins: Regulate physiological processes (e.g., insulin). Defense proteins: Protect the body (e.g., antibodies in the immune system). Protiens Page 2  Defense proteins: Protect the body (e.g., antibodies in the immune system). Enzymes and Catalysis Enzymes are specialized proteins that speed up chemical reactions without being consumed. They lower the activation energy required for a reaction to proceed. Active sites on enzymes bind to specific substrates, leading to the formation of enzyme-substrate complexes. Enzyme activity can be regulated by factors such as temperature, pH, and the presence of inhibitors or activators. Protiens Page 3 Thursday, September 5, 2024 10:23 Enzymes Enzymes are biological catalysts that accelerate chemical reactions by lowering the activation energy required. They do not alter the equilibrium of reactions but make it easier for reactants (substrates) to convert into products. Active Site The active site is the specific region of an enzyme where substrate molecules bind and undergo a chemical transformation. The enzyme-substrate interaction can follow two models: ○ Lock-and-key model: The substrate fits perfectly into the active site. ○ Induced-fit model: The enzyme undergoes a conformational change to accommodate the substrate upon binding. Enzyme Specificity Enzymes are highly specific, meaning they catalyze only one type of reaction or work with specific substrates. This specificity is due to the precise interaction between the enzyme’s active site and the substrate. Cofactors and Coenzymes Cofactors are non-protein molecules that assist enzymes in catalysis. They can be metal ions (e.g., Zn²⁺, Mg²⁺) or organic molecules. Coenzymes are organic cofactors, often derived from vitamins (e.g., NAD⁺, FAD). They play an essential role in transferring chemical groups between molecules. Factors Affecting Enzyme Activity Several factors influence enzyme activity, including: Substrate concentration: As substrate concentration increases, reaction velocity increases until the enzyme is saturated (Vmax). Temperature: Increasing temperature boosts reaction rates until a point where the enzyme denatures and loses activity. pH: Each enzyme has an optimal pH at which it functions most efficiently. Deviations can alter the ionization of the enzyme’s active site, reducing its activity. Enzyme Inhibition Inhibitors are molecules that decrease enzyme activity. They can be classified into: ○ Competitive inhibitors: Bind to the active site, competing with the substrate. They increase Km but do not affect Vmax. Their effects can be overcome by increasing substrate concentration. ○ Noncompetitive inhibitors: Bind to an allosteric site (not the active site) and reduce enzyme activity without affecting substrate binding. They lower Vmax but do not change Km. ○ Uncompetitive inhibitors: Bind only to the enzyme-substrate complex, lowering both Vmax and Km. Regulation of Enzyme Activity Enzyme activity is tightly regulated to ensure that metabolic processes occur efficiently. Mechanisms Protiens Page 4 Enzyme activity is tightly regulated to ensure that metabolic processes occur efficiently. Mechanisms include: Allosteric regulation: Allosteric enzymes have sites where molecules (effectors) bind and cause conformational changes, either activating or inhibiting the enzyme. These enzymes do not follow Michaelis-Menten kinetics. Covalent modification: Some enzymes are regulated by reversible covalent modifications, such as phosphorylation or dephosphorylation. Feedback inhibition: In some pathways, the end product of a reaction inhibits an enzyme earlier in the pathway, controlling the flow of metabolites. Proteolytic cleavage: Some enzymes are synthesized as inactive precursors (zymogens) and are activated by cleavage (e.g., digestive enzymes like trypsin). Clinical Relevance of Enzymes Measuring enzyme levels in the blood can be a diagnostic tool for diseases. For example, elevated levels of creatine kinase (CK) can indicate muscle damage, including heart attacks. Enzymes like lactate dehydrogenase (LDH) and alanine aminotransferase (ALT) are also used to diagnose liver and tissue damage. Protiens Page 5