Bio Lecture 8 - Catalysis, Enzymes, Regulation of Enzymes

Review of Biological Molecules

• Building Blocks of Living Organisms: Cells

• Building Blocks of Cells:

  • Nucleic acids

  • Lipids

  • Carbohydrates

  • Proteins (composed of monomers)

Biological Molecules: Macromolecules

• Location of Proteins: Present throughout the cell in:

  • Nucleus

  • Cytoplasm

  • Mitochondria

  • Chloroplasts

Types of Protein Structure

• Primary Structure: Sequence of amino acids in a polypeptide chain.

• Secondary Structure: Local folding into helices or sheets due to hydrogen bonding.

• Tertiary Structure: Overall three-dimensional shape of a polypeptide, influenced by side chain interactions.

• Quaternary Structure: Combination of multiple polypeptide chains into a single functional protein.

Factors Affecting Protein Folding

• Amino Acid Sequence: Determines how proteins fold.

• Interaction Between Amino Acids: Influences folding through attractions and repulsions.

• Temperature: High temperatures can denature proteins.

• pH Levels: Affects the ionization of amino acids and thus protein structure.

Functions of Proteins

• Structural Support: Example - Collagen in skin and bones.

• Transporters: Involved in moving substances across cell membranes.

• Muscle Contraction: Actin and myosin proteins.

• pH Regulators: Hemoglobin stabilizes pH via oxygen transport.

• Energy Sources: Proteins can be catabolized for energy.

• Catalysts: Enzymes accelerate chemical reactions.

Enzymes

• Definition: Typically proteins that catalyze metabolic reactions; exception is ribozymes (RNA molecules).

• Nomenclature: Enzymes typically end with "ase" (e.g., lactase, sucrase).

• Specificity: Enzymes have a unique active site for specific substrates.

Active Site

• Structure: Formed by the three-dimensional folding of the enzyme; characterized by a specific arrangement of amino acids.

• Function: Binds substrates with high affinity to enable reactions.

Catalytic Cycle

• Availability of Active Site: Active site opens to substrate.

• Substrate Interaction: Substrate binds, and enzyme aids in conversion to products.

• Reusability: Enzymes can be used multiple times without depletion.

Enzyme Mechanism

• Activation Energy: Minimum energy needed to initiate a reaction.

• Function of Enzymes: Lower activation energy, facilitating reactions by bending critical bonds.

Rate of Enzymatic Reaction

• Relation to Substrate Concentration: Reaction rates increase with substrate concentration until reaching Vmax (maximum rate).

• Michaelis-Menten Model: Describes the hyperbolic relationship between initial reaction rate (V) and substrate concentration:

  • Formula: Vo = Vmax[S]/(Vmax + [S])

  • Vmax represents maximum reaction capacity, typically achieved when substrate is abundant.

  • Km: Substrate concentration at which the rate is half of Vmax. Depending on the Km value:

    • Low Km: High binding affinity (less substrate needed).

    • High Km: Low binding affinity (more substrate needed).

Factors Regulating Enzyme Activity

• Temperature: Optimal around 37°C; higher temperatures can lead to enzyme denaturation (usually above 40°C).

• pH: Optimal range typically between 6 and 8.

• Salinity: Generally physiological salt concentration (e.g., 150 mM NaCl) is most effective.

• Cofactors:

  • Inorganic examples: Copper, zinc, manganese.

  • Organic coenzymes: Vitamins, e.g., S-adenosyl methionine (SAM), which carries methyl groups.

Regulations of Enzymatic Reactions

Competitive Inhibition

• Mechanism: Inhibitors compete with substrates for the active site.

• Structure: Structurally similar to the substrate, often reversible through increased substrate concentration.

Noncompetitive Inhibition

• Mechanism: Inhibitors bind elsewhere on the enzyme, altering its shape and preventing substrate binding.

• Nature: Typically irreversible, increasing substrate concentration does not restore activity.

Allosteric Regulation

• Function: Binding of a molecule at an allosteric site affects enzyme activity.

• Characteristics: Allosteric enzymes have multiple subunits and can exist in active or inactive forms.

  • Activators: Stabilize active form, enhancing activity.

  • Inhibitors: Stabilize inactive form, reducing activity.

Cooperativity

• Mechanism: The binding of one substrate molecule increases the binding affinity for subsequent substrates.

  • Initial binding occurs with lower affinity; subsequent binding occurs with higher affinity.

Feedback Inhibition

• Definition: End-product of a metabolic pathway inhibits an enzyme early in the pathway.

• Purpose: Prevents overproduction of substances, conserving cellular resources.