Enzymes: Biological Catalysts

Enzymes: Biological Catalysts

• Enzymes are biological catalysts accelerating reaction rates in living cells.
• They are crucial for metabolic processes and nearly every chemical reaction in a cell requires one.
• Enzymes exhibit substrate specificity, enhancing reaction rates without being consumed.
• Specificity comes from complementary shapes, charges, and hydrophilic/hydrophobic characteristics matching the enzyme and substrate

Enzyme-Substrate Interaction

• Enzymes bind substrates at the active site, forming an enzyme-substrate complex.
• The active site is a restricted region, a pocket formed by the enzyme's tertiary and quaternary structure.
• Specificity is explained by the "Lock and Key" and "Induced-fit" theories.

Enzyme Nomenclature and Classification

• Enzyme names usually end in "-ase" and indicate their function.
• They are classified using an EC (Enzyme Commission) number into six or seven main classes based on the reaction type.
• EC 1: Oxidoreductases catalyze oxidation/reduction reactions.
• EC 2: Transferases transfer chemical groups.
• EC 3: Hydrolases catalyze the hydrolysis of chemical bonds.
• EC 4: Lyases catalyze cleavage of chemical bonds without hydrolysis or oxidation.
• EC 5: Isomerases catalyze geometric and structural changes in molecules.
• EC 6: Ligases join two compounds with ATP hydrolysis involved.
• EC 7: Translocases transport substances across membranes; added in 2018
• The EC number has four digits indicating class, subclass, sub-subclass, and serial number.

Enzyme Properties and Regulation

• Enzymes are excellent catalysts and significantly speed up reactions.
• Activity is regulated by temperature, pH, and additives, functioning best at specific conditions.
• Enzymes lower activation energy by forcing molecules through different transition states.
• Enzyme activity is modulated by inhibitors, which decrease activity
• Activators are molecules increasing enzyme activity; some drugs and poisons act as inhibitors.

Enzyme Inhibition

• Reversible inhibition involves non-covalent interactions and can be reversed.
• Irreversible inhibition involves covalent bonds, preventing catalytic activity.
• Competitive inhibitors bind to the active site.
• Non-competitive inhibitors bind elsewhere, altering the enzyme's shape and reducing activity.

Enzyme Activation

• Enzymes can be activated by ions (Ca2+, Mg2+), cofactors, coenzymes, or proenzyme conversion.
• Activation converts an inactive enzyme into a metabolically active one.
• Activators bind to enzyme molecules and boost metabolic activity.

Cofactors and Coenzymes: Enzyme Helpers

• Some enzymes need cofactors or coenzymes to function.
• Cofactors are inorganic ions or organic molecules assisting enzymes.
• Coenzymes are organic molecules acting as cofactors, often vitamin-derived.
• Metalloproteins are enzymes containing tightly bound metal ions at their active sites.

Water-Soluble Vitamins as Coenzyme Precursors

• Many water-soluble vitamins are precursors to coenzymes.
• B vitamins (Thiamin, Riboflavin, Niacin, Pantothenic Acid, Pyridoxine, Biotin, Folic Acid, Cobalamin) and Vitamin C play a part.
• Vitamin B1 (Thiamin) is part of thiamin pyrophosphate (TPP) and is involved in decarboxylation.
• Vitamin B2 (Riboflavin) forms FAD & FMN and is used in redox reactions.
• Vitamin B3 (Niacin) is part of NAD+ and NADP+ and is used in redox reactions.
• Vitamin B5 (Pantothenic Acid) forms coenzyme A (CoA), for energy, lipid, and amino acid metabolism.
• Vitamin B6 (Pyridoxine) is converted to pyridoxal phosphate (PLP), for amino acid transamination and decarboxylation.
• Biotin is used in carboxyl-group transfer reactions.
• Vitamin B9 (Folic Acid) forms tetrahydrofolate (THFA), used in nucleic acid synthesis.
• Vitamin B12 (Cobalamin) is used in methyl group transfer.
• Vitamin C (Ascorbic Acid) acts as an antioxidant and is involved in collagen and biogenic amine production

Heterocyclic Compounds: Cyclic Structures

• Heterocyclic compounds have one or more carbon atoms in a ring replaced by heteroatoms (O, N, or S).
• They can be classified by ring atom number (three, five, or six-membered).
• They can also be classified based on heteroatom type (same or different) and ring number (monocyclic or polycyclic).

Biologically Important Heterocycles

• Pyrrole derivatives (Porphyrins): Pyrrole rings form building blocks of biologically important compounds.
• Heme: The iron-porphyrin complex gives arterial blood its red color, found in hemoglobin.
• Indole: A fused-ring system in tryptophan and its derivatives (serotonin).
• Pyrimidines: Cytosine, Thymine, and Uracil are bases found in nucleic acids.
• Purines: Adenine and Guanine are bases found in nucleic acids.

Nucleosides and Nucleotides

• Nucleosides: Nitrogenous base (purine/pyrimidine) linked to a sugar (ribose/deoxyribose) via a glycosidic bond.
• Nucleotides: Nucleoside with one or more phosphate groups attached to the sugar.
• Nucleotides function as building blocks for DNA/RNA, in energy transfer (ATP), and as signaling molecules.

Nucleic Acids: DNA and RNA

• Nucleic acids are nucleotide polymers linked by phosphodiester bonds storing information.
• DNA (Deoxyribonucleic Acid): a double-stranded helix containing deoxyribose sugar.
• DNA bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T) with base pairing A-T, G-C.
• The primary structure has alternating 2-deoxy-ribose and phosphate units.
• RNA (Ribonucleic Acid): single-stranded with ribose sugar.
• RNA bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U).
• RNA functions as mRNA (messenger), rRNA (ribosomal), and tRNA (transfer).

Key Differences Between DNA and RNA

• RNA is single-stranded and shorter, while DNA is double-stranded and longer.
• DNA nucleotides contain deoxyribose, phosphate, and A, G, T, or C.
• RNA nucleotides contain ribose, phosphate, and A, G, U, or C.