Enzymes: Biological Catalysts

Enzymes: Biological Catalysts

• Enzymes are biological catalysts accelerating reactions in living cells, essential for metabolic processes.
• Enzymes exhibit substrate specificity due to complementary shapes and characteristics between the enzyme and its substrates.
• Substrates bind to enzymes at the active site, forming an enzyme-substrate complex.

Enzyme-Substrate Interaction

• The active site, a pocket within the enzyme's structure, binds to the substrate.
• Specificity is explained by the "Lock and Key" and "Induced-fit" theories.

Enzyme Nomenclature and Classification

• Enzyme names usually end in "-ase" and are classified using an EC (Enzyme Commission) number based on reaction type.
• EC numbers categorize enzymes into main classes, including Oxidoreductases (EC 1), Transferases (EC 2), Hydrolases (EC 3), Lyases (EC 4), Isomerases (EC 5), Ligases (EC 6), and Translocases (EC 7).
• The EC number is composed of four digits indicating class, subclass, sub-subclass, and serial number.

Enzyme Properties and Regulation

• Enzymes are excellent catalysts regulated by temperature, pH, and additives.
• Enzymes lower activation energy by guiding reacting molecules through a different transition state.
• Enzyme activity is affected by pH, temperature, inhibitors, and activators.

Enzyme Inhibition

• Inhibitors modulate enzyme activity, with reversible inhibitors binding via non-covalent interactions and irreversible inhibitors binding via covalent bonds.
• Competitive inhibitors bind to the active site; non-competitive inhibitors bind elsewhere, altering the enzyme's shape.

Enzyme Activation

• Enzymes may be activated by ions like Ca2+ and Mg2+, cofactors, coenzymes, or proenzyme conversion.
• Activators bind to enzyme molecules, boosting metabolic activity.

Cofactors and Coenzymes: Enzyme Helpers

• Some enzymes need additional molecules, either cofactors or coenzymes, to function.
• Cofactors are inorganic ions or organic molecules assisting enzymes.
• Coenzymes are organic molecules that act as cofactors, often derived from vitamins.
• Metalloenzymes contain tightly bound metal ions at their active sites.

Water-Soluble Vitamins as Coenzyme Precursors

• Many water-soluble vitamins are precursors to coenzymes, including B vitamins (Thiamin, Riboflavin, Niacin, Pantothenic Acid, Pyridoxine, Biotin, Folic Acid, Cobalamin) and Vitamin C.
• Thiamin (Vitamin B1): Forms thiamin pyrophosphate (TPP), which is involved in decarboxylation reactions.
• Riboflavin (Vitamin B2): Forms flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), used in redox reactions.
• Niacin (Vitamin B3): Forms nicotinamide adenine dinucleotide (NAD+) and NADP+, used in redox reactions.
• Pantothenic Acid (Vitamin B5): Forms coenzyme A (CoA), involved in energy production and lipid/amino acid metabolism.
• Pyridoxine (Vitamin B6): Converted to pyridoxal phosphate (PLP), involved in amino acid transamination and decarboxylation.
• Biotin: Transfer reactions involving carboxyl-groups.
• Folic Acid (B9): Synthesis of nucleic acid using tetrahydrofolate (THFA).
• Cobalamin (Vitamin B12): Transfer of methyl groups.
• Vitamin C (Ascorbic Acid): Functions as an antioxidant and participates in collagen synthesis and biogenic amine biosynthesis.

Heterocyclic Compounds

• Heterocyclic compounds are organic compounds where one or more carbon atoms in a ring structure are replaced by heteroatoms like oxygen, nitrogen, or sulfur.
• Classified by the number of atoms in the ring, type of heteroatoms, and number of rings.

Biologically Important Heterocyclic Examples

• Pyrrole derivatives (Porphyrins): Form the building blocks of compounds in biologic processes.
• Heme: An iron-porphyrin complex that gives arterial blood its red color and is found in hemoglobin.
• Indole: Found in tryptophan and its derivatives like serotonin and is a fused-ring system.
• 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: A nitrogenous base (purine or pyrimidine) linked to a sugar (ribose or deoxyribose) via a glycosidic bond.
• Nucleotides: Nucleosides with one or more phosphate groups attached to the sugar.
• Nucleotides serve as building blocks for DNA and RNA, energy sources (ATP), second messengers, and intracellular signaling switches.

Nucleic Acids: DNA and RNA

• Polymers of nucleotides linked by phosphodiester bonds store information for cellular growth and reproduction.
• Two types include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

DNA (Deoxyribonucleic Acid)

• DNA is a double-stranded helix containing deoxyribose sugar.
• DNA contains the bases Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).
• Base pairing: A-T, G-C is held together by purine-pyrimidine base pairs connected by hydrogen bonds.
• Primary structure: Units of 2-deoxy-ribose and phosphate alternate in the backbone.

RNA (Ribonucleic Acid)

• RNA is single-stranded and contains ribose sugar.
• RNA contains the bases Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).
• Functions: mRNA (messenger), rRNA (ribosomal), tRNA (transfer).

Key Differences Between DNA and RNA

• RNA is single-stranded and shorter; DNA is double-stranded and very long.
• DNA nucleotides: Deoxyribose, phosphate, and one of four nitrogenous bases (Adenine, Guanine, Thymine, Cytosine).
• RNA nucleotides: Ribose, phosphate, and one of four nitrogenous bases (Adenine, Guanine, Uracil, Cytosine).