Enzymes: Biological Catalysts

Enzymes: Biological Catalysts

• Enzymes catalyze reactions essential for life
• Required for almost every chemical reaction in living cells
• Exhibit specificity, enhancing reaction rates without being consumed
• Specificity is due to complementary characteristics between enzyme and substrate

Enzyme-Substrate Interaction

• Enzymes bind substrates at the active site which forms the enzyme-substrate complex
• Active site is a pocket formed by the enzyme's tertiary and quaternary structure
• The Lock and Key theory and the Induced-fit theory are proposed to explain specificity

Enzyme Nomenclature and Classification

• Enzyme names typically end with "-ase"
• Enzymes are classified using an EC (Enzyme Commission) number
• There are six (now seven) main classes based on reaction type

Enzyme Classes

• Oxidoreductases (EC 1) mediate oxidation/reduction
• Transferases (EC 2) transfer chemical groups
• Hydrolases (EC 3) catalyze hydrolysis of chemical bonds
• Lyases (EC 4) facilitate cleavage of chemical bonds without oxidation or hydrolysis
• Isomerases (EC 5) affect geometric and structural changes
• Ligases (EC 6) catalyze joining of two compounds using ATP
• Translocases (EC 7) transport substances across membranes (added in 2018)
• The EC number is composed of four digits to show the class, subclass, and serial number of the enzyme

Enzyme Properties and Regulation

• Enzymes significantly speed up reactions
• Activity is regulated by temperature, pH, and additives
• Enzymes lower activation energy by altering the reaction's transition state
• Enzyme activity is strongly influenced by pH and temperature
• Specific pH and temperature ranges are optimal for enzyme function
• Enzyme activity is modulated by inhibitors and activators
• Many drugs and poisons act as enzyme inhibitors

Enzyme Inhibition

• Reversible inhibition occurs through non-covalent interactions
• Irreversible inhibition occurs through covalent bond
• Competitive inhibitors bind to the active site
• Non-competitive inhibitors bind elsewhere, altering enzyme shape and activity

Enzyme Activation

• Activation can be by ions (Ca2+, Mg2+), cofactors, coenzymes, or proenzyme conversion
• Activation converts inactive molecules into metabolically active ones

Cofactors and Coenzymes

• Some enzymes require cofactors or coenzymes to function
• Cofactors are inorganic ions or organic molecules that assist enzymes
• Coenzymes are organic molecules serving as cofactors, often derived from vitamins

Metalloproteins and Vitamins

• Metalloenzymes contain tightly bound metal ions at active sites
• Water-soluble vitamins are precursors to coenzymes
• B vitamins (Thiamin, Riboflavin, Niacin, Pantothenic Acid, Pyridoxine, Biotin, Folic Acid, Cobalamin) and Vitamin C are included

Specific Vitamins and Their Roles

• Thiamin (Vitamin B1) is part of 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) part of 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 is involved in carboxyl-group transfer reactions
• Folic Acid (B9) forms tetrahydrofolate (THFA), used in nucleic acid synthesis
• Cobalamin (Vitamin B12) is involved in methyl group transfer
• Vitamin C (Ascorbic Acid) acts as an antioxidant and is involved in collagen synthesis and biogenic amine biosynthesis

Heterocyclic Compounds

• Heterocyclic compounds have one or more carbon atoms replaced by heteroatoms
• Common heteroatoms are oxygen, nitrogen, or sulfur
• Can be classified by number of atoms in the ring, type of heteroatoms, or number of rings

Biologically Important Heterocyclic Compounds

• Pyrrole derivatives (Porphyrins): Pyrrole rings form the building blocks
• Heme: Iron-porphyrin complex, imparts the color to arterial blood and is found in hemoglobin
• Indole: A fused-ring system found in tryptophan and its derivatives
• Pyrimidines (Cytosine, Thymine, Uracil): Bases in nucleic acids
• Purines (Adenine, Guanine): Bases in nucleic acids

Nucleosides and Nucleotides

• Nucleosides are nitrogenous bases linked to a sugar via a glycosidic bond
• Nucleotides are nucleosides with one or more phosphate groups attached to the sugar

Nucleotide Function

• Nucleotides serve as building blocks for DNA and RNA
• They are intracellular energy sources (ATP)
• They are also mediators in signaling

Nucleic Acids: DNA and RNA

• Nucleic acids are polymers of nucleotides linked by phosphodiester bonds
• Store information for cellular growth and reproduction
• Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

DNA (Deoxyribonucleic Acid)

• Double-stranded helix
• Contains deoxyribose sugar
• Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T)
• Base pairing: A-T, G-C
• Primary structure: 2-deoxy-ribose and phosphate units that alternate in the backbone

RNA (Ribonucleic Acid)

• Single-stranded
• Contains ribose sugar
• Bases: Adenine (A), Guanine (G), Cytosine (C), 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 have deoxyribose and Thymine
• RNA nucleotides have ribose and Uracil

Conclusion

• Enzymes, cofactors, heterocyclic compounds, nucleotides, and nucleic acids are essential, and understanding them can develop new therapies for diseases