Enzymes: Biological Catalysts

Enzymes: Biological Catalysts

• Enzymes are biological catalysts that accelerate reaction rates in living cells.
• Enzymes are essential for almost every chemical reaction within cells.
• Enzymes exhibit substrate specificity, enhancing reaction rates without being consumed.
• Enzyme specificity comes from complementary shapes and characteristics between the enzyme and its substrate.
• Enzymes bind substrates at the active site, forming an enzyme-substrate complex.
• The active site is a pocket within the enzyme's tertiary and quaternary structure.
• The Lock and Key and Induced-fit theories explain enzyme specificity.
• Enzyme names usually end in "-ase" and indicate their function.
• Enzymes are classified using EC numbers, divided into six main classes based on reaction type.
• Oxidoreductases (EC 1) catalyze oxidation/reduction reactions
• Transferases (EC 2) catalyze the transfer of chemical groups
• Hydrolases (EC 3) catalyze the hydrolysis of chemical bonds
• Lyases (EC 4) catalyze the cleavage of chemical bonds without oxidation or hydrolysis
• Isomerases (EC 5) catalyze geometric and structural changes between isomers
• Ligases (EC 6) catalyze the joining of two compounds with ATP hydrolysis
• Translocases (EC 7) catalyze the transport of substances across membranes, added in 2018
• EC numbers have four digits, indicating enzyme class, subclass, sub-subclass, and serial number.
• Enzymes are excellent catalysts, accelerating reactions significantly.
• Enzyme activity is regulated by temperature, pH, and additives.
• Enzymes reduce activation energy by altering the reaction's transition state.
• Enzyme activity is significantly influenced by pH and temperature.
• Enzymes function optimally at specific pH and temperature levels.
• Enzyme activity can be affected by inhibitors (decrease activity) or activators (increase activity).
• Many drugs and poisons act as enzyme inhibitors.
• Enzyme activity can be modulated through inhibition.
• Reversible inhibitors bind non-covalently and can be reversed as there is no interaction between inhibitor and substrate
• Irreversible inhibitors bind via covalent bonds, preventing enzyme activity and are irreversible because of strong covalent bonding
• Competitive inhibitors bind to the active site, while non-competitive inhibitors bind elsewhere and alter the enzyme's shape, which reduce activity.
• Enzymes can be activated by ions, cofactors, coenzymes, or conversion of a proenzyme into an active molecule.
• Activators bind to enzymes and enhance their metabolic activity.

Cofactors and Coenzymes: Enzyme Assistants

• Some enzymes need cofactors or coenzymes to function.
• Cofactors are inorganic ions or organic molecules that assist enzymes.
• Coenzymes are organic molecules, often vitamin-derived, that function as cofactors.
• Metalloproteins are enzymes with tightly bound metal ions at the active sites.
• Examples of metalloenzymes contain iron, zinc, copper, or cobalt.
• Water-soluble vitamins are precursors to coenzymes.
• B vitamins (Thiamin, Riboflavin, Niacin, Pantothenic Acid, Pyridoxine, Biotin, Folic Acid, Cobalamin) and Vitamin C are water soluble-vitamins.
• Thiamin (Vitamin B1) is part of thiamin pyrophosphate (TPP) and participates in decarboxylation.
• Riboflavin (Vitamin B2) forms flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), which helps with redox reactions.
• Niacin (Vitamin B3) is part of nicotinamide adenine dinucleotide (NAD+) and NADP+ and participates in redox reactions.
• Pantothenic Acid (Vitamin B5) is part of coenzyme A (CoA) and participates in energy production and lipid/amino acid metabolism.
• Pyridoxine (Vitamin B6) is converted to pyridoxal phosphate (PLP) and participates in amino acid transamination and decarboxylation.
• Biotin participates in carboxyl-group transfer reactions.
• Folic Acid (B9) forms tetrahydrofolate (THFA) for help with nucleic acid synthesis.
• Cobalamin (Vitamin B12) participates in methyl group transfer.
• Vitamin C (Ascorbic Acid) is an antioxidant and participates in collagen synthesis and biogenic amine biosynthesis

Heterocyclic Compounds: Cyclic Structures with Heteroatoms

• Heterocyclic compounds are organic compounds where one or more carbon atoms in a ring are replaced by heteroatoms
• Common heteroatoms include oxygen, nitrogen, or sulfur.
• Heterocycles are the largest class of organic compounds, found in natural products and drugs.
• Classification is based on the number of atoms in the ring.
• Classification is also based on the type of heteroatoms and the number of rings (monocyclic or polycyclic).
• Pyrrole derivatives (porphyrins) form building blocks of biologically important compounds.
• Heme, an iron-porphyrin complex, is responsible for the red color of arterial blood and is found in hemoglobin.
• Indole is a fused-ring system found in tryptophan and its derivatives like serotonin.
• Pyrimidines such as Cytosine, Thymine, and Uracil are bases found in nucleic acids.
• Purines such as Adenine and Guanine are bases found in nucleic acids.

Nucleosides, Nucleotides, and Nucleic Acids: Building Blocks of Genetic Material

• Nucleosides consist of a nitrogenous base linked to a sugar (ribose or deoxyribose) via a glycosidic bond.
• Nucleotides are 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) are polymers of nucleotides linked by phosphodiester bonds that store information for cellular growth and reproduction.

DNA (Deoxyribonucleic Acid): The Genetic Code

• DNA has a double-stranded helix structure and contains deoxyribose sugar.
• The bases in DNA are Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).
• Base pairing in DNA follows the rule: A-T, G-C, connected by hydrogen bonds.
• DNA primary structure features alternating 2-deoxy-ribose and phosphate units in the backbone.

RNA (Ribonucleic Acid): Genetic Messenger & More

• RNA is generally single-stranded and contains ribose sugar.
• The bases in RNA are Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).
• RNA functions as mRNA (messenger), rRNA (ribosomal), and tRNA (transfer).

Key Differences Between DNA and RNA

• RNA consists of a single strand and is shorter, while DNA is double-stranded and longer.
• DNA nucleotides contain Deoxyribose, a phosphate group, and one of four nitrogenous bases like Adenine, Guanine, Thymine, or Cytosine.
• RNA nucleotides contain Ribose, a phosphate group, and one of four nitrogenous bases such as Adenine, Guanine, Uracil, or Cytosine.