ENZYME BIOCHEMISTRY(FACTOR OF AFFECTING ENZYME REACTION) GROUP MEMBERS: 1. MOHAMAD SHAHRIL BIN RASHID (2023898462) 2. NIK MOHAMAD IRWAN BIN MOHD RASANI (2023800734) 3. WAN AHMAD AMIR AKHTAR BIN ANUAR (2023800914) 4. MUHAMMAD FAKHRUL FADZLI BIN RUSNI (2023873866) 5. MUHAMMAD ZULSYAHMI BIN SHARIF (2023610302)
Contents Oxidoreductase Transferases Hydrolases Lyases Isomerases Ligases Mechanism Function Classification Application Mechanism Function Classification Application Mechanism Function Classification Application Mechanism Function Classification Application Mechanism Function Classification Application Mechanism Function Classification Application
What is Oxidoreductase ? technology in textile Medicine & synthetic enforcement technology in food b oi conversion, biocontrol & enviromenta carbohydrate conversion for biomass Application Oxidoreductase enzyme- A large class of enzymes known as oxidoreductases catalyses the transfer of electrons from compounds that are electron donors (reduction) to molecules that are electron acceptors (oxidation). Ared + Box Aox + B red Oxidant + Reductant Oxidized reductant + Reduce oxidant Oxidoreductase catalyzed by Oxidoreductase is an enzyme that catalyzes the transfer of electron from one molecule to another. This group of enzymes usually utilizes NADP+ or NAD+ as cofactors. is a broad class of biochemistry enzymes involved in redox reactions found in living things and laboratories. Proton extraction, hydride transfer, oxygen insertion, and other critical processes are catalysed by oxidoreductase enzymes. Function Play important role in aerobic and anaerobic metabolism. Can be found in glycolysis, TCA cycle, oxidative phosphorylation and amino acid metabolism. Example, In glycolysis catalyzes the reduction of NAD+ to NADH. Mechanism of Action 3 oxygenase Incorporated oxygen into organic substrates. Add hydroxyl group to substrates Oxygen as the hydrogen or electron accepter Oxidize substrates by transferring one or more hydride ions Catalyze reduction Reduction of hydrogen peroxide and hydroperoxides Hydroxylases Oxidases Dehydrogenases Reductases Peroxidases Classification
What is Transferase ? Ared + Box Aox + B red Mechanistically, an enzyme catalyzing the following reaction would be considered as a transferase: Transferase is an enzyme that catalyses the transfer of functional group from one molecule to another. The functional group such as methyl, hydroxylmethyl, formal, glycosyl, acyl, akyl, phosphate, and sulfate groups through a nucleophilic substitution reaction Mechanism of Action 4 Up to now, the classification of transferases is still under way for new ones discovered frequently. The category of transferases is described primarily according to the type of biochemical group transferred, and can be divided into ten groups based on the EC Number classification which comprises more than 450 different unique enzymes and have been assigned a number of EC 2 in the EC numbering system Single carbon transferases under EC 2.1 are enzymes that transfer single-carbon groups, which contain functional groups of hydroxymethyl, methyl, carboxy, carbamoyl, formyl, and amido substituents ec 2.1 Classification where X is the donor that is often a coenzyme, and Y is the acceptor. Group would be the functional group that is transferred on account of transferase activity. Terminal transferase Application In the Biotechnology Glutathione transferases EC 2.2 includes aldehyde and ketone transferases transferring aldehyde or ketone groups, mainly comprising a variety of transketolases and transaldolases that play important role in pentose phosphate pathway and catalyze the transfer of dihydroxyacetone functional group to glyceraldehyde 3-phosphate. ec 2.2 ec 2.3 Enzymes divided into EC 2.4 could transfer glycosyl, hexosyl and pentosyl groups. Glycosyltransferase under the subcategory of EC 2.4 takes participate in the biosynthesis of disaccharides and polysaccharides by transferring monosaccharides to other molecules. ec 2.4 Acyl transferases as key aspects of EC 2.3 could transfer acyl groups or acyl groups that are converted into alkyl groups during the process of being transferred. Furthermore, this category also distinguishes amino-acyl from non-amino-acyl groups.
What is Hydrolase ? Function Mechanism of Action Substrate binding - Formation of the Enzyme-Substrate Complex - Activation of water molecule - Nucleophilic attack - Formation of transition state - Cleavage of substrate - Release of products. A hydrolase is a type of enzyme that catalyzes the hydrolysis of chemical bonds through the addition of water. Hydrolysis is a chemical reaction in which a water molecule is used to break a covalent bond in a larger molecule, resulting in the cleavage of that bond. Hydrolases are essential in various biological processes and play a crucial role in the metabolism of cells. Hydrolase breaks down large molecules into smaller pieces, which are then utilized for synthesis, waste material excretion, or as sources of carbon to produce energy 5 Examples LIPASE Catalyze the hydrolysis of lipids into glycerol and fatty acids. Lipases play a key role in digestion and the absorption of dietary fats. Catalyze the hydrolysis of peptide bonds in proteins. Proteases are involved in the digestion of proteins into amino acids. Nucleases catalyze the hydrolysis of phosphodiester bonds in nucleic acids, such as DNA and RNA Catalysis of the glycosidic linkages present between the two monomeric units of the polysaccharides. Replace a phosphate group on the substrate with a hydroxyl group from water. involved in the degradation of off-function proteins in lysosomes, cytosol, plasma membranes, or extracellular space PROTEASE NUCELOSIDASE GLYCOSIDASE PHOSPHATASE PEPTIDASE Excretion Digestion Transport Signaling processes Carry out important degradative reactions in the body Application The industrial sectors Detergen Leather Waste treatment Textile
What is Lyases? Function Lyases is one of six types of enzymes. This enzyme works by catalyse a process that breaks down a variety of chemical bonds by “elimination” reaction, other than hydrolysis and oxidation. At the end of the reaction, it always resulting in the new formation of a new cyclic structure or a new double bond. Lyases function is to catalyse the cleavage of various chemical bonds by a method that is not hydrolysis, reduction or oxidation. It cleaves bonds by adding or removing groups directly to substrate. It catalyses the reactions either by forming a new double bond or a new ring structure. 6 Classification TCA cycles Application Cleave carbon-carbon bonds (EC 4.1) Contains the aldehyde-lyases which can catalyse the reversal of an aldol condensation Catalyse the breaks of carbon-oxygen bonds. Example of enzymes is fumarate hydratase. Contain enzymes that release ammonia or its derivatives with the formation of a double bond or ring. Some catalyse the actual elimination of the ammonia, amine or amide. Catalyse the elimination or substitution of dihydrogen sulfide from a reaction. It utilises a mechanism which eliminates hydrochloric acid from Dichloro-Diphenyl_Trichloroethane (DDT), a synthetic pesticide Catalysation of elimination diphosphate from nucleotide triphosphate such as ATP and GTP. Cleave carbon-oxygen bonds (EC4.2) Cleave carbon-nitrogen bonds (EC4.3) Cleave carbon-sulphur bonds (EC4.4) Cleave carbon-halide bonds (EC4.5) Cleave phosphorus-oxygen bonds (EC4.6) A group of other lyases (EC4.99) Production of cyanohydrins Production of (S)- malic acid from fumaric acid. Production of cyanohydrin from ketone 1 2 3 4 Mechanism of Action Mechanism of isocitrate lyase: 1. Glyoxylate bind to the enzyme isocitrate lyase. 2. Then succinate also bind to the enzyme and form tertiary complex. 3. A Claisen condensation occurs. 4. Isocitrate produced.
What is Isomerase ? Function Racemases and epimerases (EC 5.1) In biological compounds, enzymes called racemases and epimerases catalyse the inversion of stereochemistry. To catalyse an inversion of stereochemistry, an epimerase or racemase must break and reform a bond in a non-stereospecific manner. The bond could be a carbon-hydrogen bond, or a carbon-carbon bond. This class of isomerase catalyse the isomerisation of cistrans isomer or geometric isomers. They are present in several enzymes and help in the rapid and precise completion of their functions. It works by catalyse the transfer of electrons from one part of the molecule or catalyse the oxidation of one part of a molecule with corresponding reduction of another part of the same molecule This class of enzymes accelerate the transfer of functional groups from one part of a molecule to another. For example, in glycolysis pathway, 3-phosphoglycerate is converted to 2-phosphoglycerate by phosphoglyceromutase It catalyses reactions where a group can be removed from one part of a molecule, leaving a double bond, while keeping covalently attached to the molecule. Cis-trans isomerases (EC 5.2) intramolecular oxidoreductases (EC 5.3) Intramolecular transferases (EC 5.4) Intramolecular lyases (EC 5.5) Mechanism of Action Figure above shows the peptidyl prolyl isomerisation. This enzyme facilitates the cis-trans isomerisation of peptide bonds N-terminal to proline residues within polypeptide chains. Isomerase is a type of enzyme that is responsible for changing a molecule from one isomer to another. The isomerase is well-known for its capability to catalyse many other biological reactions. The example is glycolysis and carbohydrate metabolism An isomer is any of two or more variations of a molecule with an identical chemical formula but a distinct stereochemical configuration of the atoms. Isomerase enzymes catalyse the processes by which functional groups are transferred within a molecule, leading to the production of isomeric forms. 7 Examples High fructose corn syrup (HFCS) Application Ethanol production
What is Ligase ? Mechanism & Function In biochemistry, ligase, also known as synthetase, is an enzyme that facilitates the connection of two large molecules by creating a novel chemical bond, such as Carbon-Oxygen, Carbon - Sulphur, or Carbon - Nitrogen. This process often involves linking two compounds, and it typically includes the simultaneous hydrolysis of a small chemical group attached to one of the larger molecules. (DNA Ligase) 8 DNA replication involves unwinding the DNA double helix and creating new complementary strands. DNA ligase helps to connect the Okazaki fragments on the lagging strand, resulting in an unaltered and ongoing DNA strand DNA Repairing occurs once DNA is damaged, whether by outside causes or replication mistakes, DNA repair processes step in. DNA ligase is responsible for fixing single strand breaks and preserving the molecular structure of the DNA molecule. Genetic recombination occurs when DNA fragments are transferred between homologous chromosomes. DNA ligase is required to fix any damage and spaces that may form during this procedure DNA Ligase Application DNA ligase is a specialized enzyme that connects DNA strands by facilitating the creation of phosphodiester linkages between phosphate and deoxyribose. Its activity includes the replication of DNA, repair, and recombination activities. In living organisms, DNA ligase repairs single-strand breaks using the complementary strand as a template, and some forms can address double-strand damages. In molecular biology labs, purified DNA ligase is widely used for gene cloning, enabling the joining of DNA molecules to create recombinant DNA. Additionally, in the field of nanotechnology, particularly DNA origami, DNA ligase plays a vital role by assisting in the construction of DNA lattice structures from overhanging DNA ends, facilitating the assembly of nanoscale objects such as nanomachines, nanoelectronics, biomolecules, and photonic components. Classification The following are six subclasses of ligases EC=Enzyme Commission
REFERENCES Mahdi Kareem, H. (2021). Oxidoreductases: Significance for Humans and Microorganism. IntechOpen. doi: 10.5772/intechopen.93961 1. Legesse Habte, M., & Assefa Beyene, E. (2021). Biological Application and Disease of Oxidoreductase Enzymes. IntechOpen. doi: 10.5772/intechopen.93328 2. Vijay, E., V. Sangeetha, & Routhu Gyana Deepika. (2019). Emerging Trends in the Industrial Production of Chemical Products by Microorganisms. Elsevier EBooks, 107–125. https://doi.org/10.1016/b978-0-12-816328-3.00009-x 3. 1-Holmquist, M. (2000). Alpha beta-hydrolase fold enzymes structures, functions and mechanisms. Current Protein and Peptide Science, 1(2), 209-235. 4. Asbóth, B., & Náray-Szabó, G. (2000). Mechanism of action of D-xylose isomerase. Current protein & peptide science, 1(3), 237–254. https://doi.org/10.2174/1389203003381333 5. Clérat, L., Emmanuelle Rémond, Schneider, R., Cavelier, F., & Éric Vivès. (2023). Exogenous C–S Lyase Enzyme, a Potential Tool To Release Aromas in Wine or Beer? Journal of Agricultural and Food Chemistry. https://doi.org/10.1021/acs.jafc.3c02086 6. Dunbar, K. L., Scharf, D. H., Agnieszka Litomska, & Hertweck, C. (2017). Enzymatic Carbon–Sulfur Bond Formation in Natural Product Biosynthesis. Chemical Reviews, 117(8), 5521–5577. https://doi.org/10.1021/acs.chemrev.6b00697 7. Ki Hyun Nam. (2022). Glucose Isomerase: Functions, Structures, and Applications. Applied Sciences, 12(1), 428–428. https://doi.org/10.3390/app12010428 8. Martínez Cuesta, S., Rahman, S. A., & Thornton, J. M. (2016). Exploring the chemistry and evolution of the isomerases. Proceedings of the National Academy of Sciences of the United States of America, 113(7), 1796–1801. https://doi.org/10.1073/pnas.1509494113 9. Park, Y., Cho, Y., Lee, Y.-H., Lee, Y.-W., & Rhee, S. (2016). Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum. Journal of Structural Biology, 194(3), 395–403. https://doi.org/10.1016/j.jsb.2016.03.019 10. Sang Woo Kim, P.J. Stogios, Khusnutdinova, A. N., Nemr, K., T. Skarina, Flick, R., Jeong Chan Joo, Mahadevan, R., Savchenko, A., & Yakunin, A. F. (2020). Rational engineering of 2-deoxyribose-5- phosphate aldolases for the biosynthesis of (R)-1,3-butanediol. Journal of Biological Chemistry, 295(2), 597–609. https://doi.org/10.1074/jbc.ra119.011363 11. Sharma, V., Sharma, S., Hoener, K., McKinney, J. D., Russell, D. G., Jacobs, W. R., & Sacchettini, J. C. (2000). Nature Structural & Molecular Biology, 7(8), 663–668. https://doi.org/10.1038/77964 12. Tanner M. E. (2002). Understanding nature's strategies for enzyme-catalyzed racemization and epimerization. Accounts of chemical research, 35(4), 237–246. https://doi.org/10.1021/ar000056y 13. Wouters, J., Oudjama, Y., Ghosh, S., Stalon, V., Droogmans, L., & Oldfield, E. (2003). Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase. Journal of the American Chemical Society, 125(11), 3198–3199. https://doi.org/10.1021/ja029171p 14. Ligase Introduction - Creative Enzymes. (n.d.), from https://www.creativeenzymes.com/resource/ligase-introduction_24.html 15. Admin. (2020, November 12). DNA Ligase - Synopsis. BYJUS; BYJU’S. https://byjus.com/neet/dna-ligase/#DNA%20Ligase%20-%20Function 16. Image from What is DNA Ligase? (2019, July 19). Labxchange.org. https://www.labxchange.org/library/pathway/lx-pathway:eb23624c-22b2-4862-95ca4c5123008519/items/lb:LabXchange:40d24088:html:1/57791 17. Ligase - Definition and Examples - Biology Online Dictionary. (2021, July 30). Biology Articles, Tutorials & Dictionary Online. https://www.biologyonline.com/dictionary/ligase 18.