ITM 101 | Biochemistry Enzymes PDF

ITM 101 | BIOCHEMISTRY LESSON # 7 – ENZYMES 1st YEAR | A.Y. 2023-2024 | SEPTEMBER 8, 2023 DR. JACINTO NONCOMPETITIVE INHIBITION They are not competing with the same binding site. The substrate binds to the active site, the inhibitor binds to another site called the allosteric site....

ITM 101 | BIOCHEMISTRY LESSON # 7 – ENZYMES 1st YEAR | A.Y. 2023-2024 | SEPTEMBER 8, 2023 DR. JACINTO NONCOMPETITIVE INHIBITION They are not competing with the same binding site. The substrate binds to the active site, the inhibitor binds to another site called the allosteric site. When the inhibitors bind to an allosteric site, it changes the enzyme substrate binding, hence the decrease in the Vmax. The inhibitor can bind to the free enzyme; it can also bind to the enzyme that is already bound to the substrate. Inhibitors never bind to the active site. Both the EI and EIs complexes are enzymatically active. OXIDOREDUCTASE As the name implies, they catalyze redox reaction – transfer of electrons. One molecule would lose an electron and another molecule would eventually gain an electron. In organic chemistry, these are also dehydrogenation reaction. It’s easy to identify. Take the reaction or substrate, and add - ase to the end. (ATPase, Hexokinase) As a matter of fact, there is a subclass of oxidoreductase that is called dehydrogenase like malic dehydrogenase, pyruvate UNCOMPETITIVE INHIBITION dehydrogenase, succinate dehydrogenase and alcohol dehydrogenase. Occurs when the inhibitor binds only to the ES complex to form the EIS complex. When we are talking about oxidoreductase, the usual coenzymes are NAD, FAD or NADP. Whenever we see an Inhibition is irreversible. enzyme that bears the name dehydrogenase, try to look for the coenzyme, right away. There should be NAD, FAD or NADP During uncompetitive inhibition, Vmax and Km are reduced. in that particular reaction. This results in a higher affinity but slower reaction. The difference between NAD and NADP is that NAD is primarily used in metabolic reactions, whereas NADP is used in biosynthetic pathways. TRANSFERASES These enzymes catalyze the transfer of functional groups such as methyl, acetate and phosphate among other things. 101 INTRODUCTION TO MEDICINE | PHYSIOLOGY AYURA 2027 1 ITM 101 | BIOCHEMISTRY LESSON # 7 – ENZYMES 1st YEAR | A.Y. 2023-2024 | SEPTEMBER 8, 2023 DR. JACINTO There is a special class of transferases that are called kinases. They transfer phosphate usually coming from ATP onto the substrate. Hexokinase transfers the phosphate group to hexose. One example is glucose. One of the very first reactions that glucose undergoes when it enters the cell is that it will be phosphorylated at C6. Phosphate will be attached at C6. Phosphate was transferred from ATP to glucose. From ATP it became ADP. The enzyme is called hexokinase. -> phosphatase, removes phosphate HYDROLASES Main thing is that they hydrolyze, through the action or ISOMERASES addition of water. Main thing is that, an enzyme that catalyzes transformation They catalyze hydrolytic reactions, adding water across C-C between two isomers. bonds. These enzymes break bonds by adding water molecule. Example: Glucose and Fructose – these two are isomers. Also called mutases They catalyze interconversion between isomers. Isomers are molecules that have the same structure but different configuration. Example: Fumarate and Maleate In naming the product, they both can be interconverted. One of them can be the product and the other the substrate or vice versa. LYASES Main thing is that is they break bonds, but without the use of water. Very similar to the enzyme hydrolyases are the enzymes lyases. They also break C-C bonds, C-O bonds, C-N bonds and other bonds. Sometimes they generate a ring or a double bond. They break bonds but do not incorporate any water molecules This reaction is catalyzed by pyruvate decarboxylase – a special type of lyases. The bond between the 2 Cs has been cleaved, making the carboxyl group in the form of C02. There is no water molecule involved making pyruvate decarboxylase a form of lyases. The main difference of these two is how the COO- is oriented. 101 INTRODUCTION TO MEDICINE | PHYSIOLOGY AYURA 2027 2 ITM 101 | BIOCHEMISTRY LESSON # 7 – ENZYMES 1st YEAR | A.Y. 2023-2024 | SEPTEMBER 8, 2023 DR. JACINTO LIGASES Proteolytic enzymes secreted in the gastrointestinal tract are stored as zymogens or proenzymes (inactive form). They catalyze condensation (bond formation) between 2 substrates with splitting of ATP. The active sites of these zymogens are often covered by an extra peptide bond. Since it is covered, the substrate cannot Example: A condensation reaction between monosaccharides, bind to the enzyme. In the presence of HCl, in case of the it will form disaccharides and glycosidic linkages. pepsinogen, the covering is hydrolyzed which exposes the active site, making the enzyme active. But these factors vary Main thing is that, Ligases has a specific requirement, which in enzymes. is the use of ATP, wherein the ATP would be broken down and the energy released will be used up to form the bonds. Once they have been secreted, they are usually cleaved to yield the active enzyme. They form bonds between 2 molecules and there has to be a source of energy, and the usual source of energy is ATP. Example: Chymotrypsinogen One example is pyruvate carboxylase. This is stored in the pancreas. Just before it is secreted, it is cleaved between arginine 15 (Arg 15) and isoleucine 16 (lle Here, oxaloacetate is formed by condensation of bicarbonate 16) to yield active chymotrypsin. and pyruvate. A bond here has been formed and the source of energy is the splitting of ATP to ADP in Pi (inorganic ALLOSTERIC REGULATION phosphate). In this example, we can see a pathway. The initial substrate A Ligate = to tie together becomes B then becomes C and so on. The final product is E. Each step is catalyzed by a respective enzyme like A Opposite of lyase. becomes B catalyzed by enzyme A. HOW ARE ENZYMES CONTROLLED OR Product E although it is not directly related to Substrate A, it REGULATED? can bind to Enzyme A. Since Product E can bind to an allosteric site, or Enzyme A which becomes inactivated. Regulating the active site or substrate binding. What happens Product E acts as an allosteric inhibitor. here is that they get attached to, or grouped with the active site in which they can activate or inhibit. Feedback inhibition. lf there is excessive amount of the final product E, it can provide feedback inhibition to the Anchoring enzymes in membranes initial enzyme a to slow down the reaction. The cell membrane is composed of 2 layers of Precursor activation. Not all forms of allosteric phospholipid and inserted into them are integral proteins. regulation are inhibitory in nature. Sometimes they can Some of these integral proteins are actually enzymes. When activate an enzyme. This time, it is no longer called an they are inserted into membranes, it allows them to interact allosteric inhibitor but a positive modulator. efficiently with their substrate. They are locked into that particular area; having nowhere else to go therefore they can COVALENT MODIFICATION act efficiently with their substrate. Another way of regulating an enzyme is by attaching another INACTIVE PRECURSORS group on active site, which inactivates the enzyme. Phosphate is often attached from ATP. This process is known Enzymes are initially produced in inactive forms, once these as phosphorylation. enzymes are needed, they are activated. One of the functional groups in the enzyme will be attached to another functional group. In this case, phosphate was 101 INTRODUCTION TO MEDICINE | PHYSIOLOGY AYURA 2027 3 ITM 101 | BIOCHEMISTRY LESSON # 7 – ENZYMES 1st YEAR | A.Y. 2023-2024 | SEPTEMBER 8, 2023 DR. JACINTO attached to serine, rendering the enzyme active. This form of covalent modification is what is known as phosphorylation. The source of phosphate is usually ATP. Phosphorylation/dephosphorylation of an enzyme will result to either activation or inhibition depending on what enzyme. The effect will depend on whatever metabolic pathway the enzyme is involved. iPase cerebrosi atages REGULATION OF ENZYME SYNTHESIS The most sophisticated way of controlling enzymes. Enzymes are proteins. Their synthesis is similar to proteins obviously. Genes are DNA which encode for proteins. Proteins are made through a process of transcription and translation of a particular gene. So, gene encodes proteins and enzymes are proteins. 101 INTRODUCTION TO MEDICINE | PHYSIOLOGY AYURA 2027 4