Enzymes Chemistry PDF

Enzymes  Definition of an enzyme Enzyme is mostly protein catalyst (i.e. increase the rate of reactions) synthesized intracellularly (but may act extracellularly) NOT changed during the reaction Enzymes direct all metabolic reactions occurring in the cells  Mechanis...

Enzymes  Definition of an enzyme Enzyme is mostly protein catalyst (i.e. increase the rate of reactions) synthesized intracellularly (but may act extracellularly) NOT changed during the reaction Enzymes direct all metabolic reactions occurring in the cells  Mechanism of action of enzymes: 1-lock & key model (fixed theory) An enzyme binds a substrate in a region called the active site Enzyme active site is rigid (stable, not malleable) Only certain substrate can fit the active site of the enzyme (i.e. the enzyme can act on only one or few substrates. i.e. specific) P + S S P E + S ES complex E + P  2-induced fit model (flexible theory) Active site of the enzyme adjust s its shape to bind the substrate. Enzyme structure is flexible (not rigid) This mechanism gives increased range of substrate specificity (many types of substrates can bind the same enzyme) P S SS P E + S ES complex E + P  Properties of enzymes 1- All Enzymes are Proteins (except ribozymes that are RNA in structure) 2- Active Site Each enzyme molecules contain a special pocket called the active site. The substrate bind with the active site to form enzyme substrate-complex (ES) which is converted to enzyme-product complex (EP). Then, EP dissociates to enzyme and product 3-Catalytic Efficiency: Each enzyme molecule is capable of transforming 100 – 1000 substrate molecules into product each second 4- Specificity: Enzymes are highly specific i.e. each enzyme interacts with one or few type of substrates and catalyzes one type of reactions e.g urease on urea, amylase on glycogen, starch… 5- Holoenzymes: Some enzymes require molecules other than proteins for enzymic activity. Holoenzymes: apoenzyme (protein part) + nonprotein component Apoenzymes: are inactive without the nonprotein component - non-protein part: (called cofactors) 1- a metal ion as zinc or ferrous ions 2- small organic molecules (called coenzymes) Coenzymes : may be only transiently associated with the enzyme or may be permanently associated with the enzyme Coenzymes may be derived from vitamins. (e.g. NAD+ contains niacin) 6- Regulation: Enzyme activity can be regulated by activation or inhibition. 7- Location within the cell (Compartmentalization): Many enzymes are localized in specific organelles within the cell. This serves to isolate the reaction substrate or product from other opposite reactions. Factors affecting enzyme activity Each enzyme has its own optimum pH level of blood 3- Substrate concentration  Km of enzyme Km (Michaelis Constant) of an enzyme is numerically equal to the substrate concentration at which the velocity of reaction is equal to 1/2 Vmax Km is the substrate concentration at which 1/2 maximal velocity is reached If Km is small, the substrate concentration required for the reaction to reach 1/2 maximal velocity is small. i.e. the enzyme has a high affinity for the substrate. If Km is large, the substrate concentration required for the reaction to reach 1/2 maximal velocity is large. i.e. the enzyme has a low affinity for the substrate  4- Enzyme concentration Increasing enzyme concentration increases the rate of reaction (with substrate concentration is constant)  5- Inhibition of enzyme activity Inhibitor: is an any substance that can diminish the velocity of a reaction which is catalyzed by an enzyme. 1- Reversible Inhibitors: bind to enzymes through non-covalent bonds 2- Irreversible Inhibitor: bind to enzymes through covalent bonds Types of inhibitors according to site of binding of inhibitor: 1- Competitive Inhibitor: inhibitor binds at the active site of the enzyme 2- Noncompetitive Inhibitor: inhibitor binds to a site other than active site  Competitive inhibitors A competitive inhibitor: has a structure similar to substrate of the enzyme occupies active site of the enzyme competes with substrate for occupying the active site of the enzyme increases Km of the enzyme to its substrate. i.e. more substrate is required to reach ½ Vmax effect can be reversed by increasing substrate concentration.  Noncompetitive inhibitors A noncompetitive inhibitor: Has a structure different from the substrate Binds to the enzyme at a site different from active site i.e. does not compete with the substrate of the enzyme for the active site of enzyme Changes the shape of enzyme and thus active site shape is changed. Accordingly, substrate cannot fit in the altered active site So, no reaction occurs Effect is not reversed by adding more substrate Does not change Km of the enzyme (i.e. increase of substrate concentration will not lead to reaching of ½ Vmax).  Regulation of enzyme activity The regulation of the activity of enzyme is essential for coordinating the metabolic processes. Types of regulation: 1- General: (occurs in all types of enzymes in the body) increasing substrate concentration will lead to increase activity of the enzyme 2-Special regulatory mechanisms: (not all enzymes of the body) i- Allosteric effectors ii- Covalent modification iii. Increase or decrease rate of enzyme synthesis iiii. Feed back product inhibition 1- Allosteric effectors Allosteric binding sites are sites on the enzyme different from the active site. Binding of an allosteric effectors to this site will make changes in shape of the whole enzyme with an effect on activity. So, the activity may be increased (positive allosteric effector) or decreased (negative allosteric effector).  2- Covalent modification 1- Many enzymes may be regulated by addition of phosphate groups to the enzyme (modification by phosphorylation) Addition of phosphate group may cause activation or inactivation of the enzyme 2- Some enzymes are released as an inactive form (zymogen) By removal of a part of the enzyme (modification), it will be active. e.g Trypsinogen is activated by enterokinase to trypsin and pepsinogen to pepsin by HCL 3- Increasing or decreasing rate of enzyme synthesis (At Gene level) By this mechanism cells regulate the amount of enzyme by changing the rate of enzyme synthesis The increase (induction) or decrease (repression) of enzyme synthesis leads to change total amount of active site. This mechanism is slow (takes from hours or days) 4- Feed back product inhibition Medical importance of enzymes of blood Blood enzymes can be classified into two major groups: 1- Enzymes that have functions in blood (smaller group): They are present in blood in high amounts Example: liver secretes zymogens (inactive precursors) involved in blood coagulation. 2-Enzymes that do not have functions in blood (large number) These enzymes are released from cells during normal cell turn over. They have functions in cells (intracellular) BUT: they do not have a function in blood In healthy individuals, levels of these enzymes are constant. So, the presence of elevated enzyme level in blood may indicate tissue damage that leads to increase in release of these enzymes.  Many diseases that cause tissue damage results in increased release of intracellular enzymes into plasma (blood) So, the enzyme levels in blood are measured for diagnosis of these diseases Diseases of the heart, liver, skeletal muscles and other tissues are diagnosed by an elevation of a blood enzymes. The level of elevation of an enzyme correlates with the extent of tissue damage in any of these organs. Some enzymes may be available in high amount in only one organ So, the elevation of blood levels of these enzymes are diagnostic for diseases of this organ only. (specific) Example: Alanine aminotransferase (ALT) enzyme elevation in blood indicates disease of the liver (specific for liver cells).