Enzyme Biochemistry Lecture Notes PDF

Almaaqal University Biochemistry Enzymes Dr/ Wael Sobhy Darwish Biochemistry PhD Lec-3  Enzymes ❑Enzymes are proteins that acts as a bio...

Almaaqal University Biochemistry Enzymes Dr/ Wael Sobhy Darwish Biochemistry PhD Lec-3  Enzymes ❑Enzymes are proteins that acts as a biological catalyst, speeding up chemical reactions without undergoing any change themselves. ❑All enzymes are proteins. ❑Enzymes are required in very small quantities. ❑Each enzyme is very specific and only attaches to one type of molecule. ❑Enzymes possess active site, at which interaction with substrate take place. ❑The molecule the enzyme acts upon is called its substrate. ❑Our bodies naturally synthesize enzymes  The properties of enzymes Catalytic property A small amount of enzyme is enough to break large molecules down into smaller molecules. Specificity Enzymes are very specific in action, with one enzyme acting only on a particular substrate. Reversibility Most reactions that are catalyzed by enzymes are reversible. Sensitivity to temperature Enzymes are thermos-liable or very sensitive to heat and temperature. Specificity to pH Enzymes show maximum activity at an optimum pH of 6 – 8. Function of enzymes ❑They are essential for respiration, digestion of food, DNA replication, muscle contraction and nerve function. ❑Store and release energy (ATP). ❑Create larger molecules from smaller ones ❑Hormone production ❑Transporting materials around a cell Sources of enzymes Endoenzymes: enzymes that function within the cells, most of enzymes are these types. Ex: metabolic oxidase. Exoenzymes: enzymes that are liberated by cells and catalyze reactions outside the cell. Ex: digestive enzymes (amylase, lipase, protease).  Zymogen or proenzyme They are inactive enzymes. 1. Zymogens are inactive because their catalytic sites are masked by a polypeptide chain. 2. Activation of zymogen, into active enzyme is done by removal of the polypeptide chain to open the catalytic site for its substrate. 3. Examples of zymogens: are pepsinogen and trypsinogen.  Some enzymes require an additional nonprotein component for its optimum activity called cofactor which may be either loosely or tightly bound to the protein portion of the enzyme. Cofactors: are non-proteinous substances that associate with enzymes. These cofactors may be: – Organic compounds, called coenzymes, loosely attached to enzyme. Prosthetic groups: These are cofactors tightly bound to an enzyme at all times. Apoenzyme: term refers to the protein part of enzyme. without its cofactor Holoenzyme : the complete catalytically active enzyme. (Apoenzyme + cofactor)  Enzyme Conjugated Enzyme (Holoenzyme) Simple Enzyme Made up of protein + non protein part Made up of protein only Ex. Pepsin, Trypsin Protein part Non-Protein part Apoenzyme Co-factors Co-enzyme Metal activator Prosthetic group Loosely attached, Loosely attached, Tightly attached organic part of inorganic or organic, inorganic enzyme, metallic ions part, cant be easily Ex: Vitamin, AMP, Ex: Fe, Mg, Zn separated FAD, NAD  Enzyme nomenclature (Naming): 1. Trivial name: such as trypsin and pepsin. 2. Adding suffix ase to the substrate such as maltase and lactase. 3. To standardize enzyme nomenclature, the International Union of Biochemistry (IUB) made a systemic name to each enzyme that can indicate: a- The substrate acted upon. b- The coenzyme involved in the reaction. c- The type of reaction catalyzed  Classification of Enzymes Oxidoreductases These catalyze oxidation and reduction reactions, e.g. pyruvate dehydrogenase, catalysing the oxidation of pyruvate to acetyl coenzyme A. Isomerases They catalyze the formation of an isomer of a compound.  Transferases These catalyze transferring of the chemical group from one to another compound. An example is a transaminase, Hydrolases They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide bonds in proteins. Lyases These catalyze the breakage of bonds without catalysis, e.g. aldolase. Ligases Ligases catalyze the joining of two molecules. For example, DNA ligase catalyzes the joining of two fragments of DNA by forming a phosphodiester bond.  Mechanism of enzyme action 1- The Key and Lock (Fisher model) Theory The active site of the enzyme is complementary in conformation to the substrate, so that enzyme and substrate recognize each other. This theory postulates that active site has fixed shape.  2- The Induced Fit Theory (Khoshland model) It is a flexible model. The induced fit model proposes that the shape of the active site within enzymes is flexible and can be induced to fit the substrate through a variety of mechanisms (changes in temperature, pH, cofactor, or coenzyme binding) The substrate molecule does not fit exactly in the active site. This induces a change in the enzymes shape to make a closer fit.  Rate of enzyme reactions The rate of enzyme reaction is measured by the amount of substrate changed or amount of product formed during a period of time. If enzyme activity is measured over a period of time, the rate of reaction usually falls, most commonly as a result of a fall in the substrate concentration.  Temperature Raising temperature generally speeds up a reaction, and lowering temperature slows down a reaction. However, extreme high temperatures can cause an enzyme to lose its shape (denature) and stop working.  pH Each enzyme has an optimum pH range. Changing the pH outside of this range will slow enzyme activity. Extreme pH values can cause enzymes to denature.  ENZYME CONCENTRATION Enzyme concentration: Increasing enzyme concentration will speed up the reaction, as long as there is substrate available to bind to. Once all of the substrate is bound, the reaction will no longer speed up, since there will be nothing for additional enzymes to bind to.  SUBSTRATE CONCENTRATION Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate.  Denaturation: Denaturation is a process in which enzymes lose their conformational structure due to application of external stress. A denatured enzyme will not function properly because the shape of the active site has changed. If the denaturation is not severe, the enzyme may regain its original shape and become functional. Causes of denaturation: Heat Changes in pH (Acids and bases). Heavy-metal ions (lead, arsenic, mercury). Organic Solvents (Alcohol, acetone). UV radiation.