INTRODUCTION TO ENZYMES

 Can you guess???  Hints: DNA and Proteins  Yes, the whole purpose of our living lies within these 2 biomolecules  Can you explain why?? And how??? WHAT IS THE PURPOSE OF LIFE?

 One of the many tools that life uses to fulfill its purpose  Enzymes perform many important functions, but the key job it does is “Catalysis”  Think about the conversion of sugar to CO 2 and H 2 O  Does all the sugar in your pot break down spontaneously?? If so, how long does it take?  The sugar in your body (That you consume) breaks down instantaneously to give off energy  Metabolism consists of biological reactions that give us energy to lead our life  Enzymes, via their catalytic power, help to speed up these reactions  But is that the only reason they are popular??? ENZYMES

 All enzymes are proteins- True/False?  So, what are proteins?  Strings of amino acids folding up into distinct structures  The properties of a protein (Enzyme) are largely determined by its three-dimensional structure- Folding  There are several levels of protein folding 1.Primary 2.Secondary 3.Tertiary 4.Quaternary  Before we delve into Enzymes, lets recap on proteins and associated subjects! ENZYMES ARE PROTEINS

 The fluid of life  Properties of water: 1.Ionic bonding between O and H atoms 2.Asymmetric charge distribution- Polar 3.Forms Hydrogen bonding with other water molecules and polar solutes 4.Repels hydrophobic molecules WATER, WATER, EVERYWHERE

 Presence of other molecules in an aqueous solution disrupts the hydrogen bonding of water  When water surrounds a hydrophobic molecule, the optimal arrangement of hydrogen bonds results in a highly structured shell, or solvation layer, of water around the molecule  The increased order of the water molecules in the solvation layer correlates with an unfavorable decrease in the entropy of the water  When nonpolar groups cluster together, the extent of the solvation layer decreases because each group no longer presents its entire surface to the solution.  The result is a favorable increase in entropy KEY CONCEPTS OF BIOCHEMICAL BONDING

 Polar groups can generally form hydrogen bonds with water and hence are soluble in water  The number of hydrogen bonds per unit mass is generally greater for pure water than for any other liquid or solution, and there are limits to the solubility of even the most polar molecules as their presence causes a net decrease in hydrogen bonding per unit mass  A solvation layer also forms to some extent around polar molecules  The energy of formation of an intramolecular hydrogen bond between two polar groups in a macromolecule is largely canceled by the elimination of such interactions between these polar groups and water,  However, release of structured water as intramolecular interactions form provides an entropic driving force for folding  Most of the net change in free energy as weak interactions form within a protein is therefore derived from the increased entropy in the surrounding aqueous solution resulting from the burial of hydrophobic surfaces KEY CONCEPTS OF BIOCHEMICAL BONDING

 A description of all covalent bonds (Mainly peptide bonds and disulfide bonds) linking amino acid residues in a polypeptide chain  The most important element of primary structure is the sequence of amino acid residues  Each protein has a distinctive number and sequence of amino acid residues  The function of a protein depends mainly on its amino acid sequence (Primary structure) which ultimately governs its folding into higher order structures PRIMARY STRUCTURE OF PROTEINS

 Defined as the local conformation of its backbone  Particularly stable arrangements of amino acid residues giving rise to recurring structural patterns: Helices, pleated sheets, and turns  Stabilized largely by weak non-covalent interactions  α helix: The polypeptide backbone is tightly wound around an imaginary axis drawn Iongitudinally through the middle of the helix, and the R groups of the amino acid residues protrude outward from the helical backbone. The repeating unit is a single turn of the helix, which extends about 5.4 A along the long axis, slightly greater than the periodicity. The amino acid residues in the prototypical α helix have conformations with φ = -57 ˚ and ψ = -47 ˚, and each helical turn includes 3.6 amino acid residues SECONDARY STRUCTURE OF PROTEINS

 β sheet: The backbone of the polypeptide chain is extended into a zigzag form, arranged side by side to create a structure resembling a series of pleats. Hydrogen bonds form between adjacent segments of polypeptide chain. The individual segments that form a β sheet are usually nearby on the polypeptide chain, but can also be quite distant from each other in the linear sequence of the polypeptide; they may even be in different polypeptide chains. The R groups of adjacent amino acids protrude from the zigzag structure in opposite directions, the adjacent polypeptide chains in a β sheet can be either parallel or antiparallel (having the same or opposite amino-to-carboxyl orientations, respectively SECONDARY STRUCTURE OF PROTEINS

 β turn: Connects the ends of two adjacent segments of an antiparallel β sheet. The structure is a 180 ˚ turn involving four amino acid residues, with the carbonyl oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen of the fourth  Other less common structures also prevail SECONDARY STRUCTURE OF PROTEINS

 Describes all aspects of the three-dimensional folding of a polypeptide  Two major groups: 1.Fibrous proteins: Polypeptide chains arranged in long strands or sheets, usually consist largely of a single type of secondary structure, and their tertiary structure is relatively simple. Structures that provide support, shape, and external protection to vertebrates are made of fibrous proteins 2.Globular proteins: Polypeptide chains folded into a spherical or globular shape. Globular proteins often contain several types of secondary structure. Most enzymes and regulatory proteins are globular proteins TERTIARY STRUCTURE OF PROTEINS

 When a protein has two or more polypeptide subunits  Protein quaternary structure ranges from simple dimers to large complexes  Some multimeric proteins have a repeated unit consisting of a single subunit or a group of subunits, or protomer QUATERNARY STRUCTURE OF PROTEINS

 When did we come to know about them?  Enzymology, the study of enzymes  First recognized and described in the late 1700s, in studies on the digestion of meat by secretions of the stomach  In the 1850s, Louis Pasteur concluded that fermentation of sugar into alcohol by yeast is catalyzed by “Ferments”  In 1897 Bertrand, using the ‘‘Pressed juice’’ from rehydrated dried yeast, demonstrated that alcoholic fermentation could be performed in the absence of living yeast cells  “Enzyme” (Greek: en, in + zyme, yeast) was coined in 1878 by Wilhelm Friedrich Kühne LETS MOVE BACK TO ENZYMES HISTORY

 Higher reaction rates  Milder reaction conditions  Greater reaction specificity- Both for substrate and products  Capacity for control WHAT MAKES ENZYMES SO SPECIAL?

 Emil Fischer’s discovery, in 1894, that glycolytic enzymes can distinguish between stereoisomeric sugars led to the formulation of his lock-and-key hypothesis: The specificity of an enzyme (the lock) for its substrate (the key) arises from their geometrically complementary shapes  The noncovalent forces through which substrates and other molecules bind to enzymes are similar in character to the forces that dictate the conformations of the proteins themselves= Both involve van der Waals, electrostatic, hydrogen bonding, and hydrophobic interactions  A substrate-binding site consists of an indentation or cleft on the surface of an enzyme molecule that is 1.Complementary in shape to the substrate (Geometric complementarity) 2.The amino acid residues that form the binding site are arranged to interact specifically with the substrate in an attractive manner (Electronic complementarity) SPECIFICITY?

 Four distinct types of specificity: 1.Stereochemical specificity: The enzyme will act on a particular steric or optical isomer 2.Absolute specificity: The enzyme will catalyze only one reaction 3.Group specificity: The enzyme will act only on molecules that have specific functional groups, such as amino, phosphate and methyl groups 4.Linkage specificity: The enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure SPECIFICITY

 Enzymes are highly specific both in binding chiral substrates and in catalyzing their reactions  Enzymes are absolutely stereospecific in the reactions they catalyze  Consider the reaction of yeast alcohol dehydorgenase STEREOSPECIFICTY

 A substrate of the wrong chirality will not fit into an enzymatic binding site  Most enzymes are quite selective about the identities of the chemical groups on their substrates. Indeed, such geometric specificity is a more stringent requirement than is stereospecificity  Enzymes vary considerably in their degree of geometric specificity.  YADH catalyzes the oxidation of small primary and secondary alcohols to their corresponding aldehydes or ketones but none so efficiently as that of ethanol. Methanol and isopropanol, are oxidized by YADH at rates that are, respectively, 25-fold and 2.5-fold slower than that for ethanol. Similarly, NADP+, does not bind to YADH GEOMETRIC SPECIFICITY

 Some enzymes require no chemical groups for activity other than their amino acid residues  Others require an additional chemical component called a cofactor 1.One/more inorganic ions, such as Fe2+, Mg2+ 2.Complex organic or metalloorganic molecule called coenzyme  Coenzymes are chemically changed by the enzymatic reactions in which they participate. Thus, in order to complete the catalytic cycle, the coenzyme must be returned to its original state  The protein part of such an enzyme is called the apoenzyme or apoprotein  A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a holoenzyme  What’s a prosthetic group? SANTA NEEDS ELVES

 Enzymes are classified by the reactions they catalyze  By international agreement, a system has been adopted for naming and classifying enzymes  This system divides enzymes in to six ciasses, each with subclasses, based on the type of reaction catalyzed  Each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes.  For this reaction ATP + n-glucose = ADP + D-glucose 6-phosphate The enzyme is ATP:glucose phosphotransferase which indicates that it catalyzes the transfer of a phosphoryl group from ATP to glucose  Its Enzyme Commission number (E.C. number) is The first number( 2) denotes the class name (Transferase) 2.The second number (7), the subclass (phosphotransferase) 3.The third number (1), a phosphotransferase with a hydroxyl group as acceptor; 4.The fourth number (1), D-glucose as the phosphoryl group acceptor CLASSIFICATION OF ENZYMES

 Principles of Biochemistry, Lehninger, 5 th Edition, Chapters 2, 4, 6  Biochemistry, Stryer, 6 th Edition, Chapters 2, 8  Biochemistry, Voet and Voet, 4 th Edition, Chapters 8, 13 REFERENCES