Proteins are the products of structural genes, which on transcription get translated on mRNA template producing a polypeptide chain. This depending upon the amino acid sequences undergoes modifications such as splicing and secondary, tertiary structural organization. Most of the polypeptide chains based on their amino acid R groups first organize into helices (coiled structures) or extended chains called beta sheets. It is the sequences that ultimately determine the shape of proteins. Such secondary structured protein further fold into 3-D structures called tertiary structures by intra chain or inter-chain noncovalent bonds and covalent bonds. Understanding of Ramachandran’s plot is very important in understanding changes in protein structures.
Proteins are the polymers of amino acid residues held by peptide linkages. Next to carbohydrates, proteins are the major organic constituents of the cell. They are in every conceivable structural and functional components of the cell. They perform a wide variety of functions. Their role in cellular metabolism is so pervasive, if one of the proteins is missing, it will be fatal for the survival of the cell.
When proteins are hydrolyzed in the presence of strong acids or by enzymes, they yield amino acid residues. Living cells contain just twenty different kinds of amino acids, to which one more amino acid has to be added, it is Selenocysteine; so the total number of amino acids in biosystem is 21; which act of the building blocks of protein chains. However, different proteins contain different composition and different sequences of amino acid residues. A particular sequence generates a motif and several such motifs can generate a domain. There are hundred of different kinds of motifs; and it is the combination of motifs ultimately determines the structure and function of a protein. There is a distinct relationship between a motif and an exon, a coding sequence in the gene. It is the sequence of amino acids that ultimately determines the 3-D structure and the specific functions of the proteins.
The C-N linkage between the carboxyl groups of one amino acid residue with an amino group of succeeding amino acid is called peptide bond. Based on the number of amino acid residues linked, proteins are called dipeptides,
tripeptides and polypeptides. Generally an average polypeptide chain of mol. Wt of 12 KD-36 KD consists of 100-300 amino acid residues.
Sometimes certain compounds other than amino acids bind to proteins ex. Carbohydrates, lipids, sulfates, nucleic acids, metals, etc. Accordingly the proteins are called glycoproteins, lipoproteins, sulfoproteins, nucleoproteins, metalloproteins, etc. The above said compounds are added only after the synthesis of polypeptide chains. Further more a protein may be made up of a single polypeptide chain, called monomer or it may contain more than one polypeptide chains called dimers, trimers, polymers, etc. Such polymers have protein-protein interacting surfaces, they come in different forms and shapes.
The molecular weight of a protein depends upon the number and the kind of amino acid residues present in the chain. Added to this the number of sub-units present in a particular protein has to be taken into consideration for determining molecular weight of a protein complex. The molecular weight of individual polypeptides or the total mol. wt. of polymer proteins can be determined either by ultracentrifugation method or by column chromatography or electrophoretic methods. Using these methods the mol. wt. of and the number of sub-units present in various proteins have been determined. (See Table)
Name of the protein
Mol. Wt. In Daltons
The backbone of a polypeptide chain is the C-N peptide bond between amino acid residues. Every polypeptide chain possesses one amino free end and the other and contains a free carboxyl group. The peptide C-N region is planar and it is not free for rotation on its own axis. But the a carbon with its R group is pliable and it can freely rotate on its axis. Thus C-N planar group imposes significant constraints upon the shape of the polypeptide chain.
Another important factor that contributes to the orientation of the polypeptide chain in its stable from (least energy) is R groups present at a carbon of each amino acid residue. They contribute to the configuration and conformation of the polypeptide chain in its entirety. Configuration denotes
the arrangement of substituent groups in space and their position is always fixed. It cannot be change without breaking one or more covalent bonds. On the other hand conformation refers to special arrangement of substituent groups where they are free to assume different positions without breaking any bonds. The side groups i.e. R groups of each amino acid residue strongly influence the conformation of the polypeptide chain and the possible conformations is infinite. In addition, the pH of the medium, thermal rotations, electronic energy, binding of other molecules, etc have strong influence on the conformation. Basically, proteins exhibit three or four different forms i.e. primary structure, secondary structure, tertiary structure and quaternary structure.
A protein crystal
The information that can be obtained from the primary structure is the composition and sequential arrangement of amino acid residues, in the polypeptide chain. This can be established by subjecting the putative protein into ‘finger printing’ techniques, which involves the identification of amino acid sequence of the polypeptide chain. The primary structure ultimately determines the other structural forms of proteins.
If a polypeptide chain is suspended in water, due to the interaction between forces that are operating on R groups and the forces exerted by dipolar water, the protein assumes helical form; which may be right handed helix a
or left handed helix (b). ex., keratin proteins (hair proteins) assume right handed helix called a helix, in which for every 0.5 mm to 55 mm length the protein takes one complete turn consisting of +/- 3.6 amino acid residues. The R groups from each amino acid stick out of the helix. Because of this the inter chain hydrogen bond formation, between the electronegative nitrogen of one coils with the carbon oxygen of the third amino acid found in the next coil, is greatly facilitated. The hydrogen bondings are oriented parallel to the long axis of the helix. Most of the proteins exhibit right handed a helix.
It should also be noted that not all polypeptides should have helical conformation. For example polylysine polypeptides, at pH 7.0 do not assume any helical structure but remains as a random chain. Instead, the same polypeptide chain at pH 12 assumes a helical from. This is because at pH 7.0, the R group of all lysine residues having positive charges repels each other and prevents intra chain hydrogen bonding. On the contrary, at pH 12, the R groups are neutralized, and they do not exert any repelling forces, instead hydrogen bonding between intra chains is favored, hence they assume a helix. In the case of poly-isoleucine polypeptide chains. a helical conformation is prevented because of stearic hindrances exerted by bulky hydrophobic R groups.
The conformation in polyprolines is slightly different, because the N group is actually within the heterocyclic ring which forms the R group of the amino acid. This prevents the rotation on its axis which in turn prevents the hydrogen bonding within the polypeptide chain. If such proline residues are present with in a polypeptide chain, the helical confirmation at such regions is prevented and assumes B chains.
The above mentioned features strongly suggests that a polypeptide chain generally assumes a helical form, but it need not be throughout the length of the chain and a part of the chain may be in random form or it may assume and kind form which depends upon the amino acid sequences in that position. It also explains how the side groups exert influence in the 3-D conformation and stability of the protein chain.
Prof. G.N. Ramachandra from I.I.Sc, Bangalore has proposed another restraint with regard to the angle of rotation along the Ca -C1 axis. He has determined the most stable angles of rotation for the right handed helix between the C-R to C-0 = a = 47 degree and C-R to NH is Q=57 degree. The entire conformation of the protein chain falls within the allowed territory, called Ramachandran’s plot
The helical polypeptides need not be a straight helical chain and it can further fold or associate with other R- groups of the same protein chain.
Such structural form is called tertiary structure. The R groups that are responsible for such interaction may bring about hydrogen bonding, ionic interactions, hydrophobic interaction, and covalent cross bridges like sulfhydril bonds. Among the above mentioned attractive forces, sulfhydril bonding in the strongest. Such covalent S-S bonds within the chain bring about the folding of the chain into specific 3-D conformation. Such 3-D conformation is very much essential for specific structural organization and functions .
DENATURATION AND RENATURATION:
When proteins are heated or dissolved certain solvents, their 3D structure and they become linear. This phenomenon is called denaturation; as a result, proteins loose their ability to perform their specific functions. On the other hand, the temperature of the said solution is brought back to the normal temperature, the sulfhydril bonds are reformed and the 3-D shape is restored, so also its function. Such a process is called renaturation. On the contrary, if the solution is heated to boiling temperature, proteins undergo irreversible destruction.
When a solution containing proteins in their 3-D state are heated, to 40-50 degree C, the sulfhydril bonds break and polypeptides open out into straight helical structure .
user, sodium dodisulphate, methyl mercury, mercury, etc. bind to proteins and break the bonds responsible for 3-D conformation, thus they bring about denaturation. Even changes in the pH of a solution bring about denaturation. Thus, it is clear, that the intracellular environment plays an important role in the function of proteins.
A protein may be made up of one polypeptide chain or many polypeptide chains, the former is called monomer protein and the latter is referred to as polymer or oligomeric proteins.
The dimer or polymer proteins may be made up of similar polypeptides or different polypeptides, so they are called homopolymers and heteropolymers. Such an association of more than one protein is referred to as quaternary structures. The binding forces responsible for such an association may be due to metal ions, hydrophobic interactions or ionic interactions.
Globular proteins polypeptide chains which are folded into 3-D spherical structures are called globular proteins. Nearly 2000 and odd enzymatic proteins so far known are globular proteins. Such proteins are soluble in water and some are buried in the lipid core of the membranes; which depends upon the kind of peripheral amino acid residues found on proteins, ex. Hemoglobins, myoglobins, serum proteins are water soluble; Cytochrome oxidase, protein secretion proteins, etc. are lipid soluble proteins. The globular proteins contain specific areas or sites at which they bind to specific substrates for enzymatic reactions. The intergrity of the 3-D shape is essential for their normal functions.
Many globular proteins organize into fibrous proteins. For example, a and B subunits of tubulins polymerize to form tubular microtubules. Similarly the G action units polymerize into functional filament called F-actins. Such proteins are often called pseudo fibrous proteins. But polypeptide chains of a keratin and B collagen proteins are considered as true fibrous proteins
Human hairs are primarily made up of numerous a keratin helical polypeptides. Such helixes are intertwined with each other by disulphide bonds between helical chains. All the chains in such structural fibers have NH2 or Carboxyl groups at the same ends. Basically, three such a keratin helical polypeptides are coiled to each other into a rope like structures called protofibrils. Even such protofibrils associate to form a micro fibril. Many such micro fibrils join together into a macrofibril. A large number of such macrofibrils join together to form a super coiled structure called hair.
Similarly collagen is another super coiled muscle fibrous protein found in the tissues of higher vertebrates. The basic unit of collagen fibers is tropocollagen which is made up of three helical polypeptides twisted to each other. Each tropocollagen is 300 mm long and 1.5 mm thick. Many such tropocollagen fibers are longitudinally arranged head to head to form long thick fibers. Many such fibers are longitudinally oriented to form muscle fibers called collagen fibers.
Silk fibrions or fibrions secreted by silk moths, spiders and other insects are insoluble proteins but they are supple and flexible in nature. Such fibers are different from a keratin fibers in their structure and flexibility. Keratins can be stretched to greater lengths, but silk fibrions cannot be stretched.
Silk fibroins are actually made up of polypeptide chains with beta confirmation, wherein the chain is extended into zig-zag rather than helical conformations. Such zig zag fibers are oriented side by side parallel to each other and they are held to each other by interchain hydrogen bonds (See Figure). That is the reason why silk fibers look like stretched pleated sheet like structures. The most significant feature of these proteins is the total absence of intra chain sulfhydril bonds and most of polypeptide chains are arranged parallel to each other.
Most of the cellular proteins fall into either into globular or fibrous types but some of the proteins found in both the animals and the plants (rarely), contain another class of proteins which have both the features. Such proteins are called fibro globular proteins.
The best example to illustrate such structural combination is myosin. .It is made up of a head and a long tail. The tail consists of two long intertwined a helical polypeptides. On the contrary, the head consists of four polypeptide chains folded into globular structure; of which two are in continuity with tail fibers. The head proteins exhibit ATPase activity. The head and the tail protein of the myosin fibro globular proteins are inter connected by a region called hinge which exhibits random arrangement of the polypeptide chain.
The chemical composition and the structure of proteins are so diverse, their functions also vary. They are extra ordinary biomolecules endowed with a potentiality to provide structural stability to cell, determine the shape and perform myriads of functions. Though DNA act as the genetic material with all the information encoded within it, without functional protein, it is like a dummy tape without an instrument to play. No cellular component can be synthesized or processed without proteins. Their functions are pervasive; all biological activities are the functions of proteins. However there exceptions to this rule. There are many RNA molecules in their specific structural form can perform enzymatic reactions, where they can cleave a bond and make a bond. Based on protein structure and functions a simple classification has been given below.
The most specialized proteins are enzymes and they act as biological catalysts. So far 10000 or more enzymes have been identified from bacteria, fungi, animals and plants. They are mainly responsible for biochemical activities of the cell.
Seed proteins like zein, gliedin etc are called storage proteins. They provide nutritional requirement of essential amino acids for animals. Such proteins are also stored in the white of eggs. E.g. casin in milk and ferretin in animal tissues.
Proteins found in membranes, cytoskeletal fabric, capsids, collagen, elastin of muscles, mucoproteins of synovial fluids, keratin of hairs, nails, hoofs, borns, silk fibrions, spider webs, etc. are all structural proteins. They provide mechanical support and strength to various structural components of the cellular tissues.
Certain cellular components are transported from one region of the cell to the other or from one region of the body to the other. Specific proteins are responsible for the transportation of various cellular components. Such proteins are called transport proteins. Microtubules and microtrabaculae transport sucrose in sieve tubes, microtubules and action filaments are involved in protoplasmic streaming. Hemoglobin, hemoeyanin and myoglobin transport oxygen in the blood of vertebrates and invertebrates. Serum albumin and B lipoproteins transport fatty acid components in the blood. Iron binding proteins and ceruloplasmins transport iron and copper respectively.
Flagellar proteins help in the movement of cells from one place to another. Cytoskeletal fabric is responsible for the protoplasmic movement. Muscular proteins control mechanical movement of organs and the body. Most of the above said movements are due to the activity of contractile proteins like action and myosin.
DNA binding Proteins
Antibodies are a class of serum proteins which act against the invasion of pathogenic bacteria, viruses or any other foreign substances. They are highly specific to the antigens. Interferons induce antiviral proteins against the attack of certain viruses in mammalian dells. Thus such proteins provide defensive mechanism against disease causing foreign agents. Fibrinogen and thrombin are another set of proteins, which prevent hemorrhage by blood clotting.
Certain pathogenic bacteria after infection release toxins which results in dehydration or food poisoning. Snake venom is another class of proteins which can cause death in man. Ricin produced by castor seeds and gossip in from cotton can easily kills persons. Thus proteins not only act as saviors as in the case of antibodies, they can also act as killers.
Animals produce certain proteins which control physiological activities, e.g. hormonal proteins. They are synthesized and secreted by endocrinal glands. Insulin controls the blood sugar level; growth hormone controls the growth of the body. Thus many such hormones play important roles in the life cycle of animals. Further more some of the proteins control transcription and translation, thus they control gone expression and differentiation. Even such proteins are called regulatory proteins.
In olden days wine making was an art. They used to prepare wine from different sources like fruits, barley and wheat by subjecting them to a process called fermentation. But they did not know what the actual mechanism of fermentation was. It was Louis Pasteur who demonstrated that fermentation requires living micro organisms like yeast cells. Buckner extracted a juice from yeasts, which was still capable of catalyzing the fermentation reactions. Such catalytic components were earlier called, by Willy Kuhne (1878) as enzyme. Later, Sumner succeeded in isolating an enzyme called urease in pure crystalline form, since then a large number of enzymes have been isolated and identified. Their chemical composition, structure, functions and kinetic mechanisms have been elucidated.
RuBCase is the enzyme that fixes CO2 to carbohydrates; it is the most abundant protein on earth
In earlier days, nomenclature of enzymes was based on the substrate on which they acted ex. Sucrase on sucrose, lipase on lipids, protease on proteins, etc. As more and more number of enzymes was discovered in different labs all over the world, the trivial names gave rise to a lot of confusion. In order to avoid confusion and ambiguity in giving names, an international society of enzymologists was established. Based on substrate and the kind of reaction they brought about, the enzymes were given names.
In fact, naming and classification was done together. According to the internation body of enzymologists, all enzymes are basically grouped into six classes of enzymes – such as oxido-reductases, transferases, hydrolases, isomerases, ligases and lyases; further sub groups have been identified.
Enzymes responsible for oxidation either by the addition of oxygen or removal of hydrogen or electrons are called oxidases. On the contrary, the enzymes which add hydrogen or electrons are termed as reductases. Most of the enzymes which bring about oxidation or reduction perform the reaction simultaneously. Ex. Cytochrome oxidase, nitrate reductase, a ketoglutamate dehydrogenase.
Certain groups like amino groups, acyl groups, phosphates, etc can be transferred from one compound to another compound by specific transferase enzymes, ex. Aminotransferases, transcarboxylases, transhydrogenases, transacetylases etc.
The enzymes which by adding water molecules bring about breakdown of bonds are called hydrolases. Majority of lysosomal enzymes are hydrolases of one or the other kind, e.g. Lipases, proteases, DNase, RNAase, Amylase, endonuclease etc.
These enzymes add a group to compounds containing double bonds between carbon and carbon, carbon and nitrogen, carbon and oxygen, etc,
Enzymes which are capable of transforming one isomer to another are called isomerases. They a re highly specific in their substrates and reactions, ex. Glucose 6-p isomerase converts glucose 6-p to fructose 6p. Phosphoglyceraldehyde can be converted to another isomer called dihydroxyacetone phosphate by gluoco-phospho glyceraldehyde isomerase.
Ligase enzymes bring about the bond formation between different molecules by removing a molecule of water. In fact, their activities is in the opposite direction of hydrolyses. They bring about the synthesis of bigger compounds by the addition of simpler compounds. Such enzymes are also called synthetases, e.g. RNA polymerases, DNA polymerase, peptidyl transferase etc.
Almost all enzymes are made up of proteins as the major compounds. In addition some non proteinaceous compounds like vitamins or inorganic ions are also bound to be the protein part of the enzyme. The protein part of the enzyme is called ‘apoenzyme’ and the non protein parts are called as prosthetic groups, which may be metal ions like Mg2+, Ca2+, Mo2+, Mn2+, Fe2+, Cu, K, Ni, Se, Zn, etc. The apoenzyme may also contain some non proteinaceous organic compounds like NAD, FAD, NADP, FMN, coenzyme A, Biotin, TPP, Folate, pentothenic acid, etc. Such compounds are called co-enzymes. They easily dissociate from the main enzyme. The apoenzyme and prosthetic groups can be separated by dialysis; where the prosthetic groups diffuse out of the membranous bag, but the bulky apoenzyme protein part is retained within the dyalytic membranes. The enzyme containing both apoenzyme and prosthetic group together is referred to as Holoenzyme.
The main part of the enzyme is protein; it possesses a 3-D structural organization. The total surface area of the enzyme is very large, and it has specific sites at which the substrates bind to the enzyme. The apoenzyme may be made up of a single protein or it may consist two or more monomers. Still their organization and association is very important for their specific function.
However, some exhibit multiple enzyme system, where two or more different enzymes are complexed together and together they function. Such enzymes perform multi step reactions where intermediate products are retained on the enzymatic surface and only the final products are released from the surface of the multiple enzymes, ex. Pyruvate dehydrogenase, ketogluterate dehydrogenase, Fatty acid synthetase, etc.
The specificity of an enzyme and substrate and its function is determined by the enzymatic proteins’ 3-D organization. The enzyme proteins are folded in such a way, they possess specific regions in the form of clefts or grooves of particular shape and dimensions. The surface area of such sites is always complementary to their substrates, so that the substrate and enzyme form a complex similar to that of lock and key association. Within such grooves or clefts, certain amino acids with specific R groups act as binding sites to which the substrates bind transitorily and exert forces to bring about reactions.
Some of the enzymes, besides possessing specific binding sites for substrates, contain other sites at which certain molecules bind and bring about conformational changes in the 3-D confirmation of the enzymatic protein. Such bindings may activate an enzyme or inhabit the activity of the enzymes. Such enzymes are called allosteric enzymes. The components that bring about the activation or inactivation of allosteric enzymes are called allosteric affectors or effectors. The affecters block the activity and effectors activate the activity.
Multi-cellular organisms are made up of different organs containing specific tissues. Each of then perform a set of functions by producing specific enzymes. However, some of the enzymes synthesized within the cell are secreted to extra-cellular surfaces, such enzymes are called exoenzymes and those enzymes which are retained within the cell are called endoenzymes.
The enzymes present within a cell show a great range in their structures and functions. However, some of the enzymes are compartmentalized, so that each organ contains a group of enzymes which perform specific functions. For example, chloroplast contains enzymes responsible for photochemical and carbon pathways. Nucleus possesses enzymes responsible for DNA replication, transcription, processing, etc. Likewise, cytosol contains enzymes for HMP pathway, etc. Thus one can see intracellular compartmentalization of enzymes for specific functions.
A large number of enzymes present in cells are continuously made irrespective of external or internal conditions. Such enzymes are called house keeping or constitutive enzymes. But under certain conditions, specific enzymes are synthesized de novo. Such enzymes are called induced enzymes.
1. Enzymes are macromolecules and possess a large surface area with specific binding or acting sites.
2. Enzymes act as biological catalysts
(a) They increase or accelerate the rate of reaction towards equilibrium
(b) Enzymes are required in small numbers to bring about maximum rate of reaction.
This is determined by the turnover reactions. The total number of products produced by a given enzyme in a given time is called turnover number. Different enzymes exhibit different turnover rates.
Substrate molecules transformed into products per enzyme/min/
(c) Enzymes remain unaltered at the end of a reaction. Once the reaction is brought about, enzymes are ready for another sequence of reactions.
(d) Majority of the enzymes are capable of bringing about reversible reactions depending upon the concentration of substrates or products. If the concentration of substrates is more than the concentration of products, the enzyme favors forward reaction. On the contrary, if the concentration of substrates is less than the concentration of products, the enzymes favor reverse reactions. However, not all enzymes are capable of bringing about reversible reactions and they exhibit unidirectional reactions.
(e) The catalytic activity of enzymes is highly specific in terms of their substrates and the kind of reactions they bring about.
(I). General Specificity: Enzymes like RNAase degrade RNA molecules of every kind. DNAases digest all kinds of DNA molecules irrespective of their nucleotide sequences.
(ii) Absolute group specificity: Trypsin and pepsin are proteolytic enzymes, but they cleave peptide bonds at specific amino acids, ex. Trypsin is specific to the carboxyl side of arginine or lysine. Pepsin is specific to amino acids of tyrosine or phenylalanine residue in the protein.
(iii) Stereo chemical specificity: There are enzymes which recognize only specific isomers with either α or β or D or L forms. Such enzymes are called stereo specific enzymes, which are capable of transforming one isomer to another or vice versa.
The binding forces responsible for such an association may be due to metal ions, hydrophobic interactions or ionic interactions.
αβδ or B
3. Sensitive to Heat:
Enzymes being mainly made up of proteins, their 3-D organization depend upon S-S bonds. Under normal temperatures such bonds are intact and perform normal functions but at very high temperatures, the S-S bonds break open and proteins get denatured and their function is impaired. Further more, the rate of reaction depends upon the temperature. As the rate of reaction depends upon the frequency of collision between the substrate and enzymes, the rate of movement of these reactants is controlled by the kinetic energy available in the system.
4. Sensitive to pH:
As enzymes are mainly made up of proteins, the electronic charge of the R-Groups found in amino acids depends upon the intracellular pH. Every enzyme has an optimal pH for its activity. Quite a number of enzymes are active at the range of pH 5.8 to 6.8. But certain enzymes like Trypsin and chymotrypsin are active at acidic pH 3-4. On the contrary, Alkaline phosphotases are active at pH 10-12. As pH of the cytoplasm determines the activity of functional groups found in enzymes, their activity is dependent on specific pH.
5. Sensitive to Inhibitors:
Normally substrates bind to enzymatic surface at specific sites, before catalytic action. But certain molecules other than substrates sometimes bind to active site or at some other site and bring about the inhibition of enzymatic activity. Such substances are called inhibitors, which may be competitive, non-competitive or un-competitive inhibitors.
1. Competitive Inhibitors:
Competitive inhibitors are those molecules, whose structural configuration is almost similar to that of actual substrates. As enzyme active sites recognize certain specific groups found in the substrate, any inhibitor molecule which possesses such groups identical to a substrate easily binds to active site. But the enzyme fails to bring about any catalytic reactions because of the internal structure of the inhibitors. Thus competitive inhibitors, by binding to active sites prevent the binding of substrates to the enzymatic surface. Competitive inhibition could be reversed by the addition of excess amount of substrates. For example, succinate, a substrate binds to its enzyme called succinate dehydrognase. If malonate, which has carboxyl groups similar to that succinate, is added, it easily recognizes the active sites in the enzyme and prevents the binding of real substrates. Thus enzyme activity is inhibited.
2. Non Competitive Inhibitors:
Certain organic or inorganic molecules inhibit enzymatic activity by distorting the 3-D surface of the protein or by blocking the active site non-competitively. The former kinds of inhibitors bind to a site of an enzyme other than active site and induce conformational change in the structure of proteins, thus making the enzyme inactive. On the other hand, compounds like cyanide, rotenone, antimycin, etc bring to the active site of respiratory enzyme non-competitively and inhibit enzymatic activity. There are another class of compounds like Urea, Mercaptide compounds which break the S-S bonds and unfold the proteins and make it inactive.
6. Lowers the Activation Energy:
In living systems, molecules are under constant motion and exist at different energy states. Some may exist at higher energy state and some exist at may lower energy start. Without the mediation of enzymes, substrates by themselves can react with each other by collision, provided the energy required is sufficiently high, at which point, molecules are in a transitory state. The amount of energy required for a substrate to be at higher transitional state is referred to as activation energy. For example, sucrose breaks down spontaneously, if the activation energy available is of 28000 K.cals/mole. But in the presence of enzyme invertase; it performs
the same reaction with just 11000 K.cals/mole. Thus enzyme medicated
catalysis requires less energy, because the binding of substrates to enzymes, which have a large surface, renders substrate molecules to be in a transitory state, because binding brings about stretching of the substrate bonds. This greatly felicitates the reaction with minimum input of energy. Thus enzymes economize the utilization of cellular energy and also make them efficient.
An enzyme can exist in two or more different structural forms still perform the same functions. Such enzymes are called isoenzymes. Such behavior is due to changes in the amino acid composition of enzymatic proteins, ex. Lactic dehydrogenase, it is a tetramer and it exists in five different forms; which are found in different organs. Such multiple forms of enzymes may be expressed at different stages of development. Electrophoretic methods have greatly helped in identifying such isoenzymes.
In recent years, studies on biosynthesis of macromolecules like polypeptides revealed that most of the proteins that are synthesized on mRNA template are larger than the functional proteins. Such large inactive proteins are called precursor proteins or they may also exist as pre pro precursor proteins. Such proteins require enzymatic cleavage of certain part of the polypeptide chain for the activation of precursor proteins. Living organisms produce some inactive enzymes called zymogen granules, ex. Chymotrypsinogen, Trypsinogen, pepsinogen, etc. Chymotrypsinogen is activated into active Chymotrypsinogen by enzymatic cleavage of a peptide bond. Similarly trypsinogens and pepsinogen are converted to active Trypsin and pepsins by enzymatic activation. Even insulin proteins are first synthesized as inactive precursor proteins, they are then made active by elimination of a particular segment of the protein chain.
In recent years, various techniques like radioactive isotope labeling, spectrophotometric, immunoprecipitation techniques, etc. have been employed in understanding the kinetic properties and the mechanism of enzyme action. Way back, Emil fisher proposed lock key model to explain the enzyme substrate reactions. However, this model has been slightly restructured to explain certain properties of enzymes.
To going with the enzyme and substrate molecules collide with each other. If the collision brings their complementary surfaces together, the electronic forces operating upon the enzymes and substrate molecules, fecilitate the binding of substrate to the active site located on the enzymatic surface. The active site is always located in a cleft or a groove within the enzyme.
The binding, is mostly due to non covalent forces like hydrogen bonding and it is a transitory phenomenon. The R groups in amino acid residues found in the active site exert many forces like Vander wall forces, hydrogen bonding, ionic interactions, or hydrophobic interactions.
The initial binding of a substrate induces certain changes in 3-D conformation of the enzyme, which felicitates the substrate to bind to the enzyme properly, what is called ‘face to face’ binding. Such changes in enzyme topography by substrate were first proposed by Koshland Jr. This mechanism is popularly called as ‘Induced fit mechanism’. It is now believed that most of the substrate enzyme binding reactions are found to be induced fit types.
The proper binding of the substrate to the enzyme renders the substrate to be in a transitional state. The electronic forces operating in the region of active site bring about the reaction either in making of a bond or breaking off a bond or involving in the transfer of a group. The reorientation of bonds within a substrate molecule, brings about and change in the configuration, hence it becomes a product. As products are in a stable form, they are repelled and released from the surface of the enzyme and make the enzyme free for another cycle of reactions. In the said mechanism, a single substrate binds to a single enzyme and the products produced may be one or two.
But there are many enzymatic reactions, where two substrates are involved to produce one or two products. In such cases the mechanism is slightly different. They are single displacement mechanism and double displacement or ping pong mechanism.
SINGLE DISPLACEMENT MOACTIONS
These reactions involve the binding of two substrates simultaneously to two specific binding sites on the enzyme. Binding leads to enzymatic reactions and then the product are released from the enzyme surface.
In these reactions one of the two substrates binds to a specific site, first. The enzymatic reaction that ensues, results in the transfer of group from the substrate onto the enzyme surface and the substrate after donating the groups is released as the product. Then the second substrate binds to the second site at which a group found on the enzyme is transferred to the substrate and the product is released.
EVIDENCES FOR ENZYME SUBSTRATE COMPLEX FORMATION
Various methods have been employed to find out whether enzyme and substrate molecules bind to each other to bring about enzymatic reactions. Only spectrophotometric, immunoprecipitation and chemical modifications have been mentioned here.
Different organic substances in their free state absorb light at different wavelengths, and show distinct absorption spectrum. So the enzyme and substrate individually show distinct absorption spectrum, which can be easily determined by spectrophotometric studies. If an enzyme and a specific substrate are bound to each other, the absorption band shifts. This does not happen, if the enzyme and the substrate are free.
Enzymes can be immunoprecipitated by using specific antibodies. If labeled substrate is added to an enzyme solution and immediately immunoprecipitated, the substrate that just bound is also precipitated along with the enzyme. Thus the enzyme substrate complex formation can be demonstrated.
As enzymes contain specific binding sites, they can be modified chemically or they can be made inaccessible for the substrate and thus reaction can be inhabited. This is another evidence to prove that substrates bind to enzymes at specific sites.
Different events like enzyme to substrate contact, binding, reaction and the release of products are time consuming processes. The time required for a given enzyme to bind and convert the substrate to its products can be determined by various methods and by different means. However, the rate with which enzymatic reactions taken place is referred to as enzyme kinetics. The relationship between the enzyme and substrate and other factors operating in the system can be determined accurately by kinetic data. The rate of reaction is always measured in terms of conversion of a number of substrate molecules into products by a single enzyme molecule, in a given time.
Leonar MICHAELIS AND Maud MENTEN:
Using enzyme substrate complex formation as the criteria for enzymatic reaction, Michaelis and Menton developed an equation to explain the kinetic properties of various enzyme reactions. The quotation is very popularly called Michaelis Menton equation; it is possible to determine various quantitative aspects of enzymatic reactions like velocity, km value, effect of factors, temperature, inhibitors, etc.
Assume that only one substrate molecule, binds to an enzyme to form an enzyme substrate complex, which results in the formation of products. The direction of the reaction is proportional to the concentration of input or the output. It is a reversible reaction.
In this equation, enzyme combines with a substrate to form a complex the complex produces a product. The rate constants for the forward reaction are K1, K2 & K3 where (E) (S) to (ES) and (ES) to (E) +(S) are reversible but from (ES) to (E) + (P) is not reversible.
E + S ==èES==èE + P
The velocity of enzyme reaction can be studied in individual reactions. V=K3 (ES) where the rate of enzymatic reaction is equal to the products of K3 and ES – (2)
The rate of formation of enzyme substrate complex is.
ES=K1 (E) (S) – (3)
The rate of breakdown of enzyme substrate complex to products is
ES = (K2 + K3) (ES) – (4)
Therefore K1 (E) (S) = (K2+K3) (ES) - (5)
The above equation can be further simplified or modified by using another constant called Michaelis Menton constant called km. In enzymatic reaction, km refers to the concentration of the substrate at which the enzyme reaction is half the V max. V max refers to the maximal rate of reaction at which all the enzyme molecules are saturated with substrates. The modified equation can be written as
The data obtained from Michaelis Menton equation can be plotted reciprocally as reciprocal of the velocity as the function of reciprocal of substrate concentration. The reciprocal plot can be used to determine the values for V max, km turnover numbers, etc. by just varying the concentration of substrates.
Km of enzymes in mM concentration:
Catalase 25 mM
Carbonic anhydrase 26.0 mM
Hexokinase 0.4 mM
RUBP carboxylase 15 mM
RUBP carboxylase 1-2 mM
Turnover numbers, Kcat of some enzymes
Enzyme Substrate K cat (s-1
Catalse H2O2 40,000,000
Carbonic anhydrase HCO3 400,000
Acetylcholin esterase Ac,choline 14,000
b-Lactamase B,penicillin 2000
Fumerase Fumarate 800
RecA ATP 0.4
Furthermore, determination of V max gives the data for calculating the turnover number for an enzyme. The number of substrate molecules converted into products per unit time when the enzyme is fully saturated with the substrate is called turnover number. Using this method, the turnover number of different enzymes has been determined. The reciprocal plot can also be used to find out the nature of inhibitors, whether they are competitive types or non-competitive types. See the figures.
Enzyme with two or more sub-units is called multimeric or polymeric enzymes. Besides an active site, such enzymes contain another site at which molecules other than their substrates bind and bring about the modulation on the activity of the enzyme. Such sites are called allosteric sites and the enzymes are called allosteric enzymes. The phenomenon is referred as allosterism.
Certain molecules by binding to such allosteric sites induce a conformation change in the 3-D structure of the enzyme and make the inactive enzyme into an active enzyme. Such sites are called allosteric efforts or activators. Contrary to this effect some molecules may bring about the inhibition of enzyme activity, and then the said molecules are named as affectors or inhibitors.
In addition to the above said features, multimeric enzymes contain one or more binding sites for different substrates. The binding of one substrate to one of submits in the enzyme induces or felicitates the binding of the other substrates. This behavior is called co-operative effect. Thus one can observe how the enzymatic activity is modulated by various components like substrates, activators, inhibitors etc.
In biological systems, there are many biochemical reactions where a particular substrate is converted to a product not in a single step but in multiple but sequential steps of reactions. And each of these steps is controlled by a specific enzyme. Many such multi step enzymes are induced enzymes. However, these reactions show very interesting features. The enzymes are induced by a specific substrate. The product required synthesized when it is needed and the synthesis is stopped when it is not
needed. In the latter mentioned control mechanism, the ultimate product, if
it is excess, binds to the enzyme that controls the first step and makes it
inactive, thus the production of final product is inhibited. Such a phenomenon is called feed back inhibition. Similar enzyme regulatory mechanism can be applied to a branched pathway.
Molecules of various dimensions are in constant motion at different rates within a living cytosolic fluid. When such moving substrates and enzymes of right kinds collide with each other, the enzymatic reaction is initiated. Thus the frequency of such collisions determines the rate of reaction. Higher the temperature, higher the frequency of collision hence, the rate in the rate of biochemical reactions. Every enzyme has its own optimal temperature at which it shows the maximal activity. However, at very high temperatures, enzymatic proteins undergo denaturation, so the enzymatic activity is inhibited.
2. Hydrogen ion Concentration:
Intracellular ph has a profound effect on the total change of the enzyme. The structural integrity and functional capability of an enzyme depends upon its charges at specific active sites. As different enzymes contain different composition of amino acid residues, enzymes require a favorable pH for their activity. Many enzymes are active at 5.8-6.8 some have an optimal activity at acidic ph and some at alkaline ph. Thus the intracellular ph regulates enzyme mediated cellular activities.
Water is a very important component of cellular protoplasm, in which all kinds of structures and inorganic ad organic substances are in suspended or in dissolved state. Water provides the medium for the molecules to move, collide and react. If the content of water is reduced, all the components get crowded in a given area and the enzymatic activity is reduced because of lack of opportunity for the right kind of collision between the substrate and enzymes. For example dry seeds exhibit very low rate of respiration. But when dry seeds are provided with water, the cells absorb water and its content increases from 6% to 90%. With the increase in water content, respiratory activity also increases till the water content reaches saturation point.
Enzymes, being functional molecules, require substrates for their further activity. If the concentration of substrates available is less than the number of enzymes present at any given time, only few enzymes are involved in enzyme reactions and the others remain idle. On the other hand, if the concentration of substrates is increased steadily, the number of enzymes reacting with substrates increases and thus the rate also increases. At a particular concentration or higher than that, the rate of activity remains constant because all the enzymes are loaded with substrates and maximum activity is brought about; hence the rate of enzymatic activity remains constant.
On the contrary, the concentration of enzymes also has a say in the overall rate of biochemical activity. In a situation, where there is abundant supply of substrates, but the concentration of enzymes is very low. The rate achieved in such a situation is minimum, though individual enzymes show
maximum activity. If the concentration of enzymes is increased, the rate of reaction also increases tremendously. If the proportions of enzymes and substrates are equally raised, the rate of reaction steadily increases till other factors act as limiting factors.
A part from the above said factors, the enzymatic activity also requires factors, like co-enzymes, co-factors, allosteric effectors, etc. for their optimal activity, particularly the availability of metallic ion sand organic co-enzymes are very important for the maximal activity of enzymes. Similarly certain regulatory factors also control the enzymatic activity without which no enzymatic activity is normal.