Term Paper on Enzymes | Proteins | Cell | Biology

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Term Paper on Enzymes

Term Paper Contents:

1. Term Paper on the Introduction to Enzymes
2. Term Paper on the Structure of Enzymes
3. Term Paper on the Cofactors in Enzyme Action
4. Term Paper on the Effects of Temperature and pH on Enzymes
5. Term Paper on the Enzymatic Pathways
6. Term Paper on the Enzyme Deficiencies  
7. Term Paper on the Regulation of Enzyme Activity

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Term Paper # 1. Introduction to Enzymes:

Enzymes are the catalysts of biological reactions. They differ from the catalysts, that they are very selective in their action. A particular enzyme can generally catalyze reactions only between a very specific group of reactants, known as its substrate.

Otherwise, enzymes resemble the catalysts, that they are not used up in the course of the reaction and so can be used over and over again. Enzymes also, as we shall see, appear to act in part by increasing the local concentrations of the reactants or substrate.

Enzymes enormously accelerate the rate at which reactions take place. For instance, the combination of carbon dioxide with water, can take place spontaneously, as it does in the oceans.

In the human body, however, this reaction is catalyzed by an enzyme, carbonic anhydrase, which is one of the fastest enzymes known, each enzyme molecule producing 10⁵ (100,000) molecules of carbonic acid per second. The catalyzed reaction is 10⁷ times faster than the un-catalyzed one.

In animals, this reaction is essential in the transfer of carbon dioxide from the cells, where it is produced, to the bloodstream, which transports it to the lungs.

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Term Paper # 2. Structure of Enzymes:

Enzymes are large to very large, complex globular proteins consisting of one or more polypeptide chains. They are folded so as to form a groove or pocket into which the reacting molecule or molecules-the substrate-fit and where the reactions take place. This portion of the enzyme is known as the active site. The relationship between the active site and the substrate is very precise.

Emil Fischer, who postulated the existence of active sites in 1894, compared the relationship to that of a lock and a key. The active site, we know now, is a result of the very exact folding of the polypeptide chain.

The active site not only has the right three-dimensional shape, but also it has exactly the right array of charged or uncharged, hydrophilic or hydrophobic areas on the binding surface. If a particular portion of the substrate has a negative charge, the corresponding feature on the active site has a positive charge, and so on. Thus the active site not only confines the substrate molecule but also orients it in the right direction.

The amino acids involved in the active site need not be adjacent to one another on the polypeptide chains. In fact, in an enzyme with quaternary structure, they may even be on different polypeptide chains, as-shown in Figure 4.6. They are brought together at the active site by the precise folding of the molecule.

The Induced-Fit Hypothesis:

Within the last several years, studies of enzyme structure have suggested that the binding between enzyme and substrate alters the conformation of the enzyme, thus inducing the close fit between the active site and the reactants. It is believed that this induced fit may put some strain on the reacting molecules and so further facilitate the reaction.

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Term Paper # 3. Cofactors in Enzyme Action:

The catalytic activity of some enzymes appears to depend only upon the physical and chemical interactions between the amino acids of the active site and the substrate. Many enzymes, however, require additional non-protein low-molecular-weight substances in order to function. Such non-proteins that are essential for enzyme function are known as cofactors.

Ions as Cofactors:

Certain ions are cofactors for particular enzymes. For example, the magnesium ion (Mg²⁺) is required in all enzymatic reactions involving the transfer of a phosphate group from one molecule to another. Its two positive charges hold the negatively charged phosphate group in position. K⁺, Ca²⁺, and other ions play similar roles in other reactions. In some cases, ions serve to hold the protein together.

Coenzymes and Vitamins:

Non-protein organic molecules may also play a crucial role in enzyme-catalyzed reactions. Such molecules are called coenzymes. For example, in some oxidation reduction reactions, electrons-often traveling as a hydrogen ion with a pair of electrons-are passed to a molecule that serves as an electron acceptor.

There are several different electron acceptors in any given cell, each tailor-made to hold the electron at a slightly different energy level. As an example, let us look at just one, nicotinamide adenine dinucleotide (NAD⁺). At first glance, NAD⁺ looks complex and unfamiliar, but if you look at it more closely, you will find that you recognise most of its component parts.

The two units labeled ribose are five-carbon sugars. They are linked by two phosphate groups. One of the sugars is attached to the nitrogenous base adenine. The other is attached to another nitrogenous base, nicotinamide. (A nitrogenous base plus a sugar plus a phosphate is called a nucleotide, and a molecule that contains two of them is called a dinucleotide.)

The nicotinamide ring is the business end of NAD⁺, the part that accepts the electrons. Nicotinamide is a vitamin, niacin. Vitamins are compounds required in small quantities that humans and other animals cannot synthesize themselves and so must obtain in their diets.

Thus we must eat foods containing niacin (which includes both nicotinamide and nicotinic acid but should not be confused with nicotine, found in tobacco). When nicotinamide is present, our cells can use it to make NAD⁺. Many vitamins are coenzymes or parts of coenzymes.

Nicotinamide adenine dinucleotide, like other coenzymes, is recycled. That is, NAD⁺ is regenerated when NADH passes its electrons on to another electron acceptor. Thus, although this coenzyme is involved in many cellular reactions, the actual number of NAD⁺ molecules required is relatively small.

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Term Paper # 4. Effects of Temperature and pH on Enzymes:

An increase in temperature increases the rate of uncatalyzed chemical reactions. This temperature effect also holds true for enzyme-catalyze (reactions-but only up to a point. As you can see in Figure 4.8, the rate of moss enzymatic reactions approximately doubles for each 10°C rise in temperature and then drops off very quickly at about 40°C.

The increase in reaction rate occurs! Because of the increased energy of the reactants; the decrease in the reaction rat (occurs as the enzyme molecule itself begins to move and vibrate, disrupting the hydrogen bonds and other relatively fragile forces that hold it together. A molecule that has lost its characteristic three-dimensional structure in this way is said to be denatured.

Some denatured enzymes regain their activity on being cooled, indicating that their polypeptide chains have regained their necessary shape. Others, however, are permanently tangled and inactivated. The pH of the surrounding solution also affects enzyme activity. The conformation of an enzyme depends, among other factors, on attractions and repulsions between negatively charged (acidic) and positively charged (basic) amino acids.

As the pH changes, these charges change, and so the shape of the enzyme changes until it is so drastically altered that it is no longer functional. More important, probably, the charges of the active site and substrate are changed so that the binding capacity is affected.

The optimum pH of one enzyme is not the same as that of another. The digestive enzyme pepsin, for example, works at the very low (highly acidic) pH of the stomach, in an environment where most other proteins would be permanently denatured.

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Term Paper # 5. Enzymatic Pathways:

Enzymes work in series-the pathways.

As a consequence, compared to chemists in a laboratory, a living organism carries out its chemical activities with remarkable efficiency. First, there is little accumulation of waste products, since each tends to be used up in the next reaction along the pathway.

A second advantage of such sequential reactions can be understood readily if you remember the principle of reversible reactions. If product 2, for example, is used up (by being converted into product 3) almost as rapidly as it is formed, the reaction product 1 → product 2 can never reach equilibrium. If the eventual end product is also used up rapidly, the whole series of reactions will move toward completion.

A third advantage is that the groups of enzymes making up a common pathway can be segregated within the cell. Some are found in small vesicles, membrane surrounded sacs in the cytoplasm. Others are embedded in the membranes of specialised organelles.

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Term Paper # 6. Enzyme Deficiencies:

As with the hemoglobin molecule; slight variations in the amino acid sequence of an enzyme can have drastic effects on the function of the enzyme. A “mistake” involving any of the amino acids directly involved in the active site renders the enzyme less efficient or even completely inactive.

Changes in the rest of the molecule can be more or less important, depending on the extent to which they affect the tertiary or quaternary structure. For instance, one of the ways in which Siamese cats differ from their more common counterparts is that a particular enzyme, involved in controlling the synthesis of dark pigment for the coat, is especially sensitive to temperature.

It functions adequately in the cooler, peripheral areas of the body, such as the ears, nose, paws, and tip of the tail, but it becomes inactive in the warmer areas of the body. Cat fanciers who want their Siamese to be perfect specimens do not let them out in the winter because exposure to cold can make the entire coat turn darker.

Enzymes and Human Diseases:

Enzyme deficiencies are the cause of many human diseases.

One such was described in 1649:

The patient was a boy who passed black urine and who, at the age of fourteen years, was submitted to a drastic course of treatment which had for its aim the subduing of the fiery heat of his viscera, which was supposed to bring about the condition in question by charring and blackening his bile.

Among the measures prescribed were bleedings, purgation, baths, a cold and watery diet and drugs galore. None of these had any obvious effect, and eventually the patient, who tired of the futile and superfluous therapy, resolved to let things take their natural course.

None of the predicted evils ensued when he married, begat a large family, and lived a long and healthy life, always passing urine black as ink. In 1902 the cause of this disease was identified by the physician Archibald Garrod. Alcaptonuria, as it came to be called, results from deficiencies in an enzyme that opens the ring structure (a benzene ring) at step 4 in the pathway of the breakdown of phenylalanine. As a consequence, the ring-containing compound homogentisate accumulates in the urine and, on exposure to air, oxidises, polymerizes, and turns black.

Unfortunately, not all enzyme deficiencies are so benign. Loss of function of another enzyme in this same pathway, the one that converts phenylalanine to tyrosine, produces phenylketonuria, which, if untreated, produces severe mental retardation and, in half of the cases, death by age 20.

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Term Paper # 7. Regulation of Enzyme Activity:

Another remarkable feature of the metabolic activity of cells is the extent to which each cell regulates the synthesis of the products necessary to its well-being in the amounts and at the rates required, while avoiding overproduction, which would waste both energy and raw materials.

Temperature, affects enzymatic reactions, as does pH; some enzymes are usually found at a pH that is not their optimum, suggesting that this discrepancy may not be an evolutionary oversight but a way of damping enzyme activity. The availability of reactant molecules or of cofactors is a principal factor in limiting enzyme action, and most enzymes probably work at a rate well below their maximum for this reason.

Living systems also have more precise ways -of turning enzyme activity on and off. Some enzymes are produced only in an inactive form and, just when they are needed, are activated, usually by another-enzyme.

Pepsin, a digestive enzymes is controlled in this way-JA is synthesized by cells in the lining of the stomach in the form of pepsinogen, which contains 42 additional amino acids on the amino end of the molecule and is inactive. After pepsinogen is released into the stomach, a particular enzyme snips off these last 42 amino acids, converting pepsinogen to pepsin, the active form.

In this way, pepsin (and other digestive enzymes) are prevented from digesting the proteins in the cells in which they are synthesized. Once activated, these enzymes cannot again be deactivated, however.

Allosteric Interactions:

An ingenious mechanism by which an enzyme may be temporarily activated or inactivated is known as allosteric interaction. Allosteric interactions occur among enzymes that have two binding sites, one the active site and another, into which a second molecule, known as an allosteric effector, fits. The binding of the effector changes the shape of the enzyme molecule and either activates or inactivates it.

Feedback Inhibition:

Allosteric interactions are often involved in feedback inhibition, which is a common means of biological control. A familiar non-biological example of feedback inhibition is a thermostat that turns off the furnace when the room temperature reaches a desired level. In feedback inhibition of enzymatic reactions, one of the products, usually the last in the series, acts as an effector, inhibiting the function of one of the enzymes, often the first in the series. Or, in a reaction that may take one of two directions, the effector may act to shunt the reactions along another pathway.

Competitive Inhibition:

Some compounds inhibit enzyme activity by temporarily occupying the active site of the enzyme; regulation in this way is known as competitive inhibition, because the regulatory compound and the substrate compete for the active site. The result of the competition depends on how many of each kind of molecule are present.

For example, in the reaction series:

The final product F might be rather similar in structure to product D. It could occupy the active site of enzyme E₄, preventing D, the normal substrate, from binding to the enzyme. As F was used up by the cell, the active site of enzyme E₄ would once more become available to D.

Competitive inhibition probably does not play a large role in the normal life of a cell, but it is an important mechanism in the action of some drugs. For instance, bacteria can make the vitamin folic acid, which animal cells do not make (animals obtain folic acid from their food). One of the compounds in the metabolic pathway leading to folic acid is para-aminobenzoic acid.

Sulfanilamide, has a structure very similar to PABA, so similar, in fact, that the enzyme involved in converting PABA to folic acid combines with the drug rather than with the PABA. Without folic acid, the bacterial cell dies, leaving the animal cell, which lacks this enzyme, unharmed.

Noncompetitive Inhibition:

In noncompetitive inhibition, the inhibitory chemical, which need not resemble the substrate, binds with the enzyme either at the active site or elsewhere in the molecule and prevents its functioning. Lead, for instance, forms covalent bonds with sulfhydryl (SH) groups. Many enzymes contain cysteine, which has a sulfhydryl group. The binding of lead to such enzymes permanently deactivates them, producing the symptoms associated with lead poisoning.

The most potent poisons known, including arsenic, the cyanides, mercury, and the nerve gases, all combine with and prevent the functioning of enzymes necessary for survival, as do many useful drugs.

Regulation at the Source:

Many enzymes are broken down rapidly, characteristically by other enzymes. For such enzymes, a highly efficient means of enzyme regulation is to produce these large protein molecules only when they are needed.