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Enzymes-Advanced level notes

Enzymes

ENZYMES

Enzymes can be defined as biological catalysts. A catalyst is a substance that speeds up a chemical reaction but remains unchanged at the end. Enzymes are biological catalysts because they are protein molecules made by living cells.

A typical human cell contains several thousand enzymes. They are used to catalyse a vast number of chemical reactions at temperatures suitable for living organisms, that is between approximately 5 and 40 °C. High temperatures would be needed, as well as marked changes in other conditions if the same speeds of reaction were to be achieved outside the organism. These would be lethal to a living cell.

Enzymes are vitally important because in their absence reactions in the cell would be too slow to sustain life.

in this short summaries article we will be talking much about; types of enzymes, the type of reaction they catalyse, factors that affect their catalyse reactions, enzyme inhibition, enzyme cofactors and coenzymes

The chemical (or chemicals) which an enzyme works on is called its substrate. An enzyme combines with its substrate to form a short-lived enzyme/substrate complex. This proximity of the enzyme with the substrate in the complex greatly increases the chances of a reaction occurring.

Once a reaction has occurred, the complex breaks up into products and enzymes. The enzyme remains unchanged at the end of the reaction and is free to interact again with more substrate.

substrate + enzyme ↔ enzyme/substrate complex ↔ enzyme/ product complex ↔ enzyme + products

or E+S ↔ ES ↔ EPHE ↔ P

The sum total of all the chemical reactions in cells is known as metabolism. Metabolism can be divided into two types, namely anabolism and catabolism.

These two types of activity take place in different parts of the cell. Catabolic reactions involve the breakdown of molecules and usually release energy. They often involve oxidation or hydrolysis.

Anabolic reactions involve the synthesis of molecules and usually require energy. They often involve condensation.

or anabolism is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy, known also as an endergonic process. Anabolism is the building-up aspect of metabolism,All these reactions are catalysed by enzymes. An example of an enzyme involved in anabolism is glutamine synthetase, which catalyses the synthesis of the amino acid glutamine from glutamic acid and ammonia:

NB: ATP is adenosine triphosphate, ADP is adenosine diphosphate and Pi is inorganic phosphate

What are the properties of enzymes?

Properties of enzymes

  • All are glular proteins.
  • Being proteins, they are coded for By DNA.
  • They are catalyst
  • Their presence does not alter the neture of properties of the end product(s) of the reaction.
  • They are very efficient. that is a very small amount of catalyst brings about a large change, For example, one molecule of the the enzyme catalase can catalyse the decomposition of about 600 thousand molecules per second of hydrogen peroxide to water and oxygen at body temperature.
  • They are highly specific, that is an enzyme will generally catalyse only a single reaction. Catalase, for example, will only catalyse the decomposition of hydrogen peroxide.
  • Their catalyse reactions are reversible.
  • Their activity is affected by pH , temperature, substrate concentration and enzyme concentration.
  •  Enzymes lower the activation energy of the reactions they catalyse.
  •  Enzymes possess active sites where the reaction takes place

Activation energy

Consider a mixture of petrol and oxygen maintained at room temperature. Although a reaction between the two substances is thermodynamically possible, it does not occur unless energy is applied to it, such as a simple spark. The same is true of a match.

The chemicals in the match head are capable of reacting with an overall release of energy. However, a little energy must be put in to get the reaction started (heat energy generated by friction on the matchbox).

This energy is called the activation energy.  is the minimum amount of energy that must be provided for compounds to result in a chemical reaction. Enzymes, by functioning as catalysts, serve to reduce the activation energy required for a chemical reaction to take place.

The figure below shows the catalysed and uncatalysed reaction of ethene(CH2CH2) and hydrogen.

CLASSIFICATION OF ENZYMES

TypesBiochemical Property
TransferasesThe Transferases enzymes help in the transportation of the functional group among acceptors and donor molecules.
 IsomerasesThe Isomerases enzymes catalyze the structural shifts present in a molecule, thus causing the change in the shape of the molecule.
 LyasesAdds water, carbon dioxide or ammonia across double bonds or eliminate these to create double bonds.
 LigasesThe Ligases enzymes are known to charge the catalysis of a ligation process.
 HydrolasesHydrolases are hydrolytic enzymes, which catalyze the hydrolysis reaction by adding water to cleave the bond and hydrolyze it.
OxidoreductasesThe enzyme Oxidoreductase catalyzes the oxidation reaction where the electrons tend to travel from one form of a molecule to the other.

According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze. The six kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases and isomerases.

  • Transferases

These catalyze transferring of the chemical group from one to another compound. An example is a transaminase, which transfers an amino group from one molecule to another.

  • Isomerases

They catalyze the formation of an isomer of a compound. Example: phosphoglucomutase catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate (phosphate group is transferred from one to another position in the same compound) in glycogenolysis (glycogen is converted to glucose for energy to be released quickly).

  • Lyases

These catalyze the breakage of bonds without catalysis, e.g. aldolase (an enzyme in glycolysis) catalyzes the splitting of fructose-1, 6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

  • Ligases

Ligases catalyze the association of two molecules. For example, DNA ligase catalyzes the joining of two fragments of DNA by forming a phosphodiester bond.

  • Hydrolases

They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide bonds in proteins.

  • Oxidoreductases

These catalyze oxidation and reduction reactions, e.g. pyruvate dehydrogenase, catalysing the oxidation of pyruvate to acetyl coenzyme A.

ENZYME CATALYSED REACTION(Induce-fit-hypothesis)

Enzymes are very specific and it was suggested by Fischer in 1890 that this was because enzymes have specific shapes into which substrates fit. This is also called the lock and key hypothesis

The substrate is imagined to be the key which is complementary to the enzyme the lock. Most enzymes are far larger molecules than the substrates they act on and the active site is usually only a very small portion of the enzyme, between 3 and 12 amino acids.

when the substrate and product have completely reacted, the products live the active site to the surrounding medium. The induce-fit-hypothesis introduced by Koshland in 1959 which is the modification of the lock and key hypothesis.

Working from the evidence that suggested that some enzymes and their active sites were physically rather more flexible structures than previously described, he proposed that the active site could be modified as the substrate interacts with the enzyme. The amino acids which make up the active site are moulded into a precise shape which enables the enzyme to perform its catalytic function most effectively 

FACTORS AFFECTING ENZYME ACTION

When investigating the effect of a given factor on the rate of an enzyme-controlled reaction, all other factors should be kept constant and at optimum levels wherever possible, Initial rates only should be measured, as explained above,

 Enzyme concentration

Provided that the substrate concentration is maintained at a high level, and other conditions such as pH and temperature are kept constant, the rate of reaction is proportional to the enzyme concentration. Normally reactions are catalysed by enzyme concentrations which are much lower than substrate concentrations. Thus
as the enzyme concentration is increased, so will be the rate of the enzyme reaction.

  •  Substrate concentration

For a given enzyme concentration, the rate of an enzyme reaction increases with increasing substrate concentration The theoretical maximum rate (Vmax) is never quite obtained, but there comes a point when any further increase in substrate concentration produces no significant change in reaction rate.

This is because at high substrate concentrations the active sites of the enzyme molecules at any given moment are virtually saturated with substrate. Thus any extra substrate has to wait until the enzyme/substrate complex has released the products before it may itself enter the active site of the enzyme.

  •  Temperature

If the temperature is increased above this level, then a decrease in the rate of the reaction occurs despite the increasing frequency of collisions. This is because the secondary and tertiary structures of the enzyme have been disrupted, and the enzyme is said to be denatured.

In effect, the enzyme unfolds and the precise structure of the active site is gradually lost. The bonds which are most sensitive to temperature change are hydrogen bonds and hydrophobic interactions.

Heating increases molecular motion. Thus the molecules of the substrate and enzyme move more rapidly and increase the frequency at which they collide. As a result, there is a greater probability of a reaction occurring. The temperature that promotes maximum activity is referred to as the optimum temperature.

Most mammalian enzymes have a temperature optimum of about 37-40 °C, but enzymes with higher optima exist. For example, the enzymes of bacteria living in hot springs may have an optimum temperature of 70°C or higher

If the temperature is reduced to near or below freezing point, enzymes are inactivated, not denatured. They will regain their catalytic influence when higher temperatures are restored.

  •  pH

Under conditions of constant temperature, every enzyme functions most efficiently over a particular pH range. Often this is a narrow range. The optimum pH is that at which the maximum rate of reaction occurs. When the pH is altered above or below this value, the rate of enzyme activity diminishes.

As pH decreases, acidity increases and the concentration of H+ ions increases. This increases the number of positive charges in the medium. Changes in pH alter the ionic charge of the acidic and basic groups and therefore disrupt the ionic bonding that helps to maintain the specific shape of the enzyme. Thus the pH change leads to an alteration of enzyme shape, including its active site. If extremes of pH are encountered by an enzyme, then it will be denatured.

ENZYME INHIBITION

A variety of small molecules exists which can reduce the rate of an enzyme-controlled reaction. They are called enzyme inhibitors. It is important to realise that inhibition is a normal part of the regulation of enzyme activity within cells. Many drugs and poisons also act as enzyme inhibitors, Inhibition may be competitive or noncompetitive. Non-competitive inhibition may be reversible or non-reversible.

  •  Competitive inhibition

This occurs when a compound has a structure that is sufficiently similar to that of the normal substrate to be able to fit into the active site. Normally it does not take part in a reaction but while it remains there it prevents the true substrate from entering the active site.

The genuine substrate and the inhibitor, therefore, compete for a position in the active site, and this form of inhibition is called competitive inhibition. A characteristic feature of competitive inhibition is that if the substrate concentration is increased, the rate of reaction increases,

The knowledge of competitive inhibition helps us to understand the effect of a group of antibiotics known as sulphonamides. Antibiotics destroy infectious microorganisms without damaging host tissues. Sulphonamides were the first antibiotics to be used and were developed during the 1930s. During the Second World War they were used extensively to prevent the spread of microbial infection in wounds.

  • Non-competitive reversible inhibition

This type of inhibitor has no structural similarity to the substrate and combines with the enzyme at a point other than its active site. It does not affect the ability of the substrate to bind with the enzyme, but it makes it impossible for catalysis to take place.

The rate of reaction decreases with increasing inhibitor concentration. When inhibitor saturation is reached, the rate of the reaction will be almost nil. It is a characteristic of this type of inhibition that an increase in substrate concentration does not affect the rate of reaction, unlike with competitive inhibition.

  • Non-competitive irreversible inhibition:

Some chemicals cause irreversible inhibition of enzymes. Two examples will be given. Very small concentrations of chemical reagents such as the heavy metal ions mercury (Hg+), silver (Ag+) and arsenic (As+), or certain iodine-containing compounds completely inhibit some enzymes. They combine permanently with sulphydryl (-SH) groups

These may be in the active site or elsewhere. Either way, the change in structure of the enzyme makes it ineffective as a catalyst. The change may cause the protein of the enzyme molecule to precipitate. Another example of irreversible inhibition is provided by the nerve gas DFP (diisopropylfluorophosphate) designed for use in warfare.

It combines with the amino acid serine at the active site of the enzyme acetylcholinesterase. This enzyme deactivates the neurotransmitter substance acetylcholine. Neurotransmitters are needed to continue the passage of nerve impulses from one nerve cell to another across a Synaptic gap .

When the impulse has been transmitted, acetylcholinesterase functions to deactivate acetylcholine almost immediately by breaking it down. If acetylcholinesterase is inhibited, acetylcholine accumulates and nerve impulses cannot be stopped, causing prolonged muscle contraction. Paralysis occurs and death may result since the respiratory muscles are among those affected.

Some insecticides currently in use, including those known as organophosphates (such as parathion), have a similar effect on insects, and can also cause harm to the nervous and muscular systems of humans who are overexposed to them.

ENZYME COFACTOR

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme’s efficient activity. They were discovered as substances that had to be present for enzyme activity, even though, unlike enzymes, they were stable at relatively high temperatures.

Cofactors may vary from simple inorganic ions to complex organic molecules and may either remain unchanged at the end of a reaction or be regenerated by a later process. There are three recognised types of cofactor: inorganic ions, prosthetic groups and coenzymes, which will be examined in the following sections.

 inorganic ions (enzyme activators): These are thought to mould either the enzyme or the substrate into a shape that allows an enzyme/substrate complex to be formed, hence increasing the chances of a reaction occurring between them and therefore increasing the rate of the reaction catalysed by that particular enzyme. For example, salivary amylase activity is increased in the presence of chloride ions.

Prosthetic groups (for example FAD, haem): If the cofactor is tightly bound to the enzyme on a permanent basis it is known as a prosthetic group (from the Greek prosthesis, meaning ‘addition’). Prosthetic groups are organic molecules. They assist the catalytic function of their enzymes, as in flavine adenine dinucleotide (FAD). This contains riboflavin (vitamin B2), the function of which is to accept hydrogen. FAD is concerned with cell oxidation pathways and is part of the respiratory chain in respiration.

Haem: Haem is an iron-containing prosthetic group. It has the shape of a flat ring (a ‘porphyrin ring’ as is found in chlorophyll) with an iron atom at its centre. It has a number of biologically important functions.

Electron carrier: Haem is the prosthetic group of cytochromes where it acts as an electron carrier. In accepting electrons the iron is reduced to Fe(II); in handing on electrons it is oxidised to Fe(III). In other words, it takes part in oxidation/reduction reactions by reversible changes in the valency of the iron.

Oxygen carrier: Haemoglobin and myoglobin are oxygen-carrying proteins that contain haem groups. Here the iron remains in the reduced, Fe(II) form 

Other enzymes: Haem is found in catalases and peroxidases, which catalyse the decomposition of hydrogen peroxide into water and oxygen. It is also found in a number of other enzymes.

COENZYMES

Like prosthetic groups, coenzymes are organic molecules that act as cofactors, but unlike prosthetic groups, they do not remain attached to the enzyme between reactions. All coenzymes are derived from vitamins.

NAD(Nicotinamide adenine dinucleotide) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other nicotinamide. It is derived from the vitamin nicotinic acid(niacin) and exists in both reduced and oxidised form.

ATP (adenosine triphosphate) is the energy-carrying molecule used in cells because it can release energy very quickly. Energy is released from ATP when the end phosphate is removed. Once ATP has released energy, it becomes ADP (adenosine diphosphate), which is a low energy molecule.

Enzymes-Advanced level notes

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