Complete info about enzymes for beginners:

 Enzymes:

                Enzymes are globular proteins that catalyze or speed up the chemical reaction and are not changed during the reaction.

•They are biologically active.

•They tremendously increase the efficiency of a biochemical reaction.

•Enzymes are specific for each type of reaction.

•Without these enzymes, reaction would proceed at very slow speed making life impossible.

Composition of Enzyme:

                                            Enzymes are composed of hundreds of amino acids joined together and coiled upon themselves to form a globular structure.

Active site:

                   The catalytic activity is restricted the small portion of enzyme called active site. The reactant (substrate) is attached to active site consisting only few amino acids.

•Rest of bulk of amino acids (other than active site) maintain globular structure of enzyme.

Cofactor:

                Some enzymes consist only of proteins. Other have a non-protein part called cofactor. 

•Cofactor is essential for proper functioning of enzyme.

•It acts as a bridge between  substrate and  enzyme.

•It contributes directly to the chemical reactions which brings about catalysis.

•Sometimes, cofactor provides a

source of chemical energy, helping to drive reactions which would otherwise be very difficult and impossible.

•Some enzymes use metal ions

cofactor like Mg2+,Fe²+,Cu²+, Zn²+, etc.

Activator:

                 The detachable cofactor is called activator,if it is an inorganic ion.

Prosthetic Group: 

                               If the non-protein part (cofactor) is covalently bonded / tightly bonded to enzyme, it is called prosthetic group.

Co-enzyme:   

                      If the non-protein part (cofactor) is loosely bonded to enzyme it is called co-enzyme.

It is closely related to vitamins, which represent the essential raw materials from which co-enzymes are made.e.g: Riboflavin,thiamine and folic acid, etc.

Only a small quantity of vitamins, are needed because they can be used

again and again.

Apoenzyme:

                       An enzyme with no coenzyme and prosthetic group attached with it, is called apoenzyme. Adding the correct concentrated coenzyme to the apoenzyme will restore enzyme activity.

Holoenzyme: 

                        An activated enzyme with polypeptide chain and a cofactor is called called holoenzyme.

Activation energy:

                                Activation energy is the amount of energy required to start a chemical reaction.

Distribution / Location of enzymes in cells:

          Many enzymes are simply dissolved in the cytoplasm.

Other enzymes are tightly bounded to certain sub-cellular organelles. They are produced by living cells for use in or near the site of their production.

Examples:

                  1)The enzyme important in photosynthesis are found in cytoplasm.

                  2)The enzyme involved in cellular respiration are found in mitochondria.

                  3)The enzyme involved in protein synthesis are integral part of ribosomes.

Why some enzymes are present in inactive form?

Some enzymes are potentially damaging if they are manufactured in their active form.For example:Pepsin is a powerful protein digesting enzyme and is quite capable of destroying cell's integral structure and so is produced in inactive form Pepsinogen by the cell.It is converted in its active form only in the digestive tract where it is required to be active.

Characteristics/Features/Properties of Enzymes:

The important characteristics of enzymes are following:

1) Globular protein:

                                   All enzymes are globular proteins that have three dimensional structure.

2) Rate of Reaction:

                                   Enzymes increase the rate of reaction without themselves being used up. Thus enzymes can be used again and again.

3) Nature of end products:

                                           The presence of enzyme does not affect the nature and properties of end products.i.e: products will be same, in both case, if reaction is catalyzed by enzyme or not.

 

4) Acceleration of reaction:

                                               Small amount of enzyme can accelerate the chemical reaction. Reaction by enzyme is million times faster than that in which enzymes are not used.

5) Specificity of Enzyme:

                                            Enzymes are very, specific in their action.A single enzyme can catalyze only a single chemical reaction or a group of related reactions.Specificity of enzyme depends upon:

1)Number of amino acids.

2)Sequence of amino acids.

3)Shape of active site.

6) Sensitivity of Enzymes:

                                              Enzymes are sensitive to even a minor change in pH, temperature and substrate concentration. Any of these conditions, when disturbed can change the activity of enzyme.

7) Co-factor:

                      Some enzymes require co-factor for their proper functioning. Cofactor is a non-protein part that only helps enzyme to  catalyze the reaction.

8) Activation Energy:

                                     Enzymes lower the activation energy (minimum amount of energy required to start

a reaction) of the reaction.

Inhibitors:

                  These are molecules that stop the enzymatic activities.

Activators:

                   These are molecules that enhance the enzymatic activities.

Mechanism of Enzyme Action (Catalysis):

Introduction:

                       An enzyme is a three dimensional globular protein that has specific chemical composition due to its component amino acids and a specific shape.

Specificity of Enzyme:

                                       Every enzyme by virture of its specificity recognizes and reacts with special chemical substance called substrate.

Working of Enzymes: 

                                      An enzyme reacts only with specific substrate, form Enzyme - Substrate Complex (E-S complex) which is then converted into products. Enzyme is released in unchanged form and is used again and again.

          E+S🔁ES complex🔁E+P

Active Site:

                An enzyme and its substrate react with each other through a definite charge - bearing site of enzyme called active site.

Charge & Shape of active site:

                                                      The charge and shape of active site is formed by some amino acids present in the polypeptide chain of active site of enzymes. These amino acids are

brought closer and are arranged in

specific way by coiling and folding

of polypeptide chain within globular symmetry of enzyme.

Regions of active site:

                                       The active site of the enzyme is made up of two definite regions:

1)Binding Site:

•Binding Site helps the enzyme in recognition.

•Binding Site helps in proper binding of a proper substrate to produce ES- complex.

•Formation of ES-complex activates catalytic site.

2)Catalytic site:

•Catalytic site catalyzes transformation of substrates into products.

• Enzymes after catalysis detaches itself from products unchanged.

• Enzymes require aqueous medium for its activity.

Models related to enzyme action:

There are two main models according to/related to enzyme action.

1)Lock & Key model:

                                     In 1890, Emil Fischer proposed lock and key model to visulize substrate interaction. According to this model, as one specific key can open  only a specific lock, in the same way a specific enzyme can transform only one substrate into product.

Explanation:

                     According to Lock and key model, active site is a rigid structure. There is no modification or flexibility in the active site before, during or after the

enzyme action and only used as template.According to modern researches, this model is not applicable to all reactions.

2)Induced fit Model:

On the basis of new evidences, in 1959,Daniel Koshland proposed modified form of  lock and key model. This is known as induced fit model.According to this model,when a substrate combines with enzyme ,it induces changes in enzyme structure.The change in structure enables the enzyme to perform catalytic activity more effectively.

Presence of Enzymes in cell: 

•Most enzymes do not float in a kind of cytoplasmic "Soup".

•Enzymes are attached to membrane systems inside the cell in specific and orderly arrangement e.g. mitochondria and chloroplast.

Metabolic Pathway:

                                   In some cases, enzymes act in a series of chemical reactions in a particular order to complete a metabolic pathway such as respiration or photosynthesis.

Formation of Metabolic pathway:

• First of all, 1st enzyme converts substrate into products.

•Products of 1st enzyme act as substrate of other (2nd) enzymes.

• This process continues until final product is obtained.

• This is called metabolic pathway of enzyme activity.

Factors affecting rate of enzyme action:

The functional specificity of every enzyme is the consequence of its specific chemistry and configuration.Any factor that can alter alter the chemistry and shape of enzyme can affect its rate of catalysis.Some important factors that affect rate of enzyme action are listed below:

•Enzyme concentration 

•Substrate concentration 

•Temperature 

•pH value 

1)Enzyme concentration:

                                             The rate of reaction depends directly on amount of enzyme present at a specific time at unlimited substrate concentration.If the amount of enzyme is increased by two folds,the reaction is doubled.

Justification:

                       By increasing the enzyme molecules an increase in number of active site takes place. More active sites will convert substrate molecules into products, in the given period of time. After a certain limiting concentration,

the rate of reaction will no longer depend upon this increase.

2)Substrate Concentration:

                                               At low substrate concentration, the reaction rate is directly proportional to the substrate available. If the enzyme concentration is kept constant and the amount of substrate is increased, a point is reached, when further increase in substrate does not increase the rate of reaction anymore.

Justification:

In thiscase, at high substrate level, all the active sites of enzyme are occupied and further increase in the substrate does not increase the reaction rate.

3)Temperature:

                        The rate of enzyme controlled reaction may  increase with increase in temperature but upto certain limit. All enzymes can work at their maximum rate at a specific temperature called as optimum temperature. For enzymes of human body,37°C is optimum temperature.

Justification:

                       Heat provides activation energy and so chemical reactions are accelerated at high temperatures.

Heat also supplies kinetic energy to the reacting molecules,causing them to move rapidly. So, reactants move more quickly and the chances of their collision with eachother are increased.

Effect of extreme temperature:

                                                    Increase in temperature beyond a certain limit, increases vibrations of atoms which make up enzyme molecule. If the vibrations become too violent, globular structure essential for enzyme activity is lost, and enzyme is denatured.

3)pH value:

Every enzyme functions effectively

over a narrow range of pH known as optimum pH.

Justification:

A slight change in pH can change ionization of amino acids at the active site. Moreover,it may effect the ionization of the substrate.Under these changed conditions, enzyme activity is either retarted or blocked completely.

Effect of extreme pH:

                                    Extreme changes in pH, cause the bonds in the enzymes to break, resulting in the denaturation of enzymes.

Optimum pH for some common enzymes:

ENZYMES                       OPTIMUM pH

Pepsin                                       2.00

Sucrase                                     4.50

Enterokinase                            5.50

Salivary Amylase                     6.80

Catalase                                    7.60

Chymotrypsin                           7.00-8.00

Pancreatic Lipase                    9.00 

Arginase                                    9.70        

Inhibitor:

An inhibitor is a chemical substance

which can react (in place of substrate) with the enzyme but is not transferred into products and so block the active site temporarily or

permanently.

Examples:

• Poisons like cyanide 

• Antibiotics

• Antimetabolites

• Some drugs.       

Types of inhibitors:

                                   Inhibitors can be divided into two types:              

1) Irreversible Inhibitors:

                                           Irreversible inhibitors check the reaction rate by occuping the active sites or

destroying globular structure. They occupy the active sites by forming covalent bonds or they may physically block the active sites.

2) Reversible inhibitors:

                                          Reversible inhibitors form weak linkages with the enzymes. Their effect can be neutralized completely or partly by an increase in concentration of the substrate. It does not allow irreversible inhibitors to combine. They are further divided into:

1)Competitive inhibitors: (playing role of cheater)                        

Due to structural similarity with the substrate, competitive inhibitors may be selected by the binding sites, but are not able to activate the catalytic site. So, products are not formed.

2)Non-Competitive inhibitors:

                                   

Non-Competitive inhibitors form enzyme inhibitor complex at a point other than the active site. They change the structure of enzyme in such a way that if even genuine substrate binds the active site, catalysis fails to take place. In short, non-competitive inhibitor is a hacker of catalytic site.