Enzymes

• Enzymes are globular proteins that serve as biological catalysts.
• They speed up or slow down metabolic reaction, but remain unchanged

 

Active sites

• Active site is the area in enzyme’s molecule where the substrate binds to enzyme to form enzyme-substrate complex
• The R groups of amino acids at the active site form temporary bonds with the substrate molecule

 

Activation energy

• Activation energy is the energy the substrates need for changing themselves into products.
• Enzymes reduce activation energy needed

 

Enzyme specificity

 

Lock and Key hypothesis

• The shape of the active site of the enzyme and the substrate molecules are complementary.
• They possess specific 3-D shapes that fit exactly into one another.
• Like a key into a lock, only the correct size and shape of the substrate (the key) would fit into the active site of the enzyme (the lock).
• This shows the high specificity of enzymes, however it is too rigid

 

Induced fit hypothesis

• The shape of the active site of the enzyme and the substrate molecules are NOT complementary.
• In the presence of the substrate, the active site continually reshapes by its interactions with the substrate, until the substrate is completely fit into it.
• The enzyme is flexible and molds to fit the substrate molecule like gloves fitting one‘s hand or clothing on a person.
• This hypothesis is more acceptable

 

Properties of enzymes

• Enzymes possess the following properties
• They are all globular proteins
• Being proteins, they are coded for by the DNA
• They are catalyst
• They are very efficient; they have a high turnover rate.
• They are highly specific; an enzyme will only catalyze one reaction.
• Their catalyzed reaction is reversible
• They are affected by pH, temperature, substrate concentration & enzyme concentration.
• Enzyme lower Activation energy
• Enzymes possess Active sites where the reaction take place

 

Factors affecting the rate of enzyme-catalyzed reactions

• Temperature
• pH
• Enzyme concentration
• Substrate concentration
• Inhibitor concentration

 

Temperature

• As to increases, kinetic energy of reacting molecules also increases
• this increases successful collision increasing rate of reaction.
• At optimal to enzyme’s activity is maximum ie rate is maximum.
• Above this temperature, Hydrogen bonds holding enzyme molecule in shape begin to break
• this change tertiary structure of the enzyme (denaturation)
• active site is deformed, these decreases binding of substrate with enzyme hence decreases rate of reaction.

 

pH

• Enzymes are very sensitive to a slight change in pH changes & as such operate in very narrow pH ranges.
• The optimum pH is that at which the maximum rate of reaction occurs.
• When the pH is altered, above or below, the rate of enzyme activity diminishes significantly.
• Pepsin has an optimum pH of 2
• Changes in pH alter the ionic charge of acidic & basic group & therefore disrupt the ionic bonds that maintain the specific 3-D shape of the enzyme.
• Extreme pH denatures the enzyme. The peptide bond can be hydrolyzed.

Enzyme concentration

• When there are more substrate than enzyme:
• increasing concentration of enzyme also increases collisions between enzyme and substrate tus the rate of the reaction
• Increasing the enzyme concentration beyond a certain point does not change the rate of reaction because the limiting factor is Substrate concentration
• increasing concentration of enzyme does not increase the rate of reaction.

Substrate concentration

• When there is more enzyme than substrate:
• increasing concentration of substrate also increases collisions between enzyme and substrate thus the rate of the reaction
• Increasing the substrate concentration beyond a certain point does not change the rate of reaction because the limiting factor is enzyme concentration
• increasing concentration of substrate does not increase the rate of reaction.

 

The effect of competitive and non-competitive

Competitive inhibitors

• Have similar shape to the enzyme’s normal substrate.
• Can fit into the enzyme’s active site, preventing the substrate from binding.
• The greater the proportion inhibitor: substrate, the more inhibitor molecules (not substrate molecules) will bump into an active site.
• Relative concentrations of the inhibitor and the substrate will affect the degree to which a competitive inhibitor slows down a reaction.

 

Non-competitive inhibitor-reversible

• inhibitor has no structural similarity to the substrate & combines with the enzyme at a point other than the active site.
• It does not affect the ability of the substrate to bind with the enzyme but makes it impossible for catalysis for catalysis to occur.
• The rate of reaction decreases with inhibitor concentration to almost nil, when inhibitor saturation is reached.
• However, increasing substrate concentration does not increase the rate of reaction.
• When the inhibitor is removed, the enzyme regains its catalytic activity hence reversible

 

Non-competitive inhibitor/irreversible

• Some chemicals can cause irreversible inhibition of enzymes.
• Some concentration of chemicals reagents e.g. heave metals or certain iodine containing compounds, complete inhibit enzymes.
• They may be in active site or elsewhere.
• Once such reactions have occurred the enzyme loses its catalytic activity effectually
• The change may cause the enzyme protein to precipitate.

 

Allosteric enzymes

• These are enzymes which can change their shape.
• They are regulated by compound bind to the enzyme at specific site well away from the active site.
• While there, they cause the active site to change, there by affecting the ability of the substrate to bind the enzyme.
• Compounds of this nature are called allosteric inhibitor

 

Enzyme Co-factors

• Enzymes require non proteins components called co- factors for their effective activity.
• Co- factors vary from simple inorganic ions to complex organs molecules & may either remain unchanged at the end of a reaction or be generated by a later process.
• There are 3 types of co-factors & these are inorganic ions prosthetic group & coenzymes.

 

Types of cofactors

• inorganic ions
• prosthetic groups
• Coenzymes

Prosthetic group

Examples

• • Haem
  • FAD
  • hydrogen carrier molecules
• There are organic molecules that are tightly bound on a permanent basis to the enzyme.
• They assist in catalytic activity of the enzyme e.g. (FAD) which contains fluorine.
• Its function is to accept hydrogen. Haem is found in the catalase & peroxides which catalyzes the breakdown of hydrogen peroxide into water & oxygen.

Haem

Haem is an iron-containing prosthetic group. It has the shape of a flat porphyrin ring 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). It takes part in oxidation/reduction reactions by reversible changes in the valency of the iron.

 

Oxygen carrier.

Haemoglobin and myo-globin 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.

 

Inorganic ions (enzyme activators)

• These are thought to mold either the enzyme or substrate in a shape that easily allows an enzyme / substrate complex to be formed.
• Hence, they greatly increase the chance of the reaction occurring, salivary amylase is activated by chloride ions.

 

Coenzymes

Examples

• • NAD
  • NADP
  • Coenzyme A
  • ATP)
• Like prosthetic group, coenzymes are organic molecules which act as co- factors, but they do not remain attached to the enzyme between reactions.
• Coenzymes are derived from victims. NAD is derived from vitamins nicotinic & can exist in both reduced & oxidized form.
• It functions as a hydrogen acceptor.

 

NAD (nicotinamide adenine dinucleotide)

Its derived from the vitamin nicotinic acid (niacin) and can exist in both a reduced and an oxidised· form. In the oxidized scare it functions as a hydrogen acceptor.

 

---

 
Practice Questions 

Describe the secondary and tertiary structure of an enzymatic protein, such as lysozyme

• secondary
  • regular order/pattern, based on H-bonds ;
  • between CO– group of one amino acid and NH– group of another ;
  • alpha-helix and β-pleated sheet ;
• tertiary
  • folding coiling ;
  • interactions between, R groups side chains ;
  • two correctly named bonds ; e.g. hydrogen bonds, disulfide, bonds/bridges, ionic bonds, hydrophobic interactions
  • further description of bonds ; e.g.
    disulfide between cysteine (S–H) groups
    hydrogen between polar groups (NH– and CO–)
    ionic between ionised amine and carboxylic acid groups
    hydrophobic interactions between non-polar side chains
  • ref. active site, specific/precise, shape ;
  • ref. globular/AW, shape ; A spherical/ball
  • ref. amino acids with, hydrophilic/polar, R groups facing to outside ;

• With reference to molecular structure, explain the specificity of enzymes.
• With reference to a named example, describe one model of enzyme action
• Describe how you would measure the rate of a reaction catalyzed by the enzyme catalase.

 

Describe how competitive and non-competitive inhibitors affect enzyme activity.

• Competitive inhibitor
  • Competes with substrate for the site.
  • Inhibitor and substrate have similar structure/ shape
  • Enzyme-complex usually has no end product.
  • Substrate cannot occupy enzymes active site i.e reaction rate decreases with increase in inhibitor concentration
  • Increase in the substrate concentration affect the rate of reaction
• Non-competitive inhibitor
  • They have no structural similarity with substrate.
  • Non- competitive inhibitors bind to other parts of enzyme
  • Inhibitor binding on the enzyme distorts enzyme structure
  • Substrate-enzyme complex is not formed
  • The reaction rate decreases with increase in inhibitor concentration
  • Increase in the substrate concentration does not affect the rate of reaction