3.1.2 Types of Cofactors

There are three types of cofactors:

• Inorganic ions
• Organic molecules (coenzymes)
• Prosthetic group

1. Inorganic Ions

Definition: The inorganic cofactors are different metallic ions such as Fe²⁺, Mg²⁺, Cu²⁺, Zn²⁺, etc.

• These are only attached to the enzymes when substrate gets bind, i.e., they are detachable cofactors.
• Such cofactors are also called activators.

Example: Glucose + ATP Hexokinase + Mg²⁺→ Glucose-6-phosphate + ADP

2. Organic Molecules (Coenzymes)

Definition: The organic cofactors are either co-enzymes or prosthetic groups. The coenzymes are the derivatives of vitamins.

• Examples: ATP, NAD⁺, FAD⁺ are common coenzymes.
• Like inorganic cofactors, they are also attached to the enzymes when substrate gets bind, i.e., they are also detachable cofactors.

Example: Ethyl alcohol Alcohol dehydrogenase + NAD⁺→ Acetaldehyde + NADH₂

3. Prosthetic Group

Definition: A prosthetic group is a covalently bonded part of an enzyme which is permanently attached to the enzyme and does not detach after the completion of reaction.

Example: - An iron-containing porphyrin ring attached to some enzymes like cytochromes is the example of a prosthetic group.

Enzyme Activation: Holoenzyme and Apoenzyme

Key Points:

• Some enzymes also require a non-protein part (cofactor).
• The cofactor is not only responsible for the attachment of substrate to the active site but also participates in the catalytic process.
• The final shape of the active site is actually established after the attachment of the cofactor.
• An enzyme which requires a cofactor becomes active only if the cofactor is combined with it.
• Such an active enzyme is called holoenzyme.
• If the cofactor is not available, the remaining protein part of the enzyme becomes catalytically inactive and is called apoenzyme.

• The enzymes which do not require cofactor can also show active and inactive states.
• Pepsin is an example of such an enzyme.
• It is secreted by gastric glands from the stomach wall in an inactive state, the pepsinogen.
• In this state, it has an additional polypeptide fragment attached to its active site which does not allow the binding of substrate, hence it remains inactive.
• When pepsinogen is exposed in HCl (as in stomach cavity), the additional polypeptide fragment is removed.
• As a result, inactive (apoenzyme) pepsinogen is changed into its active (holoenzyme) form, the pepsin.

Intermediate Level

Enzyme Structure in Detail

Cofactors in Detail

Holoenzyme and Apoenzyme

Pepsinogen to Pepsin Conversion

Important Points

• 1. There is complete check and balance on the chemistry of the cell, which is exhibited through various enzymatic reactions going on within a cell.
• 2. The sum of all the chemical reactions going on in a cell is known as metabolism.
• 3. These reactions have to be carried out very quickly so that their products can be utilized in various life activities in the cells.
• 4. Enzymes are biological catalysts and therefore they speed up the biochemical reaction without being consumed.
• 5. The enzymes exist in the cell as colloids.
• 6. We can define enzymes as 'biological polymers that catalyse biochemical reactions.'
• 7. All the enzymes are globular proteins which are made up of one or more polypeptides.
• 8. Ribozymes are the only exception which consist of RNA and are found in ribosomes.
• - For example, peptidyl transferase is a ribozyme which forms peptide bond during protein synthesis.
• 9. The enzyme consists of a linear chain of amino acids, which form the three-dimensional structure of an enzyme.
• 10. 3.1.1 Components of an Active Site of an Enzyme:
• - Majority of enzymes are protein in nature.
• - The catalytic activity of an enzyme is located in its active site.
• - It is a specific charge bearing, three-dimensional cavity.
• - The substrate (the reactant which is to be converted into product) molecule is attached to the active site by non-covalent interactions like hydrogen bonding and hydrophobic interactions.
• - Active site consists of 3–12 amino acids which may be scattered in the polypeptide but are brought together in a particular fashion due to secondary and tertiary folding of the protein molecule.
• - e.g., the active site for aldolase consists of glycine, histidine, and alanine amino acids.
• - An active site consists of two functional regions:
• - Binding site – Some amino acids have active site which makes bonds with substrate constitute the binding site.
• - Catalytic site – The other amino acids which cause conversion of substrate into product (catalysis) constitute the catalytic site.
• - The shape of active site is designed according to the substrate therefore only a particular substrate can attach to the active site, however, sometime related substrate can also bind to the active site.
• 11. 3.1.2 Types of Cofactors:
• - There are three types of cofactors:
• - Inorganic ions
• - Organic molecules
• - Prosthetic group
• - Inorganic ions: The inorganic cofactors are different metallic ions such as Fe²⁺, Mg²⁺, Cu²⁺, Zn²⁺, etc. These are only attached to the enzymes when substrate gets bind, i.e., they are detachable cofactors. Such cofactors are also called activators.
• - Example: Glucose + ATP → (Hexokinase + Mg²⁺) → Glucose-6-phosphate + ADP
• - Organic molecules: The organic cofactors are either co-enzymes or prosthetic groups. The coenzymes are the derivatives of vitamins. For example, ATP, NAD⁺, FAD⁺ are common coenzymes. Like inorganic cofactors they are also attached to the enzymes when substrate gets bind, i.e., they are also detachable cofactors.
• - Example: Ethyl alcohol → (Alcohol dehydrogenase + NAD⁺) → Acetaldehyde + NADH₂
• - Prosthetic group: On the other hand, a prosthetic group is covalently bonded part of an enzyme which is permanently attached to enzyme and does not detach after the completion of reaction.
• - An iron-containing porphyrin ring attached to some enzymes like cytochromes is the example of prosthetic group.
• 12. Some enzymes also require a non-protein part, the cofactor which is not only responsible for the attachment of substrate to the active site but also participate in catalytic process.
• 13. The final shape of active site is actually established after the attachment of cofactor.
• 14. An enzyme which requires a cofactor becomes active only if the cofactor is combined with it. Such an active enzyme is called holoenzyme.
• 15. If the cofactor is not available the remaining protein part of enzyme becomes catalytically inactive and is called apoenzyme.
• 16. On the other hand, the enzymes which do not require cofactor can also show active and inactive states. Pepsin is an example of such enzyme.
• 17. It is secreted by gastric gland from stomach wall in an inactive state, the pepsinogen.
• 18. In this state, it has an additional polypeptide fragment attached to its active site which does not allow the binding of substrate, hence it remains inactive.
• 19. When pepsinogen is exposed in HCl (as in stomach cavity) the additional polypeptide fragment is removed and as a result inactive (apoenzyme) pepsinogen is changed into its active (holoenzyme) form, the pepsin.

Remember

• - Enzymes = biological catalysts
• - All enzymes = globular proteins (except ribozymes)
• - **Ribozymes** = RNA enzymes
• - Active site = where substrate binds
• - Active site = 3–12 amino acids
• - Binding site = holds substrate
• - Catalytic site = converts substrate to product
• - Cofactors = non-protein helpers
• - Three types of cofactors: Inorganic ions, coenzymes, prosthetic groups
• - Holoenzyme = active enzyme (apoenzyme + cofactor)
• - Apoenzyme = inactive protein part
• - Pepsinogen = inactive form of pepsin
• - Pepsin = active form

Common Mistakes

• 1. Thinking all enzymes are proteins – Most enzymes are proteins, but ribozymes are RNA enzymes.
• 2. Confusing active site and binding site – The active site has two regions: binding site and catalytic site.
• 3. Thinking the active site is a rigid structure – The active site is flexible (induced fit model).
• 4. Forgetting that active site amino acids are brought together by folding – Amino acids that are far apart in the linear sequence come together in the 3D structure.
• 5. Confusing cofactors and coenzymes – Coenzymes are a type of cofactor (organic molecules).
• 6. Thinking cofactors are always permanently attached – Inorganic ions and coenzymes are detachable; prosthetic groups are permanently attached.
• 7. Confusing holoenzyme and apoenzyme – Holoenzyme = active; Apoenzyme = inactive.
• 8. Thinking pepsinogen is active – Pepsinogen is the inactive precursor of pepsin.
• 9. Forgetting the role of HCl in pepsin activation – HCl removes the additional polypeptide fragment from pepsinogen.
• 10. Thinking all enzymes require cofactors – Some enzymes do not require cofactors (e.g., pepsin).
• 11. Confusing the types of cofactors – Inorganic ions, coenzymes, prosthetic groups.
• 12. Thinking the active site is made of the entire enzyme – The active site is only a small part of the enzyme (3–12 amino acids).

Quick Revision

• There is complete check and balance on the chemistry of cell, which is exhibited through various enzymatic reactions going on within a cell.
• The sum of all the chemical reactions going on in a cell is known as metabolism.
• These reactions have to be carried out very quickly so that their products can be utilized in various life activities in the cells.
• Enzymes are biological catalysts and therefore they speed up the biochemical reaction without being consumed.
• The enzymes exist in the cell as colloids.
• We can define enzymes as 'biological polymers that catalyse biochemical reactions.'
• All the enzymes are globular proteins which are made up of one or more polypeptides.
• Ribozymes are the only which consist of RNA and are found in ribosomes.
• For example, peptidyl transferase is a ribozyme which forms peptide bond during protein synthesis.
• The enzyme consists of linear chain of amino acids, which form the three dimensional structure of an enzyme.
• Components of an Active Site of an Enzyme:
• Majority of enzymes are protein in nature.
• The catalytic activity of an enzyme is located in its active site.
• It is a specific charge bearing, three-dimensional cavity.
• The substrate (the reactant which is to be converted into product) molecule is attached to the active site by non-covalent interactions like hydrogen bonding and hydrophobic interactions.
• Active site consists of 3–12 amino acids which may be scattered in the polypeptide but are brought together in a particular fashion due to secondary and tertiary folding of the protein molecule.
• e.g., the active site for aldolase consists of glycine, histidine, and alanine amino acids.
• An active site consists of two functional regions, i.e., binding site and catalytic site.
• Some amino acids have active site which makes bonds with substrate constitute the binding site while the other amino acids which cause conversion of substrate into product (catalysis) constitute the catalytic site.
• The shape of active site is designed according to the substrate therefore only a particular substrate can attach to the active site, however, sometime related substrate can also bind to the active site.
• Types of Cofactors:
• There are three types of cofactors: inorganic ions, organic molecules and prosthetic group.
• Inorganic ions: The inorganic cofactors are different metallic ions such as Fe²⁺, Mg²⁺, Cu²⁺, Zn²⁺ etc. These are only attached to the enzymes when substrate gets bind i.e., they are detachable cofactors. Such cofactors are also called activators.
• Organic molecules: The organic cofactors are either co-enzymes or prosthetic groups. The coenzymes are the derivatives of vitamins. For example ATP, NAD⁺, FAD⁺ are common coenzymes. Like inorganic cofactors they are also attached to the enzymes when substrate gets bind i.e., they are also detachable cofactors.
• Prosthetic group: On the other hand a prosthetic group is covalently bonded part of an enzyme which is permanently attached to enzyme and does not detach after the completion of reaction. An iron containing porphyrin ring attached to some enzymes like cytochromes is the example of prosthetic group.
• Some enzymes also require a non-protein part, the cofactor which is not only responsible for the attachment of substrate to the active site but also participate in catalytic process.
• The final shape of active site is actually established after the attachment of cofactor.
• An enzyme which requires a cofactor becomes active only if the cofactor is combined with it. Such an active enzyme is called holoenzyme.
• If the cofactor is not available the remaining protein part of enzyme becomes catalytically inactive and is called apoenzyme.
• On the other hand, the enzymes which do not require cofactor can also show active and inactive states.
• Pepsin is an example of such enzyme.
• It is secreted by gastric gland from stomach wall in an inactive state, the pepsinogen.
• In this state, it has an additional polypeptide fragment attached to its active site which does not allow the binding of substrate, hence it remains inactive.
• When pepsinogen is exposed in HCl (as in stomach cavity) the additional polypeptide fragment is removed and as a result inactive (apoenzyme) pepsinogen is changed into its active (holoenzyme) form, the pepsin.

60-Second Revision

• Enzymes = biological catalysts
• All enzymes = globular proteins (except ribozymes)
• **Ribozymes** = RNA enzymes
• Active site = where substrate binds
• Active site = 3–12 amino acids
• Binding site = holds substrate
• Catalytic site = converts substrate to product
• Cofactors = non-protein helpers
• Three types of cofactors: Inorganic ions, coenzymes, prosthetic groups
• Holoenzyme = active enzyme (apoenzyme + cofactor)
• Apoenzyme = inactive protein part
• Pepsinogen = inactive form of pepsin
• Pepsin = active form
• Warning: Not all enzymes are proteins — ribozymes are RNA. The active site has two regions: binding site and catalytic site. Cofactors are not always permanently attached — inorganic ions and coenzymes are detachable. Holoenzyme is active; apoenzyme is inactive. Pepsinogen is inactive; pepsin is active. HCl is required for pepsinogen activation.