CLASSIFICATION OF ENZYMES

1. Oxidoreductases : Act on many chemical groupings to add or remove hydrogen atoms. e.g. Lactate dehydrogenase

2. Transferases Transfer functional groups between donor and acceptor molecules. Kinases are specialized transferases that regulate metabolism by transferring phosphate from ATP to other molecules. e.g. Aminotransferase.

3. Hydrolases Add water across a bond, hydrolyzing it. E.g. Acetyl choline esterase

4. Lyases Add water, ammonia or carbon dioxide across double bonds, or remove these elements to produce double bonds. e.g. Aldolase.

5. Isomerases Carry out many kinds of isomerization: L to D isomerizations, mutase reactions (shifts of chemical groups) and others. e.g. Triose phosphate isomerase

6. Ligases Catalyze reactions in which two chemical groups are joined (or ligated) with the use of energy from ATP. e.g. Acetyl CoA carboxylase

Weak Acids and pKa

• The strength of an acid can be determined by its dissociation constant, Ka.

• Acids that do not dissociate significantly in water are weak acids.

• The dissociation of an acid is expressed by the following reaction: HA = H⁺ + A^- and the dissociation constant Ka = [H⁺ ][A^- ] / [HA]  

• When Ka < 1, [HA] > [H⁺ ][A^- ] and HA is not significantly dissociated. Thus, HA is a weak acid when ka < 1.

• The lesser the value of Ka, the weaker the acid.

• Similar to pH, the value of Ka can also be represented as pKa.

• pKa = -log Ka.

• The larger the pKa, the weaker the acid.

• pKa is a constant for each conjugate acid and its conjugate base pair.

• Most biological compounds are weak acids or weak bases.

Essential vs. Nonessential Amino Acids

*The amino acids arginine, methionine and phenylalanine are considered essential for reasons not directly related to lack of synthesis. Arginine is synthesized by mammalian cells but at a rate that is insufficient to meet the growth needs of the body and the majority that is synthesized is cleaved to form urea. Methionine is required in large amounts to produce cysteine if the latter amino acid is not adequately supplied in the diet. Similarly, phenyalanine is needed in large amounts to form tyrosine if the latter is not adequately supplied in the diet.

ISO-ENZYMES

Iso-enzymes are physically distinct forms of the same enzyme activity. Higher organisms have several physically distinct versions of a given enzyme, each of which catalyzes the same reaction. Isozymes arise through gene duplication and exhibit differences in properties such as sensitivity to particular regulatory factors or substrate affinity that adapts them to specific tissues or circumstances.

Isoforms of Lactate dehydrogenase is useful in diagnosis of myocardial infarction. While study of alkaline phosphatase isoforms are helpful in diagnosis of various bone disorder and obstructive liver diseases.

Function of Calcium

The major functions of calcium are

(a) Excitation and contraction of muscle fibres needs calcium. The active transport system utilizing calcium binding protein is called Calsequestrin. Calcium decreases neuromuscular irritability.
(b) Calcium is necessary for transmission of nerve impulse from presynaptic to postsynaptic region.
(c) Calcium is used as second messenger in system involving protein and inositol triphosphate.
(d) Secretion of insulin, parathyroid hormone, calcium etc, from the cells requires calcium.
(e) Calcium decrease the passage of serum through capillaries thus, calcium is clinically used  to reduce allergic exudates.
(f) Calcium is also required for coagulation factors such as prothrombin.
(g) Calcium prolongs systole.
(h) Bone and teeth contains bulk quantity of calcium.

Proteins are complex macromolecules composed of amino acids that perform diverse biological functions. Understanding their structure-function relationships is crucial for medical applications and biochemistry.

Levels of Protein Structure

Primary Structure

• Linear sequence of amino acids connected by peptide bonds
• Determines all higher levels of organization
• Coded by DNA sequence

Secondary Structure

• Local folding patterns stabilized by hydrogen bonds
• Alpha helix: Right-handed spiral structure
• Beta sheet: Extended polypeptide chains arranged side by side
• Beta turn: Connects different secondary structural elements

Tertiary Structure

• Three-dimensional folding of entire polypeptide chain
• Stabilized by:
  • Hydrogen bonds
  • Disulfide bridges
  • Van der Waals forces
  • Electrostatic interactions
  • Hydrophobic interactions

Quaternary Structure

• Assembly of multiple polypeptide subunits
• Present only in proteins with more than one polypeptide chain
• Examples: Hemoglobin (4 subunits), antibodies

Protein Classification

Based on Structure

1. Fibrous Proteins

   • Elongated, insoluble
   • Structural functions
   • Examples: Collagen, keratin, elastin

2. Globular Proteins

   • Compact, soluble
   • Functional proteins
   • Examples: Enzymes, antibodies, hormones

Based on Composition

1. Simple Proteins

   • Composed only of amino acids
   • Examples: Albumin, globulins

2. Conjugated Proteins

   • Contain non-protein prosthetic groups
   • Glycoproteins: Contain carbohydrates
   • Lipoproteins: Contain lipids
   • Nucleoproteins: Contain nucleic acids
   • Phosphoproteins: Contain phosphate groups
   • Metalloproteins: Contain metal ions