Protein Structure, Enzymes, and Vitamins: Comprehensive Insights

Posted on Dec 14, 2024 in Biology

Protein Structure: Levels and Significance

Protein structure refers to the multi-level spatial arrangement of proteins. There are four levels:

Primary Structure

The primary structure is the specific order in which amino acids (aa) are arranged in a polypeptide chain. Each of the 20 amino acids can join without restriction. Polarity varies among amino acid residues, and the chain has terminal carboxyl (COOH) and amino (NH2) groups. Some residues are polar and oriented outward, while others are nonpolar and oriented inward.

Secondary Structure

The secondary structure involves the initial folding of the polypeptide chain. Two common types are:

  • Alpha-helix: A right-handed helix formed by a specific amino acid sequence, with residues pointing outward. It is stabilized by hydrogen bonds between the amino group of one peptide bond and the carbonyl group of the peptide bond four amino acids away. This structure is frequently found in fibrous proteins.
  • Beta-sheet: Formed by two or more peptide chains linked by hydrogen bonds. Parallel chains are aligned, and hydrogen bonds are established between the amino and carboxyl groups of different chains. The folding points are carbon atoms, the sheets are peptide bonds, and the side chains (R groups) extend outward.

Tertiary Structure

The tertiary structure is the final spatial arrangement of all atoms in the polypeptide chain. Interactions leading to this structure include:

  • Ionic bonds between charged amino acid side chains
  • Disulfide bridges between cysteine residues
  • Hydrogen bonds between polar functional groups
  • Hydrophobic interactions and Van der Waals forces between nonpolar side chains

Tertiary structures can be classified as:

  • Globular: These proteins have high biological activity, with nonpolar R groups oriented inward and polar R groups on the surface, making them mostly water-soluble.
  • Fibrous: These proteins are elongated and insoluble in water, playing a fundamental structural role.

Quaternary Structure

The quaternary structure occurs when a protein requires the association of multiple polypeptide chains to be functional. An example is hemoglobin, which involves thousands of bonds, including covalent bonds, hydrogen bonds, Van der Waals forces, and ionic bonds.

Essential Amino Acids: These cannot be synthesized by the body and must be obtained from the diet.

Protein Properties

  • Specificity: Each protein has a unique function.
  • Solubility: Ability to dissolve in a solvent, often related to shape.
  • Acid-base behavior: Proteins can act as acids or bases.
  • Isoelectric point: The pH at which a protein has no net charge.
  • Proteins perform their functions within a narrow range of conditions.

Protein Classification

  • Hemeproteins: Contain a heme group.
  • Fibrous: Insoluble, thread-like, structural proteins (e.g., actin, myosin, collagen, elastin, keratin).
  • Globular: Involved in storage and transport.
  • Heteroproteins: Composed of a non-protein (prosthetic) group and a protein group.
  • Glycoproteins: Contain carbohydrates (e.g., antibodies, gangliosides, mucoproteins).
  • Lipoproteins: Contain lipids (e.g., chylomicrons, HDL, LDL, cell membrane components).
  • Chromoproteins: Colored substances, including porphyrins and non-porphyrins.
  • Nucleoproteins: Nucleic acids combined with histones.

Biocatalysts: Enzymes and Their Functions

Biocatalysts are organic molecules that regulate biological reactions. Enzymes constitute 99% of biocatalysts and are globular, water-soluble proteins synthesized in ribosomes. They are highly efficient, achieving nearly 100% yield without unwanted byproducts. Enzymes are advantageous because they are needed in small quantities and can facilitate numerous reactions.

Enzyme Characteristics

  • High molecular weight
  • Highly active
  • Operate at physiological temperatures
  • Highly specific

Enzyme Structure

Enzymes have a specific amino acid sequence and are grouped based on function:

  1. Catalytic groups: Part of the active site where the substrate binds.
  2. Binding sites: Regions for coenzymes and cofactors that do not bind to the active site.
  3. Structural groups: Maintain the enzyme’s 3D structure, such as the solvation layer with polar R groups on the outside and nonpolar R groups inside.

Coenzymes and Cofactors

Some enzymes are active solely based on their protein structure (apoenzyme), while others require one or more non-protein components (cofactors) to be active. These are called holoenzymes (apoenzyme + cofactor). A cofactor can be an organic molecule (coenzyme) or an inorganic ion. Important coenzymes include FAD, NAD, and NADP, which often incorporate a vitamin and a nucleotide. Coenzyme A (CoA) is involved in transferring acyl groups, such as in acetic acid. Cytochromes are coenzymes involved in electron transfer in respiration and photosynthesis.

Metabolic Regulation

  1. Primary level: Substrate concentration and pH.
  2. Secondary level: Allosteric enzymes that change their 3D conformation to become active or inactive.
  3. Tertiary level: Genetic control, including constitutive (always formed) and induced enzymes.
  4. Quaternary level: Endocrine control via hormones that stimulate or inhibit enzyme actions.
  5. Fifth level: Feedback regulation.

Enzyme Nomenclature and Classification

Enzymes are named based on their preferred substrate and action, typically ending in “-ase.” There are six major groups:

  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases

Vitamins: Essential Nutrients for Human Health

Vitamins are a diverse group of organic molecules with varied chemical structures that humans need in small amounts because they cannot be synthesized in sufficient quantities. They are classified into two groups: water-soluble and fat-soluble.

  • Deficiency: Avitaminosis or hypovitaminosis.
  • Excess: Hypervitaminosis.

Important water-soluble vitamins include C, B1, B2, B3, and B12. Fat-soluble vitamins include A, D, E, and K.