Protein

Proteins are essential molecules found in all living organisms. They are made up of smaller units called amino acids, linked together in a chain. Proteins have many important roles in the body, such as building and repairing tissues, controlling chemical reactions, and transporting molecules. They are like tiny workers that perform various tasks, helping our bodies function properly.

Proteins have four primary levels of structure

Primary Structure:

The primary structure of a protein refers to the linear sequence of amino acids in its polypeptide chain. The sequence is determined by the genetic information encoded in DNA. The specific arrangement of amino acids influences the protein’s overall folding and function.

• Amino Acids: Proteins are made up of a chain of amino acids linked together by peptide bonds. Amino acids are organic compounds that contain an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R group) that varies between different amino acids.
• Peptide Bonds: Peptide bonds form between the amino group of one amino acid and the carboxyl group of the adjacent amino acid during protein synthesis. This covalent bond results in the formation of a polypeptide chain.
• Linear Sequence: The primary structure represents the specific order and arrangement of amino acids in the protein chain. It is determined by the genetic information encoded in the DNA sequence of the gene that codes for the protein.
• Amino Acid Residues: Each position in the protein chain is referred to as an amino acid residue. The sequence of residues is written from the amino terminus (N-terminus) to the carboxyl terminus (C-terminus) of the protein.
• Protein Coding Genes: The DNA sequence in genes contains the instructions for protein synthesis. Each gene carries the information for the precise order of amino acids that will make up a specific protein.

Secondary Structure

The secondary structure describes the local folding patterns of the protein chain. The two most common types of secondary structures are alpha helices and beta sheets. Alpha helices are tightly coiled structures, while beta sheets consist of extended strands connected by hydrogen bonds. These structures are stabilized by hydrogen bonding between the amino acid residues in the polypeptide chain.

• Alpha Helix
  • Alpha helix is a right-handed coiled structure resembling a spiral staircase.
  • It forms when the polypeptide chain twists into a helical shape, with hydrogen bonds between the amino acids.
  • The hydrogen bonds form between the carbonyl oxygen of one amino acid and the amino hydrogen of another, four residues away.
• Beta Sheet
  • Beta sheet consists of extended strands of the polypeptide chain connected by hydrogen bonds.
  • It can be either parallel or antiparallel, depending on the directionality of the strands.
  • The hydrogen bonds form between the carbonyl oxygen of one strand and the amino hydrogen of an adjacent strand.
• Beta Turns
  • Beta turns, also known as hairpin turns, are short stretches in a polypeptide chain that reverse its direction.
  • They allow the chain to fold back on itself, forming a compact structure.
  • Proline and glycine are commonly found in beta turns due to their unique structural properties.

Tertiary Structure

The tertiary structure refers to the three-dimensional arrangement of the entire polypeptide chain. It results from interactions between amino acid side chains, such as hydrophobic interactions, hydrogen bonding, disulfide bonds, and electrostatic attractions. Tertiary structure determines the protein’s overall shape and functional properties.

• Hydrophobic interactions: Hydrophobic residues tend to cluster together in the protein’s core, away from the aqueous environment, promoting stability.
• Hydrogen bonds: Hydrogen bonding occurs between polar residues, contributing to the folding and stabilization of the protein.
• Disulfide bonds: Some cysteine residues can form covalent bonds known as disulfide bonds, linking different regions of the protein chain and adding further stability.
• Electrostatic interactions: Charged amino acid residues (positively or negatively charged) can attract or repel each other, influencing the protein’s overall structure.

Quaternary Structure

Some proteins are composed of multiple polypeptide chains, each with its own tertiary structure, which come together to form a functional protein complex. The quaternary structure describes the arrangement and interactions between these individual polypeptide subunits. Examples of proteins with quaternary structure include hemoglobin and antibodies.

• Polypeptide Subunits
  • The quaternary structure consists of two or more individual polypeptide chains, also referred to as subunits.
  • Each subunit may have its own primary, secondary, and tertiary structures.
  • The subunits can be identical or different in terms of amino acid sequence and structure.
• Interfaces
  • Interfaces are the regions where subunits come into contact and interact with each other.
  • Interactions at the interfaces are crucial for stabilizing the quaternary structure and maintaining the overall integrity of the protein complex.
  • Interactions can involve hydrogen bonding, ionic interactions, hydrophobic interactions, and sometimes disulfide bond formation.
• Ligand Binding Sites
  • Quaternary structures often have specific regions called ligand binding sites where molecules (ligands) can bind.
  • Ligands can include substrates, cofactors, regulatory molecules, or other proteins.
  • Binding of ligands at these sites can trigger conformational changes, modulate protein activity, or facilitate cooperative interactions between subunits.
• Symmetry
  • Some proteins with quaternary structure exhibit symmetry in their arrangement.
  • Symmetry can be rotational, such as cyclic symmetry or rotational symmetry, or it can be helical or spherical.
  • Symmetry contributes to the stability and functional properties of the protein complex.