Saturday, May 16, 2009

Understanding all about Protein. ( an introductory approach)


Proteins are the major machine through which living organisms performs most of their metabolic activities. Proteins are built up from amino acids. Amino acids can be likened to blocks of different shapes that are used to build a building of a specific designed (i.e. protein).

Since the blocks have different shape, any block can’t just be used to substitutes for another block, on the course of building up the protein to its right speciation. Since substitution of amino acid are not allowed, the absence of any amino acid in the amino acid pool on the course of protein synthesis results in incomplete and terminated synthesis.

There are 20 amino acids found naturally in plants and animal (See details on structure and other amino acids information) Plants can easily manufacture all then needed amino acid from their primary metabolite. Animals derive their amino acid partly from then diet and from direct synthesis in the body.

Still using previous illustration, the building (i.e. protein) is built by the engineering action of ribosome in the nucleus of the cell. These engineers follow strictly, the plan (blueprint) stated on the mRNA.

The tRNA assists the ribosome to transfer amino acids from the amino acid pools to the site of protein synthesis. The blue print for protein synthesis is carefully copied from the DNA during the transcription to build any protein an organism will ever need.


Protein usually has unique structure that enables them to perform their specific function. There are four levels of a protein structure.

  1. The primary structure (i.e. the amino acid sequence)
  2. The secondary structure (i.e. the alpha and Beta helices. and sheets)
  3. The tertiary structure (i.e. the domains and family)
  4. Quaternary structure (i.e. aggregate of the tertiary structure )

The Primary Structure

The primary structure of a protein specifies the sequence of amino acids that makes up the protein. Its the primary sequence that determines the overall secondary and tertiary structure of the protein and hence its function.

Representation of the Primary Sequence

Conventionally, proteins are named from the N-terminal to the C-terminal. Each amino acid that makes up the entire protein sequence are joined together with a dipeptide bond, which involves a reaction between the carboxylic acid group of one amino acid and the amino group of another amino acid.

Amino acids in a protein sequence can be named as a whole (e.g. Alanine) abbreviated (ala) or as a single lettering form (A) The frequent way of representing amino acid sequence in Bioinformatic database is the single lettering method.

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