Review of the essentials of computational Biochemistry; importance and implications. (Page 2)

Contents

• Introduction to protein molecule
• Protein structures
• Primary structure
• Characteristics of the primary structure of Protein

Introduction to Protein molecule

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 specification.

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. Plants can easily manufacture all their 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 in transferring 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 Structure

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

• The primary structure (i.e. the amino acid sequence)
• The secondary structure (i.e. the alpha and Beta helices. and sheets)
• The tertiary structure (i.e. the domains and family)
• 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. It is the primary sequence that determines the overall secondary and tertiary structure of the protein and hence its function.

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 databases is the single lettering method.

The primary structure of protein plays a significant role in the predictions made on any protein. It is usually what is used to query most protein sequence analytical tools

Characteristics of the primary structure of protein

The 20 naturally occurring amino acids have different physiochemical characteristics that makes them perform the role they play in any protein sequence. Some are acidic, basic, neutral, hydrophobic, polar etc. this different properties are bestowed on the amino acids by the kind of side chain that they have.

The amide group of asparagine and glutamine and the hydroxyl group of tyrosine, threonine and serine and the sufhydryl group of cysteine are all good hydrogen bond former hence, anywhere they are founding the protein sequence they facilitate the formation of structures that are stabilized by hydrogen bond formation such as the alpha helix.

Glycine have only a single hydrogen as its side chain and this hydrogen is not a good hydrogen bond former, expectedly, it can be classified as an helix breaker. Glycine’s flexibility makes it play important role in beta sheet formation

Aspartate and glutamate’s negatively charged acidic side chain makes them important to proteins that binds metal ion for structural or functional purpose.

Arginine and Lysine’s side chain participate in electrostatic interaction in protein.

The peptide’s backbone of protein consist of the repeated sequence
-N-Cα-C-

Where

N= amide Nitrogen
C=carbonyl carbon
Cα=alpha carbon of the amino acid

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