Protein primary structure

Under primary structure is understood in biochemistry the lowest level structure of a biopolymer, i.e., the sequence ( sequence ) of its basic building blocks. Since proteins are made of amino acids, their primary structure amino acid sequence is known. Accordingly, these in nucleic acids (DNA and RNA) is called nucleotide sequence. In chemistry and materials science, the term primary structure also indicates the sequence of synthetic polymers ( plastics).

Effects on the shape of the protein

The shape of the higher structure levels ( secondary structure, tertiary structure, quaternary structure ) of the protein is shown in the primary structure. It is already determined by the sequence of amino acids. During the translation, the secondary structure is usually in its final form as a result of interactions between the amino acids. In some cases, this process involved enzymes and other environmental influences ( see also: Prion ). From the secondary structure, in turn, performance of the spatial structure ( tertiary structure ) and, if the complex with other protein subunits into complexes ( quaternary ) is shown.

At present, there is still no reliable method to predict the exact spatial arrangement of the amino acid chain on the basis of the primary structure. From experience, however, statements about existing structural elements and the function of the protein can be found in the rule.

Relationship between nucleotide sequence and amino acid sequence

The amino acid sequence of a protein can be obtained from the nucleotide sequence of nucleic acid in which it is coded is derived, since the genetic code is known, each codon codes for only one amino acid. Conversely, this is not possible, since most of the amino acids have more than one codon. So you can be encoded by different nucleotide sequences. The genetic code is therefore referred to as degenerate.

The implementation of the genetic information of a gene in the amino acid sequence of a protein is a part of gene expression and protein biosynthesis. The first part of the processes is controlled by the transcription, the second is the translation.

For the specification of the primary structure of proteins and nucleic acids exist agreed conventions.

• The amino acid sequence of proteins is written from the amino end ( N- terminus) to carboxyl- end (C -terminus ).
• The nucleotide sequence of nucleic acids (DNA, RNA ) is written from the 5'- phosphate end to the 3 ' hydroxy terminus.

Analysis of the primary structure

Proteins

The Edman degradation is the classical method for sequencing of proteins and consists of three steps:

For sequencing of the next amino acid is followed by the repetition of three steps.

The method is highly automated, and operates for peptides up to a length of about 50 amino acids. Larger proteins are cleaved prior to analysis in fragments that are sequenced separately. Lately amplified gain mass spectroscopic methods in importance in this area.

Nucleic acids

DNA

Frederick Sanger developed in 1976 a method for sequencing DNA. This is called dideoxy method or chain termination method, since in this case a termination of the synthesis reaction is effected by the incorporation of dideoxy nucleotides into the DNA synthesis. By adding a small amount of a particular dideoxynucleotide for the synthesis reaction, the corresponding deoxynucleotide is partially replaced by the dideoxynucleotide, which causes the termination of the reaction at this point. This results in different lengths of DNA fragments from the length of the position of the replaced deoxynucleotide can be derived.

Also, this method has been largely automated. The separation by electrophoresis is usually in a common gel lane. The fragments are distinguished from each other by fluorescent labels, which are detected by a laser.

RNA

RNA can be transcribed by the reverse transcriptase enzyme in this cDNA and DNA sequencing (see above).