Get to know the structure of protein
A kind of amino acid
There are 20 kinds of amino acids, each of which is determined by the type of R group or side chain of amino acids. If the R group is different then the type of amino acid is different. For example, the serine amino acids, aspartic acid and leucine have differences only in the type of R group.
The R groups of amino acids vary in size, shape, charge, hydrogen binding capacity and chemical reactivity. The twenty types of amino acids have never changed. The simplest amino acid is glycine with H atoms as side chains. Next is alanine with a methyl group (-CH3) as a side chain.
Peptide Bonds
The twenty kinds of amino acids bind together, in a variety of order to form proteins. The process of forming proteins from amino acids is called protein synthesis. The bond between one amino acid and another is called a peptide bond. This peptide bond can also be called an amide bond.
Try to review the basic structure of amino acids. In proteins or amino acid chains, the carboxyl group (-COOH) binds to the amino group (-NH2). Each peptide bond is formed, issued 1 water molecule (H2O).
Protein Structure
Proteins made up of amino acid chains will have a variety of structures that are unique to each protein. Because proteins are composed of amino acids that are chemically different, a protein will be strung through peptide bonds and sometimes even connected by sulfide bonds. Furthermore, proteins can be folded to form various structures.
There are 4 levels of protein structure namely primary structure, secondary structure, tertiary structure and quaternary structure.
PROTEIN STRUCTURE
Primary structure
The primary structure is a simple structure with sequences of amino acids arranged in a linear fashion that is similar to the order of letters in a word and no chain branching occurs.
Primary structure
The primary structure is formed by the bond between the α-amino group and the α-carboxyl group (Figure 3). These bonds are called peptide bonds or amide bonds. This structure can determine the order of an amino acid from a polypeptide.
Peptide formation reaction
Frederick Sanger was a scientist who contributed to the discovery of methods for determining amino acid sequences in proteins, with the use of several protease enzymes that slice the bonds between certain amino acids into shorter peptide fragments to be further separated with the help of chromatographic paper. The amino acid sequence determines the function of proteins, in 1957, Vernon Ingram found that amino acid translocation would change the function of proteins, and further trigger genetic mutations.
The primary structure of a protein refers to the linear amino acid sequence of the polypeptide chain. The primary structure is caused by covalent bonds or peptides, which are made during the process of protein biosynthesis or called the translation process. The two ends of the polypeptide chain are called carboxyl (C-terminal) and amino (N-terminal) ends based on the nature of the free group. Residue calculations always begin at the end of the N-terminal (amino group, -NH2), which is the end where the amino group is not involved in the peptide bond. The primary structure of proteins is determined by genes associated with proteins. A certain sequence of nucleotides in DNA is transcribed into mRNA, which is read by ribosomes in a process called translation. Protein sequences can be determined by methods such as Edman's degradation.
Secondary structure
The secondary structure of proteins is regular, the pattern of repeated folds of the protein skeleton. The two most patterns are alpha helix and beta sheet. The secondary structure of proteins is the local three-dimensional structure of various amino acid sequences in proteins that are stabilized by hydrogen bonds. Various forms of secondary structures, for example, are as follows:
o alpha helix (α-helix, "twisting-alpha"), in the form of a spiral chain of amino acids shaped like a spiral;
o beta-sheet (β-sheet, "beta-plate"), in the form of wide sheets composed of a number of amino acid chains bound together through hydrogen bonds or thiol (S-H) bonds;
o beta-turn, (β-turn, "beta-curve"); and gamma-turn, (γ-turn, "gamma-indentation").
The secondary structure is a combination of primary structures that are linearly stabilized by hydrogen bonds between the CO = and NH groups along the polypeptide spine. One example of a secondary structure is α-helical and β-pleated (Figures 4 and 5). This structure has segments in the polypeptide that are twisted or folded repeatedly. (Campbell et al., 2009; Conn, 2008).
Secondary structure
The α-helical structure is formed between each of the carbonyl oxygen atoms in a peptide bond with hydrogen attached to the amide group in a peptide bond of four amino acid residues along the polypeptide chain (Murray et al, 2009).
In the secondary structure β-pleated formed by hydrogen bonds between linear regions of the polypeptide chain. β-pleated two forms are found, namely antiparrel and parallel (Figures 6 and 7). Both are different in terms of the hydrogen bonding pattern. In the form of antiparrel conformation has a bond conformation of 7 Å, while conformation in the parallel form is shorter which is 6.5 Å (Lehninger et al, 2004). If this hydrogen bond can be formed between two separate polypeptide chains or between two regions in a single chain that folds itself which involves four amino acid structures, then it is known as β turn shown in Figure 8 (Murray et al, 2009).