Primary structure of polypeptides and proteins

Using the techniques we described, chemists have had remarkable success in determining the primary structures of polypeptides and proteins. The compounds described in the following pages are important examples. 

Acid-Base Properties of Amino Acids Poiypeptides and Proteins Primary Structure of Polypeptides and Proteins Synthesis of Polypeptides 27.6 Three-Dimensional Shapes of Polypeptides and Proteins... 

In particular, we can now determine the main-chain conformation of various copolypeptides (and some proteins) in the solid state from the criso and labelled natural protein can be provided. As the relation between the nitrogen shielding and the structures (primary, secondary and higher ordered structures) is clarified in the future, we will be able to get more detailed information on the structure of polypeptides and proteins in the solid state. 

As the mRJSlA leaves the cell nucleus in which it was created and enters the cytoplasm, it binds with specialized structures called ribosomes, as shown in Figure 13.36. Ribosomes are microscopic complexes of rRNA and proteins, and they are the site where proteins are built. As the mRNA is scrolled sequentially over the ribosome, the anticodon end of a free tRNA molecule binds to an mRNA codon. In this manner, tRNA molecules and their tag-along amino acids are placed adjacent to one another along the mRNA strand. The amino acids then chemically bond with one another, forming a long polypeptide chain that breaks away from the tRNA as it forms. This process continues until a stop mRNA codon, for which there are no tRNA anticodons, is encountered. At this point, the primary structure of a new protein has been built. 

The enormous structural diversity of proteins begins with different amino acid sequences (primary structure) of polypeptide chains that fold into complex 3D structures. The final folded arrangement of the polypeptide chain is referred to as its conformation (secondary and tertiary structures). It appears that the information for folding to the native conformation is present in the amino acid sequences (Anfinsen, 1973) however, a special class of proteins known as chaperons is required to facilitate in vivo folding of a protein to form its native conformation (Martin and Hartl, 1997). 

The peptides obtained by specific chemical or enzymatic cleavage are separated by some type of chromatography. The sequence of each purified peptide is then determined by the Edman method. At this point, the amino acid sequences of segments of the protein are known, but the order of these segments is not yet defined. How can we order the peptides to obtain the primary structure of the original protein 7Te necessary additional infor mation is obtained from overlap peptides (Figure 3.22). A second enzyme is used to split the polypeptide chain at different linkages. For example, chy-motrypsin cleaves preferentially on the carboxyl side of aromatic and some other bulky nonpolar residues (p, 247). Because these chymotryptic peptides overlap two or more tryptic peptides, they can be used to establish the order of the peptides. The entire amino acid sequence of the polypeptide chain is then known. 

Accurate mapping of mutated genes led to the conclusion that sites of mutation in a particular gmie are also in linear formation, and are responsible for specifically l(x alized defects (amino-acid replacements) in the amino-acid sequence of the mi me product The exact topography of the amino-acid replacements deduced from the cximparison of the primary structures of the mutant proteins, made apparent the co-linearity between the gene and its polypeptide product For examide. a... 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

Whereas the primary structure of a protein is determined by the covalently linked amino acid residues in the polypeptide backbone, secondary and higher... 

Proteins are polymers made of amino acid units. The primary structure of a polypeptide is the sequence of amino acid residues secondary structure is the formation of helices and sheets tertiary structure is the folding into a compact unit quaternary structure is the packing of individual protein units together. 

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