Primary polypeptide structure

Fibrous proteins Globular proteins Alpha-amino acids Side chains Dipeptide Peptide linkage Polypeptide Primary structure Secondary structure Alpha-helix Pleated sheet Tertiary structure Disulfide linkage Denaturation Enzymes... 

N-terminal Peptide linkage Polypeptide Primary structure Protein... 

The amino acid sequence of the polypeptide primary structure is very important. Any changes in the normal sequence can have severe effects on the human body, even if only one amino acid is out of place. Sickle cell disease is one example. Sickle cell disease is a mutation of the hemoglobin, and development of the disease... 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

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... 

The folding of a single polypeptide chain in three-dimensional space is referred to as its tertiary structure. As discussed in Section 6.2, all of the information needed to fold the protein into its native tertiary structure is contained within the primary structure of the peptide chain itself. With this in mind, it was disappointing to the biochemists of the 1950s when the early protein structures did not reveal the governing principles in any particular detail. It soon became apparent that the proteins knew how they were supposed to fold into tertiary... 

The biological function of biopolymers such as polypeptides, proteins, nucleic acids etc. depends strongly on their ordered structure which is determined by the pattern of inter- and intramolecular interactions given by the primary structure. 

Human and horse insulin both have two polypeptide chains, with one chain containing 21 amino acids and the other containing30 amino acids. They differ in primary structure at two places. At position 9 in one chain, human insulin has Ser and horse insulin has Gly at position 30 in the other chain, human insulin has Thr and horse insulin has Ala. How must the DNA for the two insulins differ ... 

Remember that, by convention, the NH2 group of each amino acid is written at the left the COOH group is at the right Other reagents split the chain at different points. By correlating the results of different hydrolysis experiments, it is possible to deduce the primary structure of the protein (or polypeptide). Example 23.10 shows how this is done in a particularly simple case. 

A certain polypeptide is shown by arid hydrolysis to contain only three amino acids serine(Ser), alanine(Ala), and methionine(Met) with mole fractions of j, and respectively. Enzymatic hydrolysis yields the following fragments Ser-Ala Ser-Met Ala-Ser. Deduce the primary structure of the polypeptide. 

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. 

The preparation of polypeptide and polypeptide hybrid vesicles with predictable properties begins with proper synthesis of a primary structure. This section focuses on three different classes of procedures that are used to synthesize polypeptides. Although conjugation between the polypeptide and non-polypeptide blocks to form polypeptide hybrids is discussed briefly with the third class of synthesis procedures (Sect. 2.3), more detailed information regarding the synthesis and generation of polypeptide hybrid macromolecules are reviewed elsewhere [22-26]. 

The number and order of all of the amino acid residues in a polypeptide constitute its primary structure. Amino acids present in peptides are called aminoacyl residues and are named by replacing the -au or -ine suffixes of free amino acids with -yl (eg, alany/, asparg//, ty-... 

Knowledge of DNA sequences permits deduction of the primary structures of polypeptides. DNA sequencing requires only minute amounts of DNA and can readily yield the sequence of hundreds of nucleotides. To clone and sequence the DNA that encodes a partic-... 

The gene-encoded primary structure of a polypeptide is the sequence of its amino acids. Its secondary structure results from folding of polypeptides into hydrogen-bonded motifs such as the a helix, the P-pleated sheet, P bends, and loops. Combinations of these motifs can form supersecondary motifs. 

The primary structure of a polypeptide is its sequence of amino acids. It is customary to write primary structures of polypeptides using the three-letter abbreviation for each amino acid. By convention, the structure is written so that the amino acid on the left bears the terminal amino group of the polypeptide and the amino acid on the right bears the terminal carboxyl group. Figure 13-35 shows the two dipeptides that can be made from glycine and serine. Although they contain the same amino acids, they are different molecules whose chemical and physical properties differ. Example shows how to draw the primary stmcture of a peptide. 

A primary structure represents a polypeptide as a simple linear string of amino acids. Actually, within long polypeptides, certain sections fold into sheets or twist into coils. These regions with specific structural characteristics constitute the secondary structure of the protein. Figures 13-37 and 13-38 show the two most common secondary structures. 

Each protein has a unique three-dimensional shape called its tertiary structure. The tertiary structure is the result of the bends and folds that a polypeptide chain adopts to achieve the most stable structure for the protein. As an analogy, consider the cord in Figure 13-39 that connects a computer to its keyboard. The cord can be pulled out so that it is long and straight this corresponds to its primary structure. The cord has a helical region in its center this is its secondary structure. In addition, the helix may be twisted and folded on top of itself This three-dimensional character of the cord is its tertiary structure. 

Figure 1.3 Folding of a polypeptide chain illustrating the hierarchy of protein structure from primary structure through secondary structure and tertiary structure.

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