Sequence of amino acids

Figure C2.5.1. The 3D native stmcture of haemoglobin visualized using RasMol 2.6 [8], The linear sequence of amino acids of haemoglobin is given below tire figure.

When the cell requires instructions for protein production, part of the code on DNA, starting at an initiator and ending at a stop codon, is converted into a more mobile form by transferring the DNA code into a matching RNA code on a messenger ribonucleic acid (mRNA), a process known as transcription. The decoding, or translation, of mRNA then takes place by special transfer ribonucleic acids (tRNA), which recognize individual codons as amino acids. The sequence of amino acids is assembled into a protein (see Proteins section). In summary, the codes on DNA... 

The sequence of amino acids in a peptide can be written using the three-letter code shown in Figure 45.3 or a one-letter code, both in common use. For example, the tripeptide, ala.ala.phe, could be abbreviated further to AAF Although peptides and proteins have chain-like structures, they seldom produce a simple linear system rather, the chains fold and wrap around each other to give complex shapes. The chemical nature of the various amino acid side groups dictates the way in which the chains fold to arrive at a thermodynamically most-favored state. 

Primary structure refers to the sequence of amino acids in the polyamide chain. 

For example, a polypeptide is synthesized as a linear polymer derived from the 20 natural amino acids by translation of a nucleotide sequence present in a messenger RNA (mRNA). The mature protein exists as a weU-defined three-dimensional stmcture. The information necessary to specify the final (tertiary) stmcture of the protein is present in the molecule itself, in the form of the specific sequence of amino acids that form the protein (57). This information is used in the form of myriad noncovalent interactions (such as those in Table 1) that first form relatively simple local stmctural motifs (helix... 

Proteins are macromolecules that play many roles such as serving as enzymes or components of cell membranes and muscle. The antibodies that protect against invasion by foreign substances are themselves proteins. There are twenty-odd amino acids found regularly in most naturally occurring proteins. Because of the great length of protein chains and the various sequences of amino acids, the theoretic number of possible proteins is astronomical. The amino acid sequence is referred to as the primaiy structure of a protein. The pol eptide... 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

Gene The basic unit of inheritance a sequence of DNA coding that can be translated by the cell machinery into a sequence of amino acids linked to form a protein. 

Primary structure (Section 27.8) The sequence of amino acids in a peptide or protein. 

Amino acid analysis itself does not directly give the number of residues of each amino acid in a polypeptide, but it does give amounts from which the percentages or ratios of the various amino acids can be obtained (Table 5.2). If the molecular weight and the exact amount of the protein analyzed are known (or the number of amino acid residues per molecule is known), the molar ratios of amino acids in the protein can be calculated. Amino acid analysis provides no information on the order or sequence of amino acid residues in the polypeptide chain. Because the polypeptide chain is unbranched, it has only two ends, an amino-terminal or N-terminal end and a carboxyl-terminal or C-termuial end. 

The unique characteristic of each protein is the distinctive sequence of amino acid residues in its polypeptide chain(s). Indeed, it is the amino acid sequence of proteins that is encoded by the nucleotide sequence of DNA. This amino acid sequence, then, is a form of genetic information. By convention, the amino acid sequence is read from the N-terminal end of the polypeptide chain through to the C-terminal end. As an example, every molecule of ribonucle-... 

FIGURE 11.1 The fundamental process of information transfer in cells. Information encoded in the nucleotide sequence of DNA is transcribed through synthesis of an RNA molecule whose sequence is dictated by the DNA sequence. As the sequence of this RNA is read (as groups of three consecutive nucleotides) by the protein synthesis machinery, it is translated into the sequence of amino acids in a protein. This information tmiisfer system is encapsulated in the dogma DNA RNA protein. 

The backbone of polypeptides and, more generally, proteins is made up of a linear sequence of amino acids. 

On complete hydrolysis, a polypeptide gives two alanine, one leucine, one methionine, one phenylalanine, and one valine residue. Partial hydrolysis gives the following fragments Ala-Phe, Leu-Met, Val-Ala, Phe-Leu. It is known that the first amino acid in the sequence is valine and the last one is methionine. What is the complete sequence of amino acids ... 

Suppose that, in the polypeptide referred to in Question 31, the first amino acid is alanine and the last one is also alanine. What is the complete sequence of amino acids ... 

Domain, sequence of amino acids in a protein that can be identified as controlling a specific function, that is, recognition of ligands. 

Sequence of amino acids that determine the transport of proteins into the nucleus. Although there is no clear consensus, nuclear localization signals tend to be rich in positively charged residues, which allow interaction with proteins from the nuclear import machinery (i.e., importins). 

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 observation that a repeating, relatively short sequence of amino acids directs the spontaneous self-assembly of a large protein is shared by other structural proteins from mammalian systems [6] as well as of plant origin [16], Hence, such sequences may inspire the construction of nanostructures made of polypeptides and small proteins, as discussed later. 

This class is the most heterogeneous in size and stability. All members of the class function as messengers conveying the information in a gene to the protein-synthesizing machinery, where each serves as a template on which a specific sequence of amino acids is polymerized to form a specific protein molecule, the ultimate gene product (Figure 35-9). 

The cell must possess the machinery necessary to translate information accurately and efficiently from the nucleotide sequence of an mRNA into the sequence of amino acids of the corresponding specific protein. Clarification of our understanding of this process, which is termed translation, awaited deciphering of the genetic code. It was realized early that mRNA molecules themselves have no affinity for amino acids and, therefore, that the translation of the information in the mRNA nucleotide sequence into the amino acid sequence of a protein requires an intermediate adapter molecule. This adapter molecule must recognize a specific nucleotide sequence on the one hand as well as a specific amino acid on the other. With such an adapter molecule, the cell can direct a specific amino acid into the proper sequential position of a protein during its synthesis as dictated by the nucleotide sequence of the specific mRNA. In fact, the functional groups of the amino acids do not themselves actually come into contact with the mRNA template. 

The general structural characteristics of ribosomes and their self-assembly process are discussed in Chapter 37. These particulate entities serve as the machinery on which the mRNA nucleotide sequence is translated into the sequence of amino acids of the specified protein. 

It is possible to calculate whether a particular sequence of amino acids present in a protein is consistent with a transmembrane location. This can be done by consulting a table that hsts the hydrophobicities of each of the 20 common amino acids and the free energy val-... 

As mentioned above, which of the sequential NOEs d j, d j, and dj j is observed depends on the conformation of the backbone for the residues involved. Repetition of a particular type of connectivity for a sequence of amino acids often occurs in regions of regular secondary structure (19). For example a stretch of d jj-type NOEs is a signature of extended conformation, whereas a sequence of dj j -type NOEs is characteristic of helical conformation. Turns, on the other hand, are characterized by short, distinct patterns of dj j and d j connectivities. 

Biocatalysis refers to catalysis by enzymes. The enzyme may be introduced into the reaction in a purified isolated form or as a whole-cell micro-organism. Enzymes are highly complex proteins, typically made up of 100 to 400 amino acid units. The catalytic properties of an enzyme depend on the actual sequence of amino acids, which also determines its three-dimensional structure. In this respect the location of cysteine groups is particularly important since these form stable disulfide linkages, which hold the structure in place. This three-dimensional structure, whilst not directly involved in the catalysis, plays an important role by holding the active site or sites on the enzyme in the correct orientation to act as a catalyst. Some important aspects of enzyme catalysis, relevant to green chemistry, are summarized in Table 4.3. 

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