Monomer amino acid

The first basic tenet of protein-structure prediction is that the amino acid sequence, the primary structure, contains all of the information required for the correct folding of the polymer chain. This is a first approximation which clearly ignores the role of environment on the induction of structure or the action of chaperone proteins which assist the in vivo folding process. The wide variety of structural motifs that have been observed for proteins is derived from only twenty different monomers (amino acids), many of which are structurally quite similar (i.e., isoleucine and leucine vary only in branching of the butyl side chain). However, there are many cases in which the substitution of amino acids with structurally similar residues (so-called conservative substitution) will lead to a protein that will not properly fold. Studies involving deletion of even small portions of the termini of the protein sequence provide similar results. On the other hand there are proteins related through evolution with as little as 20% sequence identity which adopt similar three-dimensional structures. Therefore the information encoded in the primary sequence is specific for one protein fold, however, there are numerous other sequences, only remotely related at first glance, which will produce the same fold. 

Many biopolymers are heteropolymers. DNA is a heteropolymer consisting of four different types of monomers (nucleotides), while natural proteins are heteropolymers commonly consisting of 20 different types of monomers (amino acids). 

Fig. 10.34 shows the INS spectrum of ox femur as the organic component is progressively removed [83]. Fig. 10.34a is very similar to that of the protein Staphylococcal nuclease. Fig 10.32, and emphasises one of the problems of working in this field because proteins are largely made of the same monomers (amino acids), the INS spectra of very different proteins tend to look very similar. Removal of the fat results in little change in the spectrum, Fig. 10.34b. It can be seen that elimination of the protein is highly effective, Fig. 10.34c the C-H stretching modes just below 3000 cm" and the C-H deformation modes at 1200-1500 cm have both disappeared. There is a weak, broad peak at 630 cm and its overtone near 1300 cm. For comparison, the INS spectrum of a highly crystalline reference hydroxyapatite is shown in Fig. 10.34d. The frequency match of the of the residual bone peak and that of the hydroxyapatite is exact, the width of the peak is attributed to heterogeneous broadening. The spectrum demonstrates that hydroxyl groups are still present in bone.

Proteins are condensation polymers, formed by coupling amines and carboxylic acids. In proteins, the monomers (amino acids) contain both the amine and the carboxylic acid, and so they are an example of the AB type monomer shown in Figure 13.15. In fact a protein, or more specifically polyglycine, could be described as Nylon-2. Recall that Nylon-1 is the polyisocyanate structure discussed in Section 6.8.1. 

Polysaccharides (monomers, sugars), proteins (monomers, amino acids), and nucleic acids (monomers, nucleotides) are natural polymers. DNA occurs as a double helix, with bases in each strand H-bonded to specific bases in the other. The base sequence of an organism s DNA determines the amino-acid sequences of its proteins, which determine the proteins structure and function. 

L-valine, L-proline, L-leucine, and L-phenylalanine as initiators of the ROP of DTC and TMC. PTMC and poly(dimethyl trimethylene carbonate) (PDTC) with different Mn were obtained at 80 and 120 °C, respectively, in bulk by changing the molar ratio of [monomer]/[amino acid]. Among these polymers, the maximum values of A n of the PCs reached 17 800-18 900 and the dispersity index was 1.67 for [monomer]/[r-phenylalanine] molar ratio of 200. NMR spectroscopic analysis demonstrated that amino acid was incorporated into the polymer chain. 

Since proteins are composed of amino acids, many researchers have tried to develop synthetic polypeptides, which can be manufactured by polymerization of the respective monomers (amino acids) or by fermentation. It should be noted that the functional groups on the side chain (e.g., co-carboxylic groups) should be protected in different chemical forms (e.g., methyl, benzyl esters) during polymerization of amino acids. Several polypeptides have been synthesized to serve as models for structural, biological, and immunological studies. In addition, many different types of synthetic polypeptides have been investigated for use in biomedical applications. 

Most biological catalysts are enzymes, i.e., proteins, which are macromolecules (polypeptides) fonned by biopolymerization of amino acids (with elimination of water) some enzymes are huge, with hundreds of monomer units. The 20 amino acid monomers occurring in nature. 

A polymer is a macromolecule that is constructed by chemically linking together a sequent of molecular fragments. In simple synthetic polymers such as polyethylene or polystyrer all of the molecular fragments comprise the same basic unit (or monomer). Other poly me contain mixtures of monomers. Proteins, for example, are polypeptide chains in which eac unit is one of the twenty amino acids. Cross-linking between different chains gives rise to j-further variations in the constitution and structure of a polymer. All of these features me affect the overall properties of the molecule, sometimes in a dramatic way. Moreover, or... 

Polyethylene (Section 6 21) A polymer of ethylene Polymer (Section 6 21) Large molecule formed by the repeti tive combination of many smaller molecules (monomers) Polymerase chain reaction (Section 28 16) A laboratory method for making multiple copies of DNA Polymerization (Section 6 21) Process by which a polymer is prepared The principal processes include free radical cationic coordination and condensation polymerization Polypeptide (Section 27 1) A polymer made up of many (more than eight to ten) amino acid residues Polypropylene (Section 6 21) A polymer of propene Polysaccharide (Sections 25 1 and 25 15) A carbohydrate that yields many monosacchande units on hydrolysis Potential energy (Section 2 18) The energy a system has ex elusive of Its kinetic energy... 

The discussion of polyamides parallels that of polyesters in many ways. To begin with, polyamides may be formed from an AB monomer, in this case amino acids ... 

Without other alternatives, the carboxyalkyl radicals couple to form dibasic acids HOOC(CH)2 COOH. In addition, the carboxyalkyl radical can be used for other desired radical reactions, eg, hydrogen abstraction, vinyl monomer polymerization, addition of carbon monoxide, etc. The reactions of this radical with chloride and cyanide ions are used to produce amino acids and lactams employed in the manufacture of polyamides, eg, nylon. 

HO—R—COOH, or an amino acid, H2N—R—COOH. In some cases, such monomers self-condense to a cycHc stmcture, which is what actually polymerizes. For example, S-caprolactam (1) can be thought of as the self-condensation product of an amino acid. Caprolactam undergoes a ring-opening polymerization to form another... 

Biopolymers are the naturally occurring macromolecular materials that are the components of all living systems. There are three principal categories of biopolymers, each of which is the topic of a separate article in the Eniyclopedia proteins (qv) nucleic acids (qv) and polysaccharides (see Carbohydrates Microbial polysaccharides). Biopolymers are formed through condensation of monomeric units ie, the corresponding monomers are amino acids (qv), nucleotides, and monosaccharides, for proteins, nucleic acids, and polysaccharides, respectively. The term biopolymers is also used to describe synthetic polymers prepared from the same or similar monomer units as are the natural molecules. 

Proteins. The most abundant and physiologically diverse natural biopolymers are proteins, which make up enzymes, hormones, and stmctural material such as hair, skin, and connective tissue. The monomer units of natural proteins, a-amino acids, condense to form dipeptides, tripeptides, polypeptides, and proteins. 

Figure 8.6 The N-terminal domain of lambda repressor, which binds DNA, contains 92 amino acid residues folded into five a helices. Two of these, a2 (blue) and a3 (red) form a helix-turn-hellx motif with a very similar structure to that of lambda Cro shown In Figure 8.4. The complete repressor monomer contains in addition a larger C-termlnal domain. (Adapted from C. Pabo and M. Lewis, Nature 298 443-447, 1982.)...

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

Figure 14.5 The domain organization of intermediate filament protein monomers. Most intermediate filament proteins share a similar rod domain that is usually about 310 amino acids long and forms an extended a helix. The amino-terminal and carboxy-terminal domains are non-a-helical and vary greatly in size and sequence in different intermediate filaments.

Two polypeptides, A and B, have similar tertiary structures, but A normally exists as a monomer, whereas B exists as a tetramer, B4. What differences might be expected in the amino acid composition of A versus B ... 

The structure of the UQ-cyt c reductase, also known as the cytochrome bc complex, has been determined by Johann Deisenhofer and his colleagues. (Deisenhofer was a co-recipient of the Nobel Prize in Chemistry for his work on the structure of a photosynthetic reaction center [see Chapter 22]). The complex is a dimer, with each monomer consisting of 11 protein subunits and 2165 amino acid residues (monomer mass, 248 kD). The dimeric structure is pear-shaped and consists of a large domain that extends 75 A into the mito-... 

Reactions between one monomer species with two different functional groups. One functional group of one molecule reacts with the other functional group of the second molecule. For example, polymerization of an amino acid starts with condensation of two monomer molecules ... 

Nylon 6 is produced by the polymerization of caprolactam. The monomer is first mixed with water, which opens the lactam ring and gives w-amino acid ... 

Nylon 11 is produced hy the condensation reaction of 11- aminounde-canoic acid. This is an example of the self condensation of an amino acid where only one monomer is used. The monomer is first suspended in water, then heated to melt the monomer and to start the reaction. Water is continuously removed to drive the equilibrium to the right. The polymer is finally withdrawn for storage ... 

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