Chemistry, protein amino acid structures

The relationship between structure and function reaches its ultimate expression in the chemistry of amino acids, peptides, and proteins. 

Now that you have learned some of the chemistry of amino acids, it s time to study proteins, the large polymers of amino acids that are responsible for so much of the structure and function of all living cells. We begin with a discussion of the primary, secondary, tertiary, and quaternary structure of proteins. 

The applications of the chemistry of amino acids to the biological problem, protein structure and function, and folding and stability are the main focus of this article. The article is divided into hve main sections that include the biological insights on protein structures, chemical applications including protein functions, thermodynamics of proteins, protein interactions, and computational protein design. 

This chapter concentrates on the basic structures and chemistry of amino acids and on natural and synthetic proteins that have been applied as materials or in synkinesis. Biochemistry and molecular biology are touched upon occasionally. Metzler s and Voet s excellent biochemistry textbooks are recommended for these subjects. 

WE BEGIN THIS CHAPTER with a study of amino acids, compounds whose chemistry is built on amines (Chapter 10) and carboxylic acids (Chapter 13). We concentrate in particular on the acid-base properties of amino acids because these properties are so important in determining many of the properties of proteins, polymers of amino acids that have many functions in living organisms. With this understanding of the chemistry of amino acids, we then examine the structure of proteins themselves. 

As in most aspects of chemistry and biochemistry, structure is the key to function. We ll explore the structure of proteins by first concentrating on their fundamental building block units, the a-amino acids. Then, after developing the principles of peptide str-ucture, we ll see how the insights gained from these smaller molecules aid our understanding of proteins. 

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-... 

Continuing our look at the four main classes of biomolecules, we ll focus in this chapter on amino acids, the fundamental building blocks from which the 100,000 or so proteins in our bodies are made. We ll then see how amino acids are incorporated into proteins and the structures of those proteins. Any understanding of biological chemistry would be impossible without this study. 

Protein (Section 26.4) A large peptide containing 50 or more amino acid residues. Proteins serve both as structural materials and as enzymes that control an organism s chemistry. 

West, K.A. and Crabb, J.W 1990 Performance evaluation automatic hydrolysis and PTC amino acid analysis. In Vallafraca, J.J., ed.. Current Research in Protein Chemistry Techniques, Structure, and Function. San Diego, Academic Press 37-48. 

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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