what does the shading represent in a 3D structure of a protein
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Explanation:
The covalent backbone of proteins is made up of hundreds of individual bonds. If free rotation were possible around even a fraction of these bonds, proteins could assume an almost infinite number of threedimensional structures. Each protein has a specific chemical or structural function, however, strongly suggesting that each protein has a unique three-dimensional structure . The simple fact that proteins can be crystallized provides strong evidence that this is the case. The ordered arrays of molecules in a crystal can generally form only if the molecular units making up the crystal are identical. The enzyme urease (Mr 483,000) was among the first proteins crystallized, by James Sumner in 1926. This accomplishment demonstrated dramatically that even very large proteins are discrete chemical entities with unique structures, and it revolutionized thinking about proteins.
Figure 7-1 The structure of the enzyme chymotrypsin, a globular protein. A molecule of glycine (blue) is shown for size comparison.we will explore the three-dimensional structure of proteins, emphasizing several principles. First, the three-dimensional structure of a protein is determined by its amino acid sequence. Second, the function of a protein depends upon its three-dimensional structure. Third, the three-dimensional structure of a protein is unique, or nearly so. Fourth, the most important forces stabilizing the specific three-dimensional structure maintained by a given protein are noncovalent interactions. Finally, even though the structure of proteins is complicated, several common patterns can be recognized.
The relationship between the amino acid sequence and the threedimensional structure of a protein is an intricate puzzle that has yet to be solved in detail. Polypeptides with very different amino acid sequences sometimes assume similar structures, and similar amino acid sequences sometimes yield very different structures. To find and understand patterns in this biochemical labyrinth requires a renewed appreciation for fundamental principles of chemistry and physics.
Overview of Protein Structure
The spatial arrangement of atoms in a protein is called a conformation. The term conformation refers to a structural state that can, without breaking any covalent bonds, interconvert with other structural states. A change in conformation could occur, for example, by rotation about single bonds. Of the innumerable conformations that are theoretically possible in a protein containing hundreds of single bonds, one generally predominates. This is usually the conformation that is thermodynamically the most stable, having the lowest Gibbs' free energy (G). Proteins in their functional conformation are called native proteins.
What principles determine the most stable conformation of a protein? Although protein structures can seem hopelessly complex, close inspection reveals recurring structural patterns. The patterns involve different levels of structural complexity, and we now turn to a biochemical convention that serves as a framework for much of what follows in this chapter.Levels of structure in proteins. The primary structure consists of a sequence of amino acids linked together by covalent peptide bonds, and includes any disulfide bonds. The resulting polypeptide can be coiled into an a helix, one form of secondary structure. The helix is a part of the tertiary structure of the folded polypeptide, which is itself one of the subunits that make up the quaternary structure of the multimeric protein, in this case hemoglobin.
Conceptually, protein structure can be considered at four levels (Fig. 7-2). Primary structure includes all the covalent bonds between amino acids and is normally defined by the sequence of peptide-bonded amino acids and locations of disulfide bonds. The relative spatial arrangement of the linked amino acids is unspecified.
Polypeptide chains are not free to take up any three-dimensional structure at random. Steric constraints and many weak interactions stipulate that some arrangements will be more stable than others. Secondary structure refers to regular, recurring arrangements in space of adjacent amino acid residues in a polypeptide chain. There are a few common types of secondary structure, the most prominent being the a helix and the β conformation. Tertiary structure refers to the spatial relationship among all amino acids in a polypeptide; it is the complete three-dimensional structure of the polypeptide. The boundary between secondary and tertiary structure is not always clear. Several different types of secondary structure are often found within the three-dimensional structure of a large protein. Proteins with several polypeptide chains have one more level of structure: quaternary structure, which refers to the spatial relationship of the polypeptides, or subunits, within the protein.
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Answer:
Teteriary and secondary