Tertiary structure, of a protein

Protein tertiary structure is also influenced by the environment In water a globu lar protein usually adopts a shape that places its hydrophobic groups toward the interior with Its polar groups on the surface where they are solvated by water molecules About 65% of the mass of most cells is water and the proteins present m cells are said to be m their native state—the tertiary structure m which they express their biological activ ity When the tertiary structure of a protein is disrupted by adding substances that cause the protein chain to unfold the protein becomes denatured and loses most if not all of Its activity Evidence that supports the view that the tertiary structure is dictated by the primary structure includes experiments m which proteins are denatured and allowed to stand whereupon they are observed to spontaneously readopt their native state confer matron with full recovery of biological activity... 

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

Name the amino acids in Table 19.4 that contain side groups capable of forming hydrogen bonds. This interaction contributes to the tertiary structure of a protein. 

The tertiary structure of a protein is the overall shape of its polypeptide chain. 

Several types of bonding might be utilized to bind substrates to enzymes. These are analogous to the bondings that contribute to the secondary and tertiary structures of a protein and include the following non-covalent interactions ... 

The binding of a protein to nucleic acid is accomplished by weak, non-covalent interactions. The interactions are the same as those involved in the formation of the tertiary structure of a protein ... 

Another method of determining the secondary and tertiary structure of a protein is NMR (nuclear magnetic resonance) spectroscopy. NMR spectroscopy reveals detailed information on specific sites of molecules without having to solve then-entire structure. 

N-Terminal nucleophile hydrolases autoactivation of 621 Termites, protozoa in 19 Tertiary structure of a protein 59 TES buffer 99... 

Tertiary Structure of Proteins The tertiary structure of a protein refers to how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact or globular structure. Two-dimensional representations of the three-dimensional tertiary structures of proteins are, well, pretty two dimensional. If you want to better understand tertiary structure, you can view interactive, three-dimensional models of a large variety of proteins at the RCSB Protein Data Base at http //www.rcsb.org. 

Describe, using a suitable example, each of the following (a) a prosthetic group, (b) a peptide link, (c) a S-S bridge and (d) the tertiary structure of a protein. 

According to Owusu and Makhzoum (20) AH values of about 200-300kJ/mol would lead to unfolding of the tertiary structure of a protein. However, the Dowex-lx4-200/invertase complex had a AH 37% lower than these values, indicating that the declining invertase activity vs temperature is probably owing to the breakup of the supramolecular structures of invertase rather than to the irreversible unfolding of the macromolecular tertiary structure. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

When a protein possesses two or several Trp residues, when quenchers such as iodide, cesium, or acrylamide are used, and if all Trp residues are not accessible to the quencher, the Stern-Volmer equation yields a downward curvature. In this case, we have selective quenching (Figure 10.5b). From the linear part of the plot, we can calculate the value of the Stern-Volmer constant corresponding to the interaction between the quencher and accessible Trp residues. Upon complete denaturation and loss of the tertiary structure of a protein, all Trp residues will be accessible to the quencher. In this case, the Stern-Volmer plot will show an upward curvature. In summary, inhibition of the protein fluorescence with two or several Trp residues can yield three different representations for the Stern-Volmer equations, depending on the accessibility of the fluorophore to the quencher. 

The tertiary structure of a protein is its complete three-dimensional conformation. Think of the secondary structure as a spatial pattern in a local region of the molecule. Parts of the protein may have the a-helical structure, while other parts may have the pleated-sheet structure, and still other parts may be random coils. The tertiary structure includes all the secondary structure and all the kinks and folds in between. The tertiary structure of a typical globular protein is represented in Figure 24-17. 

Ornithine (C) is a nonstandard amino acid that occurs in metabolic processes. Which amino acid does it most closely resemble Estimate pKa values and p/ for ornithine, and draw the major form present at pH = 2, pH = 6, and pH = 11. If ornithine were a component of proteins, how would it affect the tertiary structure of a protein ... 

The secondary and tertiary structures of a protein can modulate the reduction potential of a single cofactor by more than 500 mV. The Fe(IIEII) reduction potential of a free heme in aqueous solution is approximately -200 mV... 

Summary of the various types of interactions that stabilize the tertiary structure of a protein (a) ionic, (b) hydrogen bonding, (c) covalent, (d) London dispersion, and (e) dipole-dipole. 

Distinguish between the primary, secondary, and tertiary structures of a protein. Give examples of the types of forces that maintain each type of structure. 

Tertiary structure (of a protein) the overall shape of a protein, long and narrow or globular, maintained by different types of intramolecular interactions. (22.6)... 

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