Organic chemistry proteins

Carey Organic Chemistry I 27 Ammo Acids Peptides I Text Fifth Edition and Proteins... 

Many globular proteins are enzymes They accelerate the rates of chemical reactions m biological systems but the kinds of reactions that take place are the fundamental reactions of organic chemistry One way m which enzymes accelerate these reactions is by bringing reactive func tions together m the presence of catalytically active functions of the protein... 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

The Novosibirsk Institute of Organic Chemistry has developed a method for computer-aided retrieval of stmctural information from H-nmr using its database of 50,000 spectra (72). Eraser WUHams Ltd. (Scientific Systems) has special software to search its E-nmr database (73). Protein nmr data have been compiled into a relational database at the University of Wisconsin (74). 

The chemical properties of peptides and proteins are most easily considered in terms of the chemistry of their component functional groups. That is, they possess reactive amino and carboxyl termini and they display reactions characteristic of the chemistry of the R groups of their component amino acids. These reactions are familiar to us from Chapter 4 and from the study of organic chemistry and need not be repeated here. 

Comprehensive Organic Chemistry , Pergamon, Elmsford, NY, 1979, is a six-volume treatise on the synthesis and reactions of organic compounds. The first three volumes cover the various functional groups, vol. 4, heterocyclic compounds, and vol. 5, biological compounds such as proteins, carbohydrates, and lipids. Probably the most useful volume is vol. 6, which contains formula, subject, and author indexes, as well as indexes of reactions and... 

George M. Whitesides is Mallinckrodt Professor of Chemistry at Harvard University. He received his A.B. from Harvard College in 1960 and his Ph.D. from the California Institute of Technology in 1964. His research areas are Materials Science and Organic Chemistry, with specific focus in surface chemistry, materials science, self-assembly, capillary electrophoresis, organic solid state, molecular virology, directed ligand discovery, and protein chemistry. He is a member of the National Academy of Sciences, and he received the U.S. National Medal of Science in 1998. 

Nuclear magnetic resonance (NMR) spectroscopy in pharmaceutical research has been used primarily in a classical, organic chemistry framework. Typical studies have included (1) the structure elucidation of compounds [1,2], (2) investigating chirality of drug substances [3,4], (3) the determination of cellular metabolism [5,6], and (4) protein studies [7-9], to name but a few. From the development perspective, NMR is traditionally used again for structure elucidation, but also for analytical applications [10]. In each case, solution-phase NMR has been utilized. It seems ironic that although —90% of the pharmaceutical products on the market exist in the solid form, solid state NMR is in its infancy as applied to pharmaceutical problem solving and methods development. 

Koing, S. 2005. Functional protein analysis using mass spectrometry. Current Organic Chemistry 9(9), 875-887. Osguthorpe, D. 2000. Ab initio protein folding. Current Opinion in Structural Biology 10(2), 146-152. 

Our goal in this chapter is to help you learn about organic chemistry, the chemistry of carbon. You will learn about the different types of organic compounds. We will also discuss biochemistry, including some biologically important compounds, such as proteins, carbohydrates, and so on. We will also familiarize you with some organic reactions. And finally, to do well, you must Practice, Practice, Practice. 

---