322 / Biochemistry protein digestion

Taurine is a rather specialized topic in the nutritional biochemistry of digestion. Taurine, 2 aminoethane sulfonic acid, is synthesized from cysteine, as shown in Figure 2AI). I hc taurine molecule contains an amino group as well as an acidic group. Taurine has not been found in proteins, although some evidence suggests that it occurs in certain polypeptides. Taurine t ccurs as a component of bile salts and plays an important role in the transport and absorption of lipids. 

Yeung, Y.G., Nieves, E., Angeletti, R.H., Stanley, E.R. (2008) Removal of detergents from protein digests for mass spectrometry analysis. Analytical Biochemistry, 382 (2), 135-137. 

Henzel WJ, Bourell JH, and Stubs JT (1990) Analysis of protein digests by capillary high-performance liquid chromatography and on-line fast atom bombardment mass spectrometry. Analytical Biochemistry 187 228. 

Biochemistry is carbonyl chemistiy. Almost all metabolic pathways used by living organisms involve one or more of the four fundamental carbonvl-group reactions we ve seen in Chapters 19 through 23. The digestion and metabolic breakdown of all the major classes of food molecules—fats, carbohydrates, and proteins—take place by nucleophilic addition reactions, nucleophilic acyl substitutions, a substitutions, and carbonyl condensations. Similarly, hormones and other crucial biological molecules are built up from smaller precursors by these same carbonyl-group reactions. 

A family of 100 hybridoma antibodies can typically provide 20 tight binders and these need to be assayed for catalysis. At this stage in the production of an abzyme, the benefit of a sensitive, direct screen for product formation comes into its own. Following identification of a successful catalyst, the antibody is usually recloned to ensure purity and stabilization of the clone, then protein is produced in larger amount (—10 mg) and used for determination of the kinetics and mechanism of the catalysed process by classical biochemistry. Digestion of such protein with trypsin or papain provides fragment antibodies, Fabs, that contain only the attenuated upper limbs of the intact IgG (Fig. 1). It is these components that have been crystallized, in some... 

This biology/biochemistry of the whelk is of some commercial importance because a related species, the sting winkle, sometimes attacks and devours oysters in oyster farms by boring a hole in the shell in order to digest the protein inside and then absorb the digested peptides and amino acids. It is the radular retractor muscle that is the culprit ... 

Rosenfeld, J., Capdevielle, J., Guillemot, J.C. and Ferrara, P. (1992) In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Analytical Biochemistry 203, 173-179. 

Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-mass spectrometry (MS) is now routinely used in many laboratories for the rapid and sensitive identification of proteins by peptide mass fingerprinting (PMF). We describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by one- or two-dimensional gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and de-stain-ing, reduction and alkylation, in-gel trypsin digestion, MALDI-TOF MS of the tryptic peptides, and database searching of the PMF data. Up to 96 protein samples can easily be manually processed at one time by this method. 

The International Union of Biochemistry has recommended that enzymes have three names, namely a systematic name, which shows the reaction being catalysed and the type of reaction based on the classification in Table A7.1, a recommended trivial name and a four figure Enzyme Commission code (EC code). Nearly all systematic and trivial enzyme names have the suffix -ase. Systematic names show, often in semi-chemical equation form, the conversion the enzyme promotes and the class of the enzyme. Trivial names are usually based on the function of the enzyme but may also include or be based on the name of the substrate. However, some trivial names in current use are historical and bear no relationship to the action of the enzyme or its substrate, for example, pepsin and trypsin are the names commonly used for two enzymes that catalyse the breakdown of proteins during digestion. The Enzyme Commission s code is unique for each enzyme. It is based on the classification in Table A7.1 but further subdivides each class of enzyme according to how it functions. The full code is... 

The fourth section deals with various aspects Digestion, Absorption, and Nutritional Biochemistry. The chapter Obesity considers current problems with respect to the ever-increasing incidence of imbalance between energy intake and utilization. Key problems of undemutrition are discussed in the chapters Protein-Energy Malnutrition and Vitamin A Deficiency in Children. The chapters Lactose Intolerance, Pancreatic Insufficiency, and Abetalipoproteinemia focus on the biochemical processes underlying food digestion and absorption. Calcium Deficiency Rickets, Vitamin B12 Deficiency, and Hemochromatosis provide discussions of absorption and utilization of vitamin D, vitamin B12, and iron, respectively. 

Kim, S. Y., Je, J. Y., and Kim, S. K. 2007. Purification and characterization of antioxidant peptide from hoki (Johnius belengerii) frame protein by gastrointestinal digestion. /. Nutrit. Biochemistry, 18, 31-38. 

Proteins [From proteios, Greek for primary) are considered the primary material of life, and the relevance and ubiquitous role of peptides (from peptein, Greek for digestion) have been investigated in biochemistry and drug research since their... 

A brilliant success of modern biochemistry has been to show that all or almost all proteins of bovine pancreatic juice are enzymes (1). It may be said in a cursory way that this juice is a solution of enzymes in bicarbonate and that its composition is strictly utilitarian. Bicarbonate is present in order to neutralize hydrochloric acid coming from the stomach and to keep enzymes in solution. Enzymes are present for digesting alimentary products in the intestine. On the other hand, pancreatic juice seems to have been created for the protein chemist s delight, since its proteins are biologically active, relatively simple, and endowed with unusual properties. 

Amide hydrolysis, a very important reaction in biochemistry, is a central reaction in the digestion of proteins and the breakdown of proteins within cells. However, most amide hydrolysis in the body is catalyzed by enzymes rather than by strong acids or bases. 

Developments in mass spectrometry technology, together with the availability of extensive DNA and protein sequence databases and software tools for data mining, has made possible rapid and sensitive mass spectrometry-based procedures for protein identification. Two basic types of mass spectrometers are commonly used for this purpose MALDI-TOF-MS and ESI-MS. MALDI-TOF instruments are now quite common in biochemistry laboratories and are very simple to use, requiring no special training. ESI instruments, usually coupled to capillary/nanoLC systems, are more complex and require expert operators. We will therefore focus on the use of MALDI-TOF-MS, although the sample preparation is identical for both methods. The principle behind the use of MALDI-TOF-MS for protein identification is that the digestion... 

---