The Protein Book: A Complete Guide for the Athlete and Coach Paperback – November 20, The Protein Book: A Complete Guide for the Athlete and Coach examines the topic of protein nutrition for both endurance and strength/power athletes. His other books The Ultimate Diet Consuming the proper amounts, types and timing of protein can impact on all aspects of strength and endurance performance, along with recovery, immune. The Protein Book is a comprehensive look at the issue of protein intake for both strength/power and endurance athletes. Coaches looking for the latest scientific.

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The Protein Book

Title, The Protein Book: A Complete Guide for the Athlete and Coach. Author, Lyle McDonald. Publisher, Lyle McDonald, download a cheap copy of The Protein Book: A Complete Guide for by Lyle McDonald . Free shipping over $ The Paperback of the The Protein Book: A Complete Guide for the Athlete and Coach by Lyle McDonald at Barnes & Noble. FREE Shipping on.

The following is an excerpt from Chapter 3: Basic Protein Metabolism: Protein turnover: The link between protein synthesis and breakdown. Although the amount of tissue in the body tends to remain fairly constant over time, those tissues are actually undergoing an essentially continuous process of breakdown and resynthesis; the two processes together are generally referred to as tissue turnover. This holds for protein-based tissues such as plasma proteins and skeletal muscle which undergo a continuous process of breakdown and resynthesis. Fundamentally what occurs in terms of the amount of these tissues present depends on the long-term relationship between protein synthesis and breakdown. If synthesis exceeds breakdown, there will be an increase in the amount of that protein.

Full-fat cheese is high in both protein and fat while fat-free cheese is almost pure protein. Milk and yogurt contain carbohydrates in addition to the protein; fat content can vary from high to low or zero depending on whether full-fat, low-fat or skim products are chosen. There are also vegetable sources of proteins w i t h beans also called legumes being the primary source; nuts and seeds also contain protein.

Fruits and vegetables both contain trace amounts of protein as well. Since they tend to be a staple of athletic nutrition, I should discuss protein powders and supplements.

In the most general terms, protein is available in supplemental form as either protein powder or free form amino acids. Free form amino acids are simply individual amino acids, either by themselves e. L-glutamine or tyrosine or in some combination. Some companies now sell products containing powdered essential amino acids EAAs or branched chain amino acids BCAAs either alone or in combination.

Other products containing various mixes of amino acids either free form or bonded to one another are also often available. I should mention that, although food technologies and flavoring are improving by leaps and bounds, free form amino acids tend to be fairly vile tasting.

Arginine and ornithine, sold as Growth Hormone GH releasers for years, are both disgustingly bad; quite in fact one company sells a separate product meant solely to cover up their taste.

A product that was once popular, ornithine keto-glutarate OKG has a taste that has been likened to bleach. In contrast, glutamine is very mild and glycine is said to be somewhat sweet. Readers may be wondering what the L- that comes before most amino acids e. L-leucine, L-glutamine stands for.

The Protein Book

Chemically speaking, many molecules in the body come in one of two different shapes, D- or L-. In the human body, only the L-form of nutrients is used; quite in fact, the D-form of some nutrients such as D-carnitine can be toxic to the body. In general, throughout this book I'll drop the L- before individual amino acid names. Protein powders come in three primary forms which are isolates, concentrates and hydrolysates. Hydrolysates are simply isolates or concentrates which have been pre-digested digestion of protein is called hydrolysis by subjecting them to specific enzymes.

Practically speaking, you will typically pay the least for a protein concentrate, more for an isolate and the most for a protein hydrolysate. Because of the presence of free form amino acids in protein hydrolysates, they often have a more bitter taste than either concentrates or isolates. Amino acids: The building blocks of protein Proteins are made up of individual components called amino acids AAs that are attached together in long chains.

In the food supply, there are 20 AAs although more occur within the body 1. For example, 3-methylhistidine is an amino acid generated during muscle protein breakdown; hydroxyproline is made from the breakdown of connective tissue.

Individual amino acids are referred to as peptides. When two amino acids are attached, it is called a di-peptide di means two. Three aminos are a tri-peptide tri means three and anything longer than that is usually just referred to as an oligo or polypeptide oligo means few and poly means many.

Readers may have seen the terms essential amino acids often abbreviated to EAAs and inessential amino acids tossed around the newer terms for this are indispensable and dispensable.

In dietary terms, an essential nutrient is one that is not only required by the body for survival but cannot be made by the body; thus it is essential that they are obtained from the diet. In contrast, inessential nutrients can be made within the body but are still required for health or survival ; thus it is not essential that they be obtained from the diet.

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Of the 20 total amino acids, 8 are considered essential with the other 12 being inessential. Although I don't want to get into huge detail here, this topic is actually a bit more complicated than I've made it sound. Under specific circumstances, an inessential amino acid can become essential 2 and there are other categories that are sometimes used. For example, glutamine is normally considered an inessential AA, the body can make sufficient amounts from other sources and it needn't be obtained from the diet.

However, under specific conditions such as high stress, trauma, or burn damage, the body may require more glutamine than it can produce. Under those conditions, extra glutamine must come from the diet typically via supplementation. Thus glutamine is described as being conditionally essential: under certain conditions, it becomes an essential AA.

For the most part, athletes on high protein intakes from quality sources won't need to worry about such details and I'm mentioning it here only for completeness. A list of the essential and inessential AAs appears in Table 1. These are sometimes referred to as the branched chain amino acids BCAAs and play a special role in human physiology and muscle growth.

I'll discuss the BCAAs in some detail in a later chapter. What is protein used for in the body Protein's primary use in the body is structural; that it, protein is used for the production of other substances in the body 1.

Most athletes are probably aware that their skeletal muscles are made up of protein but that's not all. Both cardiac heart and smooth surrounding blood vessels and such muscle are made of protein. Skin and hair both contain a lot of protein as well.

Additionally, many of the hormones in the body called peptide hormones are made from protein. This includes insulin, glucagon, growth hormone GH and insulin like growth factor IGF which are all simply long chains of amino acids linked together, catecholamine hormones, adrenaline and noradrenaline, are made from the amino acid tyrosine.

Albumin, which is used to transport many hormones in the bloodstream, is also made from protein. This change in shape is often crucial to the function of the protein, as we see later.

Although a protein chain can fold into its correct conformation without outside help, protein folding in a living cell is often assisted by special proteins called molecular chaperones. These proteins bind to partly folded polypeptide chains and help them progress along the most energetically favorable folding pathway. Chaperones are vital in the crowded conditions of the cytoplasm , since they prevent the temporarily exposed hydrophobic regions in newly synthesized protein chains from associating with each other to form protein aggregates see p.

However, the final three-dimensional shape of the protein is still specified by its amino acid sequence: chaperones simply make the folding process more reliable. Proteins come in a wide variety of shapes, and they are generally between 50 and amino acids long. Large proteins generally consist of several distinct protein domains—structural units that fold more or less independently of each other, as we discuss below. Panel pp. Constructed from a string of amino acids, the structure is displayed as A a polypeptide backbone model, B a ribbon model, C a wire model that includes the amino acid side chains, and D a space-filling model.

Each of the three horizontal rows shows the protein in a different orientation, and the image is colored in a way that allows the polypeptide chain to be followed from its N-terminus purple to its C-terminus red. But the description of protein structures can be simplified by the recognition that they are built up from several common structural motifs, as we discuss next. Both patterns were discovered about 50 years ago from studies of hair and silk. Thus, they can be formed by many different amino acid sequences.

In each case, the protein chain adopts a regular, repeating conformation. These two conformations, as well as the abbreviations that are used to denote them in ribbon models of proteins, are shown in Figure Both of these structures are common in proteins. This gives rise to a regular helix with a complete turn every 3.

Long rodlike coiled-coils provide the structural framework for many elongated proteins. The structure of a coiled-coil. The Protein Domain Is a Fundamental Unit of Organization Even a small protein molecule is built from thousands of atoms linked together by precisely oriented covalent and noncovalent bonds, and it is extremely difficult to visualize such a complicated structure without a three-dimensional display.

For this reason, various graphic and computer-based aids are used. A CD-ROM produced to accompany this book contains computer-generated images of selected proteins, designed to be displayed and rotated on the screen in a variety of formats. Biologists distinguish four levels of organization in the structure of a protein.

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The amino acid sequence is known as the primary structure of the protein. Studies of the conformation , function, and evolution of proteins have also revealed the central importance of a unit of organization distinct from the four just described.

This is the protein domain , a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure.

A domain usually contains between 40 and amino acids, and it is the modular unit from which many larger proteins are constructed. The different domains of a protein are often associated with different functions. This protein has four domains: the SH2 and SH3 domains have regulatory roles, while the two remaining domains are responsible for the kinase catalytic activity.

Later in the chapter, we shall return to this protein, in order to explain how proteins can form molecular switches that transmit information throughout cells. Figure A protein formed from four domains.

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In the Src protein shown, two of the domains form a protein kinase enzyme, while the SH2 and SH3 domains perform regulatory functions. A A ribbon model, with ATP substrate in red. B A spacing-filling model, with more The smallest protein molecules contain only a single domain , whereas larger proteins can contain as many as several dozen domains, usually connected to each other by short, relatively unstructured lengths of polypeptide chain.

Figure presents ribbon models of three differently organized protein domains. Each different combination is known as a protein fold. So far, about different protein folds have been identified among the ten thousand proteins whose detailed conformations are known. Ribbon models of three different protein domains. A Cytochrome b, a single-domain protein involved in electron transport in mitochondria.

B The NAD-binding domain of the enzyme lactic more For a typical protein length of about amino acids, more than different polypeptide chains could theoretically be made.

This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe. Only a very small fraction of this vast set of conceivable polypeptide chains would adopt a single, stable three-dimensional conformation —by some estimates, less than one in a billion.

The vast majority of possible protein molecules could adopt many conformations of roughly equal stability, each conformation having different chemical properties. And yet virtually all proteins present in cells adopt unique and stable conformations.

How is this possible? The answer lies in natural selection. A protein with an unpredictably variable structure and biochemical activity is unlikely to help the survival of a cell that contains it. Such proteins would therefore have been eliminated by natural selection through the enormously long trial-and-error process that underlies biological evolution. Because of natural selection, not only is the amino acid sequence of a present-day protein such that a single conformation is extremely stable, but this conformation has its chemical properties finely tuned to enable the protein to perform a particular catalytic or structural function in the cell.

Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost. Proteins Can Be Classified into Many Families Once a protein had evolved that folded up into a stable conformation with useful properties, its structure could be modified during evolution to enable it to perform new functions. This process has been greatly accelerated by genetic mechanisms that occasionally produce duplicate copies of genes, allowing one gene copy to evolve independently to perform a new function discussed in Chapter 7.

This type of event has occurred quite often in the past; as a result, many present-day proteins can be grouped into protein families, each family member having an amino acid sequence and a three-dimensional conformation that resemble those of the other family members.

Consider, for example, the serine proteases, a large family of protein -cleaving proteolytic enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, and several proteases involved in blood clotting. When the protease portions of any two of these enzymes are compared, parts of their amino acid sequences are found to match.

The similarity of their three-dimensional conformations is even more striking: most of the detailed twists and turns in their polypeptide chains, which are several hundred amino acids long, are virtually identical Figure The many different serine proteases nevertheless have distinct enzymatic activities, each cleaving different proteins or the peptide bonds between different types of amino acids.

Each therefore performs a distinct function in an organism. Figure The conformations of two serine proteases compared. The backbone conformations of elastase and chymotrypsin. Although only those amino acids in the polypeptide chain shaded in green are the same in the two proteins, the two conformations are very similar more The story we have told for the serine proteases could be repeated for hundreds of other protein families.

In many cases the amino acid sequences have diverged much further than for the serine proteases, so that one cannot be sure of a family relationship between two proteins without determining their three-dimensional structures. Because they are identical in only 17 of their 60 amino acid residues, their relationship became certain only when their three-dimensional structures were compared Figure Figure A comparison of a class of DNA-binding domains, called homeodomains, in a pair of proteins from two organisms separated by more than a billion years of evolution.

A A ribbon model of the structure common to both proteins.

The various members of a large protein family often have distinct functions. Some of the amino acid changes that make family members different were no doubt selected in the course of evolution because they resulted in useful changes in biological activity, giving the individual family members the different functional properties they have today.

In addition, since mutation is a random process, there must also have been many deleterious changes that altered the three-dimensional structure of these proteins sufficiently to harm them. Such faulty proteins would have been lost whenever the individual organisms making them were at enough of a disadvantage to be eliminated by natural selection.

The Protein Book: A Complete Guide for the Athlete and Coach

Protein families are readily recognized when the genome of any organism is sequenced; for example, the determination of the DNA sequence for the entire genome of the nematode Caenorhabditis elegans has revealed that this tiny worm contains more than 18, genes. Through sequence comparisons, the products of a large fraction of these genes can be seen to contain domains from one or another protein family; for example, there appear to be genes containing protein kinase domains, 66 genes containing DNA and RNA helicase domains, 43 genes containing SH2 domains, 70 genes containing immunoglobulin domains, and 88 genes containing DNA-binding homeodomains in this genome of 97 million base pairs Figure Figure Percentage of total genes containing one or more copies of the indicated protein domain, as derived from complete genome sequences.

Note that one of the three domains selected, the immunoglobulin domain, has been a relatively late addition, and its relative more In , we did not know the order of the amino acids in a single protein , and many even doubted that the amino acids in proteins are arranged in an exact sequence.

In , the first three-dimensional structure of a protein was determined by x-ray crystallography. Now that we have access to hundreds of thousands of protein sequences from sequencing the genes that encode them, what technical developments can we look forward to next? It is no longer a big step to progress from a gene sequence to the production of large amounts of the pure protein encoded by that gene. Thanks to DNA cloning and genetic engineering techniques discussed in Chapter 8 , this step is often routine.

But there is still nothing routine about determining the complete three-dimensional structure of a protein. The standard technique based on x-ray diffraction requires that the protein be subjected to conditions that cause the molecules to aggregate into a large, perfectly ordered crystalline array—that is, a protein crystal.

Each protein behaves quite differently in this respect, and protein crystals can be generated only through exhaustive trial-and-error methods that often take many years to succeed—if they succeed at all. Membrane proteins and large protein complexes with many moving parts have generally been the most difficult to crystallize, which is why only a few such protein structures are displayed in this book. Increasingly, therefore, large proteins have been analyzed through determination of the structures of their individual domains: either by crystallizing isolated domains and then bombarding the crystals with x-rays, or by studying the conformations of isolated domains in concentrated aqueous solutions with powerful nuclear magnetic resonance NMR techniques discussed in Chapter 8.

From a combination of x-ray and NMR studies, we now know the three-dimensional shapes, or conformations, of thousands of different proteins. By carefully comparing the conformations of known proteins, structural biologists that is, experts on the structure of biological molecules have concluded that there are a limited number of ways in which protein domains fold up—maybe as few as As we saw, the structures for about of these protein folds have thus far been determined ; we may, therefore, already know half of the total number of possible structures for a protein domain.

A complete catalog of all of the protein folds that exist in living organisms would therefore seem to be within our reach.

Sequence Homology Searches Can Identify Close Relatives The present database of known protein sequences contains more than , entries, and it is growing very rapidly as more and more genomes are sequenced—revealing huge numbers of new genes that encode proteins. Powerful computer search programs are available that allow one to compare each newly discovered protein with this entire database, looking for possible relatives.

Homologous proteins are defined as those whose genes have evolved from a common ancestral gene , and these are identified by the discovery of statistically significant similarities in amino acid sequences.

With such a large number of proteins in the database, the search programs find many nonsignificant matches, resulting in a background noise level that makes it very difficult to pick out all but the closest relatives.

Figure The use of short signature sequences to find homologous protein domains. The two short sequences of 15 and 9 amino acids shown green can be used to search large databases for a protein domain that is found in many proteins, the SH2 domain. Here, the more These protein comparisons are important because related structures often imply related functions.

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