Amino Acids and Proteins

Since proteins constitute the majority of tissues in the body and since these tissues are constantly in protein flux, proteins are degraded and synthesized within all tissues on a regular basis. Some of the amino acids that are degraded can be recycled by the liver and used again for other biosyntheses, but a significant portion of this protein cannot be replaced.

Through a process known as transamination, the liver synthesizes amino acids. During this reaction, an amino group from glutamic acid is transferred to an alpha keto acid, which is a precursor for amino acid sythesis. Aminotransferases, which are derived from vitamin B6, are the enzyme responsible for the reaction. The amino acids that can be produced through transanimation include alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine. These are obviously the non-essential amino acids, since they can be synthesized in the body.

When the body's energy sources are low, it begins to degrade proteins for use as an alternative energy source. Amino acids can be classified as glucogenic or ketogenic.

Glucogenic amino acids can be degraded to pyruvate or an intermediate in the Krebs Cycle. They are named glucogenic because they can produce glucose under conditions of low glucose. This process is also known as gluconeogenesis, or the production of "new glucose." Amino acids form glucose through degradation to pyruvate or an intermediate in the Krebs Cycle. The intermediates can then be converted to oxaloacetate, the main precursor for gluconeogenesis. The following amino acids are glucogenic: alanine, cysteine, glycine, serine, threonine, tryptophan, asparagine, aspartate, phenylalanine, tyrosine, isoleucine, methionine, threonine, valine, arginine, glutamate, glutamine, histidine, and proline.

In contrast, ketogenic amino acids can produce ketones when energy sources are low. Some of these amino acids are degraded directly to ketone bodies such as acetoacetate (see ). They include leucine, lysine, phenylalanine, tryptophan, and tyrosine. The other ketogenic amino acids can be converted to acetyl CoA. Acetyl CoA has several different fates, one of which is the conversion to acetoacetate. Although not a preferential energy source, acetoacetate can be metabolized by the brain and muscle for energy when blood glucose is low. Acetoacetate cannot be used in gluconeogenesis, since acetyl CoA cannot be converted directly to oxaloacetate.

When energy sources are high, both glucogenic and ketogenic amino acids are converted to fatty acids through the intermediate acetyl CoA. Other amino acids that are degraded to intermediates in the Krebs Cycle are siphoned off into the production of urea, a nitrogenous carboxyl compound that is filtered through the kidneys and secreted in the urine.

Blood proteins such as albumin and globulin function to maintain fluid balance in the body. When the concentrations of proteins in the bloodstream are low, the fluid in the blood (serum) begins to seep into surrounding tissue. Proteins in the blood can counteract this effect by increasing the osmotic potential and forcing fluid back into the bloodstream. Therefore, low amounts of protein in the blood cause edema, a condition that is characterized by an abnormal amount of fluid in the tissue and extracellular space. Edema is seen in starvation, low calorie diets, and diseases like AIDS that decrease the amount of circulating antibodies and albumin.

Many hormones are composed of polypeptide chains. The beta cells in the pancreas produce the peptide hormone insulin. Insulin facilitates glucose uptake in cells and promotes the synthesis of glycogen and fatty acids. Diabetics must inject the peptide hormone insulin because it will be degraded into amino acids in the stomach and small intestine if taken orally. Other examples of peptide signal molecules include neurotransmitters, a class of molecules that are produced and released at nerve endings in the brain and autonomic nervous system.

Enzymes are an entirely different class of proteins. Enzymes catalyze biological reactions by increasing the reaction rates by factors of at least a million. Since most reactions in the body proceed at imperceptible rates without enzymes, it is critical that these proteins be present in sufficient quantities for proper functioning of cells.

How are enzymes so efficient and fast? First, enzymes are highly specific for their substrates. Substrates are any molecules for which the enzyme binds preferentially or with a high affinity. Enzymes are able to bind specific substrates because they form deep pockets or clefts that are complementary to the three dimensional substrate conformations. Since the enzyme pocket is complementary to the substrate, a large number of noncovalent, dipole-dipole, and Van der Waal interactions can occur, favoring enzyme-substrate binding.

The second reason for the high catalytic rate of enzymes is that they are able to stabilize transition state intermediates. By stabilizing these intermediates, enzymes are able to decrease the activation energy required for the reaction to occur. Upon reaching its high-energy transitional state, the bound substrate can be easily converted to the cell's desired product, which is then released to meet the needs of the cell. These reactions can take place on the order of microseconds to nanoseconds. In fact, many enzymes are so efficient and fast that they approach the diffusion-controlled limit, the rate at which substrate diffusion cannot keep up with the rate at which the enzyme catalyzes the reaction. Enzymes like these have reached catalytic perfection.

Besides their active sites, many enzymes have other locations or crevices where molecules can bind. Regulatory sites, also called allosteric sites, are places other than the active site of the enzyme that serve to regulate enzymatic activity.

The end product in a series of reactions catalyzed by different enzymes at each step may bind to the allosteric site and inhibit the activity of the first enzyme in the pathway. When an inhibitory molecule binds to an allosteric region on the enzyme it can cause the active site of the enzyme to close up and become inactive. This type of negative feedback is used to control levels of products from reaching levels that are too high or unnecessary.

Allosteric sites can also be areas that cause the stimulation of enzymatic rates. When these allosteric sites are occupied, the enzyme's active site may change in shape, becoming more efficient or receptive as a catalyst.

Further regulation of enzymes comes in the form of covalent modification. Many enzymes are regulated by reversible attachment of phosphoryl groups to serine andthreonine amino acid residues. Specific types of enzymes called kinases phosphorylate add phosphoryl groups to other enzymes while phosphatases remove phosphate groups. By adding just one covalent bond to the enzyme, its activity can be drastically changed. For example, during levels of low blood glucose, glucagon and epinephrine are secreted into the blood and bind to muscle and brain cell receptors. Upon binding, these hormones cause a cascade of effects within the cell, which results in the phosphorylation of a number of proteins, including a series of enzymes involved in metabolism. All phosphorylations act to increase the rate of enzymes involved in glycogen and triglyceride degradation while inhibiting the rate of enzymes involved in glycolysis and the Citric Acid Cycle. In effect, the addition of phosphate groups to these enzymes causes the level of blood glucose to increase.

Proteins are also abundant within biological membranes. Many cellular receptors, channels, and pumps are bound to membranes. Since these proteins span across a nonpolar environment, many of their residues facing this environment are also nonpolar, allowing more favorable interactions to occur. Both channels and pumps are involved in the regulation of fluids and ions within and outside the cell. However, they differ in many key respects. Channels allow ions to flow from an area of high concentration to an area of low concentration. This is a completely passive process. Pumps, on the other hand, force ions up their concentration gradient from a region of lower concentration to a region of higher concentration. This process is called active transport and usually requires the energy of adenosine triphosphate (ATP) in order to overcome the energy barrier.

A classic example of a pump is the sodium potassium pump. Since during the excitation of neurons sodium ions are constantly traversing into the cell and potassium ions are leaving the cell, the resting levels of these ions must be constantly restored. Unlike potassium, which is present in larger proportions outside the cell, sodium is in much higher concentrations outside the cell. The sodium potassium pump pushes sodium and potassium against their concentration gradients by binding ATP and hyrolyzing it for energy.

Proteins are also important in the immune response. There are two types of important proteins the immune system uses to scan the vast network of molecules in our body and determine self from nonself. In the first stage of the immune response, the body recognizes circulating foreign particles (antigens) through antibodies, which are produced by plasma cells (B lymphocytes). The ability of plasma cells to produce millions of different antibodies is inherent from birth; virtually any circulating antigen will be bound by its complementary antibody. Once bound by antibody, the antigen can be either consumed by macrophages or be further bound by mature plasma cells to stimulate the production of even more antibodies. Mature cells are stimulated to divide and form clones, which act as an immunological memory against further attack from identical antigens. Like enzymes, the amino acid sequence of the antibody determines its specificity. The whole recognition and response of plasma cells to a new infection is called the humoral response.

The second stage of immune response is called the cellular immune response. In the cellular response, T lymphocytes (killer T cells) bind to foreign particles displayed on the surface of cells and destroy the contaminated cell. Helper T cells also bind to the foreign particles displayed on the surface of cells and stimulate the humoral response by helping plasma cells to proliferate. Why is the cellular response necessary if antibodies can recognize antigens and mark them for destruction? The answer lies in the fact that many of the viruses and bacteria that invade the body are found in greater concentrations within cells, preventing antibodies from reaching them. The immune system has adapted to this problem by cutting some of the foreign particles up into peptides to be displayed at the surface of the infected cell by a protein known as the major histocompatibility complex (MHC). Killer and helper T cells are specialized for recognizing peptides bound to these proteins, increasing the speed and effectiveness of the immune response.