Proteins are polymers of amino acids
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Polypeptide Chain
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Proteins are of either a globular shape with the chain of amino acids folded back on itself, or of a rod shape with the chain of amino acids stretched out linearly.
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Ligand Binding
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Ligand is the general term for an atom or molecule that binds with the protein - a single protein may have several binding sites for several ligands - specifically bind to binding sites of a protein due to the shape of the ligand and the complementary shape of the protein. Since the ligand binds loosely, the binding is almost always reversible. Except for a very few ligands, the binding of a ligand to a protein is very specific; that is, only certain molecules can bind with a particular protein and only at specific sites.
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Protein Binding
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Some protein binding sites can bind with several different ligands, and when more than one ligand is present, there is a competition by the ligand for the binding site. As a result of the competition, the biological effects of one ligand may be diminished by the presence of another.
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Binding Site Affinity
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Following binding with a ligand, proteins will undergo a conformational change in their tertiary structure, and, if there are several proteins that have combined to form one larger entity (quaternary structure), the orientation of the proteins with each other will change once a ligand binds. This change in shape will affect the activity or action of the protein.
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Ligand Concentration
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As more substrate is available, more becomes bound to the protein. Typically, this is referred to as saturation. As more of the possible binding sites are filled the saturation becomes greater. If all of the sites are occupied, we have 100% saturation. When we are determining saturation, we do not care what ligand is occupying the site, only that the site is occupied.
Affinity of a ligand determines what percent of the available sites are taken by a particular ligand. A ligand that has greater affinity, will displace those with a lesser affinity. Therefore, in an over saturated solution, that is one where there are more ligands than binding sites, given equal concentrations of ligands, the ligands with the greatest affinity will occupy the most binding sites. The ligand with greater affinity, more than the one with lesser affinity.
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Saturation/Competition
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This set of events is known as competition. That is, ligands compete for the available sites. The ligands with the greatest affinity will bind more often than those with lesser affinity and, thus, occupy a greater number of sites, This is, even though they are both present at the some concentration. As a result of competition, the biological effects of one ligand may be diminished by the presence of another. For example, many drugs produce their effects by competing with the body's natural ligaqnds for binding sites. By competing, occupying the binding sites, the drug decreases the amount of natural ligand that can be bound.
Some reactions within the body are spontaneous such as oxygen dissolving into water; however, most metabolic reactions would occur too slowly to be of benefit were they to occur without the aid of enzymes - enzymes are constructed of protein
Enzymes speed up rates of metabolic reactions by serving as a surface on which the reaction may occur. The molecule [ligand] that binds to an enzyme [protein] is called the substrate. The location of binding of the substrate to the enzyme is called the active site of the enzyme.
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Substrate Enzyme Product
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When an enzyme binds to a substrate [ligand], not only does the enzyme [protein] change shape, but also the substrate changes shape. This change in shape of the enzyme-substrate complex serves to strain specific bonds connecting certain atoms that make up the substrate together. It is this straining that facilitates the breakdown of substances, to produce the product, during catabolism.
Generally, there are unique enzymes for particular substrates; that is, an enzyme required to modify glucose would not be able to modify fructose. This is termed enzyme specificity. Some enzymes can modify more than one substrate, but there is always a preference for one substrate to be modified by a particular enzyme.
The substance interacting with the enzyme is modified; however, except for the reversible conformational change in the protein tertiary or quaternary structure, the enzyme is not modified. Since the enzyme assists to change a substance, but is not itself changed, the enzyme is said to be a catalyst. This catalytic action only increases the rate of reactions; enzymes cannot cause reactions to occur that could not take place without the enzyme. Since the enzyme [catalyst] is not changed, the enzyme may be used multiple times.
If a larger molecule is broken down during catabolism by enzymatic action, energy is released. Anabolism requires energy input in order to allow the enzyme to be effective. Other than this synthesis of new molecules [anabolism], energy is also required for movement (i.e., muscle contraction), and for active transport of substances across membranes.
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Modulation
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Regulation of binding site characteristics is known as modulation. When a ligand binds to a protein, the attracting forces tent to alter the protein's shape. This may occur both at the binding site itself and at other locations on the protein. The term for shape alteration is allosteric. This may change the active, functional site as well as a second regulatory binding site. The ligand that binds to this regulatory site is known as a modulator molecule.
A second way of altering the shape of a protein is by covalent bonding. This is generally of the charged chemical groups to some of the protein's side chains. Such shape alteration and protein activity is known as covalent modulation. The most frequent reaction of this type is accomplished by the addition of a phosphate group, phosphorylation. Any enzyme that mediates protein phosphorylation is called a protein kinase. These enzymes catalyze the transfer of phosphate from a molecule of adenosine triphosphate (ATP) to a hydroxyl group present on the side chain of certain amino acids.
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Site Factors
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There is also a mechanism for removing the phosphate group and returning the protein to its original shape. This dephosphorylation is accomplished by a second enzyme known as phosphoprotein phosphatase.
A reaction will occur more rapidly if there is more substrate present than product, if the energy required for the reaction is low, if the temperature is high, if the proper catalyst [enzyme] is present, and if the proper enzyme is in an active form. The metabolic reactions occurring in the body are reversible; however, if large amounts of energy are required for a particular reaction to occur, the reaction is said to be irreversible.
C O2 + H2O
+ some energy substrate - C02 + H20 protein substrate - protein
H2CO3
product - H2C03
amino acid + large amount of energy
product - amino acid + large amount of energy
The requirements are simple trace elements such as magnesium, iron, zinc, or copper. These cofactors bind to specific binding sites on the enzyme protein causing a conformational change in the enzyme and enabling it to serve as the proper catalyst. Other cofactors include vitamins, which are organic substances that are required in the diet.
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Coenzymes
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In other cases the cofactor is an organic molecule that directly particpates as one of the substrates in the reactionis case the cofactor is termed a coenzyme. Enzymes that require coenzymes catalyze reactions in which a few atoms are either removed from or added to a substrate.
Metabolism are the chemical changes that occur in the body.
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Enzyme Product
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Kinetics has to do with how fast a reaction occurs. We have mentioned that the purpose of the enzyme is to catalyze a reaction and increase the speed, reaction rate.
An enzyme catalyzed reaction will occur when there are both substrate and enzyme available. As substrate is added, more substrate-enzyme complexes are formed, and more product is produced. As the concentration of substrate increases it saturates all of the available binding sites. This is the maximum velocity, Vm, of product production.
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Enzyme Concentration
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If more enzyme is available, the amount of product produced increases. Therefore, although Vm does not change, more product is produced. If we double the amount of enzyme, in a substrated saturated solution, we double the amount of product produced.
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Enzyme Affinity
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Affinity has to do with how well a substrate binds to the enzyme. A substrate with an increased affinity will turnover quicker and thus increse the amount of product produced, Vm is increased.
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Enzyme Factors
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As mentioned previously, modulation impacts the enzyme activity, and, thus, the reaction rate. Modulation is used to control the rate of reaction.
A sequences of reactions called metabolic pathways. Each reaction in the pathway has its own reaction rate. This rate is controlled by the factors previously mentioned. the interesting thing about a pathway is that the speed of the slowest reaction rate in the pathway is the rate limiting step for the whole pathway. That is, the amount of product produced by a series of steps, cannot proceed any faster than the slowest of steps!
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Feedback Inhibition
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Finally, an interesting development with metabolic pathways, is that it is possible for a product of a subsequent step to modulate a previous step. That is, it is possible for a reaction product to inhibit the whole pathway and thus limit the rate of product production.
