The Effects of Ph and Salinity on Enzyme Function free essay sample

Metabolism is the totality of all of an organism’s chemical reactions. Chemical reactions occur due to enzymes, a substance which acts as a catalyst in driving chemical reactions in order to produce a desired product (Campbell and Reece, 2002). A catalyst is usually a protein; however, some catalytic molecules counter this generalization. A discovery made in the early nineteen- nineties revealed that ribozymes, molecules made of ribonucleic acid (RNA), act as a catalyst in the transformation of an RAN molecule. Scientists concluded from the new discovery that the informational molecule RNA may have once been able to function without proteins (Dousti, 1995). However, enzymes are strictly proteins, and thus are subject to denaturation in certain conditions (Campbell and Reece, 2002). 1 Figure 1 Enzymes are granted the task of breaking bonds within the monomers of substrate, the molecule upon which the enzyme is acting. When the substrate and the enzyme bind, the substrate-enzyme complex is formed. We will write a custom essay sample on The Effects of Ph and Salinity on Enzyme Function or any similar topic specifically for you Do Not WasteYour Time HIRE WRITER Only 13.90 / page The substrate binds to the enzyme’s active site, which is the part of the protein in which the enzyme fits. Scientists have introduced multiple models that attempt to illustrate exactly how the enzyme and substrate fit together (See figure 1). In the lock and key model, the substrate and enzyme fit together perfectly. In the induced fit model, however, the enzyme changes to fit the substrate, which secures the substrate-enzyme complex even further. Induced fit allows the enzyme to position the substrate so that its ability to catalyze is enhanced (Campbell and Reece, 2002). Once the enzyme has broken down or built up the reactant(s) and released the product(s), it bonds, unaffected, to another substrate (What are Enzymes? , 2010). In order for an enzyme to work efficiently, it must reduce the activation energy, or the initial energy input to start the reaction and break or form the bonds between monomers. The quantity of activation energy needed to start a reaction is very great, which is the reason that reactions do not occur by themselves. The enzyme applies stress to certain chemical bonds of the molecules. The bending of such bonds decreases the amount of energy, which is usually thermal, needed to begin the reaction. Less input is required for the same reaction (See figure 2). A real life situation to describe this is pushing a boulder up a hill. The initial energy input is great and may require the use of machinery or many men. However, if the hill were to be diminished, the boulder would be able to get to its desired location with much less effort. In enzymes, a catalyzed reaction still has the same change in free energy or energy available for use (called ? G) as an unanalyzed one, but with less free energy going into the reaction. Figure 2 When a reaction is endergonic, free energy is made available (as shown by –? G, see figure 2). An exergonic reaction requires an input of energy and in the end does not make any energy available. Enzymes are very specific in the molecules with which they bind. In fact, they can even recognize very similar molecule, such as isomers, as not being their substrate â€Å"partner†. This specificity leads to many different types of enzymes all contributing to the chemical processes of life. A complex molecule is passed through a metabolic pathway consisting of many enzymes in order to get to the final product. Figure 2 Enzymes are naturally controlled so that only needed products are made. Allosteric enzymes, which are constructed from a few polypeptide chains, control the rates of reactions in metabolic pathways and when enzymes are active. Allosteric enzymes consist of inhibitors as well as activators. They bind to a specific site on an enzyme, called the allosteric site, and change the enzymes shape so that it is either active or inactive, depending on the allosteric device type. Feedback inhibition makes sure that chemical resources are not wasted. In this type of inhibition, the end product of a metabolic pathway binds to the allosteric site on the enzyme in order to make sure that the enzyme does not continue to make more of the primary intermediate, the resultant molecule after the first reaction on a metabolic chain of reactions (Campbell and Reece, 2002). Competitive and non-competitive inhibitors affect enzymatic behavior as well. Competitive inhibitors bind directly to the active site of an enzyme, impeding the substrate’s access. Some inhibitors are irreversible, and therefore are toxic to the body. However, others can be reversed, usually by the substrate becoming greater in concentration and gaining more access to the enzyme when it releases the inhibitor. A non-competitive inhibitor binds to a site other than the active site, but in doing so changes the enzyme’s shape so that it is less effective or completely unable to create a complex with the substrate. Cofactors, inorganic molecules, and coenzymes, organic, bind either temporarily or permanently to the enzyme’s active site and help the enzyme in catalysis (Campbell and Reece, 2002). Their presence is required for some enzymes; for others, they expedite the reaction. In certain reactions, their role is simply to carry electrons and transfer them to certain compounds (Nishiura, UCNY). Certain conditions are instrumental to enzymatic functions because of their complex structure as a protein. These conditions include pH, temperature, salinity, enzyme concentration, and substrate concentration. 3 Figure 3 Because it is a protein, an enzyme is affected by pH. The amounts of hydrogen cations, which can make a substance more or less acidic, disrupt the protein’s structure. The acidity affects the structure because it changes bonds between amino acids that were originally formed in response to the charges of the radical groups. Every enzyme has an optimal pH, or a value at which it performs the most efficiently (See figure 3). In human enzymes, for example, the optimal pH ranges from 6 to 8. Regarding temperature, the optima value is known by the greatest number of collisions made between molecules. Extreme heat as well as coldness contribute to the decrease of collisions, although each in a different manner. When a substance is heated up, the atoms move faster. Bonds within the amino acids and the polypeptide chain are affected by the increase in heat. The bonds between the enzyme and substrate are affected as well; the hydrogen and ionic bonds break. The enzymes are not able to function because their active site is disoriented, and the amount of product production decreases. In cold temperatures, the cause is simpler; the enzymes and substrates simply move slower, which allots more time per reaction. Changes in salinity add or remove cations and anions, which, as previously stated about pH, change all protein structures, especially secondary and tertiary structures. The concentrations of enzymes and substrates rely heavily on each other for their efficiencies. For a given amount of substrate, the reaction rate increases as the enzyme increases until all substrate is being broken down and some enzymes are unable to bind with substrate. Likewise, for a given amount of enzyme, the reaction rate increases as more substrate is added, until all enzymes are occupied (Trice, 2012). In part one of the lab, enzyme reaction rate was determined by observing the amount of oxygen released. Guaiacol, an indicator for oxygen production, was used so that data could be collected in the form of color. The absorbance level of the solution was taken at each given time for concrete data. No variables were tested, but the equipment (a spectrometer) was engaged and the rate of enzyme reaction was proven to increase and decrease with time. This lab constituted the rate of reaction without any variable affecting the results. Its purpose was to establish a baseline to which further data could be compared. In part two of the lab, pH’s effect on enzymes was tested in order to determine optimal pH. It was hypothesized that the greatest reaction would occur at pH 7 of the three pH’s tested (pH4 and pH 10 were also tested) because it lies in the center of the pH scale and traditionally the graph of pH in relation to enzymatic rate is a bell curve, signifying that the more basic or acidic a substance becomes, the less reactions take place. The majority of enzymes are in q rather neutral environment. In the third part of the lab, salinity’s affects on enzymes were explored. It was hypothesized that the rate of reaction would steadily decrease because of previous knowledge that salinity’s charges affects charged amino acids negatively. With the results came a better understanding of enzymatic function, experimental process, and an illustration of the measure of enzymatic reaction. Methods Part One- Control Group: How does peroxidase function under normal conditions? Materials: Turnip peroxidase; 0. 1% hydrogen peroxide; guaiacol; distilled water; three test tubes and test tube rack; timer; 1, 5, and 10 mL graduated pipettes; and a spectrometer. Two test tubes were marked with one labeled â€Å"substrate† and the other â€Å"enzyme†. To the substrate test tube, 7 mL of distilled water, 0. 3 mL of 0. 1% hydrogen peroxide, and 0. 2 mL of guaiacol were added and then gently mixed. To the enzyme tube, 6 mL of distilled water and 1. 5 mL of peroxidase were added and then the tube was gently mixed. Next, the two test tubes were combined at the same time and the time immediately began to be recorded. For five minutes after the initial observation, the color was observed at one minute increments and recorded in photo format. The reading of absorbance level, or the amount of light that a substance absorbs, was taken every minute as well to determine more specifically the shade of color that the guaiacol propagates. This was done through the aid of a spectrometer. Part Two- pH: How does acidity affect enzymatic function? Materials: Turnip peroxidase; 0. 1% hydrogen peroxide; guaiacol; buffers of pH: 4, 7, and 10; distilled water; 9 test tubes and a test tube rack; timer; 1, 5, and 10 mL graduated pipettes; and a spectrometer. To prepare the test tubes, follow the procedure for the initial test, substituting the appropriate pH solution (of the procedure is to test pH 4, add pH 4) for distilled water in the enzyme tube. Next, combine the substrate and enzyme tubes into a clean test tube and immediately begin to record the time. For five minutes after the initial observation, the color was observed at one minute increments and recorded in photo format. The reading of absorbance level, or the amount of light that a substance absorbs, was taken every minute as well to determine more specifically the shade of color that the guaiacol propagates. This was done through the aid of a spectrometer. Do the same for each pH solution. Part Three- Salinity: How does salt concentration affect the reaction rate of enzymes? Materials: 13ml of water, . 3ml of hydrogen peroxide, guaiacol, clean pipettes, 1. 5 ml of turnip peroxidase, 10% salt concentration solution (. 6 ml of salt in 6 mL of water), 5% salt concentration solution(. 3ml of salt in 6 mL of water), 2% salt concentration solution (. 12ml of salt in 6 mL of water), Spectrometer, 9 test tubes, 10ml graduated cylinder. One test tube was labeled substrate and the other enzyme. To make substrate, 0 . 7ml of water, 0. 3ml of hydrogen peroxide, and 0. 2ml of guaiacol were added to the substrate test tube and were gently mixed. To make enzyme, add 6 ml of water with salt solution (2%, 5%, or 10% depending on the experiment) and 1. 5ml of peroxidase to the test tube containing the peroxidase. Next, the substrate and enzyme tubes were combined into a clean test tube and immediately begin to record the time. For five minutes after the initial observation, the color was observed at one minute increments and recorded in photo format.