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Protein Structure Lab Report Essay

Task 1 • Describe the structure of an enzyme as a protein, in terms of tertiary/ quaternary structures. 1) Primary Structure This is in reference to the order of way that amino acids are connected to form a protein. These are built up from 20 amino acids, and follow these structures o A carbon (the alpha carbon) bonded to the four groups below: 0 A hydrogen atom (H) o A Carboxyl group (-COOH) o An Amino group (-NH2) OA “variable” group or “R” group 2) Secondary Structure This is in reference to the fold like structure of a polypeptide chain that gives the protein a 3d like shape. There is 2 types of secondary structure which are: Alpha Helix This would resemble a coiled spring which is secured by hydrogen bonding in a polypeptide chain.

Beta Pleated Sheet This would resemble folds/pleats that is held together again by a hydrogen bond between a polypeptide of the folded chain that lie next to each other. 3) Tertiary Structure This is in reference to the 3d structure. This contains 7 types of bonds that hold the protein within the structure. Hydrophobic interactions contribute to the shape of the protein. The R group of the amino acids can be hydrophobic (water disliking) or hydrophilic (water liking). The hydrogen bonds within the polypeptide chain and between the r groups will avoid water and move to the centre of the protein the hydrogen bond assists to stabilize the structure by holding the protein in shape which are created by the hydrophobic reactions.

Ionic Bonding can develop because of the protein folding as the positive and negative charged R groups come close to one another. Folding can also result in Covalent bonding between the R groups of Cysteine amino acids. This forms a disulphide bridge. Interactions called Van der Waals force assist in the stabilization of protein structure. These interactions become polarised. These forces contribute to the bonding that occurs between the molecules. 4) Quaternary Structure This is in reference to the structure of a protein macromolecule formed by interactions. These interactions are between multiple polypeptide chains. Each polypeptide chain is referred to as a subunit. Proteins with quaternary structure may consist of more than one of the same type of protein subunit.

They may also be composed of different subunits. Haemoglobin is an example of a protein with quaternary structure. Haemoglobin, found in the blood, is an iron containing protein that binds oxygen molecules. It contains four subunits: tw subunits and two beta subunits. • Explain the active site of an enzyme and why and how it is able to bond to its substrate molecule. The specific reaction they speed up takes place in a small part of the enzyme which is the active site while the rest of the protein holds the active site within shape. In the chemical reaction a substrate S is converted to a product P S-P and vice versa. Within an reaction which can be catalysed by an enzyme the substrate binds to the active sire of an enzyme to form enzyme substrate complex. • Describe both the ‘lock and key’ and ‘induced fit’ models of enzyme action.

The enzyme will only bind that particular substrate because other molecules cannot fit into the active site the substrate then reacts and turns into a product which is still attached to the enzyme. The final product is then released. This is the lock and key mechanism. The enzyme is left with an empty active site that then starts the process again. The active site changes shape when the substrates molecules fits into it. This distorts the substrate in the active site, turning the molecule half way through into the product. This distorted substrate is called the transition state. The transition state is more likely to turn into the product than the substrate. This is called the induced fit mechanism.

If the reaction is made more likely for a variety of reasons If a bond in the substrate needs to be broken then the enzyme might stretch and weaken it Alternatively the enzyme can change the ph water concentration or change the active site. • Make use of good illustrations and diagrams throughout. The diagram below shows the lock and key mechanism: Task 2 • You will demonstrate from a series of practical exercises how pH and temperature affect enzyme activity. Complete the two practical experiments attached to the assignment. • Using the results you obtained in practical 1 (Investigating the effects of temperature on enzyme activity), write a conclusion that includes: a. A graph to illustrate what happens to enzyme activity with increasing temperature and PH. b. Indicate from your results, what the optimal temperature for enzyme activity was. PH was 4 and Temperature was 70 degrees C.

What happens to the enzyme activity at temperatures higher than the optimal temperature/PH? PH Most proteins, and therefore enzymes, are active only within a narrow pH range usually between 5 and 9. Several factors are influenced directly by the pH in which the reaction takes place.. the binding of substrate to the enzyme • The ionization states of the amino acid residues involved in the catalytic activity of the enzyme. • the ionization of the substrate • Variation in the protein structure at extreme pH. Temperature The temperature range over which enzymes show activity is limited between the melting point (0oC) and boiling point (1000C) of water. If a temperature is too low, there can be no noticeable reaction rate since the enzyme is operating at a temperature far below its optimum. If the temperature at which the enzyme is operating at is well above 1000C, then thermal deactivation can occur.

Thermal deactivation of enzymes limits their useful lifetime in processing environments. Therefore, it is important in many process design and manufacturing levels to have the correct temperature of reaction. If the reaction temperature is too high, the enzymes will eventually deactivate in an irreversible way and thus halting the reaction from taking place. For many enzymes found within mammals, the optimum temperature is 370C, but deactivation can occur as low as 45 to 550C. Deactivation of enzymes may be irreversible or reversible. In terms of enzyme structure, explain in detail how the enzyme rates are affected by temperature. An increase in temperature results in more kinetic energy of the enzyme and the substrate.

More kinetic energy results in more collisions between the enzyme and the substrate. In turn, the number of successful collisions increases and more enzyme-substrate complexes form. Therefore an increase in temperature increases the rate at which enzyme substrate complexes form. However, all enzymes have an optimum temperature at which it will work best and favour the activity. Eg. Pepsin, an enzyme which works in the stomach has an optimum temperature of between 30-40oC,. Although, beyond this optimum temperature, enzyme activity starts to decrease. This is due to the atoms in the proteins making up the enzyme having too much kinetic energy. The atoms start to vibrate a lot, and bonds holding the protein together begin to break.

This changes the shape of the enzyme, and in turn changes the shape of the active site, hence enzyme-substrate complexes can no longer form. So, the rate of enzyme activity decreases once temperature is above its optimum temperature. There is a general rule that every 100C increase makes the rate double, until the optimum temperature of course. This is known as the Q10 effect. Explain how and why changes in pH detrimentally affect enzyme structure. Changes in pH also alter an enzyme’s shape. Different enzymes work best at different pH values. The optimum pH for an enzyme depends on where it normally works.

For example, intestinal enzymes have an optimum pH of about 7.5. Enzymes in the stomach have an optimum pH of about 2. Outside these ranges they would denature. Changes in pH may not only affect the shape of an enzyme but it may also change the shape or charge properties of the substrate so that either the substrate cannot bind to the active site or it cannot undergo catalysis. Furthermore the pH changes cause the breaking of the ionic bonds in the tertiary structure of the enzyme, meaning it loses shape and changes to the amino acids within the active site mean its substrate will no longer fit, therefore enzyme-substrate complexes can no longer be formed and eventually, enzyme function stops and the enzyme is denatured.

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