Biological+Chemicals+and+enzymes

** 3.6 **** Enzymes **
Globular protein Biological catalyst Speeds up biochemical/ metabolic reactions Unaltered in reaction
 * 3.6.1 Define enzyme and active site **
 * __ Enzymes __**



Specific area where substrate binds Specific for a specific substrate Depends on protein structure.
 * __ Active Site __**

**3.6.2 Explain enzyme-substrate specificity (the lock-and-key model can be used as a basis for the explanation. Refer to the 3-D struc**ture).

Substrate fits into the active site As the substrate fits into the active site – it is known as the ‘lock-and-key’ hypothesis. 3D-shape of protein determines shape of active site Other substrates will not fit into the active site – hence enzymes are specific for their substrate.

**3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity.**

Enzymes have an optimum temperature at which they work At low temperatures enzymes are inactive <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Body temperature in humans is around 37oC and enzymes will denature at about 40oC <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Most denature at 60oC
 * __ Temperature __**

<span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">All have a <span style="background-attachment: initial; background-clip: initial; background-color: yellow; background-image: initial; background-origin: initial; background-position: initial initial; background-repeat: initial initial;">optimum pH <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Depends on where enzyme is secreted. <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Denatured if move either side of pH range.
 * __ pH __**

As substrate concentration increases so will rate of enzyme action <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Up until enzyme saturation is reached. Enzymes are working at maximum rate.
 * __ Substrate Concentration __**

<span style="color: #00ff00; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.5in; text-indent: -0.5in;">3.6.4 Define denaturation

<span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Protein loses 3D structural shape <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Active site loses its shape – no longer fits around substrate <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Prevents reactions from happening. <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Changes in pH or high temperature cause denaturation <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Breaking bonds which hold the folding of the protein <span style="color: blue; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.25in; text-indent: -0.25in;">Permanent damage

<span style="color: #00ff00; font-family: 'Comic Sans MS'; font-size: 10pt; margin-left: 0.5in; text-indent: -0.5in;">3.6.5 Explain the use of lactase in the production of lactose-free milk Cannot make lactase Can’t break down lactose – milk disaccharide (glucose + galactose) Industrial process – add lactase to milk or milk product Digest lactose à glucose + galactose

**7.5 Protein structure**

 * 7.5.1 Explain the four levels of protein structure, indicating the significance of each level **

__**Primary**__


 * __Secondary__**

__**Tertiar**__**y**

Maintained in part by weak Van der Waals interactions: N.B the following website is for interest and background but goes into far more detail than is needed at IB level: @http://antoine.frostburg.edu/chem/senese/101/liquids/faq/h-bonding-vs-london-forces.shtml

__**Quaternary**__


 * 7.5.2 Outline the difference between fibrous and globular proteins, with reference to two examples of each protein typ e.**

<span style="color: #0000ff; font-family: Tahoma,Verdana,Helvetica,Arial; font-size: 10pt;">__[]__


 * 7.5.4 State four functions of proteins, giving a named example of each. **



** 7.6 ****Enzymes**


 * // 7.6.1 //// State that metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. // **

** Orange book **** à **** pg. 81 ** ** Green book **** à **** pg. 131 **

__Globular Proteins__
 * Enzymes** are **globular proteins** that function as **biological catalysts**. They permit biological reactions to occur very rapidly at normal body temperatures. The globular shape of the protein plays a key role in the action of the enzyme. Due to the specific globular shape the enzyme will have an active site, which will accommodate only one type of substrate and so carry out a very specific function.

There are about 40,000 different enzymes in human cells, each controlling a different chemical reaction. They increase the rate of reactions by a factor of between 106 to 1012 times. As well as catalysing all the metabolic reactions of cells (such as respiration, photosynthesis and digestion), they also act as motors, membrane pumps and receptors.

__Naming__ Many enzymes still have their ‘old names’ however there is a modern system of naming them. It identifies the substance the enzyme acts upon, called its **substrate** and adds the suffix –**//ase//**. Thus lipase digests lipids and protease digests proteins. This information is much more relevant when we do digestion.

__The Role of Enzymes__ To appreciate the effect of an enzyme, think of what happens when paper burns. Paper is composed many of glucose (in the form of cellulose). The burning of glucose can be represented by the equations.

C6H12O6 + 6O­2 à 6CO2 + 6H2O

Paper does not spontaneously burst into flame because few of its molecules have enough kinetic energy to react. Lighting the paper with a match, however, raises the kinetic energy enough to initiate combustion (rapid oxidation). The energy needed to get the reaction started, supplied by the match, is called the **activation energy**.

In the body, we carry out the same reaction and oxidize glucose to water and carbon dioxide to extract its energy. We could not tolerate the heat of combustion in our bodies, however, so we must oxidize glucose in a more controlled way at a biological feasible and safe temperature. Enzymes enable this to happen by lowering the activation energy – by reducing the barrier to glucose oxidation – and by releasing the energy in small steps rather than a single burst of heat.

o A ** metabolic pathway ** is a chain of reactions with each step usually catalyzed by a different enzyme. A simple metabolic pathway can be symbolized: α β γ A à B à C à D
 * Metabolic Pathways**

where A is the initial reactant, B and C are intermediates and D is the end product. The Greek letters above the reaction arrows represent enzymes that catalyze each step of the reaction.

o Such a pathway can be turned on or off by altering the conformation of any of these enzymes, thereby activating or deactivating them. This can be done by such means as the binding or dissociation of a cofactor or by an end product of the pathway binding to an enzyme at an earlier step.

__Animation__ Biochemical Pathways [|http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter8/animations.html#]


 * 7.6.2 Describe the induced-fit model **




 * 7.6.3 Explain that enzymes lower the activation energy of the chemical reactions they ** **catalyze**


 * 7.6.4 Explain the differnce between competitive and non-competitive inhibition, with reference to one example of each **


 * As promised! **
 * Q.4 What should be measured in order to determine the rate of reaction? **
 * At each substrate concentration the time taken for the substance to be used up or the time taken for the product to be produced should be measured!**
 * Q.5 On the graph draw the curve expected in the presence of the inhibitor. Explain your predictions. **
 * When inhibitor is present, the reaction is slow at low substrate concentrations because the inhibitor and substrate are competing for the active site. As the concentration of substrate increases, the rate increases. At high concentrations of substrate the rate is the same as when there is no inhibitor because the substrate occupies all the active sites**
 * Q.6 In a second investigation, the same concentration of a non-competitive inhibitor was added at each substrate concentration. On the graph draw the curve expected in the presence of this inhibitor. Explain your predictions. **
 * Non-competitive inhibitors bind at a second binding site on the enzyme (i.e. not the active site) When the inhibitor binds to the enzyme it causes the shape of the active site to change and so prevents the binding of the substrate. The rate of reaction is therefore lower.**

Competitive, non-competitive, reversible, non-reversible - disentangle these words here: []


 * 7.6.5 Explain the control of metabolic pathways by end-product inhibition including the role of allosteric sites. **

Many metabolic reactions occur in an assembly-line type of process so that a specific end-product can be achieved (see above). Each step is catalyzed by a specific enzyme.

To avoid excess product being produced (wasteful); an end product often acts to inhibit an enzyme earlier on in the process.

The enzyme that is inhibited and reactivated is an __**allosteri**__c enzyme. When in higher concentrations, the end-product binds with the allosteric site of the first enzyme, thus bringing about inhibition.

An Allosteric inhibitor is often a non-comptetive inhibitor

__** Use off immobilised enzymes investigation **__

Immobilized enzymes have a wide range of commercial applications, such as their use in the production of lactose-reduced milk, using immobilised lactase (B-galactosidase). Immmobilised enzymes are attached to inert, insoluble materials and have a number of advangeages over enzymes in free solution, including hte ability to re-use the enzyme, which reduces the overall cost of the process. Immobilised enzymes can also be used in continuous processes, which can be automated, and some enzymes are more stable when immobilised and are therefore less likely to be denatured. Enzymes can be immobilised in a range of materials, including agar gels, cellulose and polyacrylamide.

The purpose of this practical is to produce immobilized amylase and to evaluate this method as an investigative tool for IA's.

We will simply see how many times the solution has to be rinsed through the beads before the achromatic point is reached.

You can also see the effect on the colour of the iodine solution as the concentration of starch gets lower and lower.

Record your observations clearly

__** Method **__ 1) Add the prepared sodium alginate to water as demonstrated drop by drop into the calcium chloride solution. Alginate beads containing the immobilised enzyme will form immediately. Leave them to harden for 10 minutes. 2) Strain off the beads and rinse with distilled water. 3) Put a piece of Nylon gauze in a 10cm3 syringe barrel, to prevent the beads becoming stuck in the outlet, then add the beads to the syringe, Hold the syringe using a retort stand. 4) Fill the syringe with starch solution and allow it to drain though capturing the product 5) Test the product using a dropping tile and iodine solution (decide how many drops you will use) record the color as accurately as possible - a camera from your laptop could be used? 6) Be sure that you reach the achromatic point by repeating three times and observing the same colour every time and note how many times the solution went through before it changed.