Biological Molecules - Enzymes

Question 1

What is an enzyme?

Answer 1

• A protein that acts as a biological catalyst and so lowers the activation energy needed for a reaction by providing an alternate pathway.
• All enzymes are 3D tertiary structured globular proteins whose shape is determined by the primary sequence of amino acids.
• An organism’s metabolism is made up of thousands of these enzyme reactions.
• They speed up the rate of reaction but are not used up. This means they can be used again after a reaction.
• A small amount of enzyme affects a large amount of substrate.
• An enzyme will only catalyse one reaction, and this may be reversible. They are specific to their substrate.
• If the shape changes, it can’t perform its job.

Question 2

What is activation energy?

Answer 2

The minimum amount of energy required to bring about a successful collision (get the substrates to react).

Question 3

What is the active site?

Answer 3

A group of amino acids that make up the region of an enzyme into which the substrate fits in order to catalyse a reaction (also known as a depression).

Question 4

What is a substrate?

Answer 4

A substance that is acted on or used by another substance or process. Fits into the active site of an enzyme.

Question 5

What is an enzyme-substrate complex?

Answer 5

The intermediate formed when a substrate molecule interacts with the active site of an enzyme. The chance of a reaction occurring is greatly increased in this complex.

Question 6

What does complementary mean?

Answer 6

Describes the relationship between the active site of an enzyme and the substrate molecule - the way in which they fit together. The substrate does not have to be the “same shape” as the active site, the substrate has a complementary shape to the active site.

Question 7

What does specific mean?

Answer 7

Describes how enzymes catalyse a certain chemical reaction.

Question 8

What is the induced fit hypothesis? (Koshland 1959)

Answer 8

A mechanism of interaction between an enzyme and a substrate. As the substrate fits into the active site, the active site of the enzyme changes shape in order to allow an enzyme-substrate complex to be formed.

When a substrate combines with an enzyme, it “induces” a change in the enzymes shape. This is because the proximity of the substrate (a change in the environment of the enzyme) leads to a change in the enzyme that forms the functional active site. The enzyme is flexible and can mould itself around the substrate. The amino acids in the active site form a precise arrangement that allows the enzyme to perform its catalytic function.

Question 9

What is the lock and key hypothesis? (Fischer 1890)

Answer 9

An analogy for how enzymes work - only the correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme). This model was supported by the observation that enzymes are specific in the reactions that they catalyse.

The substrate binds to the enzyme’s active site. The active site is only 3-12 amino acids in size. The shape of the active site is complementary to the shape of the substrate. The shape of the enzyme determines its function.

Question 10

What is the rate of reaction?

Answer 10

The speed of a chemical reaction - can be worked out by looking at the decrease in concentration of a reactant over time or increase in concentration of a product over time.

Question 11

What is kinetic energy?

Answer 11

The energy of motion, observable as the movement of an object, particle or set of particles.

Question 12

What is pH?

Answer 12

A figure expressing the acidity or alkalinity of a solution on a logarithmic scale on which 7 is neutral, lower values are more acidic and higher values are more alkaline. Equivalent to -log10(H+).

Question 13

What is an inhibitor?

Answer 13

A substance which reduces the activity of an enzyme.

Question 14

What is a competitive inhibitor?

Answer 14

A form of inhibitor which binds to the active site of the enzyme preventing the binding of substrate.

Question 15

What is a non-competitive inhibitor?

Answer 15

A form of inhibitor which does not bind at the active site of the enzyme which prevents the binding of substrate.

Question 16

What affects the rate of a reaction?

Answer 16

• temperature
• concentration of reactants
• surface area of reactant
• catalyst

Question 17

What do you need to do in order to increase the rate of reaction?

Answer 17

To increase the rate of reaction, you need to increase the number of successful collisions per unit time.

Question 18

How does an enzyme affect the activation energy?

Answer 18

• At a given temperature, the greater the activation energy, the slower the reaction.
• An enzyme provides an alternate pathway that requires a lower activation energy.
• An enzyme does not change the energy level of the substrate or product.

Question 19

What is a conformational change?

Answer 19

a change in shape

Question 20

How is the substrate molecule held within the active site?

Answer 20

The substrate molecule is held within the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule. These are non-covalent forces such as hydrogen bonds, ionic and van der Waals forces.

Question 21

What happens when the active site changes shape in the induced fit model?

Answer 21

As the enzyme changes its shape, the enzyme puts a strain on the substrate molecule. This strain distorts a particular bond or bonds in the substrate and consequently lowers the activation energy needed to break the bond.

Any change in an enzyme’s environment is likely to change its shape. The very act of colliding with its substrate is a change in its environment and so its shape changes (induced fit).

Question 22

Do all proteins have an active site?

Answer 22

Enzymes have an active site but not all proteins are enzymes. Many proteins have binding sites or receptor sites that are not active sites. Some hormones are proteins and these have receptor sites but they are not active sites.

Question 23

What is a limitation of the lock and key model of enzyme action?

Answer 23

One limitation of this model is that the enzyme is considered to be a rigid structure. However, scientists had observed that other molecules could bind to enzymes at sites other than the active site. In doing so, they altered the activity of the enzyme. This suggested that the enzyme’s shape was being altered by the binding molecule. This led to an alternative model being proposed, one that better fitted the current observations. The induced fit model is therefore a modified version of the lock and key model.

Question 24

What can impact the tertiary structure of enzyme produced?

Answer 24

Primary structure is determined by a gene. Therefore, mutations in genes impacts the tertiary structure of enzyme produced.

Question 25

How do enzymes join molecules?

Answer 25

Enzyme holds them close together and reduces repulsion so they can bond more easily.

Question 26

How do enzymes break down molecules?

Answer 26

Fitting into the active site puts a strain on the bonds in the substrate and so breaks up easily.

Question 27

How can you measure enzyme activity?

Answer 27

By measuring the amount of product formed or the amount of substrate used up. Both can be measured over time and therefore will identify changes in reaction rate. Given time and constant conditions, the rate of reaction will slow down.

Question 28

What factors affect enzyme activity?

Answer 28

• temperature
• concentration of substrate
• concentration of enzyme
• pH

Question 29

Explain the shape of the graph of volume of oxygen produced on the y-axis and time/min on the x-axis.

Answer 29

• At first there is a lot of substrate (hydrogen peroxide or starch) but no product (water and oxygen, or maltose).
• It is very easy for substrate molecules to come into contact with the empty active sites on the enzyme molecules.
• All enzyme active sites are filled at any given moment and the substrate is rapidly broken down into its products.
• The amount of substrate decreases as it is broken down, resulting in an increase in the amount of product.
• As the reaction proceeds, there is less and less substrate and more and more product.
• It becomes more difficult for the substrate molecules to come into contact with the enzyme molecules because there are fewer substrate molecules and also the product molecules may ‘get in the way’ of substrate molecules and prevent them reaching an active site.
• It therefore takes longer for the substrate molecules to be broken down by the enzyme and so its rate of disappearance slows, and consequently the rate of formation of product also slows. Both graphs plateau.
• The rate of reaction continues to slow until there is so little substrate that any further decrease in its concentration cannot be measured.
• The graphs flatten out because all the substrate has been used up and so no new product can be produced.

Question 30

What is the effect of temperature on enzyme action?

Answer 30

A rise in temperature increases the kinetic energy of molecules. As a result, the molecules move around more rapidly and collide with each other more often. In an enzyme-catalysed reaction, this means that the enzyme and substrate molecules come together more often in a given time. There are more effective collisions resulting in more enzyme-substrate complexes being formed and so the rate of reaction increases.

Shown on a graph, this gives a rising curve. However, the temperature rise also begins to cause the hydrogen and other bonds in the enzyme molecule to break. This results in the enzyme, including its active site, changing shape. At first, the substrate fits less easily into this changed active site, slowing the rate of reaction. For many human enzymes this may begin at temperatures around 45 degrees Celsius.

At some point, usually around 60 degrees Celsius, the enzyme is so disrupted that it stops working altogether. It is said to be denatured. Denaturation is a permanent change and, once it has occurred, the enzyme does not function again. Shown on a graph, the rate of this reaction follows a falling curve.

Question 31

Why have our body temperatures evolved to be 37 degrees Celsius?

Answer 31

• Although higher body temperatures would increase the metabolic rate slightly, the advantages are offset by the additional energy (food) that would be needed to maintain the higher temperature.
• Other proteins, apart from enzymes, may be denatured at higher temperatures.
• At higher temperatures, any further rise in temperature, for example during illness, might denature the enzymes.

Question 32

Why do birds have a normal body temperature of around 40 degrees Celsius?

Answer 32

They have a high metabolic rate for the high energy requirement of flight.

Question 33

What is the effect of pH on enzyme action?

Answer 33

The pH of a solution is a measure of its hydrogen ion concentration. Each enzyme has an optimum pH, that is a pH at which it works fastest. The pH of a solution is calculated using the formula: pH = -log10[H+]. In a similar way to a change in temperature affecting the rate of enzyme action, a change in pH away from the optimum affects the rate of enzyme action. An increase or decrease in pH reduces the rate of enzyme action. If the change in pH is more extreme then, beyond a certain pH, the enzyme becomes denatured.

Question 34

How does the pH affect how an enzyme works?

Answer 34

• A change in pH alters the charges on the amino acids that make up the active site of the enzyme. As a result, the substrate can no longer become attached to the active site and so the enzyme-substrate complex cannot be formed.
• Depending on how significant the change in pH is, it may cause the bonds maintaining the enzyme’s tertiary structure to break. The active site therefore changes shape.

Question 35

How does a change in pH cause the active site to change shape?

Answer 35

The arrangement of the active site is partly determined by the hydrogen and ionic bonds between -NH2 and -COOH groups of the polypeptides that make up the enzyme. The change in H+ ions affects this bonding, causing the active site to change shape.

Question 36

How large are the pH fluctuations inside organisms?

Answer 36

pH fluctuations inside organisms are usually small, this means they are far more likely to reduce an enzyme’s activity than to denature it.

Question 37

What is the effect of enzyme concentration on the rate of reaction?

Answer 37

Once an active site on an enzyme has acted on its substrate, it is free to repeat the procedure on another substrate molecule. This means that enzymes, being catalysts, are not used up in the reaction and therefore work efficiently at very low concentrations.

As long as there is an excess of substrate, an increase in the amount of enzyme leads to a proportionate increase in the rate of reaction. A graph of the rate of reaction against enzyme concentration will initially show a proportionate increase. This is because there is more substrate than the enzyme’s active site can cope with. If you therefore increase the enzyme concentration, some of the excess substrate can now also be acted upon and the rate of reaction will increase. If, however, the substrate is limiting (in other words there is not sufficient to supply all the enzyme’s active sites at one time), then any increase in enzyme concentration will have no effect on the rate of reaction. The rate of reaction will therefore stabilise at a constant level, meaning the graph will level off. This is because the available substrate is already being used as rapidly as it can be by the existing enzyme molecules.

Question 38

What is the effect of substrate concentration on the rate of enzyme action?

Answer 38

If the concentration of enzyme is fixed and substrate concentration is slowly increased, the rate of reaction increases in proportion to the concentration of substrate. This is because, at low substrate concentrations, the enzyme molecules have only a limited number of substrate molecules to collide with, and therefore the active sites of the enzymes are not working to full capacity. As more substrate is added, the active sites gradually become filled, until the point where all of them are working as fast as they can. The rate of reaction is at its maximum. After that, the addition of more substrate will have no effect on the rate of reaction. In other words, when there is an excess of substrate, the rate of reaction levels off.

Question 39

What are enzyme inhibitors?

Answer 39

Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity.

Question 40

What is a competitive inhibitor?

Answer 40

Competitive inhibitors have a molecular shape similar to that of the substrate. This allows them to occupy the active site of an enzyme, but no reaction occurs once bound. This prevents the enzyme from carrying out its function. They therefore compete with the substrate for the available active sites. It is the difference between the concentration of the inhibitor and the concentration of the substrate that determines the effect that this has on enzyme activity. If the substrate concentration is increased, the effect of the inhibitor is reduced. The inhibitor is not permanently bound to the active site and so, when it leaves, another molecule can take its place. This could be a substrate or inhibitor molecule, depending on how much of each type is present. Sooner or later, all the substrate molecules will occupy an active site, but the greater the concentration of inhibitor, the longer this will take. This makes competitive inhibition reversible.

Question 41

What are the features of competitive inhibition?

Answer 41

• it is reversible
• the inhibitor competes with the substrate
• the effect of the inhibitor can be overcome by increasing the concentration of the substrate

Question 42

What is a non-competitive inhibitor?

Answer 42

Non-competitive inhibitors attach themselves to the enzyme at a binding site which is not the active site (away from the alive site - the allosteric site). Upon attaching to the enzyme, the inhibitor alters the tertiary shape of the enzyme and thus its active site in such a way that substrate molecules can no longer occupy it, and so the enzyme cannot function. As the substrate and the inhibitor are not competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor.

Question 43

What are the features of non-competitive inhibition?

Answer 43

• increasing inhibitor concentration decreases the rate of reaction
• when the enzyme is saturated with inhibitor, the rate of reaction will be zero
• increasing substrate concentration will have no effect when the enzyme is saturated with inhibitor

Question 44

What is irreversible inhibition?

Answer 44

The inhibitor binds permanently to the -SH (sulfhydryl) group on cysteine. If this is part of the active site, it will inhibit the enzyme (e.g. silver, mercury, arsenic).

Question 45

What is product inhibition and end-production inhibition?

Answer 45

Product inhibition and end-production inhibition are reversible and is an example of non-competitive inhibition. To prevent the products accumulating at the end of the reaction, the final product of the enzyme controlled reaction attaches to the first enzyme in the metabolic pathway, and acts as an inhibitor. After the reaction has reached completion, this final product inhibits the enzyme and so controls the amount of end-product that is made. The more product that is formed, the more the pathway is inhibited. If the product is used up or transported away, the pathway will speed up again. This regulation is an example of negative feedback.

Question 46

What is the purpose of enzymes?

Answer 46

Enzymes catalyse a wide range of intracellular and extracellular reactions that determine structures and functions from cellular to whole-organism level.