Chapter 4 - Enzymes

Roles of enzymes in reactions

• Anabolic reactions - The synthesis of large polymer-based components.

• Catabolic reactions - Reactions to break down large organic molecules along metabolic pathways to release energy for processes.

• Digestion - We get these large organic molecules from digesting food.

Define metabolism

The sum of all the different reactions and reaction pathways happening in a cell/organism because reactions are usually part of multi-step pathways.

What is Vmax

The maximum initial velocity (the highest point an enzyme can increase its ROR to).

Mechanism of enzyme action

-For a reaction to happen molecules need to collide in right orientation.

-Increasing temp and pressure increases speed and therefore successful collisions and ROR.

-Each enzyme catalyses a biochemical reaction which is its specificity

-Reactions need activation energy, enzymes reduce activation energy needed.

Lock and key hypothesis

- An area within the tertiary structure of the enzyme has a shape complementary to the shape of a specific substrate molecule, known as active site.

- Only the specific substrate will fit into enzyme active site.

- When the two are joined they form an enzyme-substrate complex then forming products in an enzyme-product complex. Enzyme can then take part in subsequent reactions.

- Substrate held in enzyme so that right atom-groups are close to react.

- R-groups in enzyme interact with substrate, forming temporary bonds.

Induced-fit hypothesis

- This suggests active site of enzyme changes shape slightly to fit substrate.

- Weak interactions between enzyme and substrate rapidly induce changes in enzyme's tertiary structure which strengthen binding putting strain on substrate.

- This strain can weaken particular bonds in substrate therefore lowering activation energy for reaction.

What are intracellular enzymes

Enzymes acting within the cells catalysing metabolic reactions like respiration. The synthesis of polymers from monomers requires enzymes.

What are extracellular enzymes

Enzymes which work outside the cell that made them, breaking down large molecules into smaller components.

What do single-celled organisms do

They release enzymes into the environment so these enzymes can be used to break down larger molecules.

What do multi-celled organisms do

They eat food to gain nutrients, the nutrients are broken down by enzymes then absorbed into the bloodstream and transported around the body.

Describe the digestion of starch

1. Starch partially broken down into maltose. The enzymes that does this is called amylase which is produced in the salivary glands and pancreas and released in saliva into the mouth, and in pancreatic juice into small intestine.

2. Maltose broken down into glucose. This enzyme is maltase present in small intestine. Glucose is then small enough to be digested into the bloodstream.

Describe the digestion of proteins

The enzymes trypsin (protease) catalyses the digestion of proteins into peptides then amino acids. Produced in the pancreas, released into small intestine. Amino acids produced are then small enough to be absorbed into bloodstream.

Name 4 similarities between Lock and Key model and Induced fit model

• Both models which describe mechanism of enzyme action.

• Both depend on degree of precise binding of substrate to enzyme.

• Both important in describing how enzymes increase rate of reaction.

• Both reduce activation energy

Name a differences between Lock and Key model and Induced fit model

• Induced fit refers to a model for enzyme-substrate interaction in which the active site of the enzyme doesn’t completely fit substrate. Lock and key refers to a second model for enzyme substrate interaction in which active site of enzyme completely fits with substrate.

Define temperature coefficient

A measure of how much the rate of a reaction increases with a 10 degrees celsius rise in temperature.

How does temperature affect enzyme activity

Increasing the temperature of a reaction increases kinetic energy of particles meaning more frequent successful collisions between substrate and enzyme meaning an increased rate of reaction.

Define denature

When the temperature gets too high above an enzyme’s optimum temperature, the bonds holding the protein together vibrate more so they are put under strain and eventually break. The breaking of these bonds results in change in tertiary structure which is why the enzyme denatures at high temperature.

How does pH affect enzyme activity

H bonds and ionic bonds between amino acid R-groups hold proteins in their specific 3D shape. These bonds occur due to interactions between polar R-groups present on amino acids forming primary structure. When pH increases the more the R-groups interact meaning the enzyme will denature. If pH is only slightly changed from the optimum the enzyme and active site is altered but can return to normal shape (renaturation), but if the pH changes significantly the enzyme is irreversibly altered.

Describe substrate enzyme concentration

When concentration of substrate increases, number of substrate molecules increases so higher collision rate and formation of enzyme-substrate complexes hence ROR increases. ROR increases to Vmax at which the only way to increase rate is to add more enzyme or increase temperature. If more enzyme or substrate is added then the Vmax can increase to a new higher Vmax.

Define an inhibitor

A molecule that can prevent enzymes from carrying out their normal function of catalysis.

What is a competitive inhibitor

A molecule or part of a molecule that has a similar shape to substrate so can fit into the active site of an enzyme.

How does a competitive inhibitor work

- It fits into the active site of an enzyme and blocks the substrate from entering active site, preventing catalysis

- Substrate and competitive inhibitors compete to bind to active sites which reduces number of substrates binding and slows down reaction.

- Most competitive inhibitors only bind temporarily but there are some exceptions

- Competitive inhibitors reduce rate of reaction but they do not change Vmax. If substrate concentration is increased enough, Vmax can still be reached.

2 examples of competitive inhibitors

Statins

Aspirin

What is a non-competitive inhibitor

Inhibitor binds to enzyme at a location other than the active site. This is called the allosteric site.

How does a non-competitive inhibitors work

- They bind to the allosteric site of an enzyme. This causes the tertiary structure of the enzyme to change so active site changes shape.

- Active sites is no longer complementary so substrate is unable to bind so enzyme can’t carry out its function.

- Increasing concentration of an enzyme or substrate has no effect on a non-competitive inhibitor as it does not compete for the active site.

- However, increasing the concentration of the inhibitor will decrease the rate of reaction further.

Examples of non-competitive inhibitors

Organophosphate

Proton pump inhibitors

What is end product inhibition

This is enzyme inhibition that occurs when the product of a reaction acts as an inhibitor to the enzyme that produces it. This is a negative feedback control mechanism, excess products are not made and resources are not wasted.

What is a cofactor

Some enzymes need a non-protein component to help them carry out their function. These may transfer atoms or groups from one reaction to another or they may form part of the active site of an enzyme.

What is the difference between a cofactor and a coenzyme

Coenzymes are organic molecules.

How are inorganic cofactors obtained

These are obtained via diet as minerals including iron, calcium, chloride, zinc.

How are organic coenzymes obtained

These are obtained from vitamins, a class of organic molecule found in the diet.

What are prosthetic groups

These are cofactors, required by certain enzymes to carry out their catalytic function. Some cofactors can be loosely or temporarily bound to the enzyme in order to activate them but prosthetic groups are tightly bound and form a permanent feature of the protein.

What are precursor enzymes and why are they produced

These are enzymes produced in an inactive form. This is mostly because some enzymes can cause damage within the cells producing them or to tissues where they are released or enzymes whose action needs to be controlled and activated under certain conditions.

How are precursor enzymes activated

They often undergo a change in the shape of the active site. This can be achieved by the addition of a cofactor. Before the cofactor is added the protein is an apoenzyme, after it is known as a holoenzyme.

Sometimes this change can be brought about by action of another enzyme. Sometimes it is a change in conditions. Precursor enzymes are called zymogens or proenzymes.