Enzymes

Question 1

Why are enzymes important?

Answer 1

• To emulate conditions needed for certain metabolic reactions to occur as quickly as needed would be impossible. Instead enzymes can catalyse reactions making them faster and easier to occur.

Question 2

What is the role of enzymes in reactions?

Answer 2

• Catalyses anabolic reactions which are the chemical reactions required for growth
• Catalyses catabolic reactions which are the chemical reactions required which are vital in releasing energy and breaking down components.

Question 3

What does metabolism mean?

Answer 3

• Metabolism = sum of all different reactions and reaction pathways happening in a cell or an organism - can only happen as a result of the control and order imposed by enzymes.

Question 4

What is Vmax?

Answer 4

• Vmax is the maximum point to which enzymes can increase the rate of reaction.

Question 5

What is the specificity of enzymes?

Answer 5

• This refers to how only one enzyme can catalyse only one biochemical reaction because of it`s specific tertiary shape complementary to the substrate.
• It needs to have a tertiary structure to build such specificity

Question 6

Very generally, How do enzymes catalyse reactions?

Answer 6

• By decreasing the activation energy of the reaction by helping the molecules collide successfully

Question 7

Describe and explain the lock and key hypothesis in 4 steps

Answer 7

• The substrate binds into the specific active site on the enzyme like only the right key fits the right lock forming an enzyme-substrate complex
• The substrate is held in such a way by the enzyme that the right atom groups are close enough to react. The R-groups in the active site of the enzyme also form temporary bonds with the substrate thus putting a strain on the bonds within a substrate.
• The substrate(s) then react and the product(s) are formed in an enzyme-product complex
• The product(s) are then released - leaving the enzyme unchanged and able to take part in subsequent reactions

Question 8

What is the active site of an enzyme

Answer 8

• An area within the tertiary structure of the protein complementary to the substrate this is the active site

Question 9

Describe and explain the induced fit hypothesis

Answer 9

• Initial interaction between enzyme and substrate = weak
• The weak interactions induce changes in the enzyme`s tertiary structure - strengthens binding and puts strain on substrate molecule
• Thus it weakens a particular bond or bonds in the substrate hence lowering the activation energy for the rxn

Question 10

What are intracellular enzymes using Catalase as an example

Answer 10

• Intracellular enzymes = enzymes inside cells
• Catalase is found inside cells and breaks down hydrogen peroxide a toxic by product of respiration harmful if allowed to accumulate into water and oxygen

Question 11

What are extracellular enzymes and why are they important?

Answer 11

• Extracellular enzymes = enzymes outside cells
• ## Nutrients often come in large molecules and need to be broken down before being able to come into cells to break these down enzymes are released outside the cells they were made in, in fungi they work outside the body

Question 12

Describe and explain the role of amylase in breaking down starch.

Answer 12

• Starch polymers are partially broken down into maltose by amylase enzymes produced in the salivary gland and pancreas and released in saliva into the mouth and pancreatic juice in the small intestine.

Question 13

Present trypsin as an extracellular enzyme

Answer 13

• Trypsin is a protease and therefore catalyses the breakdown of amino acids by other proteases
• Trypsin is produced in the pancreas but released in the pancreatic juice into the small intestines

Question 14

What is the effect of temperature of enzyme action? (can make logical refs to extremophiles but not necessary)

Answer 14

• At first it increases the rate of reaction since the increasing temperature results in increasing kinetic energy of the molecules which increases the amount of successful collisions between enzymes and substrates in a given time
• But at higher temperatures bonds holding the protein enzyme together vibrate more making them come under more strain and eventually breaking - this changes the tertiary structure of the protein enzyme particularly it`s active site meaning the enzyme cannot fit with the substrate(s) and catalyse the reaction- the enzyme has become denatured.
• Temperature coefficient (Q10) = the measure of how much the rate of rxn increases with a 10c rise
• Q10 = R2/R1

Optimum temps

• 40c in humans
• 70c in thermophilic
• below 5c in psychrophilic

Adaptations

• Enzymes adapted to the cold tend to have more flexible structures - esp. Active site - resulting in them being less stable than enzymes at higher temp.
• Enzymes present in V. hot enviros = more stable (than other enzymes) due to increased no. of bonds - esp. Hydrogen & sulfur bridges in the tertiary structures (obvs) - shapes & active site = more resistant to change as temp rises

Question 15

What is the effect of pH on enzyme action?

Answer 15

• When an enzyme is not in its optimum pH its active site will be altered and it will not work but should its environments pH go back to optimum it will start working again - renaturation

This happens by:

• pH changes significantly to alter the structure of the active site of the enzyme and the rate of reaction stops
• This is because Hydrogen ions interact with polar and charged r-groups affecting their previous degree of interaction which also affects the interaction r-groups with each other which affects the tertiary structure of the enzyme
• The more hydrogen ions present (low pH) = less R-group interactions with one another
• The less hydrogen ions present (high pH) = More R-group interactions with one another

Question 16

What is the effect of enzyme and substrate on enzyme action?

Answer 16

• Increased substrate concentration = higher successful collision rate with active site of enzymes leading to increased rate of enzyme-substrate complexes = increased rate of rxn
• Increased enzyme concentration = higher successful collision rate between active site of enzyme and substrates leading to increased rate of enzyme-substrate complexes = increased rate of rxn
• Rate of reaction increases up to it`s maximum called Vmax
• Vmax = all active sites are occupied by substrate particles and no more enzyme-substrate complexes can be formed until products are released from active sites - The only way to increase the rate of rxn in such cases is to add more enzymes or increase temp

Question 17

PAGs

Answer 17

PAG 4

Question 18

What is a co-factor. where do they come from and how are they relevant - use Amylase as an example

Answer 18

• Some enzymes need a non-protein helper component to carry out their function - these components are called co-factors
• They may transfer atoms or groups from one reaction to another in a multi-step pathway or they may actually form part of the enzyme`s active site.
• Inorganic co-factors are obtained through our diet as minerals - such as zinc, iron, calcium and chloride ions -
• Amylase contains a chloride ion which is a co-factor in order to help it form a correctly shaped active site.

Question 19

What is a co-enzyme, where do they come from (you do not need to cite an example)

Answer 19

• A co-enzyme is a co-factor but with organic molecules instead of inorganic molecules
• They are derived from vitamins
• Vitamin B5 is used to make coenzyme A - essential in the breakdown of fatty acids and carbs in respiration

Question 20

What are prosthetic groups - use Carbonic Anhydrase as an example

Answer 20

• These are co-factors that tightly bound to the enzyme and form a permeant feature of the protein
• Zinc ions form an important part of the structure of Carbonic anhydrase, an enzyme necessary for the metabolism of Carbon dioxide

Question 21

Generally, why are inhibitors important?

Answer 21

• From preventing the production of excess products which would be a wastage of resources

Question 22

What is competitive inhibition, how does it work and what are it`s effects - try to ref some medicinal uses

Answer 22

• Competitive inhibition is when a molecule competitively competes to occupy the active site of an enzyme

This is how it works:

• Molecule or part of the molecule that has a similar shape to the substrate of an enzyme fits into the active site of the enzyme
• This blocks the substrate from producing an enzyme-substrate complex with the enzyme
• The enzyme cannot carry out it`s function - it is inhibited
• The inhibitor is thus competing for the active site of the enzyme and thus competitively inhibits and slows down the rate of reaction particularly when there is an excess of products
• The degree of inhibition depends on the concentration of substrate, inhibitor and enzyme
• Most competitive inhibitors only bind temporarily to the active site apart from a few exceptions including aspirin.
• It does not change the Vmax of the enzyme
• examples - aspirin (COX enzymes preventing synthesis of postagladins and thuromboxane - pain and fever) and statins

Question 23

What is non-competitive inhibition, how does it work and what are it`s effects - try to ref some medicinal uses

Answer 23

• Here the inhibitor does not competitively compete for the active site against the substrate or at all thus it is non-competitive inhibition

This is how it works:

• Inhibitor binds to the enzyme at the allosteric site (location other then the active site on enzyme)
• The binding of the inhibitor at the allosteric site results in a change in the tertiary structure of the protein - causing a change in the shape of the active site making in inhibited
• increasing the concentration of substrate or enzyme will not affect the effect of the non-competitive inhibitor but changing the concentration of the non-competitive inhibitors will decrease the rate of reaction even more
• non-competitive inhibition can be non-irreversible or reversible
• PPIs (proton pump inhibitors) are used to treat long-term indigestion - these irreversibly inhibit the enzyme from secreting hydrogen ions into the stomach preventing the build up of excess acids and thus stomach ulcers

Question 24

What is end product inhibition, how does it work and what are it`s effects

Answer 24

• This is when the product of the reaction acts as an inhibitor to the enzyme that produces it
• Negative-feedback control system

Example - PFK (phosphofructokinase) - Respiration - thus controls production of ATP

• When ATP levels are high - more ATP bind to the allosteric -preventing addition of second phosphate group to glucose
• When ATP levels are low - less ATP binds to PFK thus allowing the addition of second phosphate group to glucose allowing production of ATP to continue

Question 25

What is precursor activation, how does it work and what are it`s effects

Answer 25

• Many enzymes are produced in an inactive form called inactive precursor enzymes
• This is done to those enzymes that could damage their producer cells or tissues and/or to those enzymes whose action needs to be controlled and only active under certain conditions
• Precursor enzymes therefore often need to undergo a change in their tertiary structure - particularly to the active site in order to be activated.
• Precursor protein = apoenzyme
• activated enzyme = holoenzyme

The change necessary in the tertiary structure could come about in several ways:

• The addition of a cofactor
• Action of another enzyme - protease cleaves certain bonds in the mol
• Change in condition - pH or temperature - zymogens/proenzymes