Enzymes & metabolism

Question 1

What are the things that speed up reaction rates?

Answer 1

• Temperature and pressure
• pH
• High reactant concentration
• Catalyst

Question 2

What kind of proteins are enzymes?

Answer 2

Globular proteins

Question 3

Compare anabolic and catabolic reactions

Answer 3

Catabolic:
*Break down large molecules into smaller ones
*Exergonic (energy release)
*Output energy as heat, movement, activate transport (etc) for processes like cell respiration, excretion, digestion.
*Hydrolysis reaction

Anabolic:
*They build up larger molecules from smaller ones
*Endergonic (energy input)
*Store energy in chemical form for reactions like photosynthesis, growth, repair, protein synthesis, glycogen formation by glucose
*Condensation reaction

Question 4

What is the induced-fit hypothesis?

Answer 4

*The active site in an enzyme undergoes conformational changes to its shape when a substrate is binding as to ensure ideal binding arrangement and maximise catalyst ability

Question 5

Ways of immobilising an enzyme

Answer 5

*Attachment to inert substance like glass through covalent bonds
*Entrapment within a matrix like alginate glass
*Entrapment within a partially permeable membrane

Question 6

Advantages of immobilising an enzyme

Answer 6

*The product is uncontaminated as there are no enzymes in it, so there is no need to further filter
*Can be reused multiple times which makes it
-Efficient and cost-effective
-Avoids need to separate enzyme in downstreaming
*Have a greater tolerance for temperature and pH changes, so they are more stable
*Substrates can be exposed to higher enzyme concentration, increasing rate of throughput
*Conditions can be controlled carefully, so enzymes work close to their optimum conditions and are more stable

Question 7

How/why does denaturation happen?

Answer 7

Temperature:
*The H+ bonds in the r-group of amino acids begin to vibrate more, which causes them to break
*Is irreversible because the bonds break, the enzyme loses its shape forever and the active site no longer works

pH:
*The increased H+ or OH- (depending on pH) interact with the hydrogen bonds in the alpha helix or beta-pleated sheet, which distorts their shape
*Is reversible because you simply remove H+ / OH- and you get original shape back

Denaturation causes enzyme to become insoluble and form precipitates

Question 8

How can progress of an enzyme-catalysed reaction be measured by product formation?

Answer 8

• Hydrogen peroxide is a common but toxic by-product of metabolism
  *Catalase breaks it down into oxygen and water
  *H2O2 and catalase are combined and the volume of oxygen generated is measured in a set time = rate of reaction is calculated

Question 9

How can progress of an enzyme-catalysed reaction be measured by substrate disappearance?

Answer 9

*Amylase hydrolysis starch into maltose and glucose
*It functions best at 37ºC and pH 7
*Amylase and starch are combined, then mixture is tested for starch in regular intervals with potassium iodide solution

Question 10

What is the formula for rate of reaction

Answer 10

1/Time taken (s^-1)

Question 11

Metabolic pathways are controlled by what?

Answer 11

Enzymes in a biochemical cascade of reactions

Question 12

What is non-competitive inhibition

Answer 12

*Effectors bind to an allosteric site, causing conformational changes to the enzymes active site.
*Prevent the intended substrate from binding as long as the effector is bound to the allosteric site
*Is reversible

Question 13

What is competitive inhibition?

Answer 13

*A competitive inhibitor has a similar shape to the substrate.
*This allows them to bind with the active site and interfere, inhibiting the substrate from interacting with the enzyme as long as it is bound.

Question 14

What is an example of competitive inhibition?

Answer 14

Statins are drugs prescribed to lower high cholesterol levels
*Statins bind to the active site of the enzyme needed to synthesise cholesterol
*Binding is possible because statins have a similar shape to the substrate of the enzyme
*The enzyme cannot catalyse the cholesterol-making reaction as long as statin is bound

Question 15

What happens if you increase substrate concentration in both competitive and non-competitive inhibition?

Answer 15

Non-competitive:
*The effect of non-competitive inhibitors will not be affected
*As the effector changes the active sites shape, regardless of whether there is more or less substrate they will still be unable to bind to the enzyme

Competitive:
*The effect of competitive inhibitors will decrease as more substrate-active site collisions will happen
*As you increase the substrate concentration, it will exceed the inhibitor concentration and thus the reaction will proceed and maximum rate will be achieved

Question 16

Compare non-competitive and competitive inhibition

Answer 16

Non-competitive:
*Bind to allosteric site, changing the active site’s shape
*Are chemically unlike the substrate
*Not affected by increasing substrate concentration

Competitive:
*Bind to the active site, interfering and competing with the substrate
*Are chemically like the substrate
*Are affected by increasing the substrate concentration

Question 17

What is feedback inhibition?

Answer 17

The end-product of a reaction is present in excess and begins to act as a non-competitive inhibitor itself, called allosteric inhibitor.
It prevents the build-up of intermediate products.

The inhibition of the enzyme causes product level to fall, and since the product is also needed elsewhere by the cell, they detach and allow enzyme to begin catalysing the reaction again

Question 18

Explain feedback inhibition using isoleucine and threonine deaminase

Answer 18

*Amino acid isoleucine can bind to the allosteric site of the enzyme it is made out of: threonine deaminase.
*Once enzyme is inhibited, isoleucine production stops
*Isoleucine is essential for cell protein synthesis. When it is needed its concentration decreases, decreasing the number of occupied allosteric sites

Question 19

Explain mechanism-based inhibition

Answer 19

*There is a substrate analogue, which is a molecule that is similar to the substrate but is not the substrate.
*It binds to the enzyme and creates a reactive group in the active site, which is a part of a molecule that is more prone to have their atoms bind/interact with other substances more
*In the reactive group it forms covalent bonds, which ‘lock’ the interaction as they are very strong
*This changes the chemical environment of the active site, and binds the enzyme to the substrate analogue forever, effectively rendering it a stable enzyme-inhibitor complex, rendering the enzyme useless forever.
*It is thus irreversible

Question 20

How do normal substrates bind

Answer 20

*Hydrogen bonding
*Ionic bonding
*Hydrophobic bonding

Question 21

Describe how penicillin acts as a mechanism-based inhibitor

Answer 21

*Penicillin is an antibiotic.
*The bacterial cell walls are made up of peptidoglycan molecules held together by cross-links. When a new bacterium is growing it secretes an enzyme called autolysin, creating small holes in the bacterium wall which allow bacterium to stretch, with new peptidoglycan molecules joining via cross-links.
*Penicillin interferes with this process as it binds with DD-transpeptidase which catalyses the formation of the cross-links because it has a similar structure to the peptide chain. Penicillin will bind to DD-transpeptidase and modify its active site. No more cross-links.
*This means the bacterium is still growing and autolysins are still creating the holes, making the cell wall weaker until the bacterium bursts because it cannot withstand the water pressure being exerted from within the cell by H2O taken up by osmosis.