2.1.4 Enzymes

Question 1

What are enzymes?

Answer 1

• enzymes are biological catalysts that speed up a chemical reaction without being used up in the reaction itself
• they catalyse metabolic reactions, both at cellular level (e.g. respiration) and for the organism as a whole (e.g. digestion in mammals)

Question 2

Where can the enzyme action be?

Answer 2

• both intracellular and extracellular

Question 3

Give an example of an intracellular enzyme

Answer 3

• catalase:
• hydrogen peroxide is the toxic by product of several cellular reactions. if left to build up, it can kill cells
• catalase works inside cells to catalyse the breakdown of H2O2 to oxygen and water

Question 4

Give examples of extracellular enzymes

Answer 4

• amylase and trypsin both work outside cells in the human digestive system
• amylase is found in saliva: it is secreted into the mouth by cells in the salivary glands
• amylase catalyses the hydrolysis (breakdown) of starch into maltose
• trypsin catalyses the hydrolysis of peptide bonds, turning polypeptides into smaller ones
• trypsin is produced by cells in the pancreas and secreted into the small intestine

Question 5

What type of protein structure are enzymes?

Answer 5

• they are globular proteins

Question 6

Describe the structure of an enzyme

Answer 6

• enzymes have an active site, which has a specific shape that substrate molecules with a complementary shape bond to
• the specific shape of an active site is determined by the enzyme’s specific tertiary structure

Question 7

How do enzymes speed up chemical reactions?

Answer 7

• activation energy is a certain amount of energy needed to be supplied to the chemicals before the reaction starts
• often provided as heat
• enzymes reduce the amount of activation energy needed, making reactions happen at a lower temperature than they could without an enzyme. this speeds up rate of reaction
• when a substrate binds to an enzyme’s active site, an enzyme substrate complex is formed
• it is the formation of the ESC that lowers the activation energy

Question 8

Why does the formation of the enzyme-substrate complex lower the activation energy?

Answer 8

• if two substrate molecules need to be joined, attaching to the enzymes hold them close together, reducing any repulsion between the molecules so they can bond more easily
• if the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on bonds in the substrate. This strain means the substrate molecule breaks up more easily.

Question 9

Interpret an energy level diagram

Answer 9

Go!

Question 10

Describe the lock and key model

Answer 10

• The shape of the active site will only allow one shape of molecule to fit in it
• the substrate shape is complimentary to the shape of the active site.

Question 11

What is the problem with the lock and key model?

Answer 11

• new evidence showed that the enzyme substrate complex changes shape slightly to complete the fit
• this locks the substrate even more tightly to the enzyme.

Question 12

Describe the induced-fit hypothesis

Answer 12

• substrate with a complimentary shape to the enzyme collides with enzyme active site
• enzyme molecule changes shape slightly
• active fits more closely around substrate
• enzyme substrate complex forms

Question 13

Why is the induced fit hypothesis better theory?

Answer 13

• change shape stabilises substrate molecule, reaction occurs more easily and products formed
• Products are different shape from substrate and no longer fit active site, so move away

Question 14

Explain why increased kinetic energy increases the rate of an enzyme controlled reaction

Answer 14

• as temperature rises, the enzyme and substrate molecules move faster due to increased kinetic energy
• collisions between the substrate molecules and the active site occur more often, and so more enzyme substrate complexes form
• they collide with more energy so more of them will have sufficient activation energy to react

Question 15

What is an enzyme’s optimum temperature?

Answer 15

• the temperature at which an enzyme catalyses at the maximum rate

Question 16

Explain in detail how increasing temperatures can reduce the activity of enzymes

Answer 16

• the structure of the enzyme molecules vibrates so energetically that some of the bonds holding the enzyme in its precise shape will break
• Bonds holding secondary structure together and bonds between R-groups break, particularly the hydrogen bonds
• the enzyme loses its tertiary shape and is denatured
• the substrate no longer fit into the active site

Question 17

Sketch a graph showing the effect of temperature on the rate of reaction catalysed by an enzyme

Answer 17

Go!

Question 18

Sketch a graph showing the effect of pH on enzyme activity

Answer 18

Go!

Question 19

How does reducing or increasing the pH away from the optimum pH reduce the rate of reaction?

Answer 19

• the concentration of H + ions in solution affects the tertiary structure of the enzyme molecule
• H+ ions are attracted to the negatively charged group and so cluster round it. This interferes with binding of the substrate to the active site
• these ions break up the ionic and hydrogen bonds that hold the enzyme’s tertiary structure in place
• this makes the active site change shape so the enzyme is denatured

Question 20

What is the temperature coefficient?

Answer 20

• this refers to the increase in the rate of a process when the temperature is increased by 10 degrees
• how much the rate of reaction changes when temp raised by 10 degrees
• at temperatures before the optimum, a Q10 value of 2 means that rate doubles when temp raised by 10 degrees
• above optimum temp, Q10 drops

Question 21

Sketch a graph showing how substrate concentration affects the rate of reaction

Answer 21

GOOOOOO

Question 22

How does substrate concentration affect rate of reaction

Answer 22

1.

• collision between substrate and active sites of the enzyme occur more frequently
• more ESCs are formed, so more product formed
• rate of reaction increases

2. when the graph steadies
   - substrate concentration is no longer the limiting factor
   - all enzyme molecules are forming ESC as fast as possible
   - all active sites are occupied all the time
   - increase in substation concentration has no further effect on rate of reaction

Question 23

Sketch a graph showing how enzyme conc. affects rate of reaction for:

1. a fixed concentration of substrate
2. a large excess of substrate/substrate continually added

Answer 23

GOOOOOOOOOO

Question 24

How does enzyme concentration affect rate of reaction when there is a fixed concentration of substrate?

Answer 24

1. Growing curve
   - more active sites become available
   - more successful collision between enzyme’s active site and substrate
   - more ESCs formed per unit time
   - enzyme conc. is the limiting factor
2. steadies
   - eventually, all substrate molecules will be occupying an active site
   - or will have already even released as products
   - the substrate concentration is now the limiting factor
   - lack of substrate prevents the rate of reaction increasing

Question 25

How does enzyme concentration affect rate of reaction when there is a large excess of substrate/substrate continually added?

Answer 25

• 1. Growing curve
• more active sites become available
• more successful collision between enzyme’s active site and substrate
• more ESCs formed per unit time
• enzyme conc. is the limiting factor
• rate of reaction increases

Question 26

Describe two ways of measuring the rate of an enzyme-controlled reaction

Answer 26

1. • you can measure how fast the product of the reaction appears
   • using catalase as it catalyses the breakdown of H2O2, oxygen can be collected in a measuring cylinder through delivery tube setup
2. • measure the disappearance of the substrate and compare rate of reaction under different conditions
     - e.g. amylases catlyses starch to maltose
     - detect starch using potassium iodide and iodine
     - time how long it takes for the starch to disappear (when iodine solution no longer turns blue-black)
     - regularly sampling solution

Question 27

Investigate the effect of temperature on catalase activity

Answer 27

• set up boiling tubes containing same volume and concentration of hydrogen peroxide
• to keep pH constant, add equal volumes of a buffer solution to each tube
• set apparatus to measure volume of oxygen produced e.g. delivery tube to an upside cylinder
• put each boiling tube in water bath set at different temperatures along with another tube containing catalase
• use a pipette to add the same volume and concentration of catalase to each boiling tube
• record how much oxygen is produced in the first 60s
• repeat three times to find a mean volume of O produced
• calculate mean rate of reaction

Question 28

What are cofactors and coenzymes?

Answer 28

• some enzymes will only work if there is another non-protein substance bound to them, called cofactors

Question 29

Describe the different type of molecules cofactors can be

Answer 29

• inorganic molecules or ions: they work by helping the enzyme and substrate bind together and increase rate of reaction. they don’t directly participate in the reaction, so aren’t used up or changed. e.g. chloride ions are cofactors for the enzyme amylase
• organic molecules: these are called coenzymes. they participate in the reaction and are changed by it. they often act as carriers, moving chemical groups between enzymes. they’re continually recycled during this process. vitamins are sources of coenzymes

Question 30

What is a prosthetic group?

Answer 30

• if a cofactor is tightly bound to enzyme, it is a prosthetic group
• it is a permanent part of an enzyme molecule
• contribute to the final 3D shape and charges
• e.g. zinc ions for canonic anhydrase (an enzyme if reed blood cells)

Question 31

What are enzyme inhibitors>

Answer 31

• molecules that bind to the enzymes that inhibits enzyme activity
• they can be competitive or non-competitive inhibitors

Question 32

Describe competitive inhibition

Answer 32

• competitive inhibitor molecules have a similar shape to that of substrate molecules
• they compete with the substrate molecules to bind to the active site, but no reaction takes place
• instead they black the active site, so no substrate molecules can fit in it
• so fewer ESCs formed per unit time
• high concentration of inhibitor means more active sites are taken up
• increasing the concentration of the substrate will increase the chance of the substrate binding to the enzyme

Question 33

Describe non-competitive inhibition

Answer 33

• non-competitive inhibitor molecules bind to the enzyme away from its active site
• the site they bind to is known as the enzyme’s allosteric site
• this distorts the tertiary structure and therefore the 3D shape of the enzyme
• changes shape of active site
• slows rate of reaction
• increasing substation concentration has no effect
• level of inhibition depends on the concentration of non-competitive inhibitor

Question 34

What makes inhibition irreversible?

Answer 34

• if the covalent bond between enzyme and inhibitor is strong

Question 35

What makes inhibitor reversible?

Answer 35

• if there are weaker hydrogen bonds, or weak ionic bonds between the inhibitor and enzyme

Question 36

Give examples of medicinal drugs that are enzyme inhibitors

Answer 36

• some antiviral drugs: e.g. reverse transcriptase inhibitors prevent the enzyme reverse transcriptase, which catalyses the replication of viral DNA, preventing virus from replicating
• some antibiotics: e..g. penicillin inhibits the enzyme transpeptidase, which catalyses the formation of proteins in bacterial cells walls. this weakens the cell wall and prevents the bacterium from regulating its osmotic pressure. as a result cell bursts and bacterium removed

Question 37

Give examples of poisons that interfere with metabolic reactions and act as enzyme inhibitors

Answer 37

• cyanide: an irreversible inhibitor of cytochrome c oxidase, an enzyme that catalyses respiration reactions
• arsenicL inhibits the action of pyruvate dehydrogenase, another enzyme that catalyses respiration reactions

Question 38

What is a metabolic pathway?

Answer 38

• a metabolic pathway is a series of connected metabolic reactions
• the product of the first reaction takes part in the second reaction etc
• each reaction is catalysed by a different enzyme

Question 39

What is product inhibition?

Answer 39

• many enzymes are inhibited by the product of the reaction they catalyse

Question 40

What is end-product inhibition

Answer 40

• end-product inhibition is when the final product in a metabolic pathway inhibits an enzyme that acts earlier on in the path way

Question 41

What is end-product inhibition used for?

Answer 41

• regulates the metabolic pathway and controls the amount of end product that gets made
• e.g. phosphofructokinase is an enzyme involved in the metabolic pathway that breaks down glucose to make ATP
• ATP inhibits the action of phosphofructokinase, so a high level of ATP prevents more ATP from being made

Question 42

Is product and end-product inhibition reversible?

Answer 42

• yes
• example of negative feedback
• when product starts to drop, level of inhibition starts to fall, enzyme functions again, more product made

Question 43

What are inactive precursor?

Answer 43

• some enzymes are synthesised and produced in an inactive precursor form
• before they are active, some of their amino acids have to be removed
  e. g. digestive enzyme are produced like this so they don’t digest cells molecules
• trypsin is produced as trypsinogen: then a portion of it is removed by another enzyme to from active trypsin
• pepsin is produced as pepsinogen: converted to pepsin by action of HCl in the stomach