Module 2, Chapter 4: Enzymes

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Non Competitive Inhibition
- non competitive inhibition molecules bind to the enzyme away from its active site
the site they bind to is known as the enzyme's Allosteric Site

- this causes the active site to change shape so the substrate molecules can no longer bind to it

- they don't "compete" with the substrate molecules to bind to the active site because they are a different shape

- increasing the concentration of substrate won't make any difference to the reaction rate - enzyme activity will still be inhibited
What do catalysts do?
speed up chemical reactions by lowering activation energy
Reactions that are catalysed
- cellular level (respiration)

- organisms as a whole (digestion)
Intracellular
within the cell
Example of Enzymes inside of Cell
catalase
Function of Catalse
- hydrogen peroxide is the toxic by product of several cellular reactions

- if left to build up, it can kill cells

- Catalase is an enzyme that works inside cells to catalyse the breakdown of hydrogen peroxide to harmless oxygen and water
Extracellular
outside the cell
Examples of Extracellular Enzymes
Amylase and trypsin
Function of Amylase
- found in saliva

- secreted into mouth by cells in the salivary glands

- catalyses the hydrolysis of starch into maltose in the mouth
Function of Trypsin
- catalyses the hydrolysis of peptide bonds

- turns big polypeptides into smaller ones

---which then get broken down into amino acids by other enzymes

- produced by cells in the pancreas and secreted into the small intestines
What are biological catalysts?
globular proteins
What is the active site of an enzyme?
is part of the enzymes that the substrate molecules bind to
What is the specific shape of the active site is determined by?
the enzyme's tertiary structure
Activation Energy
the minimum amount of energy required to start a chemical reaction
How is the Activation Energy often provided as?
as heat
How do Enzymes speed up the rate of reaction?
- enzymes reduce the amount of activation energy needed

- often making reactions happen at a lower temperature than they could without an enzyme
What is formed when an substrate binds to an enzyme's active site?
an enzyme - substrate complex is formed
What lowers the activation energy?
the formation of the enzyme's substrate complex
How does the formation of the enzyme's substrate complex lower the activation energy?
- if 2 substrate molecules need to be joined, attaching them to the enzyme holds them close together, reducing any repulsion between the molecules so they can bond more easily

- if the enzyme is catalysing a breakdown, fitting into the active site puts a strain on bonds in the substrate

- this strain means the substrate molecule breaks up more easily
Lock and Key Model
- enzymes only work with substrates that fit their active site
Induced Fit
- this locks the substrate even more tightly to the enzyme

- substrate does not only have to be the right shape to fit the active site, it has to make the active site change shape in the right way as well

- as the substrate binds, the active site changes shape slightly to fit the substrate more closely
How does temperature affect the rate of reaction?
- more heat = more kinetic energy = molecules move faster

- enzymes more likely to collide with the substrate molecules

- energy of these collisions also increases

- each collision is more likely to result in reaction

- if temperature gets too high, the reaction stops
How do enzymes become denatured?
1. The rise in temperature makes the enzyme's molecules vibrate more

2. If the temperature goes above a certain level, this vibration breaks some the bonds that hold the enzyme in shape

3. The active site changes shape and the enzyme and substrate no longer fit together
Temperature Coefficient
- Q10

- shows how much the rate of reaction changes when temperature is raised by 10 degrees
Q10=
r2 (rate at higher temperature) / r1 (rate at lower temperature)
What pH does Pepsin work best at?
pH 2
Above and Below the Optimum pH of enzymes
- the H+ ions and OH- ions found in acids and alkalis can mess up ionic bonds and hydrogen bonds that hold the enzyme's tertiary structure

- this makes active site change shape, so enzyme is denatured
Enzyme Concentration on Rate of Reaction
- more enzyme molecules = more likely substrate molecule is to collide with one

- form enzyme substrate complex

- increasing conc of enzyme = increasing rate of reaction

- if amount of substrate is limited, more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further effect
Substrate Concentration on Rate of Reaction
- the higher the substrate concentration, the faster the reaction

- more substrate means a collision between substrate and enzyme is more likely
more active sites used

- only true up until a 'Saturation Point'
after that, there are so many substrate molecules that the enzymes have about as much as they can cope with (all the active sites are full)

- adding more substrate makes no difference to the rate

- substrate concentration decreases with time during a reaction (unless more substrate is added), so if no other variables are changed, the rate of reaction will decrease over time

- this makes the initial rate of reaction, the highest rate of reaction
How to measure the Rate of an Enzyme Controlled Reaction
- Measure how fast the product of the reaction appears

- Measure disappearance of the substrate
How to Measure how fast the product of the reaction appears
1. upside down measuring cylinder

2. container with water

3. delivery tube (with hydrogen peroxide solution and catalase enzyme) under cylinder

4. measure amount of oxygen produced
Measuring disappearance of the substrate
- Use this to compare rate of reactions under different conditions

1. put potassium iodide in spotting tile

2. mix starch solution and amylase enzyme

3. using dropping pipette, put drops of iodine in spotting tile each minute

4. time when iodine solution no longer turns blue / black

- starch has then been broken down

- alter conditions
Control Variables when Investigating the Effect of Temperature on Catalase Activity
- pH

- enzyme concentration

- Substrate concentration
Method on how to Investigating the Effect of Temperature on Catalase Activity
1. Set up boiling tubes containing the same volume and concentration of hydrogen peroxide

- keep pH constant, add equal volumes of buffer solution to each tube

- buffer solution is able to resist changes in pH when small amounts of acid or alkali are added

2. Set up the apparatus to measure the volume of oxygen produced from each boiling tube

- e.g. use a delivery tube upside down measuring cylinder

3. Put each boiling tube in a water bath set to a different temperature, along with another tube containing catalase

- wait 5 minutes before moving on to the next step to allow the enzyme to reach the set temperature

4. Use a pipette to add the same volume and concentration of catalase to each boiling tube

5. Record how much oxygen is produced in the first 60 seconds of the reaction

6. Repeat the experiment at each temperature 3 times and use the results to find out the mean volume of oxygen produced at each temperature

7. Calculate the mean rate by dividing the volume of oxygen produced by the time taken
How to Investigate the Effect of Substrate Concentration
- prepare boiling tubes with different concentrations of hydrogen peroxide (serial dilutions)
How to Investigate the Effect of pH
add a buffer solution, with a different pH to each tube
Cofactors
- non protein substances that bind to enzymes to make them work

- inorganic molecules or ions
How do Cofactors work?
- they work by helping the enzyme and substrate to bind together

- they don't directly participate in - the reactions so aren't used up or changed in anyway way
What is the cofactor for amylase?
chloride ions (Cl-)
Coenzymes
cofactors that are organic molecules
How do Coenzymes work?
- they participate in the reaction and are changed by it (like a second substrate, but they aren't called that)

- they often act as carriers, moving chemical groups between different enzymes

- they're continually recycled during this process
Sources of Coenzymes
vitamins
Prosthetic group
the term if a cofactor is tightly bound to the enzymes
Examples of a Prosethic Group
- zinc ions are a prosthetic group for carbonic anhydrase (an enzyme in red blood cell, which catalyses the production of carbonic acid from water and carbon dioxide

- this zinc ions are a permanent part of the enzyme's active site
How can enzyme activity can be prevented?
Enzyme Inhibitors
Enzyme Inhibitors
- molecules that bind to the enzymes that they inhibit

- can be competitive or non competitive
Competitive Inhibition Molecules have....
a similar shape to that of the substrate molecules
Function of Competitive Inhibition Molecules
- they compete with the substrate molecules to bind to the active site, but no reaction takes place

- instead they block the active site, so no substrate molecules can fit in it

- how much the enzyme is inhibited depends on the relative concentrations of the inhibitor and substrate
High Concentration fo Competitive Inhibitors
- it'll take up nearly all the active sites and hardly any of the substrate will get to the enzyme

- but if there's a higher concentration of substrate, then the substrates chances of getting to an active site before the inhibitors increase

- so increasing the concentration of substrate will increase the rate of reaction
Metabolic Pathway
a series of connected metabolic reactions
Allosteric Site
the site the non competitive inhibition molecules bind to
Phosphofructokinase
an enzyme involved n the metabolic pathway that breaks down glucose to make ATP
What inhibits the action of Phosphofructokinas?
ATP
Is product and and product inhibition reversible?
yes
What happens when the level of product starts to drop?
the level of inhibition will start to fall and the enzyme can start to function again = more product made
Why are enzymes sometimes synthesized?
to act as inactive precursors in metabolic pathways to prevent them causing damage to cells
Examples of Synthesized Enzymes
some proteases are synthesised as inactive precursors to stop them damaging proteins in the cell in which they are made
Examples of Enzyme Inhibitors
- medicinal drugs

- metabolic poisons
Antiviral Drugs acting as Enzyme Inhibitors
- Reverse transcriptase inhibitors inhibit the enzyme reverse transcriptase, which catalyzes the replication of viral DNA

- prevents the virus from replicating
Antibiotics acting as Enzyme Inhibitors
- e.g. Penicillin

- inhibits the enzyme transpeptidase, which catalases the formation of proteins in bacterial cell walls

- weakens the cell wall and prevents the bacterium from regulating its osmotic pressure

- as a result the cell bursts and the bacterium is killed
What do Reverse transcriptase inhibitors inhibit ?
the enzyme reverse transcriptase, which catalyzes the replication of viral DNA
What does the Enzyme Reverse Transcriptase do?
catalyses the replication of viral DN
What enzyme does penicillin inhibit?
the enzyme transpeptidase
What does the enzyme transpeptidase do?
catalyses the formation of proteins in bacterial cell walls
What do Metabolic Poisons do?
interfere with metabolic reactions, causing damage, illness or death (often enzyme inhibitors)
Examples of Metabolic Poisons?
- cyanide

- malonate

- arsenic
Cyanide Function
- irreversible inhibitor of cytochrome c oxidase

- an enzyme that catalyses respiration reactions

- cells that can't respire die
Function of Malonate
inhibits succinate dehydrogenase (catalyses respiration reactions)
Function of Arsenbic
inhibits the action of pyruvate dehydrogenase (catalyses respiration reactions)
Enzymes that Catalase Respiration Reactions
- cytochrome c oxidase

- succinate dehydrogenase

- pyruvate dehydrogenase
Anabolic
where small molecules are built up into larger, more complex ones.
Catabolic
where larger molecules are broken down into smaller ones.
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