2.1.4 Enzymes

Question 1

Enzyme deffinition

Answer 1

A globular protein, made up of living cells. It is a biological catalyst meaning it can speed up a chemical reaction by reducing the activation energy, but is not used up itself. USED IN METABOLIC REACTIONS.

Question 2

where are enzymes mostly used?

Answer 2

is metabolic reactions

Question 3

What is a catabolic reaction?

Answer 3

When a large substrate ,p;ecule is broken down into smaller product molecules

Question 4

what type of reaction is a catabolic reaction?

Answer 4

Hydrolysis

Question 5

give an example of a catabolic reaction

Answer 5

ATP hydrolysis

Question 6

is catabolic exo or endo thermic? plus example

Answer 6

they are exothermic, since they release energy, ie the release of energy from glucose and its trandser to the energy currency molecule ATP

Question 7

What is a anabolic reaction?

Answer 7

The joinging together of small substrates into a larger product

Question 8

when are anabolic reactions required?

Answer 8

During growth and repair of the organism body

Question 9

what type of reaction is a anabolic reaction?

Answer 9

condensation

Question 10

give an example of a anabolic reaction

Answer 10

the condensation of amino acids to form a polypeptide, catalysed by the peptidyl transferase enzyme.

Question 11

is anabolic exo or endo thermic? plus example

Answer 11

endothermic, since it needs an input of energy from atp

Question 12

what is oxidation?

Answer 12

The loss of electrons, loss of hydrogen atom, gain oxygen atom

Question 13

what catalyses oxidation?

Answer 13

dehydrogenase enzyme

Question 14

what is reduction?

Answer 14

the gain of electrons, gain hydrogen atom, loss of oxygen atom

Question 15

what catalyses reduction?

Answer 15

hydrogenase enzyme

Question 16

when is redox important in biology?

Answer 16

in respiration and photosynthesis

Question 17

what is an intracellular enzyme?

Answer 17

An enzyme which remains in the cell that produced them, carrying out their function in that cell

Question 18

give an example of an intracellular enzyme

Answer 18

Catalase - It catalyses the breakdown of hydrogen peroxide, a toxic wasste product of metabolism, into non-toxic water and hydrogen.

Question 19

what is an extracellular enzyme?

Answer 19

An enzyme secreted out of the cell its made in, and carrys its role outside its original cell.

Question 20

give an example if extracellular enzyme

Answer 20

Trypsin - secreted by the pancrease or small intestine, catalyses the hydrolysis of proteins into amino acids.

Question 21

Draw a catabolic reaction graph

Answer 21

Question 22

draw a anabolic reaction graph

Answer 22

Question 23

Why is induced-fit better than lock-and-key?

Answer 23

Induced fit explains how an enzymeis able to decrease the amount of activation energy requird for a reaction

Question 24

what are the 8 steps of the induced-fit hypothesis?

Answer 24

1. Prior to the binding of the substrate to the active site, the active site is NOT already the perfect complementary shape for the substrate molecule to fit into
2. The substrate collides with the active site of the enzyme
3. As the substrate begins to bind with the active site, this acts as a trigger causing (‘inducing’) the active site to change shape. The active site thus becomes the complementary shape to fit with the attached substrate and an ESC is formed
4. As the shape of the active site changes, the substrate may itself be pushed into a slightly distorted shape; this could cause bond strain , i.e. bonds become weaker and break more easily ,with less energy required (hence a decrease in activation energy occurs , explaining how the enzyme is increasing reaction rate)
5. The reaction takes place, with the substrate converted to products; briefly , an EPC exists
6. The product molecules are not a good complementary fit with the active site, so they leave the active site
7. As the products detachs from the active site , this triggers a change in shape of the active site , back to its origina lshape (i.e.not yet complementary to the substrate)
8. The enzyme can now catalyse another reaction, when a new substrate molecule (of the correct type) collides with the active site.

Question 25

what is the lock and key hypothesis

Answer 25

The active site is already 100% complementary to the substrate, and it doesnt need to change at all. Like a real lock and key only the specific substrate will bind with the active site of the enzyme. When the substrate binds to the active sire, its called the enzyme-substrate complec, and then with the product its called the enzyme-product complex

The enzyme holds the substrate in a way so that the right atom-groups react together. The R groups in the active site will also react with the substrate forming tempory bonds, putting stain on the substrate.

Question 26

what is the shape of the active site?

Answer 26

complementary to the substrate

Question 27

rate of reaction equation

Answer 27

(change of substrate or product concentration) / Time

Question 28

examples of pH change from enzymes

Answer 28

more acidic = fatty acids frim hydrolysis of triglycerides
more basic = ammonia breakdown from urea

Question 29

how do you calculate the rate of reaction at a specific time from a graph?

Answer 29

Draw a tangent to the curve at this specific time, and then working out its gradient

Question 30

How does one determine the optimum of an enzyme

Answer 30

1. To obtain the most accurate vaulkes for the optimum, we would test more intermedicate values ie every 1 degree celcius or 0.1 pH wiothin the range in which the optimum is most likely to lie from rough trails.
2. We can use quantitative data rather than qualitative data, such as using a colorimiter or a pH probe
3. For valadility, we can use a control test tube, where there is the same volume of enzyme, but it is denatured through boiling. All the other controls and variables should be exactly the same.

Question 31

what does optimum mean?

Answer 31

the condition at which the rate of reaction of an enzyme is the highest

Question 32

what is the point of a control test tube?

Answer 32

Usually, no (detectable) conversion of substrate to product will be observed in the control test. This demonstrates clearly that the reaction observed in the experimental tubes must be due to the presence of the active enzyme in those tubes
The reaction is not observed in the absence of the active enzyme. The control is important because now, when you find the optimum temperature or pH, or look at the effect of a factor on the rate, you can be sure that this does relate specifically to the enzyme‐catalysed reaction and not to some chemistry that is happening without enzyme‐catalysis.

Question 33

What is the conecentration of H+ ions in acidic conditions?

Answer 33

High

Question 34

How many H+ ions are in basic conditions?

Answer 34

low

Question 35

Give an exmaple of enzyme with its optimum pH

Answer 35

Pepsin - pH 2 - a protease enzyme - most active in a very acidic environment, this is approprraite since in the stomach where it works has concentrated hydrochloric acid

Question 36

what happens to the enzyme if the pH decreases or increases away from the optimum? 5 points

Answer 36

1. The rate of reaction falls, this is becuase the changes to the pH cause alterations in the postive and negative charges on some amino acid R-groups in the enzyme
2. The changes to the R groups cause ionic bonds and hydroge bonds to break, which are a key feature in holding the specific tertiary structure in place.
3. The breaking of these bonds results in changes to the 3D shape of the enzyme, including the active site. As the enzyme active site is no longer compleementary to the specific substrate, the enzyme-substrate complex can no longer form.
4. The rate of reaction decreases (sometimes to zero), as no substrate can be converted into product
5. The enzyme has been denatured due to the pH being significantly higher or lower than the optimum ; it is no longer active. This will be irreversible (permanent), meaning that even if the pH later returns to the optimum, the specific 3D shape of the active site will not be restored and the enzyme will not regain its activity.

Question 37

small changes in pH effect on the enzyme

Answer 37

Even quite small changes to pH can alter the positive and / or negative charges of R groups that are found in the lining of the active site. This can mean that the substrate is not attracted to, or cannot attach to the active site , so no ESC is able to form. However, this effect maybe reversible if the change in pH was minor: returning the pH to optimum will restore the ‘correct’ charges and allow the substrate to bind to the active site and form an ESC.

Question 38

pH on enzyme activity graph

Answer 38

look in notes :(

Question 39

effect of heavy metal ions on enzyme strucuture

Answer 39

The presence of heavy metal ions (e.g. cadmium or lead ions) has a similar effect on enzyme structure to high / low pH : hydrogen bonds and ionic bonds will be broken, resulting in permanent changes to enzyme’s tertiary structure and corresponding loss of catalytic function. Heavy metal ions are therefore toxic to most organisms since they act as metabolic inhibitors.

Question 40

what is the optimum temperature of our enzymes?

Answer 40

37 degrees celcius

Question 41

what happens to the rate of reaction if temperature decreases?

Answer 41

If temperature decreases to values below the optimum, reaction rate will gradually decrease, this is due to the decrease in the rate of collision, as the particles have less kinetic energy, therefore there are less frequents and less successful collions, and less enzyme-substrate complexes are formed.

Question 42

what happens if temperature rises above the optimum? 4 points

Answer 42

1. If temperature rises above the optimum, reaction rate also decreases, often very steeply.
2. At temperatures significantly above the optimum, the reaction rate becomes zero, i.e. the enzyme is no longer able to catalyse the reaction, which therefore stops. This happens because the excessive kinetic energy causes vibrations within the protein structure of the enzyme, leading to the breaking of some of the bonds that were holding the enzyme’s specific tertiary structure in place: hydrogen bonds break first as these are the weakest. The enzyme now undergoes changes to its 3D shape (i.e. its specific tertiary structure is lost), resulting in alteration of the shape of the active site in particular.
3. The active site will no longer be complementary to the substrate(s), which therefore can nolonger fit into it; no ESC can form. This means that the enzyme is no longer active : it cannot catalyse the reaction which would convert substrate(s) to product(s). The enzyme is said to be denatured.
4. This denaturation is irreversible, i.e. permanent. This means that the enzyme will never have catalytic activity again, even if the temperature is returned to the optimum.

Question 43

Draw the effect of tempertaure on enzyme activity graph

Answer 43

look in notes :(

Question 44

what is the Q 10 equation?

Answer 44

Q10 = (reaction rate at t°C) ÷ (reaction rate at t‐10°C)

ie at 40°C the rxn is 50 au, but at 30°C the rxn is only 25 au, therefore the Q10 is 50/25 = 2

Question 45

Effect of enzyme concentration on rate of an enzyme-catalysed reaction

Answer 45

If we increase the number of enzymes are present in a solution (higher concentration of enzymes), the reaction rate is expected to increase, as there will be more active sites available for substrate molecules to collide with and so a higher rate of ESC formation. However, at very high enzyme concentrations, the rate may not continue to increase if enzyme concentration continues to increase ; the rate will remain constant, as the limited substrate availability may
become a limiting factor, preventing any further increase in the rate which can be achieved.

Question 46

Draw the enzyme concentration and rxn graph

Answer 46

look in notes :(

Question 47

Effect of substrate concentration on rate of an enzyme‐catalysed reaction

Answer 47

If substrate concentration is increased, the rate of the reaction is expected to increase. This is because the collision rate between substrates and the active sites of enzymes increases, giving a higher rate of ESC formation. Hence there is a higher rate of conversion of substrates to products. However, at very high substrate concentrations, the rate may not further increase if substrate concentration continues to increase; the rate will remain constant, as the active sites of all enzymes are now saturated. This means that as soon as one reaction has completed, and products have left the active site, another substrate immediately collides and undergoes conversion to products. The enzymes are all now working at their maximum rate (also called maximum velocity , or Vmax); further increases in concentration will not cause an even higher rate of reaction.

Question 48

draw the substrate concentration graph

Answer 48

look in notes :(

Question 49

what is an inhibitor?

Answer 49

Inhibitors are molecules (or ions) which bind to enzymes and cause a decrease in the rate of the reaction that the enzyme catalyses. Inhibitors can be competitive or non‐competitive (with respect to the substrate) and can bind reversibly or non‐reversibly to the enzyme they target.

Question 50

Competitive inhibitor

Answer 50

A molecule which can act as a competitive inhibitor will have a similar shape / structure to the genuine substrate (or at least similar to the part of the substrate that fits into the active site); hence thisi nhibitor molecule is able to bind with the enzyme’s active site(as it is complementary to the active site and so fits into it). This blocks the active site, preventing the substrate from binding. Hence no ESC can form and the substrate is not converted to product. The reaction rate is therefore decreased as the competitive inhibitor and substrate are competing to bind to the active site of the enzyme.

Question 51

what occurs if more substrate is added with a competitive inhibitor?

Answer 51

The greater the concentration of substrate (relative to inhibitor) the greater the probability that a substrate will collide with the active site and form an ESC, rather than the inhibitor colliding with the active site and blocking it such that substrate cannot bind.

In fact, if the substrate is present in excess quantities (i.e. at a massively greater concentration than that of the inhibitor), the reaction rate will theoretically reach the same maximum rate (Vmax) that is obtained when no inhibitor is present at all.

Question 52

are competitive inhibitors reversible or irreversible?

Answer 52

Most competitive inhibitors bind temporarily to the active site (i.e. their effect are reversible and short‐lived); others bind permanently (i.e.their effects are irreversible, meaning that the inhibited enzyme will never functionagain).

Question 53

Give an example of a competitive inhibitor

Answer 53

Reversible competitive inhibitor : Statins are drugs used to reduce a person’s cholesterol (and hence decrease their risk of heart disease). Statins are competitive inhibitors of the enzymes in the liver that produce cholesterol.

Question 54

draw the competitive inhibitor graph

Answer 54

look in notes :(

Question 55

Non-competitive inhibitors

Answer 55

Non‐competitive inhibitors bind to a different region of the enzyme (away from the active site); this is called the allosteric site. The binding of the inhibitor to the allosteric site triggers a change in the tertiary structure (3D shape) of the enzyme; this includes distortion of the active site, such that it is no longer complementary to the substrate.

The substrate cannot form an ESC and hence no substrate is converted to product. The reaction rate is therefore decreased.

Question 56

what occurs if more substrate is added with a non-competitive inhibitor?

Answer 56

Unlike competitive inhibitors, the extent of inhibition of an enzyme by a non‐competitive inhibitor does not decrease when substrate concentration increases. This is due to the inhibitor and substrate binding to different parts of the enzyme, and hence not competing, as the active site is no longer complementary so the substrate cannot fit.

Question 57

are non-competitive inhibitors reversible or irreversible?

Answer 57

Some non‐competitive inhibitors bind temporarily to the allosteric site of the enzyme (i.e. their effects are reversible); others bind permanently (i.e. their effects are irreversible).

Question 58

Give an example of a non-competitve inhibitor

Answer 58

Reversible non‐competitive inhibitors: ATP, the energy currency molecule which is the product of respiration, inhibits one of the enzymes involved in respiration and in hence production of ATP

Question 59

Draw a non-competitive inhibitor graph

Answer 59

look in notes :(

Question 60

what is the significance of enzyme inhibitors?

Answer 60

Some enzyme inhibitor act as poisons, whilst others have been found to be useful medicinal drugs; inhibitors occurring naturally the body play important roles in the control and regulation of metabolism.

Question 61

Metabolic poisions and an example

Answer 61

Metabolic poisons are enzyme inhibitors which disrupt vital chemical reactions in the organism’s body, such as respiration.

Example: Cyanide is a competitive inhibitor of an enzyme involved in aerobic respiration in the mitochondria, leading to decreased ATP production.

Question 62

Medicinal drugs

Answer 62

Some medicinal drugs are in fact enzyme inhibitors which can be taken as medicines in order to treat health problems.

Example: Statins - Statins are drugs used to reduce a person’s cholesterol (and hence decrease their risk of heart disease). Statins are competitive inhibitors of the enzymes in the liver that produce cholesterol.

Question 63

what is end product inhibition?

Answer 63

End‐productinhibition is a mechanism where by the end (final) product of a metabolic pathway (i.e.a sequence of chemical reactions) inhibits an enzyme earlier in the pathway, leading to decreased production of that product.

Question 64

what is end product inhibition an example of? and what is the point of it?

Answer 64

This is a type of negative feedback and it ensures that a particular product does not get over‐produced, leading to excessive levels building up. This mechanism also avoids wasting resources.

Question 65

how does end product inhibition work?

Answer 65

The product usually acts as a reversible non‐competitive inhibitor, binding to an allosteric site on one of the enzymes involved in its own synthesis

Question 66

Give n example of end product inhibition

Answer 66

ATP acts as a reversible non‐competitive inhibitor of one of the
enzymes involved in ATP production.

Question 67

what is an inactive precursor enzyme?

Answer 67

Many important enzymes are initially produced in an inactive precursor form and need to be activated in order for their active sites to be complementary to their substrates so that they can now catalyse reactions.

Question 68

why are enzymes produced inactive?

Answer 68

This mechanism is often used for extracellular enzymes, because if the enzyme were active before it left the cell it could do damage to components of the cell; it is also used when an enzyme should only be active in very specific conditions.

Question 69

how are inactive precurosr enzymes activated? 3 points

Answer 69

1. Activation of an enzyme sometimes involved the attachment of a co‐enzyme or the binding of a molecule (e.g. cyclic AMP) to an allosteric site on the enzyme, resulting in a change to its tertiary structure.
2. Another way that an inactive precursor enzyme can be activated is to have part of its structure modified or removed by another enzyme (e.g.a section of the polypeptide chain may be removed by a protease, which hydrolyses the relevant peptide bonds).
3. Alternatively, a change in temperature or pH may trigger the changes to tertiary structure which activate the precursor enzyme (which can also be called a pro enzyme

Question 70

give an example of a precursor enzyme please :)

Answer 70

pepsinogen is an inactive precursor enzyme secreted by cells in the lining of the stomach; once it comes into contact with the low pH conditions (HCl in the stomach), it undergoes a change in tertiary structure, such that its active site now becomes the appropriate complementary shape for its substrate. The active form of this extracellular digestive enzyme is called pepsin and it catalyses digestion (hydrolysis) of protein in the stomach.

Question 71

what is a coenzyme?

Answer 71

Coenzymes are organic (carbon‐containing) molecules which some enzymes require in order for them to catalyse the conversion of their substrate to product, but which is not a permanent part of its structure.

Many of the coenzymes required by enzymes in the human body have their origin as vitamins in our diet. i.e NAD from vitamin B3 and CoA from Vitamin B5

Question 72

what is a cofactor?

Answer 72

Cofactors are inorganic ions which some enzymes require in order for them to catalyse conversion of their substrate to product. The cofactor ion will be necessary for the activity of the enzyme, but is not a permanent part of its structure.

We obtain cofactor ions. in the form of minerals in the food and drink we consume. For example, iron (Fe2+) ions are found in high quantities in spinach and in red meat, calcium (Ca2+) ions are found in dairy products and chloride (Cl‐) ions are found in any salty food.

Question 73

what is a prosthetic group?

Answer 73

A prosthetic group is a permanent part of a protein’s structure, but is not itself made of a chain of amino acids. Some enzymes have permanently attached prosthetic groups, which are necessary for their function; such enzymes are therefore examples of conjugated proteins.

Question 74

give an example of a coenzyme

Answer 74

NAD derived from Vitamin B3 - It transfers protons and electrons during respiration

Coenzyme A (CoA) from Vitamin B5 - it transfers acetyl groups during respiration.

Question 75

give an example of a cofactor

Answer 75

Amylase - it requires a chloride ion to be active, and it bonds into the active site of the enzyme, which is required for it to form its complementary sago into which amylose cab bind to be hydrolysed into maltose

Question 76

give an example of a prothetic group

Answer 76

Catalase - breaks down hydrogen peroxided into water and hydrogen. Its described as a conjugated protein, since it contains a prothetic group, this being a ham group which contains Fe 2+ ions, this is necessary for hydrogen peroxide to bind into the active site.

Question 77

enzyme effect on activation energy

Answer 77

Enzymes speed up the rate of a chemical reaction by lowering the activation energy. Activation energy is the additional energy that must be supplied to enable the reaction to proceed, e.g. the energy needed to break bonds in the substrate molecules.

Question 78

How do enzymes work? …points

Answer 78

1. An enzyme has a groove in its surface called the active site. This active site of a particular enzyme has a specific complementary shape, meaning that only the ‘correct’ substrate can fit into this active site.
2. The consequence is that a particular type of enzyme can only catalyse the conversion of this particular substrate into product(s); other molecules will not fit into the active site, and so cannot be converted into products. This idea is called specificity: each type of enzyme is highly specific, in that it can only catalyse one type of reaction, involving a specific substrate.
3. This specificity is due to the active site of the enzyme being a particular shape, which is only complementary to one type of substrate molecule.
4. When a substrate molecule collides with an active site of the appropriate complementary shape, the substrate binds (temporarily) with the active site; this forms an enzyme‐substrate complex (ESC).
5. The reaction catalysed by the enzyme now takes place, in the active site. This typically involves some chemical bonds breaking and some new bonds forming: their action converts the substrate(s) to the product(s).
6. The products formed briefly occupy the active site, as an enzyme‐product complex (EPC). However, the products are a different shape compared to the substrates, hence they are not actually a good fit with the active site (not complementary in shape); the active site is specifically shaped so as to be complementary to the substrates only. This means that the products will immediately leave the active site, i.e. they are released.
7. As soon as the products leave the active site, another substrate can collide with the active site, forming ESC, and then be converted to products.
8. Enzymes are not ‘used up’ or altered when they catalyse a reaction, meaning that, as long as there is sufficient substrate remaining, and as long as the enzyme does not become denatured, it will keep converting substrate to products, often at a rate of millions of conversions per second.