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OCR AS LEVEL BIOLOGY > Chapter 6- ENZYMES > Flashcards

Chapter 6- ENZYMES Flashcards

1
Q

What are enzymes

A

These are globular proteins and biological catalysts that speed up reactions without undergoing permanent change.
These are specific; an enzyme only binds with a single type of substrate since their active site has a specific and complimentary shape to only one type of substrate. Different enzymes bind to different type of substrate.
They are needed to catalyse reactions at a cellular and whole organism level.

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2
Q

How are enzymes effective?

A

The energy required to break the original bonds, so that a reaction can proceed, is called the activation energy.
Enzymes speed up reactions by reducing the amount of activation energy needed.

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3
Q

The stages of substrate to product

A

Substrate + enzyme -> enzyme-substrate complex -> enzyme-product complex -> products

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4
Q

Lock and Key hypothesis

A

The shapes of the substrate and the active site of the enzyme is complimentary and specific. The substrate fits the active site of the enzyme like a fitting key does in a lock.
The interactions of the R groups within the active site and the substrate stabilise the enzyme-substrate complex.

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5
Q

What are the two types of enzyme reactions?

A

Catabolic and anabolic reactions
Catabolic reaction breaks down the substrate into two products
Anabolic reaction joins two substrates into one product

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6
Q

How does a catabolic reaction occur

A

The formation of the enzyme-substrate complex causes conformational changes in the shape of the substrate. This weakens the bonds holding together.
Less activation energy is now needed to break the bonds and for the reaction to proceed.

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7
Q

Why do the products leave the active site of the enzyme?

A

The products no longer fit into the active site so they move away, allowing the enzyme to be reused.

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8
Q

How does an anabolic reaction work

A

ATP is required to change the shape of the substrate and synthesise a larger molecule or product.
This product leaves the enzyme’s active site since it no longer fits

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9
Q

Why does each enzyme’s active site have a specific shape?

A

An enzyme is a globular protein which is formed at the tertiary structure.
The DNA structure determines the sequence, number and type of amino acids, forming the primary structure. This then determines the folds of the beta pleated sheets and the alpha helix, in the secondary structure. This then influences how this structure folds more to form the globular shape; as well as the position of the disulphide bonds, hydrogen bonds and the hydrophobic/hydrophilic interactions

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10
Q

How does the graph of rate of reaction look like

A

X axis- time (secs)
Y axis- Amount of product

The rate of an enzyme-catalysed reaction is higher at the start because the concentration of substrate molecules higher at start
At this stage, this is a higher chance of substrate molecules entering the active site.

This soon decreases and then levels off because active sites are occupied
So increasing the substrate conc has no effect
So enzyme conc is the limiting factor

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11
Q

What is the Q10 temperature coefficient

A

This is a measure of the rate of change of a biological or chemical system as a consequence of increasing the temperature by 10 degrees centigrade.
A temperature increase of 10 degree centigrade is equal to the Q10 coefficient for that enzyme and can be used to compare the rate of reaction for different enzymes.
This is the ratio between the rates of that process at two different temperatures.

Temperature coefficient= rate of reaction at (x+10) degrees centigrade / rate of reaction at x degrees centigrade

Where x is any given temp

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12
Q

What is the Brownian Motion

A

Molecules, in solution move randomly and continuously, colliding with each other.

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13
Q

How does increasing the temperature affect the particles

A

Heat increases the kinetic energy of molecules, they move faster and collide more often and with a greater force

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14
Q

How is glucose produced

A

In a solution of water molecules and maltose molecules, add maltase enzyme molecules
This will cause all of these three types of molecules to continually collide with each other.
the collision between the water molecule and a maltose molecule with the active site of a maltase enzyme molecule, a reaction will take place and the product glucose will be produced.

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15
Q

Exam question: how does optimum temperature affect enzyme activity

A

Increased kinetic energy
Increased number of collisions and successful collisions ( those reaching activation energy) in a given time
More successful collisions means more enzyme-substrate complexes are formed. Maximum rate of reaction is achieved
more product

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16
Q

What does an optimum temp give you

A

At optimum temperature, the maximum rate of reaction is occuring

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17
Q

Why does an enzyme denature at a high temperature (above optimum)

A

Heat vibrates molecules straining bonds
Weak H bonds and ionic interactions break first, breaking the tertiary protein structure

Eventually the active site loses its 3D conformational shape; the tertiary structure unravels.
The enzyme is denatured and its irreversible

The heat does not affect the primary structure; the covalent peptide bonds are not broken

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18
Q

Exam question: how does a higher temperature affect the enzyme activity

A

Molecules have more kinetic energy
Collisions occur more frequently with more energy
Molecules vibrates which strains the bonds
H bonds and ionic interactions are broken
(Covalent peptide bonds are not broken)
Tertiary structure pr globular shape altered
Active site looses its complimentary shape
Substrate molecule no longer fits active site
Enzyme is denatured
Rate decreases
Irreversible so reaction really slows down

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19
Q

Effect of temperature on enzyme sctivity

A 
Slow rate of reaction or activity
Less kinetic energy 
Molecules moving slowly
Few collisions (collisions less likely) 
Less collisions with sufficient activation energy
Few enzyme-substrate complex formed 
Enzyme still works; not denatured
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20
Q

What is pH

A

It is a measure of H+ ion concentration

The higher the H+ concentration the lower the pH (acidic)

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21
Q

What can the H+ ions do

A

Disrupt the H bonds keeping the secondary structure in place

Ionic bonds holding the tertiary structure together

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22
Q

How can H bonds disrupt the alpha helix

A

As the conc of H+ ions is increased, the positive charge of this ion is attracted to the electronegative atoms, NOF. This ends up replacing the hydrogen bond.

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23
Q

How are the ionic bonds disrupted by H+ ions

A

H+ ions are attracted to the negatively charged group and so ‘cluster’ around it. This interferes with binding of the substrate to the active site.

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24
Q

Effect of pH at optimum

A

The solution contains the ideal no. Of H+ ions
The ionic bonding of the enzyme is not disrupted
The shape of the active site is not changed
Substrate fits forming enzyme-substrate complexes
Product is formed
Rate of reaction is at its max

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25
Q

Effect of pH either side of the optimum

A

Change in pH either side of the optimum provides less/more H+ ions
Ionic bonding is disrupted changing the tertiary protein structure
Active site changes shape so the substrate no longer fits
No enzyme-substrate complexes formed
No product formed
Mild pH change effects are reversible
Extreme pH can cause irreversible denaturation

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26
Q

What is enzyme inhibitor

A

It is a molecule that binds to an enzyme and decreases its activity
Since blocking an enzyme’s activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors.
They are also used to pesticides.

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27
Q

What are competitive inhibitors

A

The competitive inhibitor fits into the active site and so a substrate molecule cannot enter

It has a similar shape to the substrate
So it has a complimentary shape to the active site

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28
Q

What affects the effect of inhibition

A

The relative concentration of substrate and inhibitor molecules
More inhibitor molecules means more inhibitors collide with active sites and so the effect of inhibition is greater

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29
Q

What does increasing substrate concentration do?

A

Increasing substrate concentration effectively ‘dilutes’ the effect of the inhibitor.
If there are more substrates in the solution, the inhibitor is unlikely to collide with the enzyme

30
Q

What are non-competitive inhibitors

A

The inhibitor binds to the enzyme, not at the active site. (Alosteric site)
Binding of this inhibitor changes the shape of the active site.

31
Q

What happens to an enzyme which was bound to a non-competitive inhibitor

A

This enzyme cannot catalyse a reaction.

The substrate concentration has no effect on the rate of the reaction

32
Q

How does the rate of reaction graph look like for a non-competitive inhibitor

A

Y axis- rate of reaction
X axis- substrate concentration

The line without an inhibitor will be steep at first and then will curve to a level and then remain constant
The line with a non-competitor inhibitor will increase only slightly and then curve to level off
The height of the non-competitor inhibitor will be much shorter than the height of the without inhibitor

33
Q

How does the line with a competitive inhibitor look like?

A

Y axis- initial rate of reaction
X axis- substrate concentration

The line without an inhibitor will be steep at first and then will curve to a level and then remain constant. The height is high.
The line with a fixed concentration of competitive inhibitor is constant straight line until it levels off at the same level as the line with no inhibitor. However, the it levels off at a much higher substrate concentration

34
Q

Reversible or irreversible

A

Non-competitor inhibitors are irreversible and permanent and effectively denature the enzymes which they inhibit. This is because these inhibitors form covalent bonds with enzymes.
Ex: heavy poisonous ions such as mercury and lead form strong covalent bonds with sulfur-R groups on proteins.
But there are a lot of non-permanent and reversible non-competitive inhibitors which are vital in controlling metabolic functions in organisms.
By controlling metabolic reactions, product is produced in very specific amounts.

35
Q

Enzyme inhibitors in metabolic control

A

Enzymes vastly increase the rate of a metabolic reaction, often by a factor of 10 million.
Therefore enzyme activity must be very tightly controlled, since uncontrolled reactions can be fatal.

36
Q

Enzyme inhibitors as metabolic poisons

A

Many poisons work by inhibiting the action of enzyme involved in metabolic processes, which disturbs an organism.
Ex: potassium cyanide is an irreversible inhibitor of the enzyme Cytochrome C oxidase, which takes part in respiration reactions in cells. If this enzyme is inhibited, ATP cannot be made since oxygen use is decreased. This means that cells can only respire anaerobically leading to a lactic acid build up in the blood. This is potentially fatal.

Cyanide is a metabolic poison because it prevents a metabolic reaction from taking place.
Malonate is another metabolic poison and a competitive inhibitor of succinate dehydrogenase.

37
Q

Enzyme inhibitors as medicine

A

Ex: infection by viruses can be treated by (competitive) inhibitors binding to the active site of the viral enzyme Protease. This means that viruses cannot build new protein coats and therefore cannot replicate.

Penicillin works by inhibiting a bacterial enzyme that is responsible for forming cross-links in bacteria cell walls. This therefore halts reproduction.

38
Q

Why does enzyme activity completely halt as soon as optimum temperature has been crossed

A

The rate of reaction decreased sharply but doesn’t halt because not all enzymes denature at the same time together. They slowly, one by one, loose their structure.

39
Q

What are inactive precursors

A

Some enzymes are produced in an inactive form-particularly digestive enzymes where they can be produced safely in cells but only start working when at the site of action.

Some of the amino acids on the precursor enzyme must be removed to convert it into the active form.

Ex: trypsinogen (inactive) is converted into trypsin (active) by another enzyme in the small intestine.

Pepsinogen (inactive) is converted into pepsin (active) by HCl in the stomach.
The pH in the stomach is very low.

40
Q

Example of enzyme (fireflies)

A

Luciferase is found in the cells of special organs in their abdomen.
These cells also produce the substrate, luciferin which luciferase can only catalyse.
These are kept apart from the cells but when stimulated by nerve impulses, luciferin is released. This is broken down under the presence of ATP bound to magnesium ions.

This complex is used as a sensitive test for ATP. Each time a molecule is detected, a flash of light is given off.
Used to detect ATP made by bacteria and fungi.
Useful for cleanliness of kitchens, sustainability of water for drinking, and the effectiveness in water treatment plants.

41
Q

Definition of Catalysts

A

This is a chemical that speeds up a chemical reaction without changing the nature of the reaction or being changed itself; so it can be used over and over again.

42
Q

Are the reactions that enzymes catalyse, reversible or irreversible

A

Reversible

43
Q

What are intracellular enzymes

A

These enzymes exclusively function within cells and so catalyse the metabolic reactions that occur at low temperatures, low concentration and a pH near 7.0

44
Q

How does catalase function

A

Intracellular enzyme
Acts on the waste product of metabolic processes, hydrogen peroxide. It is a strong oxidising agent and very toxic, so it needs to be removed and destroyed pretty quickly.
Catalase breaks it down to water and oxygen in seconds; without this enzyme, it would taken months for this to degrade

45
Q

Where are intracellular enzymes found within a cell

A

In the cytosol, nucleoplasm, mitochondrial matrix and the stroma of chloroplasts.

Other enzymes are fixed to either side of the cell surface membrane and in the inner membranes of mitochondria and chloroplasts.

Others of the digestive system are fixed to the cell membrane
Ex: sucrase attached to cell membranes of the lining of the gut

46
Q

What are extracellular enzymes

A

Catalyses reactions outside cells
Ex: breakdown of food in the gut

Are needed to digest the food we eat because large molecules cannot be absorbed until they are broken down into simple ones.

Many digestive enzymes are secreted from cells to the gut lumen where they can act on the food

47
Q

Examples of extracellular enzymes

A

Amylase hydrolyses starch into maltose

Trypsin breaks down protein molecules into peptides and amino acids.

48
Q

How does fungal hyphae work

A

Secrete enzymes directly on the food they need to digest. First the food is broken down to small molecules and then absorbed through hyphae walls

49
Q

What determines the shape of the active xite

A

Active sites are also known as grooves or clefts
The features of the active site and the type of substrate that it accepts are determined by the R groups of the amino acids.
Non-polar R groups-> hydrophobic interior to the active site-> non-polar substrates

Polar R groups forms temporary ionic bonds with substrate molecules

50
Q

How specific are all enzymes

A

Different degrees of specificity.
Some are only specific to one reaction.
Others are less specific and catalyse a number of reactions of the same type or act on a particular linkage
Ex: protease acts on a peptide bond

Subtilisin is the enzyme in the cleaning fluid for contact lenses. It is a general protease that breaks bonds between any pair o& amino acid residues in a polypeptide.

Trypsin and chymotrypsin are mammalian proteases which are secreted into small intestine and are more specific. They only break peptide bonds between certain amino acids.

51
Q

Why is the Induced-fit hypothesis better than lock and key theory

A

Since collision are random, it would be difficult for enzymes and substrate molecules to collide and form an enzyme-substrate complex if the active site were a fixed shape.
Proteins are also not fixed structures. So the lock and key theory is inadequate to explain this complex.

52
Q

Induced-fit theory

A

An active site does not have a complimentary shape to the substrate until it has moulded around the substrate so the two fit together closely.
It can adjust very little depending on how specific the enzyme needs to be for its function

Amino acids with closer to the substrate, hold it in place and put the substrate under strain, so making the reaction proceed to form the product(s).
The charges on R groups are important in the formation of the enzyme-substrate complexes: in the induced-fit model these charges allow the substrate to enter and become linked within the active site.

53
Q

Activation Energy

A

Enzymes do not lower the overall energy change of the reaction, instead they provide an alternative pathway with a lower activation energy. This allows reactions to occur without the extreme conditions that would kill cells.
A different pathway is created once the enzyme-substrate complex has formed.
This is created by the tension within the complex by charges within the amino acids at the active site and the links between the amino acids and the substrate.
Enzymes provide a lower activation energy for substrate molecules to react and form the product.

54
Q

What is the optimum temperature for many plants?

A

About 20 degrees celsius

55
Q

Optimum temp for bacterial enzymes

A

Excess of 80 degrees celsius

56
Q

How do you find the optimum temp from a range

A

Repeat the investigation, taking readings at smaller intervals of temperature within that range

57
Q

What are the enzymes called that can withstand extreme temp

A

Thermostable

Found in bacteria living in extreme conditions

58
Q

What factors with temp, contribute to how many enzymes denature

A

The temp and how long they were left for at that temp

59
Q

How does a difference of one between pH values affect the number of H+ ions

A

As the pH decreases by 1, the H+ ion conc increases by x10

60
Q

How can you work Q10 (temp coefficient) if the rate of reaction is not given in the vertical axis

A

Use a ruler and measure the distance. Use these as rates of reaction.

61
Q

What pH does a gastric protease (pepsin) have

A

Found in the stomach and has an optimum of pH of 2

62
Q

What optimum pH does a pancreatic protease have

A

8.5

63
Q

What optimum pH do most intracellular enzymes have

A

6.5 which is the pH of cytosol

64
Q

Is the denaturing of enzymes because of a pH close to the optimum, reversible or irreversible

A

Unlike with the effect of temp this is likely to be reversed

65
Q

How does enzyme conc affect enzyme activity

A

High enzyme conc
More active site will be available for substrate molecules to fit in
More enzyme-substrate complexes will form

66
Q

What are cofactors

A

Some enzymes can only function if another non-protein substance is present with them that helps the enzyme to function correctly

Some enzymes require inorganic ions to function correctly. These ions help to stabilise the enzyme structure or take part in the reaction at the active site.
Ex: Amylase requires calcium ions to hydrolyse starch to maltose

67
Q

What are coenzymes

A

These are large organic cofactors
Some of these are bound permanently to the enzyme, often in or near the active site.
Other bind to the enzyme temporarily to the active site during the reaction.
Coenzymes are used to link different enzyme-catalysed reactions in a metabolic sequence, such as respiration and photosynthesis.

68
Q

Name the three B group vitamins used to make important coenzymes in metabolic reactions

A

Pantothenic acid is a component of coenzyme A

Nicotinic acid is used in the synthesis of the coenzymes NAD and NADR

The coenzyme FAD is based on vitamin B- riboflavin

NAD and FAD are alternately reduced and oxidised in the reactions in which they take part, which transfers energy in the form of hydrogen ions in respiration.

69
Q

Examples of other coenzymes

A

ATP and coenzyme A, transfer chemical groups
ATP transfers phosphate groups between respiration and energy- consuming processes in cells.
Coenzyme A transfers the acetyl group (-CH2CO) from glucose and from fatty acids during respiration.

70
Q

What is a prosthetic group

A

Any cofactor that becomes a permanent part of an enzyme is a prosthetic group.
Contribute to the 3D shape of the enzyme
Vital for the enzyme to function
Ex: carbonic anhydrase, found in red blood cells is important in the conversion of carbon dioxide and water to carbonic acid.
Its prosthetic group is a zinc ion.

Ex: FAD is the prosthetic group of the mitochondrial enzyme succinate dehydrogenase.

71
Q

Product inhibition

A

When the product acts as an inhibitor to prevent excess products
Ex: galactose acts as a competitive inhibitor which is also a product formed by the hydrolysis of the glycosidic bond in lactose. It inhibits the enzyme beta-galactosidase which catalyses this reaction.

72
Q

Enzyme activity practical

A

Add 10cm3 of a solution of a milk powder to test tube 1
Add 1cm3 of protease solution to test tube 2

Put both test tubes in a water bath at 25 degrees centigrade for 5 mins to equilibrate

After 5 min, pour the contents of test tube 2 into test tube 1, return test tube 1 to the water bath and start a timer.

Watch carefully and time how long it takes for the cloudiness to disappear.
Use a test tube of water to judge when the end point has been reached

OCR AS LEVEL BIOLOGY (22 decks)

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