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Biology > C1.1: Enzymes and Metabolism > Flashcards

C1.1: Enzymes and Metabolism Flashcards

1
Q

Define Catalyst

A

A substance that increases the rate of chemical reactions but is not used up in the reaction

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2
Q

What is the active site

A
  • Sequence of amino acids responsible for the catalytic activity of enzymes
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3
Q

State the role of enzymes in the chemical reactions on which life is based. ​

A

Enzymes catalyse metabolic reactions by binding onto a substrate at the active site

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4
Q

What do enzymes do to chemical reactions

A

Enzymes speed up chemical reactions without being altered, so can be reused.

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5
Q

Define metabolism.

A

The complex network of interacting chemical reactions that occurs in living organisms

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6
Q

Define specificity in relation to enzyme structure and function.

A

Each enzyme catalyses one specific reaction or a specific group of reactions - because of enzyme specificity, living organisms have to make large numbers of different enzymes

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7
Q

What allows for specific binding to occur between active site and the substrate

A
  • Similarity in chemical and physical properties between active site and the substrate
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8
Q

Outline how control of metabolism is regulated by enzymes.

A

An enzyme can catalyse a specific reaction to take place thus, cells can control the rate of metabolic reactions by producing more or less of the enzyme

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9
Q

Contrast anabolic and catabolic reactions.

A

Catabolic reactions: breakdown of complex molecules into simpler molecules and includes the hydrolysis of macromolecules into monomers
- Releases Energy

Anabolic reactions: Synthesis of complex molecules from simpler moleculesand includes the condensation reaction of monomers into macromolecules
- Consumes Energy

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10
Q

List three examples of anabolic processes.

A
  • Protein synthesis by ribosomes (translation)
  • DNA synthesis (replication)
  • Synthesis of complex carbs including starch, cellulose and glycogen
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11
Q

List three examples of catabolic processes.

A
  • Digestion of food (happens in mouth, stomach and small intestine)
  • Cell respiration (glucose/lipids are oxidised to CO2 and H2O)
  • Digestion of complex carbon compounds (decomposers)
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12
Q

Outline properties of globular proteins.

A
  • Enzymes are globular proteins
  • Contain a 3d structure and chemical properties that allow them to function as catalysts
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13
Q

Explain the relationship between enzyme structure and enzyme specificity, including the structure and function of the active site.​

A
  • Amino acids form the active site
  • Substrates must bind to the active site for a reaction to be catalysed - the shape and chemical properties of the active site & substrate match one another.
  • When the substrate is bound to the active site, it is converted into products as bonds in the substrate are broken
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14
Q

Outline the stages of enzyme catalysis of a chemical reaction.

A
  • A substrate approaches the active site (the substrates direction of movement is random)
  • shape and properties of the substrate and active site are complementary resulting in enzyme-substrate specificity
  • Active site undergoes a conformational change to optimally interact with the substrate (induced fit occurs)
  • This conformational change weakens the chemical bonds within the substrate which lowers the activation energy
  • Substrate converts into product and thus, products disassociate from the active site and the enzyme’s active site returns to its original state
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15
Q

Describe the induced fit model of enzyme binding.​

A
  • Substrate binds to active site hence, forming an enzyme-susbtrate complex which triggers a conformational change in the enzyme
  • When the substrate and enzyme fit tightly together, there is a weakening of bonds within the molecules of the substrate thus, lowering the activation energy.
  • Bonds in the substrates are broken and enzyme-product complex forms where the substrate converts to product
  • When the enzyme-catalysed reaction is completed, the products disassociate from the enzyme
  • Enzyme’s active site goes back to original shape
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16
Q

Explain the role of random collisions in the binding of the substrate with the enzyme active site.

A
  • The random collisions occur usually in a watery environment (cytoplasm)
  • The collisions allow the substrate to bind to the active site on the enzyme so that the reaction can occur
  • Active site and substrate should collide in the correct orientation and with enough energy for the reaction to start
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17
Q

Compare enzyme and substrate movement involved in reactions that occur in the cytoplasm, with large substrates and with immobilized enzymes.

A
  • Substrates may be immobilised
  • In this case, the enzyme has to move in relation to the substrate
  • Enzymes can be immobilised by being embedded in membranes
  • In this case, the enzyme can’t move and the substrate has to move
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18
Q

Discuss variation in specificity of different enzymes.

A
  • Enzymes exhibit specificity due to the matching chemical and physical properties between the substrate and the active site
  • Certain enzymes are capable of binding to a single substrate exclusively whereas others can bind to a range of similar substrates
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19
Q

Define denaturation.

A

Irreversible change to an enzyme which changes the shape of its active site hence, it can no longer function

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20
Q

Outline the causes and effects of denaturation on enzyme structure and function.

A

Causes:
- Extreme pH, heat and the presence of heavy metals

Effects:
- Destroys the tertiary or quaternary structure of a protein or if the temperature or pH is extreme, the secondary structure of a protein can be altered too

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21
Q

Explain the effects of temperature on enzyme structure and function

A

Low temp:
- Molecules tend to move slowly hence, collisions between substrate and enzyme molecules are not frequent, reduces rate of reaction

Higher temp:
- Molecules move faster hence, collisions between substrate and enzyme molecules are more frequent, rate of reaction increases

If the temperature gets too high (higher than the optimal which is 37*C), enzyme denatures

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22
Q

Outline the equipment used to set up a study into the effect of temperature on amylase activity up to the point of getting results

A
  • Measuring cylinder used to measure equal volumes of substrate
  • 5 different water baths at a range of at least 5 different range of temperatures
  • Control substrate concentration and pH by ensuring they stay the same
  • Amylase and starch is mixed in each water bath for at least 5 mins
  • Test for starch by adding drops of iodine and if positive, iodine turns blue-black
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23
Q

Identify the manipulated (independent), responding (dependent) and controlled variation in experiments of enzyme catalyzed reactions.

A

Manipulated variation:
- Factors that can change; Temp, pH or substrate conc.

Responding variation:
- Measurable factor; Time, mass or volume (quantitative data)

Controlled variation
- Factors that may alter the responding variation; if temp is manipulated variable, mass is responding variable then pH, substrate conc and enzyme conc. must be controlled and stay the same

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24
Q

Define quantitative data

A

Information that can be measured and recorded with numbers

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25
Q

State the unit for enzyme reaction rate.

A

s^-1

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26
Q

Define what the reaction rate is

A

A quantitative measurement of the speed at which the product is produced or the substrate is consumed

  1. Quantity of the produced product / change in time
  2. Quantity of consumed reactants / change in time
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27
Q

State two methods for determining the rate of enzyme reaction rates.

A
  1. Allow reaction to happen for fixed time and measure amount of substrate used up or product formed. Time should be short so substrate conc. remains high
  2. Start with known amount of substrate and allow the reaction to continue until all substrate has been converted to products. Measure time taken for the reaction to go to completion.
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28
Q

Describe at least three investigative techniques for measuring the activity of an example enzyme.

A

Example enzyme: Catalase (converts hydrogen peroxide to water and oxygen gas which bubbles out the solution)

  1. Time to float an enzyme saturated filter disc
  2. H2O displacement in by formation of O2 gas
  3. O2 gas bubble volume
  4. Change in pressure due to O2 gas
  5. Change in O2 levels with sensor

All these methods measure amount of O2 formed in a set amount of time.

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29
Q

Define activation energy

A

The minimum amount of energy required to reach the transition state in which the bonds of the substrate are broken

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30
Q

What is activation energy used for

A

The activation energy is used to break or weaken bonds in the substrate.

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31
Q

Explain the role of enzymes in lowering the activation energy of a reaction.

A
  • Activation energy required to reach transition state is lowered by enzymes in the catalysed reaction due to binding of the substrate to the active site which weakens bonds in the substrate
  • Thus, this increases the rate of reaction
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32
Q

Interpret graphs showing the effect of lowering the activation energy by enzymes.

A

Substrates are at the higher base
Products are at the lower base
- Curved line with peak is drawn from substrates to products to show without enzyme and curved line has a smaller peak with enzyme

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33
Q

Compare the location of synthesis of enzymes used within and outside of a cell

A

Intracellular enzyme-catalysed reactions:
- Metabolic reactions that take place inside the cell
- Catalysed by enzymes produced by free ribosomes

Extracellular enzyme-catalysed reactions:
- Metabolic reactions that take place outside the cell
- Catalysed by enzymes produced by bound ribosomes + ribosomes secreted outside the cell by exocytosis

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34
Q

State an example of an intracellular metabolic reaction and an extracellular metabolic reaction.

A

Intracellular metabolic reactions
- Glycolysis (linear reaction): Takes place in the cytoplasm and breaks down glucose into pyruvate molecules which releases energy
- Krebs Cycle (cyclical reaction): Takes place in the mitochondria and oxidises acetyl CoA to produce CO2, electron carriers and energy-rich molecules

Extracellular metabolic reaction
- Digestive enzymes like lipase, amylase and proteases are secreted by acinar cells in pancreas to catalyse these reactions in the gut

35
Q

Outline the generation of heat energy by the reactions of metabolism

A

As energy conversions are never 100% efficient there is always a loss of energy as heat in metabolic reactions as heat energy is generated and to be used to maintain body temperature in animals and birds

36
Q

Describe how birds and mammals maintain a body temperature greater than that of their environment

A
  • Warm blooded animals (birds and mammals) use the heat generated from metabolic reactions to maintain a constant body temperature that’s higher than the ambient temperature
37
Q

Outline an example of maintaining temperature homeostasis using heat generated by reactions of metabolism.

A
  • Body temperature must be maintained for optimal physiological activities
  • Hyperthermia (high temperatures) can cause protein denaturation
  • Hypothermia (low temperatures) can slow down metabolic processes
38
Q

Describe the response of the human body to low external temperatures (4 marks)

A
  • Metabolic rate increases
  • Goosebumps
  • Vasoconstriction of skin arterioles
  • Heat is transferred in blood
  • The hypothalamus acts as a thermostat
39
Q

State the reason for metabolic pathways

A

Metabolic pathways allow for a greater level of regulation as the chemical change is controlled by numerous intermediates (products formed between starting product and final product)

40
Q

Describe cyclical reaction pathways

A

Cyclical reaction pathways:
- Cycles of enzyme-catalysed reactions that involve a starting compound being converted into an intermediate product, which is processed to regenerate the original starting compound, completing the cycle
- Different substrates in the reaction are used at each step thus, separate enzymes are required

41
Q

Describe linear reaction pathways

A

Linear reaction pathways:
- Chains of enzyme-catalysed reactions that involve a starting compound progressively converting into distinct intermediate products that form a final product without regenerating the original starting compound
- Different substrates in the reaction are used at each step thus, separate enzymes are required

42
Q

State an example of a linear metabolic pathway and a cyclic metabolic pathway.

A

Linear metabolic pathway:
- Glycolysis

Cyclic metabolic pathway:
- Krebs Cycle

43
Q

Outline the structure and function of an allosteric site

A

Structure:
- A regulatory site in the enzyme

Function:
- Allows non-competitive inhibitors to bind to it

44
Q

Define enzyme inhibitor.

A
  • A molecule that disrupts the normal reaction pathway between an enzyme and a substrate
  • Enzyme inhibitors can be either competitive or non-competitive
45
Q

Describe mechanism of action of non-competitive enzyme inhibitors.

A
  • Instead of an active site, a molecule (inhibitor) binds to an alternative site (called the allosteric site)
  • The binding of the inhibitor to the allosteric site causes a conformational change to the enzyme’s active site
  • This conformational change means the active site and substrate no longer share specificity meaning substrates can’t bind anymore
  • As the inhibitor is not in direct competition with the substrate, increasing substrate concentration can’t reduce the inhibitor’s effect
46
Q

Describe mechanism of action of competitive enzyme inhibitors.

A
  • Instead of a substrate, a molecule (enzyme inhibitor) is involved which binds to the enzyme’s active site
  • The enzyme inhibitor is structurally and chemically similar to the substrate
  • The competitive inhibitor blocks the active site and prevents the substrate from binding
  • Thus, as the inhibitor is in competition with the substrate, its effects can be reduced by increasing substrate concentration
47
Q

How do inhibitors affect the rate of reaction

A
  • They reduce the rate of reaction
48
Q

Compare and contrast competitive and non-competitive inhibitors

A

Competitive inhibitors:
- chemically similar to substrate
- binds to active site of enzyme
- binding of the inhibitor doesn’t modify active site
- As substrate conc increases, effect of the inhibitor on the reaction is reduced

Non-competitive inhibitors:
- no similarity to substrate
- binds to enzyme at a site other than the active site
- binding of the inhibitor modifies active site which prevents binding of substrates
- As substrate conc increases, effect of the inhibitor on the reaction is not impacted thus, RoR is lower than normal at all substrate concentrations

49
Q

Outline the function of statins as an example of a competitive inhibitor.

A
  • Statins lower cholesterol levels
  • Statins competitively inhibit the enzyme HMG CoA reductase thus, binding to the active site of the enzyme prevents the substrate from binding which therefore, reduces cholesterol production
50
Q

Explain why the rate of reaction with increasing substrate concentration is lower with a non-competitive inhibitor compared to a competitive inhibitor

A

In non-competitive inhibition, increasing the substrate concentration doesn’t impact the inhibitor thus, the rate of reaction is lower as compared to a competitive inhibitor which binds to the active site and so as the substrate concentration increases the effect of the inhibitor on the reaction is reduced.

51
Q

How does the graph connecting rate of reaction and substrate concentration look with and without the 2 inhibitors?

A
  • Competitive inhibitor has a steeper curve and levels of later than if there was no inhibitor
  • Non-competitive inhibitor has a less steeper and the lowest curve but levels off the same time as if there was no inhibitor
52
Q

Outline the mechanism and benefit of feedback inhibition (end-product inhibition)

A

Mechanism:
- The final product, in a series of reactions, inhibits an enzyme from an earlier step in the sequence
- The product binds to an allosteric site and temporarily inactivates the enzyme via non-competitive inhibition
- As the enzyme can’t function, the reaction sequence stops and the rate of product formation is decreased

Benefit:
- Ensures level of an essential product are always tightly regulated

53
Q

An example of inhibition that is negative feedback regulation

A

End-Product inhibition

54
Q

Illustrate end-product inhibition of the threonine to isoleucine metabolic pathway.

A
  • In plants & bacteria, isoleucine may be synthesised from threonine
  • 5 step pathway
  • Isoleucine can bind to an allosteric site on the first enzyme and function as a non-competitive inhibitor
  • Threonine is the initial reactant and isoleucine is the end product
55
Q

Compare reversible and irreversible enzyme inhibition.

A

Reversible enzyme inhibition:
- Temporary binding of inhibitors to the active site or another site on a specific enzyme through a non-covalent interaction
- E.g. End-product inhibition

Irreversible enzyme inhibition:
- irreversible binding of inhibitors to the active site of a specific enzyme through a covalent bond.
- E.g. Mechanism-based inhibition

56
Q

Describe what mechanism-based inhibition is

A
  • Occurs when an inhibitor binds to an enzyme and is then chemically modified by the enzyme to produce a reactive species that covalently modifies and inactivates the enzyme.
57
Q

Outline the cause and consequence of mechanism-based inhibition.

A

Cause:
- Caused by irreversible binding of the inhibitor to the active site of a specific enzyme through a covalent bond hence, producing an inhibitor-enzyme complex

Consequence:
- Enzyme loses its catalytic activity permanently
- Harmful to organisms

58
Q

Illustrate mechanism-based inhibition using penicillin as an example.

A
  • Polysaccharide chain on either end
  • Peptide binded to Carbon3 on each monosaccharide with Oxygen just opposite it
  • Active transpeptidase binded to monosaccharide on top of opposing polysacchatide chain having an area to fit the peptide from the opposing monosaccharide
  • Inactivated transpeptidase drawn floating on the right side with penicillin in its area instead of the peptide
59
Q

What are the enzymes formed in the small intestine and stomach and what conditions do they have

A
  • Stomach: Low pH (pH = 2) for enzyme pepsin
  • Small intestine: High pH (pH = 7.5) for enzyme trypsin
60
Q

Explain the effects of pH on enzyme structure and function

A

Changing the pH affects charges on the amino acid molecules

Too low pH:
- Attraction between amino acids is too weak, reduces rate of reaction

Too high pH:
- Attraction between amino acids may no longer exist, reduces rate of reaction

61
Q

Explain the effects of substrate concentration on enzyme structure and function

A

Substrate concentration too low:
- More enzyme molecules available than substrate, decreases chances of collisions between substrate and enzyme molecule, reduces rate of reaction

Increasing substrate concentration causes more chances of collisions between substrate and enzyme molecule hence, increasing the rate of reaction

Active site fully occupied:
- Rate of reaction is halted as the substrates have to wait for enzyme active sites to become available before they can bind to them.

62
Q

Draw and interpret graphs showing the effects of temperature of the activity of enzymes

A

y axis is enzyme activity
x axis is temperature

Slope is in the shape of a steep hill going straight down

63
Q

Draw and interpret graphs showing the effects of pH of the activity of enzymes

A

y axis is enzyme activity
x axis is pH

Shape is that of a hook held by the left hand for a more alkaline enzyme like trypsin which is made in the small intestine and opposite for a more acidic enzyme like pepsin which is made in the stomach

64
Q

Draw and interpret graphs showing the effects of substrate concentration of the activity of enzymes

A

y axis is enzyme activity
x axis is substrate concentration

Shape is an upwards sloping line and then levelling off horizontally

65
Q

Define specificity in relation to enzyme structure and function.

A

All enzymes have an indentation to which the substrate can bind with high specificity and this is called the active site

66
Q

What is the activation energy is used for

A

Activation energy is used to break or weaken bonds in the substrate.

67
Q

Explain how enzymes bind to the substrate

A
  • Substrate binds to the active site on enzyme
  • Shape of active site is complimentary to shape of substrate
  • Enzymes decrease activation energy required to change a substrate into a product
  • Enzyme and product disassociate and release from the active site thus, freeing enzyme active site to bind to another substrate molecule
68
Q

What enzyme breaks down the substrate starch and what is the product

A

Enzyme = Amylase
Product = Maltose

69
Q

What enzyme breaks down the substrate protein and what is the product

A

Enzyme = Pepsin ( a type of protease )
Product = Short Polypeptides

70
Q

What enzyme breaks down the substrate hydrogen peroxide and what is the product

A

Enzyme = Catalase
Product = O2 and H2O

71
Q

3 advantages of enzyme substrate specificity

A
  • Only one specific substrate can bind to the active site of an enzyme
  • Specificity allows to control when a reaction takes place
  • and which reaction takes place
72
Q

Outline two ways enzyme catalysed reactions can be measured.

A
  • Mass of product formed over time
  • Amount of substrate used over time
73
Q

What occurs during denaturation

A
  • Change to the 3d structure of the protein (tertiary structure)
  • Changes in the properties of the protein
74
Q

What enzyme breaks maltose into glucose

A

Maltase

75
Q

Compare the induced fit model of enzyme activity with the lock and key model (4 marks)

A
  • in both models substrate binds to active site
  • in both models an enzyme - substrate complex is formed
  • substrate fits active site exactly in lock and key, whereas fit is not exact in induced fit
  • substrate / active site changes shape in induced fit, whereas active site does not change shape in lock and key
  • induced fit explains competitive inhibition, whereas lock and key does not
76
Q

Explain, using one named example, the effect of a competitive inhibitor on enzyme activity (6 marks)

A

-Statins competitively inhibit the enzyme HMG CoA

  • competitive inhibitor has similar
  • shape/structure to the substrate
    therefore it fits to the active site
  • substrate cannot bind as long as the inhibitor remains bound
  • substrate and inhibitor compete for the active site
  • therefore high substrate concentrations can overcome the inhibition
  • only one active site per enzyme molecule
77
Q

Explain how proteins act as enzymes, including control by feedback inhibition in allosteric enzymes (9 marks)

A
  • Enzymes are globular proteins
  • There’s an active site
  • Substrates bind to active site
  • Shape of substrate has an induced fit
  • Bonds in substrate are weakened
  • Activation energy gets reduced
  • In feedback inhibition, the end-product binds to the enzyme
  • End-product binds at the allosteric site
  • Binding of end-product to allosteric site causes allosteric site to change shape
  • The higher the conc. of end-product, the lower the enzyme activity
  • Allosteric inhibition is non-competitive
78
Q

Outline how enzymes catalyze reactions (4 marks)

A
  • Increased rate of reaction
  • Enzyme remains unchanged at the end of reaction
  • Substrate joins enzyme at active site
  • Enzyme-substrate complex forms
  • Active site is specific for certain substrates
79
Q

Outline the role of condensation and hydrolysis in the relationship between amino acids and dipeptides (4 marks)

A
  • Draw diagram of peptide bond
  • Condensation: Water is produced
  • Hydrolysis: Water is consumed to break the bond
  • Dipeptide to amino acids, hydrolysis occurs
  • Amino acids to dipeptide, condensation occurs
80
Q

What does the graph of substrate concentration and time show (2 marks)

A
  • As time increases, concentration of peptides increases
  • Reaction rate is fastest at the start
81
Q

State why temperature must be maintained throughout (2 marks)

A
  • At higher temperatures, enzymes denature
  • As temperature increases, rate of reaction increases
82
Q

How can enzymes be immobilised in cells

A
  • By being embedded in the membranes of cells
    (e.g: ATP Synthase - aka ATPase}
83
Q

Example of competitive inhibition

A

An example of a use for a competitive inhibitor is in the treatment of influenza via the neuraminidase inhibitor, Relenza

84
Q

Example of non-competitive inhibition

A

An example of a use for a non-competitive inhibitor is in the use of cyanide as a poison (prevents aerobic respiration)

Biology (20 decks)

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