B.7.1
Describe the characteristics of biological catalysts (enzymes).
Include:
enzymes are proteins; activity depends on tertiary and quaternary structure;
and the specificity of enzyme action.
They are specific for a reaction and can be individually controlled.
Enzymes
- are proteins
- usually with several hundred amino acids
- have a tertiary structure (hence, are globular proteins, soluble in water)
- exist in cytoplasm
- 3D shape called 'conformation', determined by interaction between R groups and is essential for its function
- some made by more than 1 polypeptide, and so they have a quaternary structure (that is also important in determining their function)
e.g. enzymes in glycolysis (respiration) are dimeric proteins and contain 2 polypeptide chains.
- some require binding of non-protein molecules for activity, called 'cofactors',
Cofactors may be organic, 'coenzymes', or inorganic, metal ions. e.g. Vitamins, many are precursors for enzymes.
They are specific for a reaction and can be individually controlled.
Enzymes
- are proteins
- usually with several hundred amino acids
- have a tertiary structure (hence, are globular proteins, soluble in water)
- exist in cytoplasm
- 3D shape called 'conformation', determined by interaction between R groups and is essential for its function
- some made by more than 1 polypeptide, and so they have a quaternary structure (that is also important in determining their function)
e.g. enzymes in glycolysis (respiration) are dimeric proteins and contain 2 polypeptide chains.
- some require binding of non-protein molecules for activity, called 'cofactors',
Cofactors may be organic, 'coenzymes', or inorganic, metal ions. e.g. Vitamins, many are precursors for enzymes.
Markscheme:
- enzymes are proteins;
- enzymes are proteins;
- temperature dependent;
- pH dependent;
- uses lock and key mechanism/ has an active site;
- works as a catalyst and lowers Ea;
- pH dependent;
- uses lock and key mechanism/ has an active site;
- works as a catalyst and lowers Ea;
B.7.2
Compare inorganic catalysts and biological catalysts (enzymes).
Enzymes are biological catalysts and control all biochemical reactions.
- increase rate of the reaction, the reactant that is catalysed is called the 'substrate'.
- lowers Ea, so the reaction happens quicker at the same temperature
- temporarily binds to the substrate, held by weak forces of attraction forming and enzyme substrate complex.
- binding is at the enzyme's active site
- usually a much larger molecule than the substrate.
Formation of the complex depends on the compatibility ('chemical fit') of the substrate and R groups on the active site on the enzyme. Includes hydrophobic interactions, dipole-dipole attraction, hydrogen bonds and ionic attraction
- binding strains the substrate, hence aids in the breaking and forming of bonds
- once reacted it doesn't fit the active site so it detaches
- the enzyme is unchanged and can catalyze other reactions.
- all reactions are equilibrium reactions (all reversible depending on the conditions)
- increase rate of the reaction, the reactant that is catalysed is called the 'substrate'.
- lowers Ea, so the reaction happens quicker at the same temperature
- temporarily binds to the substrate, held by weak forces of attraction forming and enzyme substrate complex.
- binding is at the enzyme's active site
- usually a much larger molecule than the substrate.
Formation of the complex depends on the compatibility ('chemical fit') of the substrate and R groups on the active site on the enzyme. Includes hydrophobic interactions, dipole-dipole attraction, hydrogen bonds and ionic attraction
- binding strains the substrate, hence aids in the breaking and forming of bonds
- once reacted it doesn't fit the active site so it detaches
- the enzyme is unchanged and can catalyze other reactions.
- all reactions are equilibrium reactions (all reversible depending on the conditions)
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| Lock and key mechanism Source: IB Chemistry Textbook |
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| Summary comparing inorganic and organic catalysts Source: IB Chemistry Textbook |
Similar to Ch. 6 reactions
Velocity (V) used to describe the rate of reaction.
The curves in the graph shows the distinctive shape due to saturation.
The graph suggests:
Velocity (V) used to describe the rate of reaction.
The curves in the graph shows the distinctive shape due to saturation.
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| Substrate concentration against rate of reaction |
- low substrate concentration: rate of reaction is proportional to the substrate concentration, enzyme can bind to the substrate
- as substrate concentration increases: rate decreases, no longer proportional to the substrate concentration, some of the enzymes have their active sites occupied (by a substrate) and is not available
- high concentration: rate is constant and independent of substrate concentration, enzyme is now saturated with substrate
B.7.4
Determine Vmax and
the value of the Michaelis constant (Km) by graphical means and explain its significance.
All enzymes can be saturated, but widely vary depending on the substrate concentration required to produce saturation, called Michaelis-Menten equation (Leonor Michaelis and Maud Menten)
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| Graph showing Vmax and Km on the rate-concentration. Source: IB Chemistry Textbook |
Michaelis-Menten kinetics features:
Mzximum velocity (Vmax)
- max velocity of the enzyme under the conditions of the experiment
- units of rate (amount of product/time)
- varies between enzymes, and pH and temperature
- rate of enzyme reactions sometimes called turnover number (the no. molecules of substrate that can be processed into products per enzyme molecule per unit of time) e.g. catalase, very fast enzyme with turnover rate up to 100 000 molecules of substrate H2O2 per second
Michaelis constant (Km)
- substrate concentration at which reaction rate is equal to one half its max value.
[S] = Km when the rate is Vmax/2
- units of concentration
- varies with pH and temperature
- information about enzyme's affinity for its substrate
- inverse relationship, low value of Km means reaction is going quickly even at low substrate concentration (higher affinity); higher value means lower affinity for its substrate.
Differences between Km values
- determine enzyme's responsiveness to changes in substrate concentration
- low Km (e.g. hexokinase & glucose, 0.15 Km/mmoldm-3), is saturated with substrate under most cell conditions, so acts at a constant rate regardless of variations in substrate concentration
- high Km (e.g. catalase & hydrogen peroxidem, 25 Km/mmoldm-3), not normally saturated with substrate so activity is more sensitive to changes in substrate concentration.
- varies with pH and temperature
- information about enzyme's affinity for its substrate
- inverse relationship, low value of Km means reaction is going quickly even at low substrate concentration (higher affinity); higher value means lower affinity for its substrate.
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| Rate-concentration graphs of two different enzymes (A and B) For A, rate is higher at a lower concentration, so its Km value is lower. Source: IB Chemistry Textbook |
- determine enzyme's responsiveness to changes in substrate concentration
- low Km (e.g. hexokinase & glucose, 0.15 Km/mmoldm-3), is saturated with substrate under most cell conditions, so acts at a constant rate regardless of variations in substrate concentration
- high Km (e.g. catalase & hydrogen peroxidem, 25 Km/mmoldm-3), not normally saturated with substrate so activity is more sensitive to changes in substrate concentration.
B.7.5
Describe the mechanism of enzyme action, including enzyme substrate complex,
active site and induced fit model.
Enzymes are very specific to their substrate.
E.g. sucrose and maltose (both isomers)
- hydrolysed by sucrase and maltase
- sucrase cannot catalyse maltase breakdown, and vice versa
- specificity depends on its shape, the arrangement of R groups of the amino acids at the active site and so its precise binding ability with the substrate.
Emil Fischer - Lock and key mechanism model (above)
- recently proteomics (study of proteins and their structures/functions) suggest enzymes are less rigid structures than that model
Daniel Koshland - induced-fit mechanism
- in the presence of the substrate, the active site undergoes some conformational changes so it is a better fit
- more dynamic relationship (amino acids R groups at the active site change into the precise binding position)
E.g. sucrose and maltose (both isomers)
- hydrolysed by sucrase and maltase
- sucrase cannot catalyse maltase breakdown, and vice versa
- specificity depends on its shape, the arrangement of R groups of the amino acids at the active site and so its precise binding ability with the substrate.
Emil Fischer - Lock and key mechanism model (above)
- recently proteomics (study of proteins and their structures/functions) suggest enzymes are less rigid structures than that model
Daniel Koshland - induced-fit mechanism
- in the presence of the substrate, the active site undergoes some conformational changes so it is a better fit
- more dynamic relationship (amino acids R groups at the active site change into the precise binding position)
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| Induced-fit mechanism Source: IB Chemistry Textbook |
B.7.6
Compare competitive inhibition and non-competitive inhibition.
Activity affected by chemical inhibitors, able to modify an enzyme by binding to it.
Inhibition not always linked to illness/harm, often is important for controlling metabolic activity in healthy cells.
E.g. product of reaction sometimes acts as an inhibitor of the enzyme for its synthesis, a negative feedback loop to regulate its concentration
Product inhibition:
- product of reaction acts as an inhibitor for the first enzyme leading to its production
- concentration of product builds up and 'switches off' its own synthesis
- many amino acids synthesis are regulated this way
Competitive inhibitors
- bind irreversibly at the active site
- competes with substrate for the binding position
- usually has a chemical structure similar to the substrate (mimics ability to bind)
- does not react to form products, blocks active site to make it unavailable to the substrate
- increasing substrate concentration reduces inhibition, fewer inhibitors able to bind
- Vmax is not altered, still has a substrate concentration where the enzyme's full activity can be reached, but takes higher substrate concentration to reach this rate, Km increased.
e.g. malonate inhibits succinate dehydronase, converts enzyme into fumarate during aerobic respiration. Malonate and succinate have similiar structures so they are able to bind to the same active site.
Non-competitive inhibitors
- bind reversibly away from the active site
Inhibition not always linked to illness/harm, often is important for controlling metabolic activity in healthy cells.
E.g. product of reaction sometimes acts as an inhibitor of the enzyme for its synthesis, a negative feedback loop to regulate its concentration
Product inhibition:
- product of reaction acts as an inhibitor for the first enzyme leading to its production
- concentration of product builds up and 'switches off' its own synthesis
- many amino acids synthesis are regulated this way
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| Product inhibition Source: IB Chemistry Textbook |
Competitive inhibitors
- bind irreversibly at the active site
- competes with substrate for the binding position
- usually has a chemical structure similar to the substrate (mimics ability to bind)
- does not react to form products, blocks active site to make it unavailable to the substrate
- increasing substrate concentration reduces inhibition, fewer inhibitors able to bind
- Vmax is not altered, still has a substrate concentration where the enzyme's full activity can be reached, but takes higher substrate concentration to reach this rate, Km increased.
e.g. malonate inhibits succinate dehydronase, converts enzyme into fumarate during aerobic respiration. Malonate and succinate have similiar structures so they are able to bind to the same active site.
Non-competitive inhibitors
- bind reversibly away from the active site
- causes conformation change that alters the active site
- increasing substrate concentration does not reduce the inhibition, the enzyme has been decommissioned and is unavailable
- Vmax decreased, cannot be restored
- Km unchanged, because working enzymes are fully functional
Metal ions can be non-competitive inhibitors. Antibiotics (penicillin) kills bacteria by inhibiting one of their key enzymes. Many anti-cancer drugs also work the same way to block cell division in tumour.
- increasing substrate concentration does not reduce the inhibition, the enzyme has been decommissioned and is unavailable
- Vmax decreased, cannot be restored
- Km unchanged, because working enzymes are fully functional
Metal ions can be non-competitive inhibitors. Antibiotics (penicillin) kills bacteria by inhibiting one of their key enzymes. Many anti-cancer drugs also work the same way to block cell division in tumour.
B.7.7
State and explain the effects of heavy metal ions, temperature changes and pH
changes on enzyme activity.
Enzyme activity
- influenced by physical and chemical environment
- depends on conformational shape (to bind), hence any condition that affects its shape and binding affects catalytic property.
Temperature (Ch.6)
- rate of reaction increased by rise in temperature, due to increase in average kinetic energy of the particle
- more frequent collisions between enzyme and substrate greater than Ea (higher rate of reaction), BUT only up to a certain temperature
- effect of increase in kinetic energy is to change the conformation of the protein by disrupting the bonds and forces holding its tertiary structure
- enzyme no longer able to bind, catalytic activity decreases/ no more. (shown by the curve in a graph).
- optimum temperature: when max rate of reaction for a particular enzyme occurs. Most in the human body is around 37`C (body temperature), other organisms have enzymes with optimum temperatures closer to their ambient temperatures.
Denaturation
Enzyme activity
- influenced by physical and chemical environment
- depends on conformational shape (to bind), hence any condition that affects its shape and binding affects catalytic property.
Temperature (Ch.6)
- rate of reaction increased by rise in temperature, due to increase in average kinetic energy of the particle
- more frequent collisions between enzyme and substrate greater than Ea (higher rate of reaction), BUT only up to a certain temperature
- effect of increase in kinetic energy is to change the conformation of the protein by disrupting the bonds and forces holding its tertiary structure
- enzyme no longer able to bind, catalytic activity decreases/ no more. (shown by the curve in a graph).
- optimum temperature: when max rate of reaction for a particular enzyme occurs. Most in the human body is around 37`C (body temperature), other organisms have enzymes with optimum temperatures closer to their ambient temperatures.
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| Temperature on enzyme activity Source: IB Chemistry Textbook |
- loss of tertiary structure
- not the loss of the covalent backbone of the protein molecule (digestion)
- irreversible (e.g. cooking an egg)
- lowering temperature causes deactivation not denaturation, prevents it from working but does not change the tertiary structure, usually reversible e.g. thawed food may spoil quick because of resumption of microbial activity as temp increases
- one of the main reasons why controlling body temperature is important, and why a few degrees change in body temperature is fatal.
pH
- change in [H+] ions, affects equilibrium of ionization reactions
- involves R group of amino acids, change in ionic charge alters attraction forces stabilizing molecule, hence shape and binding ability
- specific pH depends on pKa and pKb of R groups (esp. in the active site), so different for each enzyme
- usually clear optimum pH value
- different enzymes, different pH is one way of controlling activity
e.g. pepsin is active in the stomach (low pH), but inactive when it moves to the intestines (more alkaline environment) where trypsin is ative
- extreme pH denatures enzymes like high temperatures
Presence of heavy-metal ions
- lead, copper, mercury, silver: POISONOUS, mainly bc of their effects on enzymes
- when they are present as positive ions, they react with sulfhydryl groups, -SH, in the side chains of cysteine in the protein, covalently bonds with the sulphur atoms and displaces a hydrogen ion.
- distrupts protein folding, changes shape of active site and binding ability, called non-competitive inhibition
- one of the main reasons why controlling body temperature is important, and why a few degrees change in body temperature is fatal.
pH
- change in [H+] ions, affects equilibrium of ionization reactions
- involves R group of amino acids, change in ionic charge alters attraction forces stabilizing molecule, hence shape and binding ability
- specific pH depends on pKa and pKb of R groups (esp. in the active site), so different for each enzyme
- usually clear optimum pH value
- different enzymes, different pH is one way of controlling activity
e.g. pepsin is active in the stomach (low pH), but inactive when it moves to the intestines (more alkaline environment) where trypsin is ative
- extreme pH denatures enzymes like high temperatures
Presence of heavy-metal ions
- lead, copper, mercury, silver: POISONOUS, mainly bc of their effects on enzymes
- when they are present as positive ions, they react with sulfhydryl groups, -SH, in the side chains of cysteine in the protein, covalently bonds with the sulphur atoms and displaces a hydrogen ion.
- distrupts protein folding, changes shape of active site and binding ability, called non-competitive inhibition
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