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[h] IB DP Biology HL C1.1 Enzymes and metabolism Flashcards
[q] C1.1.1 What is the role of enzymes as catalysts?
[a] Enzymes are biological catalysts;
that speeds up reactions;
in living cells;
which allows reactions to occur at much lower temperatures than would be possible otherwise;
[q] C1.1.2—What is metabolism? What is the role of enzymes in metabolism?
[a] metabolism is the complex network of interdependent and interacting chemical reactions occurring in living organisms;
because of enzyme specificity (where one enzyme catalyzes on reaction);
many different enzymes are required by living organism;
control over metabolism can be brought about through these enzymes;
[q] C1.1.3—What are anabolic reactions? (Anabolism)
[a] anabolic reactions are those that build up larger molecules from smaller ones;
when macromolecules are built from monomers by condensation reactions;
including protein synthesis, glycogen formation and photosynthesis;
[q] C1.1.3 What are catabolic reactions? (Catabolism)
[a] catabolic reactions are those that break down larger molecules into smaller ones;
this includes hydrolysis of macromolecules into monomers in digestion;
and oxidation of substrates like glucose in respiration;
[q] C1.1.4 What is an active site? What is its role in enzyme catalysis?
[a] An active site is composed of a few amino acids only;
and is part of a globular protein’s structure;
many interactions between amino acids within the overall three-dimensional structure of the enzyme ensure that the active site has the necessary properties for catalysis;
the active site binds to substrates;
allowing for reactions to occur;
[q] C1.1.5 How do interactions between substrate and active site to allow induced-fit binding?
[a] As substrates bind to active sites;
both substrate and enzymes change shape;
so that bonds within the substrate are weakened;
in this way the fit is induced;
allowing for catalysis to take place; at a lower energy level than normal;
[q] C1.1.6 What is the role of molecular motion and substrate-active site collisions in enzyme catalysis?
[a] Molecular motion is required for enzyme-substrate collisions to occur successfully;
in order for reactions to occur;
substrates need to collide with the enzyme active site with sufficient energy and at the correct orientation;
however, enzymes can be immobilized by being embedded into membranes;
and sometimes large substrates are immobilized, with enzymes colliding with them instead; e.g. glycogen which is too large to move;
[q] C1.1.7—What is the relationship between the structure of the active site, enzyme-substrate specificity and denaturation?
[a] active sites have a precise shape;
due to the amino acids that make them up;
leading to a shape that only fits a particular substrate;
they are therefore highly specific;
with one enzyme fitting one substrate(s);
if the shape changes due to denaturing, then the shape of the active site no longer fits the substrate;
leading to a loss of activity of the enzyme;
[q] C1.1.8—What are the effects of temperature on the rate of enzyme activity?
[a] increased temperature increases the chance of enzyme substrate collisions;
so, enzyme activity increases as temperature increases;
up to an optimal temperature;
beyond the optimum temperature, increased molecular motion leads to disruption of intermolecular interactions;
loss of tertiary and secondary structure;
therefore, changes shape of active site;
so, it can no longer bind to substrate;
leading to decreased activity;
until enzyme is completely denatured; and there is no activity;
[q] C1.1.8—What are the effects of pH on the rate of enzyme activity?
[a] altering pH can alter intermolecular interactions within the protein;
between R groups;
e.g. hydrogen bonding;
or within the active site;
enzymes have an optimum pH;
away from this optimum, enzyme activity decreases;
this can be irreversible, leading to total loss of activity;
[q] C1.1.8—What are the effects of substrate concentration on the rate of enzyme activity?
[a] the more substrate, the more product forms;
more substrate-active site collisions;
more substrates can bind to the enzyme active site, so therefore rate of reaction increases;
after a point, all enzyme active sites are bound to substrate (full occupancy of enzyme active sites);
additional substrate will not lead to a greater rate of product formation at this point;
[q] C1.1.9 How can we measurements the rate of enzyme-catalyzed reactions?
How is it calculated?
[a] by measuring either product formation in a given time;
or substrate usage;
1/time taken gives a measure of the rate of the reaction;
[q] C1.1.10 What is activation energy?
What are the effects of enzymes on activation energy?
[a] Activation energy is the amount of energy required to allow a particular reaction to occur;
energy is required to break bonds in substrates;
energy is given out when bonds are formed;
the overall yield (net amount) of energy released or taken in by a reaction can be calculated or shown on a graph;
enzymes reduce the amount of activation energy required;
this means reactions can happen at s sufficient rate at much lower temperatures;
[q] C1.1.11— HL ONLY – What are intracellular and extracellular enzyme-catalyzed reactions? What is an example of each?
[a] Intracellular enzyme catalyzed reactions take place in cells;
e.g. glycolysis in the cytoplasm and Kreb’s cycle in the mitochondria;
extracellular enzyme catalyzed reactions take place outside of cells;
e.g. chemical digestion in the gut;
[q] C1.1.12— HL ONLY -What is generated by all reactions of metabolism?
Why is this inevitable?
How is this useful?
[a] Heat generation is inevitable;
because metabolic reactions are not 100% efficient in energy transfer;
Mammals, birds and some other animals depend on this heat production for maintenance of constant body temperature;
homeostasis;
[q] C1.1.13— HL ONLY —What are the two major types of pathways in metabolism?
[a] linear, where one product becomes the reactant in the next reaction;
proceeding to a final product;
e.g. glycolysis
and cyclical, where the final product is again fed back to become the reactant in the first step;
e.g. Krebs cycle and Calvin cycle;
[q] C1.1.14— HL ONLY -What are allosteric sites?
What is non-competitive inhibition of enzymes?
[a] allosteric sites are binding site(s) away from the active site of an enzyme;
non-competitive inhibitors are substances that can bind to allosteric site;
this binding is reversible;
the binding causes conformational (shape) changes in the enzyme due to interactions (with tertiary and secondary structures);
which change the shape of the active site enough to prevent catalysis;
reducing the rate of reaction;
but non-competitive inhibitors do not compete with substrate for the active site;
[q] C1.1.15— HL ONLY -What is competitive inhibition?
What is an example of one?
[a] competitive inhibition is when a molecule structurally similar to the substrate binds to the active site;
this prevents the substrate from binding;
e.g. Statins;
where they compete for the active site of an enzyme involved in cholesterol synthesis, therefore reducing it;
[q] C1.1.15— HL ONLY – How do competitive inhibitors affect the rate of reactions?
What does the graph look like and why?
[a] Because non-competitive inhibitors bind at allosteric sites, away from the active site, they do not compete for the active site with the substrate;
they are therefore their binding is not affected by substrate concentration in the same way as competitive inhibitors;
this means inhibition of enzyme activity is maintained even at very high substrate concentration;
meaning a lower rate of enzyme activity; at all substrate concentrations;
[q] C1.1.16— HL ONLY – How are metabolic pathways regulated by feedback inhibition?
Use isoleucine as an example
[a] a non-competitive inhibitor binds to allosteric site;
non-competitive inhibitor changes shape of active site;
non-competitive inhibitors do not compete with substrate for the active site;
this means end-product of a pathway can inhibit enzyme needed for the first step in metabolic pathway;
this is negative feedback since increased level of product formation decreases rate of its own production;
the metabolic pathway regulated according to the requirement for its end-product;
the inhibition is reversible;
e.g. Isoleucine is end product;
binds to threonine deaminase enzyme;
stopping threonine from being converted;
which is turn stops production of isoleucine;
[q] C1.1.17— HL ONLY – How is penicillin an example of mechanism-based inhibition?
What does it block?
[a] penicillin binds irreversibly;
to transpeptidase enzymes in bacteria;
which are involved in cell wall synthesis;
by creating cross-links between cell walls polysaccharides;
penicillin therefore weakens the cell wall and they burst;
killing bacteria;
[q] C1.1.17— HL ONLY – How does resistance to penicillin develop in bacteria?
[a] mutations can occur in bacteria which change the shape of the transpeptidase enzymes;
therefore, penicillin cannot bind;
and cell walls are synthesized as normal, making the bacteria penicillin resistant;
[q] What is metabolism?
[a] The sum of all chemical reactions taking place in a cell at one time.
[q] What does it mean that metabolic pathways are interdependent?
[a] They rely on each other to occur. e.g. A+B=C then C+D=E
[q] What is anabolism and some examples?
[a] The joining together of monomers to form complex molecules in condensation reactions.
It requires energy from ATP to occur.
Some examples of this are protein synthesis, glycogen formation, and photosynthesis.
[q] What is catabolism and some examples?
[a] Catabolism is the breaking apart of complex molecules into smaller components in a hydrolysis reaction.
It releases energy as it occurs.
Some examples of this are digestion and oxidation of substances in respiration.
[q] What are 4 different forms of energy that are important to organisms?
[a] 1. Kinetic energy: energy of motion
2. Potential energy: stored energy/energy in a form that isn’t being used at a point of time
3. Chemical energy: potential energy available for release when a chemical reaction occurs
4. Thermal energy: a form of kinetic energy stored within objects.
It is capable of being transferred from one object to another as heat.
[q] What is the structure and function of ATP (adenosine triphosphate)?
[a] Adenosine triphosphate:
– Supplies the energy needed to synthesize macromolecules
– Supplies the energy needed for mechanical work e.g. muscle action
– Provides energy to move substances across the cell membrane e.g. sodium-potassium pump
[q] Why are many different enzymes needed in the body?
[a] Enzymes are highly specific so different enzymes are needed to bind to different proteins and carry out different chemical reactions.
[q] What are enzymes and what is their function?
[a] Enzymes are globular, 3D proteins and compact molecules.
They are biological catalysts, speeding up the rate of already existing chemical reactions in the cell by lowering the activation energy needed for them to take place and are NOT used up in the process.
They have specific active sites where a substrate binds.
[q] What is the benefit of enzymes?
[a] Enzymes force a collision between molecules which speeds up the reaction.
This is useful because it allows reactions to occur at a fast enough rate to sustain life but at lower temperatures and lower energy inputs that they would need otherwise.
Essentially, they increase the rate of reaction without raising temperatures (as this would damage and denature proteins).
Also, if we didn’t have enzymes, we would constantly be eating to supply enough glucose for respiration.
[q] What is needed for a substrate molecule and active site to come together?
[a] Movement
[q] What is activation energy?
[a] The energy input required to start a reaction, much of which comes from the collisions of the reactants.
[q] How do enzymes bind to substrates?
[a] They have an active site which is complementary to the substrate molecule.
[q] What is an active site?
[a] A small indentation on the surface of the enzyme, forming a hollow depression in the molecule.
The substrate molecule fits into this depression to form a enzyme-substrate complex and temporary bonds form between the substrate and certain amino acids of the active site.
[q] How much of the enzyme molecule is involved in binding to the substrate?
[a] Only a small number of the amino acids of the enzyme are significant in forming bonds with the substrate;
however other sites on the molecule are responsible activating the enzyme or preventing the active site from working.
[q] What are the two models for enzyme-substrate binding?
[a] – Lock in key
– Induced fit/Hand in glove
[q] What is the most accepted model for substrate-enzyme binding?
[a] The induced fit model
[q] Why is this more widely accepted?
[a] It shows how the enzyme and substrate are flexible and slightly change shape as the enzyme-substrate complex is formed.
It therefore implies that the substrate isn’t perfectly complimentary but that it changes shape slightly to accommodate the substrate.
[q] Summary of the mechanisms of enzyme action:
[a] 1. The surface of the substrate makes contact with the active site of the enzyme.
2. The enzyme and substrate change shape, forming a temporary enzyme-substrate complex.
3. The activation energy is lowered, and the substrate is altered by the rearrangement of the existing atoms.
4. The transformed substrate, the product, is released from the active site.
5. The unchanged enzyme is free to combine with other substrate molecules.
[q] How does an enzyme actually work?
[a] As the enzyme and substrate slightly change shape, the enzyme exerts stress on the bonds between the substrate molecules, weakening them and meaning that the substrate molecule requires less energy to break these bonds and form the products.
The opposite happens when molecules are forming- the enzyme pushes them together to encourage a bond to be formed. As such enzymes lower the amount of activation energy needed for a reaction.
[q] What does a graph of activation energy with an enzyme VS without an enzyme look like?
[a]
[q] What factors affect the rate of enzyme-controlled reactions?
[a] – Temperature
– pH
– Substrate concentration
– Enzyme concentration
[q] How to ‘describe’ a graph?
[a] – Use phrases such as ‘Between x and y on the graph’ and ‘At x degrees C’
– Use adjectives to describe the line e.g. gradual, steep
– Talk in terms of their words (labels on the axes)
[q] How can rate be measured?
[a] The amount of product produced or the substrate breakdown in a given length of time (per second/per minute)- dy/dx.
[q] How does temperature affect the rate of enzyme-controlled reactions?
[a] As the temperature rises, the substrate molecules gain more energy in their kinetic energy stores and so move more quickly, colliding more frequently and with more power with the active site of the enzymes, thus increasing the rate of reaction.
When the enzymes reach their optimum temperature, their activity is at its peak.
After this, the high temperatures cause the active site to change shape and denature as the intramolecular hydrogen and ionic bonds begin to break, changing its tertiary structure, therefore the rate of enzyme activity decreases until finally the substrate molecule can no longer bind to the active site and no enzyme-substrate complexes are formed.
[q] How does pH affect the rate of enzyme-controlled reactions?
[a] An active site of an enzyme must have the same charge as the charged areas of the substrate that bind to it.
If pH is too acidic or basic, this can interfere with these charges and even cause the bonds between the proteins in the enzyme to break, denaturing it.
Often enzymes work in quite a narrow pH range, but this differs between enzymes as they work in different environments
e.g. enzymes in the stomach will work in acidic conditions whereas enzyme in bile are alkaline
[q] How does substrate concentration affect the rate of enzyme-controlled reactions?
[a] As substrate level increases, the rate of reaction also increases.
It does this to a certain point at which the rate of reaction will reach a maximum rate and stop increasing because there would not be enough enzyme to catalyze the reaction, and this would now become the limiting factor.
All the active sites of the enzymes are saturated (occupied), meaning they can’t work any faster.
[q] How does enzyme concentration affect the rate of enzyme-controlled reactions?
[a] As enzyme level increases, the rate of reaction also increases.
It does this to a certain point at which the rate of reaction will reach a maximum rate and stop increasing because there would not be enough substrate to for enzyme-substrate complexes with the enzyme so the substrate would now become the limiting factor.
[q] What happens when bonds are broken?
[a] Energy is taken in from the surroundings (endothermic).
Therefore, the temperature of the products is higher than the reactants.
[q] What happens when bonds are made?
[a] Energy is released to the surroundings (exothermic).
Therefore, the temperature of the products is lower than the reactants.
[q] How can the rate of an enzyme-controlled reaction be measured?
[a] There are 2 ways to measure the rate of an enzyme-controlled reaction:
1. The rate at which the substrate is used up e.g. rate at which starch is broken down by amylase
2. The rate at which the product is made e.g. rate at which lactase produces glucose.
[q] What is an intracellular enzyme and examples of reactions catalyzed by them?
[a] An intracellular enzyme is one which occurs within a cell.
Examples of reactions catalyzed by intracellular enzymes are: glycolysis and the Krebs cycle.
Glycolysis takes place in the cytoplasm of the cell. The Krebs cycle takes place in the matrix of the mitochondria.
[q] What is an extracellular enzyme and examples of reactions catalyzed by them?
[a] An extracellular enzyme occurs outside a cell.
Examples of reactions catalyzed by extracellular enzymes are: chemical digestion within the gut/digestive system.
[q] Why is heat generation an inevitable consequence of metabolic reactions?
[a] The energy transfer in metabolic reactions is not 100% efficient and there is a great variation in the efficiency of the different metabolic reactions, therefore heat generation (energy transfer via heat) is an inevitable consequence of metabolic reactions.
[q] Why is heat generation important to endotherms (warm-blooded animals)?
[a] It maintains their constant internal body temperature so without the release of heat from these inefficient reactions, these organisms could not survive the low temperature extremes they can currently tolerate.
[q] What are the 2 different types of metabolic pathways?
[a] – Linear
– Cyclical
[q] What is a linear metabolic pathway and one example?
[a] A series of metabolic reactions that begin with one substance and end with another.
An example is glycolysis as part of respiration.
Glycolysis begins with one 6-carbon compound and ends with the final products being 2 3-carbon compounds.
[q] What is a cyclical metabolic pathway and two examples?
[a] A series of metabolic reactions which begin and end with the same substance.
An example is the Krebs cycle as part of respiration.
It begins and ends with the same 4-carbon compound.
Another example in photosynthesis is the Calvin cycle which begins and ends with the same 5-carbon compound.
[q] What is an inhibitor?
[a] A molecule which decreases enzyme activity, slowing down the rate of reaction, by binding to it and altering/occupying the active site.
[q] What are non-competitive inhibitors?
[a] Non-competitive inhibitors hinder the activity of an enzyme by binding to the allosteric site and thus altering the tertiary structure of the protein and its active site so the substrate can no longer bind to it and form enzyme-substrate complexes as it ceases to be complementary.
This binding is reversible.
[q] What is an example of a non-competitive inhibitor?
[a] Metallic ions such as mercury bind to the sulphur groups of the amino acids in the enzyme which results in a change in the shape of the enzyme, inhibiting it.
[q] What factors affect non-competitive inhibition and how?
[a] – Concentration of substrate: by increasing the substrate concentration, this will increase the rate of reaction to an extent but eventually an increase will make no difference since the inhibitor binds to the allosteric rather than active site.
– Concentration of enzyme: by increasing the substrate concentration, this increases the number of enzymes available to bind to the substrate and form enzyme-substrate complexes with it.
[q] Therefore, how is the effect of non-competitive inhibition overcome?
[a] By increasing the enzyme concentration.
[q] What are competitive inhibitors?
[a] Competitive inhibitors hinder the activity of an enzyme by competing directly with the usual substrate for the active site, preventing the substrate from binding to it and forming an enzyme-substrate complex.
Part of the inhibitor is complementary to the enzyme.
This binding is reversible.
[q] What is an example of a competitive inhibitor?
[a] Statins:
People with high blood cholesterol can develop coronary heart disease.
When people have these high levels of cholesterol, doctors will prescribe a group of drugs known as statins.
Statins act as competitive inhibitors as they combine with the active site of enzymes which catalyze the synthesis of cholesterol.
Thus, they cause a reduction in the production of cholesterol therefore lowering the risk of cardiovascular disease.
[q] What factors affect competitive inhibition and how?
[a] – Concentration of substrate molecules: when there is a considerably higher concentration of substrate molecules, the substrate will outcompete the inhibitor.
This doesn’t particularly affect the rate of the reaction.
– Concentration of competitive inhibitor: when there is a considerably higher concentration of competitive inhibitor molecules, the inhibitor will outcompete the substrate for the active site of the enzyme and slow the rate of reaction.
[q] Therefore, how is the effect of competitive inhibition overcome?
[a] By increasing the concentration of the substrate.
[q] What is feedback/end-product inhibition?
[a] This is a process where a high concentration of a product of a metabolic pathway acts as an inhibitor (usually of the first enzyme) in the reaction that was making it.
This is achieved by the end-product binding with the allosteric site of the first enzyme, thus bringing about inhibition.
As the existing end-product is used up by the cell, the first enzyme is reactivated.
[q] What are the advantages of end-product inhibition?
[a] It can be used to regulate the chemical reactions in the cell to save energy and materials.
[q] What is an example of end-product inhibition?
[a] The synthesis of isoleucine in plants and bacteria:
1. Threonine combines with the enzyme threonine deaminase.
2. It goes through several intermediate conversions before producing isoleucine as its product.
3. The isoleucine combines with the allosteric site of the threonine deaminase, altering the active site so it can no longer combine with threonine.
4. This renders the path inactive, and no more isoleucine is produced.
5. When isoleucine is used up the path reactivates.
[q] What is mechanism-based inhibition?
[a] The irreversible binding of an inhibitor with the active site of an enzyme, permanently changing its tertiary structure so the substrate cannot bind to it.
[q] What is an example of mechanism-based inhibition?
[a] Penicillin:
Penicillin irreversibly binds to the active site of an enzyme called transpeptidase that catalyzes the last step in the formation of bacterial cell walls, inhibiting it.
The defective cell wall prevents bacterial reproduction and causes the death of bacterial cells.
[q] How can resistance to penicillin arise in bacteria?
[a] – Certain strains of bacteria have developed a mutation that allows them to produce an enzyme called penicillinase.
This enzyme breaks down penicillin.
– Certain strains of bacteria have developed mutations in the transpeptidase active site so that penicillin can no longer bind it, resulting in bacterial resistance.
[q] Metabolism
[a] All the chemical reactions of life; all various processes by which you obtain energy, grow, heal, feel and dispose of waste, for the organism to maintain life.
[q] State the role of enzyme in metabolism.
[a] Metabolism consists of pathways which one type of molecule is transformed into another.
Each step catalyzed by an enzyme.
Without enzymes, reactions would not proceed quickly enough (at all).
Enzymes speeds up chemical reaction without being altered themselves.
[q] Compare and contrast metabolic chain reaction pathways with cyclical reaction pathways.
[a] Chemical reaction of metabolism always consists in a sequence of small steps.
Most metabolic pathways involve chain of reactions with the starting reactant different from the final product.
E.g. Glycolysis (cell respiration) or the coagulation cascade (blood clotting).
– Same metabolic pathway involves cycle of reactions where the end product is the same as starting reactants (Kerbs cycle).
[q] State the relationship between enzyme substrate and enzyme product.
[a] Substrate + Enzyme = Product.
Each enzyme is specific to a substrate or reactant in a metabolic reaction.
Thus, living organisms produces thousands of different enzymes.
[q] Explain the relationship between enzyme structure and enzyme specificity, including the role of active site.
[a] The substrate must bind to a special region on the surface of the enzyme called the active site.
The shape and chemical properties of the active site match each other. This allows the substrate to bind but not other substances.
– Substrates are converted into product while they are bound to the active-site, and the product are then released, freeing the active-site to catalyze another reaction.
[q] Outline the 3 stages of enzyme activity
[a] Collision: substrate(s) enter the active site in a specific orientation.
Catalysis: substrate(s) and active site change shape, promoting the reaction.
Release: the new chemical substance(s), the product(s), leaves the enzyme.
The enzyme can take new substrates.
[q] Explain the role of random collision in the binding of the substrate with enzyme active site.
[a] A substrate can only bind to the active site it it’s really close to it.
With most reactions, the substrates are dissolved in water, so reactions are aqueous.
All molecules in the solution are in continuous motion.
Due to that, the collision between the substrate and enzyme’s active site are random.
When they happen to successfully collide and the substrate ends up in the active-site, reaction starts.
Manipulative factors: molecule concentration, energy etc.
[q] Describe the induced fit model of enzyme reaction.
[a] The two models used to demonstrate induced fit are: lock and key or induced fit.
Lock and key: The enzyme’s active sit complements the substrate precisely.
Induced fit: The active site is not a rigid fit for the enzyme.
Instead the active site will undergo a conformational change when exposed to an substrate and improve binding.
[q] Define activation energy
[a] The energy which is required for a chemical reaction to proceed from the reactants to product.
Even when energy is released in a reaction, some energy is required for substrates to reach a transition state. it’s used to break or weaken the bonds in the substrate.
[q] Explain the role of enzymes in lowering the activation energy of a reaction.
[a] Enzymes speeds up the rate of metabolic reactions by lowering the activation energy.
When an enzyme binds to a substrate, it stresses and destabilizes the bond in the substrate.
This reduces the overall energy of the level of substrate transition state.
[q] Draw the structure of an amino acid
[a]
[q] State the unit for enzyme reaction rate
[a] The reaction rate is the amount of reaction over time.
Amount of reaction / per unit time.
[q] State two methods for determining the rate of enzyme-controlled reactions.
[a] 1. Measure the disappearance of the substrate.
2. Measure the rate of appearance of product.
[q] Given data, calculate and graph the rate of an enzyme catalyzed reaction.
[a] If the raw data is quantity, then divide by set amount of time (1cm/s)
If the raw data is time, take unit by time.
If raw data is graph over time, rate can be found by taking a slope of initial reaction.
[q] Explain how temperature affect the rate of enzyme activity.
[a] The increase of temperature means the increase of enzyme and substrate activity.
More collision would happen which then increases enzyme activity.
At an optimal or maximum, the enzyme activity would peak.
If the temperature continues on higher above the optimal, the enzymes would be unstable, and it loses its shape.
[q] Draw a graph depicting the effect of temperature on the rate of enzyme activity.
[a]
[q] Explain how pH affects the rate of enzyme activity
[a] Enzymes has an optimum pH that maximizes enzyme activity.
If it moves out of the optimum range, there will be a decrease in enzyme shape activity because the pH would alter the charges, thus affecting its shape, solubility and ability of enzyme activity.
[a] The structural change in a protein that results (often perm.) in their ability to perform their function.
• Affects the way the proteins are folded and their structure, which changes its shape and activity.
• Tertiary folds are stabilized by R-groups and if their charges are messed up, it messes up the folding.
[a] Heat: causes vibration within the protein which breaks intermolecular bonds and interactions that holds the protein together.
pH: causes the charge in the R-groups to change, which interrupts ionic bonds or causes new ones to form, altering protein structure.
[a] Competitive: This is when a molecule that’s not the substrate binds onto the enzyme’s active site with a similar structural and chemical form.
It blocks the substrate form binding.
To outcompete this, more substrate concentration would increase its chances on reaction.
Non-competitive: A molecule binds to a site other than the active site (eg. allosteric) causing the enzyme to change shape so that the substrate can no longer bind onto it.
Increasing substrate concentration wouldn’t help because the substrate and inhibitor isn’t competitive.
This is a way to REGULATE metabolism.
[a] Competitive: since it binds onto the active site, by increasing the substrate concentration it increases the probability of an enzyme colliding with the substrate, and eventually enzymes would be at their max. capacity.
Non-competitive: since the chemicals binds onto the enzyme and inhibits is form performing its task, therefore maximum capacity is reduced.
[a] For the end-product inhibition, the final product in a series of reaction acts as a chemical substance that binds to the allosteric site of an enzyme.
This ensures that production of products is regulated. If product builds up, it slows down reaction pathways so intermediate products are limited.
Once levels of product drops, reactions begin again.
[a] Isoleucine is an essential amino acid in humans, can’t be synthesized in our bodies.
Threonine attaches to threonine deaminase and produces products which gets modified a few more times before producing isoleucine, which can act as an allosteric inhibitor to the deaminase.
[a] Chemogenomics is a study of chemicals that can influence metabolic pathways.
Scientists look to develop new drugs and test massive libraries of chemicals on a range of organisms to find which ones are effective on particular parts of different metabolic pathways.
There’s often a huge database and metabolic pathways they affect.
[a] Malaria is a disease caused by a parastic protozon called plasmodium falciparum.
• They have become immune to some treatment/drugs.
• There’s only a few drugs that is currently available for treatment.
• Global effort to eradicate the disease.
• Kills hundreds/thousands of people per year (kids).
[a] What: attachment of enzyme to another substance so that its movement is restricted.
How: attaching to flass surface, trapping in gel.
Why: They enzyme can be separated from the products so reactions can be stopped at any time.
You can reuse the enzymes and prevents contamination of the products.
[a] 1) after the enzyme is purified, they’re immobilized onto gel-like beads.
2) milk then gets repeatedly poured over the immobilized enzymes so that it makes lactose-free milk
[a] • Lactose-intolerance people can get a source of dairy.
• Make the milk sweeter so that no additional sweetener is needed.
• Prevent crystallization of the milk when making ice-cream.
• A way to reduce production time of cheese/yogurt.
Krebs: cellular respiration
Calvin: photosynthesis.
[a] Non-competitive binds onto the enzyme away from the active site but only impairs the function.
Allosteric inhibition binds onto the enzyme away from the active site but prevents substrates from binding.
[q] C1.1.1—Enzymes as catalysts
Students should understand the benefit of increasing rates of reaction in cells.
[a] Catalysts are substances that increase the rate of a chemical reaction without being used up in the reaction itself.
Enzymes are a type of catalyst (proteins made by living organisms) used by cells due to:
• Faster energy production to support muscles during exercise and other energy-heavy activities
• Faster waste removal to prevent their accumulation and toxicity
• Faster response to injury, such as the blood clotting cascade
• Faster homeostatic responses to maintain internal conditions like temperature and pH
• Faster cellular communication during signaling pathways and transduction
• Faster cellular regeneration and repair of tissues
[q] C1.1.2—Role of enzymes in metabolism
Students should understand that metabolism is the complex network of interdependent and interacting chemical reactions occurring in living organisms.
Because of enzyme specificity, many different enzymes are required by living organisms, and control over metabolism can be exerted through these enzymes.
[a] Metabolism is a term that describes all enzyme-catalyzed chemical reactions that sustain the life of a living organism.
Because of enzyme specificity, many different enzymes are required by living organisms, and control over metabolism can be exerted through these enzymes
[q] C1.1.3—Anabolic and catabolic reactions
Examples of anabolism should include the formation of macromolecules from monomers by condensation reactions including protein synthesis, glycogen formation and photosynthesis.
Examples of catabolism should include hydrolysis of macromolecules into monomers in digestion and oxidation of substrates in respiration.
[a] There are two types of metabolism: Anabolism describes the enzyme-catalyzed chemical reactions that synthesize macromolecules (big, complex ones) from monomers (small, simple molecules). Examples include photosynthesis, protein synthesis, and glycogen formation.
Catabolism describes the enzyme-catalyzed chemical reactions that break down macromolecules into monomers (a cat like to breaks stuff, like catabolism).
Examples include digestion and cellular respiration.
Organic molecules are synthesized by condensation reactions (removing a water molecule from the monomers to join them, i.e. forming a peptide bond) and broken down by hydrolysis reactions (using water, hydro, to break the molecule down, lysis).
[q] C1.1.4—Enzymes as globular proteins with an active site for catalysis
C1.1.4—Enzymes as globular proteins with an active site for catalysis
[a] Enzymes are globular proteins composed of peptide chains. Of the many amino acids within its structure, a special few are involved in catalyzing chemical reactions.
The region in which these special, few amino acids exist is called the active site of the enzyme, as it is the site that carries out the enzyme’s activity.
Despite this, molecular interactions between all of the amino acids within the enzyme determine whether the active site is actually ‘active’ and able to catalyze the chemical reaction.
[q] C1.1.10—Effect of enzymes on activation energy
Application of skills: Students should appreciate that energy is required to break bonds within the substrate and that there is an energy yield when bonds are made to form the products of an enzyme-catalyzed reaction. Students should be able to interpret graphs showing this effect.
[a] Enzymes increase the rate of a chemical reaction by decreasing its activation energy, which is the minimum energy required for the reaction to take place.
They do this by providing an alternative mechanism/pathway for the reaction that requires less activation energy than the one that would have occurred without an enzyme.
[q] C1.1.5—Interactions between substrate and active site to allow induced-fit binding
Students should recognize that both substrate and enzymes change shape when binding occurs.
[a] The induced-fit theory is a model postulating that the substrate, the chemical substance that binds to the enzyme’s active site, does more than simply fit perfectly into the active site – it causes a change in the enzyme’s shape so as to properly align the special few amino acids (called catalytic groups) on its surface.
The substrate also changes its shape when binding occurs to further optimize the fitting.
Analogy: when you put on a glove, your hand induces slight changes to the glove’s shape so as to perfectly fit it, even though the glove already is shaped like a hand.
Similarly, although an enzyme’s active site is already a very good match for the substrate, the binding of the substrate to it induces slight conformational changes so as to ensure optimal fitting.
[q] C1.1.6—Role of molecular motion and substrate-active site collisions in enzyme catalysis
Movement is needed for a substrate molecule and an active site to come together.
Sometimes large substrate molecules are immobilized while sometimes enzymes can be immobilized by being embedded in membranes.
[a] Brownian motion is a phenomenon in which a chemical substance is naturally in a constant state of random movement, colliding with other molecules as they move.
This movement is how a substrate and enzyme come together; if they collide at the correct orientation (i.e. the substrate must collide with the active site of the enzyme body at the correct angle) with sufficient energy (enough to bypass the activation energy), the catalyzed reaction will take place.
Enzymes and substrates can either be present within the cell’s cytoplasm, embedded within the plasma membrane, or fixed onto a solid surface (i.e. algae balls) – if they are fixed in a particular place, they are immobilized, which incurs several benefits:
• Greater resistance to temperature and pH fluctuations
• Reduced costs when separating enzyme from substrate in industrial production
• Greater reusability as immobilized enzymes last longer
• Ability to perform localized reactions in specific parts of the cell or organelle
[q] C1.1.7—Relationships between the structure of the active site, enzyme–substrate specificity and denaturation
Students should be able to explain these relationships.
[a] The chemical structure of the enzyme’s active site determine its shape and thus the substrate that can bind to the enzyme, leading to enzyme-substrate specificity.
Some enzymes are so specific they can only fit one specific substrate, while others can bind to an entire (but specific) group of substrates.
Figure 2: the same enzyme bound to two different but similar substrates- notice how the amino acids on the active site (G121, V81, R180) form hydrogen bonds with the substrates. “The unique combination of amino acids, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site” that only specific substrate(s) can fit into (Libretexts).
[q] C1.1.8—Effects of temperature, pH and substrate concentration on the rate of enzyme activity
The effects should be explained with reference to collision theory and denaturation.
Application of skills: Students should be able to interpret graphs showing the effects.
[a] Temperature: increasing the temperature increases the probability of successful collisions between the enzyme and substrate, leading to greater enzyme activity.
Once the optimum temperature is surpassed, the enzyme begins to irreversibly denature, decreasing the concentration of functioning enzymes thus lowering enzyme activity.
pH: H+ concentration interferes with the interactions between amino acids within the enzyme’s structure.
Any deviation away from the optimum pH (in which H+ concentration enables amino acid interactions that optimize the shape of the active site), whether an increase or decrease, will denature and decrease enzyme activity.
Substrate concentration: increasing substrate concentration increases the probability of successful collisions between the enzyme and substrate, leading to greater enzyme activity.
As the active sites of the enzymes become saturated, the rate of reaction starts to gradually level off and eventually plateau when all active sites are occupied.
[q] NOS: Students should be able to describe the relationship between variables as shown in graphs.
They should recognize that generalized sketches of relationships are examples of models in biology.
Models in the form of sketch graphs can be evaluated using results from enzyme experiments.
[a]
The above graphs are general sketches of relationships that are examples of mathematical models in biology.
A model of enzyme-catalyzed reactions is hyperbolic, while a model of bacterial population growth is exponential, and so on.
Quantifying observations of biological phenomena into such models allows us to predict trends and better understand experimental results
[q] C1.1.9—Measurements in enzyme-catalyzed reactions
Application of skills: Students should determine reaction rates through experimentation and using secondary data
[a]
[q] C1.1.11—Intracellular and extracellular enzyme-catalyzed reactionsInclude glycolysis and the Krebs cycle as intracellular examples and chemical digestion in the gut as an extracellular example.
[a] 1. Glycolysis is the breakdown of glucose into two pyruvate molecules in the cytoplasm, which involves phosphorylation of the glucose molecule. This step is catalyzed by the enzyme hexokinase.
2. Fumarase catalyzes the conversion of fumarate to L-malate in the mitochondria in the Krebs Cycle.
3. Amylase,lipase, and proteases catalyze the extracellular digestion of food in humans.
[q] C1.1.12—Generation of heat energy by the reactions of metabolism
Include the idea that heat generation is inevitable because metabolic reactions are not 100% efficient in energy transfer. Mammals, birds and some other animals depend on this heat production for maintenance of constant body temperature.
[a] Chemical reactions are never 100% efficient, so some energy is lost as heat. Mammals, birds and some other animals depend on this heat production for maintenance of constant body temperature, i.e. when humans are cold, they shiver as the energy produced from muscle movement heats the body up.
[q] C1.1.13—Cyclical and linear pathways in metabolism
Use glycolysis, the Krebs cycle and the Calvin cycle as examples.
[a] Cyclic metabolic pathways involve reactions in which the product of one step is a reactant in another.
Linear metabolic pathways involve reactions in which the reactant is transformed through a series of steps into a final product.
[q] C1.1.14—Allosteric sites and non-competitive inhibition
Students should appreciate that only specific substances can bind to an allosteric site. Binding causes interactions within an enzyme that lead to conformational changes, which alter the active site enough to prevent catalysis. Binding is reversible.
[a] Enzymes can be regulated in ways that either promote or reduce their activity in order to cater for the metabolic needs of the cell.
Competitive inhibition: occurs when an inhibitor molecule is structurally similar to the substrate and is able to bind (and compete against the substrate) to the active site of the enzyme, effectively blocking the substrate from binding to the enzyme thus leading to a lower reaction rate.
Noncompetitive inhibition: occurs when an inhibitor molecule is not structurally similar to the substrate and binds reversibly to the allosteric site of the enzyme, causing chemical interactions with the enzyme that lead to conformational changes, which alters the active site an enough of an extent to prevent catalysis.
An allosteric site is a distinct region within the enzyme’s structure where regulatory molecules, like noncompetitive inhibitors, can bind to the enzyme and change the active site’s conformation so as to increase or decrease the enzyme’s affinity to its substrate.
Enzyme affinity is a measure of how readily an enzyme binds to its substrate; the higher the affinity the more optimal the active site’s conformation is for the substrate.
When noncompetitive inhibitors bind to the allosteric site, they decrease the enzyme’s affinity as they induce a conformational change in the active site that makes its shape less optimal for fitting the substrate
[q] C1.1.15—Competitive inhibition as a consequence of an inhibitor binding reversibly to an active
site
Use statins as an example of competitive inhibitors. Include the difference between competitive and noncompetitive inhibition in the interactions between substrate and inhibitor and therefore in the effect of substrate concentration
[a] Statins competitively inhibit HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A), the enzyme catalyzing the rate-determining (major) step in cholesterol synthesis, which is useful in patients with high cholesterol levels.
The maximum rate of reaction with an enzyme can be restored during competitive inhibition by simply increasing the concentration of the substrate, but not in noncompetitive inhibition.
Figure 3: effect of type of inhibition on maximum rate of reaction (Khan Academy).
[q] C1.1.16—Regulation of metabolic pathways by feedback inhibition
Use the pathway that produces isoleucine as an example of an end product acting as an inhibitor.
[a]
Metabolic pathways can be regulated by end-product feedback inhibition in which the last/end product inhibits the enzyme catalyzing the first step of the metabolic pathway.
This is done in order to ensure controlled amounts of reactants and products in the pathway; there is enough of each substance but not too much or too little.
For example, the metabolic pathway converting the amino acid threonine into isoleucine is regulated by endproduct inhibition.
When isoleucine accumulates and is in excess, it noncompetitively inhibits the enzyme threonine deaminase until isoleucine concentrations drop or until threonine amounts are sufficient again.
[q] C1.1.17—Mechanism-based inhibition as a consequence of chemical changes to the active site caused by the irreversible binding of an inhibitor
Use penicillin as an example. Include the change to transpeptidases that confers resistance to penicillin.
[a] Mechanism-based inhibition is an irreversible type in which the inhibitor molecule binds permanently to the active site of the enzyme, usually leading to lethal effects.
For example, in gram-positive bacteria, the links between the carbohydrates making up the cell wall are broken to allow the bacteria to grow and expand, then transpeptidase cross-links them back together.
Penicillin is a mechanism-based inhibitor which binds irreversibly (through a covalent bond) to transpeptidase, preventing the carbohydrates from re-linking. This weakens the cell wall, eventually leading to bursting (lysis).
[x] Exit text
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