8.1 Metabolism Flashcards
Diagram showing the different sources of ATP in the human body
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What is a metabolic pathway?
A sequence of enzyme-catalyzed biochemical reactions in cells (can be chains or cycles).
Characteristics of metabolic pathways
- Sometimes there is a substrate, which is converted into an end product in a few steps.
- However, more often, a pathway can be quite complex, with many intermediate products before an end product is produced.
- Glycolysis, the conversion of glucose into pyruvate, is a great example.
Diagram showing glycolysis- an example of a metabolic pathway showing all the enzymes involved
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Some metabolic pathways are linked to ___
Other pathways
Give an example of how some metabolic pathways are linked to other pathways
- For example, glycolysis is directly linked to the Krebs cycle.
- This reaction is known as the link reaction.
Diagram of the Krebs cycle
Metabolic reactions can be ___
Linear, for example glycolysis, or cyclic, for example the Krebs cycle
What is the role of enzymes in metabolic pathways?
- Most of the reactions in metabolic pathways would not proceed without the presence of enzymes.
- Enzymes speed up these reactions by lowering the activation energy.
Define activation energy
The minimum energy required by a substrate molecule before it can undergo a chemical change.
Diagram showing how an enzyme lowers the activation energy of a reaction
A ______ begins with a particular substrate, terminates with an end product, and has many minute steps in between.
Metabolic pathway
Some of the most poisonous substances known are ___
Enzyme inhibitors
Example of how some of the most poisonous substances known are enzyme inhibitors
- For example, the poison that probably killed the Roman emperor Claudius came from the death cap mushroom, which contains the toxic peptide alpha-amanitin.
- This is a potent enzyme inhibitor, stopping RNA polymerase II enzyme from transcribing DNA.
What are the two types of enzyme inhibitors?
- Competitive
- Non-competitive
What do competitive inhibitors do?
They compete with the substrate for the same active site
What do non-competitive inhibitors do?
They bind at a site away from the active site, altering the shape of the enzyme
Diagram of competitive and non-competitive inhibition of enzymes
Give two examples of enzyme inhibitors
- Disulfiram (inhibits acetaldehyde dehydrogenase)
- Alanine (inhibits pyruvate kinase)
What is Acetaldehyde dehydrogenase’s substrate?
Acetaldehyde
What is Pyruvate kinase’s substrate?
Phosphoenol pyruvate
What are Acetaldehyde dehydrogenase’s products?
Acetic acid
What are Pyruvate kinase’s products?
Pyruvate
What is Acetaldehyde dehydrogenase’s inhibitor?
Disulfiram (competitive)
What is Pyruvate kinase’s inhibitor?
Alanine (non-competitive)
Binding of Acetaldehyde dehydrogenase
Reversible binding to the active site
Binding of Pyruvate kinase
Reversible binding to a site away from the active site
Maximum rate of reaction in competitive inhibition
- The maximum rate of reaction (V max) is eventually the same as the reaction without an inhibitor.
- When the substrate concentration increases, the rate will increase, because there is more available substrate than an inhibitor.
- Therefore, there is a greater chance of the substrate binding to the enzyme’s active site and forming product(s).
Maximum rate of reaction in non-competitive inhibition
- In non-competitive inhibition, the rate levels off and never reaches the same level that it would without inhibitor.
- This difference is caused by the fact that all enzyme molecules to which the inhibitor is attached are effectively blocked from reacting with the substrate due to modification of their active site.
- Therefore, fewer enzyme molecules (free of inhibitor) are available to catalyse the reaction.
Graph showing the rate of reaction versus substrate concentration
Characteristics of competitive inhibitors
- It is chemically quite similar to the substrate
- It binds to the active site of the enzyme
- Binding of the inhibitor to the enzyme does not modify its active site
- As the concentration of substrate is increased, the effect of the inhibitor on the reaction is reduced
Characteristics of non-competitive inhibitors
- It has no similarity to the substrate
- It binds to the enzyme at a site other than the active site
- Binding of the inhibitor to the enzyme modifies its active site, hence preventing binding of substrate (if it does bind, the enzyme will not be able to catalyse the reaction)
- Increasing the concentration of the substrate does not decrease the impact of the inhibitor. Therefore, the rate of reaction is lower than normal at all substrate concentrations
What can reduce the effect of competitive inhibition of an enzyme?
Increasing the substrate concentration
The non-competitive inhibitor distorts the ___
Active site of the enzyme
What is the difference between a competitive and a non-competitive inhibitor?
The competitive inhibitor binds to the active site while the non-competitive inhibitor binds to a site other than the active site.
How can cells be economical with their resources?
- One of the ways is end-product inhibition.
- When the end-product of a pathway is no longer needed, it makes sense to stop the reactions at the first step of the pathway.
- For example, serotonin is needed for the synthesis of the hormone melatonin.
Diagram showing melatonin synthesis
What will happen once the body has enough melatonin?
Production will shut down
In most cases, the enzymes that catalyse the first reaction of the pathway are ___
Allosterically inhibited (a form of non-competitive inhibition) by the end product of the pathway.
Example of an enzyme being allosterically inhibited
In the example of melatonin synthesis, the enzyme that is allosterically inhibited is serotonin-N-acetyltransferase, the product that will be the inhibitor is melatonin.
What is an allosteric site?
- A binding site on the surface of an enzyme other than the active site.
- In the end-product inhibition, the product of the last reaction of an enzyme binds to the allosteric site.
- In non-competitive inhibition, when the inhibitor binds to an allosteric site, it blocks the activity of the enzyme.
Binding of a regulatory molecule in an allosteric inhibition
- In an allosteric inhibition, the binding of a regulatory molecule (which is often the end product of the pathway) to the allosteric site changes the overall conformation of the enzyme.
- This, in turn, can either enable the substrate to bind to the active site or prevent the binding of the substrate.
Diagram showing the pathway of the synthesis of isoleucine from threonine (a good example of end-product inhibition)
What is isoleucine?
- An essential amino acid.
- It cannot be made by the human body so it must be consumed from food.
- Some organisms such as bacteria can synthesise isoleucine from threonine.
Explain the pathway of the synthesis of isoleucine from threonine
- The normal pathway starts at (a), then to (b), and continues through each step to (e).
- Isoleucine can bind to the enzyme that catalyses the first step of the pathway in a non-competitive way.
- It binds allosterically to the enzyme and changes the conformation of the active site.
- As a result, the substrate can no longer bind to the enzyme, as shown in (f), (h) and (i).
In the enzyme-controlled pathway shown below, which compound is most likely to inhibit enzyme (w)?
- IV
- IV is the end product and in end-product inhibition, this is normally the compound that inhibits the enzyme of the first reaction.
What happens during end-product inhibition of the pathway shown below?
Enzyme I is inhibited by substance Z
In the pathway that converts threonine to isoleucine, name the enzyme inhibited by the end-product isoleucine.
Threonine deaminase
Describe the branch of bioinformatics that is concerned with the binding of certain compounds to target sites
- This means that if a chemical binds to a receptor, or another part of the cell wall of a parasite, bacterium or the protein coat of a virus, it may change the infectivity of that pathogen (disease-causing agent).
- Another interaction could be between a chemical and an enzyme of a metabolic pathway, or with an enzyme involved in the metabolism of nucleic acids.
- Therefore, such interactions are studied to find potential cures for certain diseases.
Some databases can be used to search for particular ___
Combinations of chemicals and target sites of pathogens.
Example of how some databases can be used to search for particular combinations of chemicals and target sites of pathogens
This approach has been used to find new drugs that could treat malarial infections.
What is Malaria?
- A disease caused by the parasite Plasmodium falciparum.
- It is a major world health issue that causes the deaths of over 400,000 people every year, mostly children under five years of age in developing countries.
- The Plasmodium falciparum parasite is transmitted from an infected person to another by blood-sucking mosquitoes.
- The malarial parasite invades the red blood cells and feeds on the proteins of these cells.
Use of databases in Malaria research
- The Plasmodium falciparum parasite has been extensively studied and the genome has been sequenced for the particular strain 3D7.
- The genome sequence information, together with the protein sequences generated from the database, were used to screen many thousands of chemicals for possible interactions.
- Chemicals, based on the predicted interactions, could then be tested in the lab to confirm whether those interactions did take place, and whether their effect is sufficiently promising to warrant further research.
What progress has been made in Malaria research?
- At least 35 new chemicals that show promise in treating malaria have been found through chemical testing (previous flashcard).
- As the malarial parasite has become resistant to most antimalarial drugs, it is necessary to find new, effective treatments quickly to stop this disease, which affects so many people worldwide.
Where has funding for Malaria research come from?
The Bill and Melinda Gates Foundation has donated millions of (US) dollars to fund this area of research.
What does successful research require?
The collaboration of software developers, engineers (for hardware), statisticians, biochemists and medical doctors.
Which parasite causes malaria?
Plasmodium falciparum
Explanation of how databases are used to identify potential new antimalarial drugs
Databases with Plasmodium falciparum genome and protein sequence information were used to screen chemicals for possible interactions before starting lab research.
What can be measured in most enzyme-catalyzed reactions?
- The time taken for a particular substrate to be used up
- The time taken for a specific product to be made
- Amount (mass or volume) of substrate used up over a specific amount of time
- Amount (mass or volume) of product made over a specific amount of time.
In the case of finding the time taken for a particular substrate to be used up or the time taken for a specific product to be made, what formula can be used to work out the rate of reaction?
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In the case of finding the amount (mass or volume) of substrate used up over a specific amount of time or the amount (mass or volume) of product made over a specific amount of time, how can the rate of reaction be found?
The mass or volume can be divided by time to obtain the rate of reaction per second
Graph showing the rate for the decolourisation of the iodine–starch complex at different temperatures (with error bars showing standard deviation)
When plotting a graph of the rate of an enzyme-controlled reaction, what variable should always be plotted on the x-axis (horizontal axis)?
Independent
The following shows a metabolic pathway:
What would be the effect on the reaction of adding a competitive inhibitor to enzyme 2?
- The concentration of intermediate X would increase.
- If the rate of the first reaction from Substrate to Intermediate X is not changed, the slowing down of the second reaction means that you will get a build-up of Intermediate X molecules as they waits for molecules of Enzyme 2 to become available.
A competitive inhibitor resembles the ___
Substrate
In the liver, alcohol breaks down to acetaldehyde, which is broken down by aldehyde dehydrogenase to acetic acid. Disulfiram is a drug that binds to aldehyde dehydrogenase and prevents acetaldehyde from being converted to acetic acid. What is the effect of disulfiram?
- Increases acetaldehyde concentration in blood.
- Disulfiram is a competitive inhibitor and when it binds to aldehyde dehydrogenase, acetaldehyde will not be converted to acetic acid, and so acetaldehyde will build up in the blood.
Structure of non-competitive inhibitor
Does not resemble the substrate
Serotonin is needed for the synthesis of the hormone melatonin as indicated below:
What will happen once the body produces enough melatonin?
- Melatonin binds to serotonin-N-acetyltransferase.
- This is end product inhibition, where the end product (melatonin) binds to the first enzyme (serotonin-N-acetyltransferase) to inhibit the increased production of melatonin.
Define a link reaction
The reactions that connect glycolysis to the reactions of the Krebs cycle by producing acetyl coenzyme A from pyruvate
Inhibition of the enzyme Acetaldehyde dehydrogenase
Substrate: Acetaldehyde
Products: Acetic acid
Inhibitor: Disulfiram (competitive)
Binding: Reversible binding to the active site
Inhibition of the enzyme Pyruvate kinase
Substrate: Phosphoenol pyruvate
Products: Pyruvate
Inhibitor: Alanine (non-competitive)
Binding: reversible binding to a site away from the active site
