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8.1 Metabolism

Essential idea: Metabolic reactions are regulated in response to the cell’s needs.

Enzymes, Feedback Inhibition, and Allosteric Regulation - YouTube

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TREAD

BLINK

_____

_____

_____

_____

_____

8.1 Metabolism

Challenge: by changing just one letter at a time, get from ‘TREAD’ to ‘BLINK’. All intermediates must be real English words.

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

Metabolic pathways*: cycles or chains of enzyme catalysed reactions. The small steps together form what is called a metabolic pathway.

Metabolism: the sum total of all chemical reactions that occur within an organism.

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TREAD

BLINK

BREAD

BREED

BLEND

BLEED

BLIND

end product

intermediates

Initial substrate

8.1 Metabolism

Challenge: by changing just one letter at a time, get from ‘TREAD’ to ‘BLINK’. All intermediates must be real English words.

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__a_biochemical_pathway.html

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Look underneath your chairs and try to piece together 3 words

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Allosteric

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Statement

Guidance

8.1.U1

Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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8.1.U2

Enzymes lower the activation energy of the chemical reactions that they catalyse.

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8.1.U3

Enzyme inhibitors can be competitive or non-competitive.

Enzyme inhibition should be studied using one specific example for competitive and non-competitive inhibition.

8.1.U4

Metabolic pathways can be controlled by end-product inhibition.

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8.1.A1

End-product inhibition of the pathway that converts threonine to isoleucine.

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8.1.A2

Use of databases to identify potential new anti-malarial drugs.

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8.1.S1

Calculating and plotting rates of reaction from raw experimental results.

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8.1.S2

Distinguishing different types of inhibition from graphs at specified substrate concentration.

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8.1 Metabolism

Syllabus Reference

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8.1 Metabolism

Vocabulary

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Reactions that build up molecules

Anabolic reactions:

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Catabolic reactions:

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Metabolism:

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Metabolic pathway:

Reactions that break down molecules

The combination of anabolic and catabolic reactions in the cell

A series of enzyme controlled reactions, may be cycles or chains

8.1 Metabolism

Define the following

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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8.1 Metabolism

Look at this diagram which summarises the enzyme catalysed reactions that break down alcohol into water and carbon dioxide...

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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  1. Which enzyme has the product acetaldehyde?

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  • Which enzyme has the substrate acetaldehyde?

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  • How do the enzymes link together to form a metabolic pathway?

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8.1 Metabolism

Look at this diagram which summarises the enzyme catalysed reactions that break down alcohol into water and carbon dioxide...

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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  1. Which enzyme has the product acetaldehyde?

alcohol dehydrogenase

2. Which enzyme has the substrate acetaldehyde?

acetaldehyde dehydrogenase

3. How do the enzymes link together to form a metabolic pathway?

The first enzyme produces the substrate of the second enzyme and so on. Each enzyme catalyses one reaction in a chain of reactions

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8.1 Metabolism

Look at this diagram which summarises the enzyme catalysed reactions that break down alcohol into water and carbon dioxide...

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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  • The overall activity of enzymes, and therefore metabolism, is controlled by a number of factors:
  • The rate of enzyme production and breakdown.
  • Enzyme interaction with the products of the reaction.
  • The influence of inhibitors.

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  • Sometimes genes are induced (“turn on” to be transcribed) only when an enzyme product is required to catalyze reactions that may occur infrequently, e.g. use of a particular substrate that is not always available.

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8.1 Metabolism

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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Glycolysis, a part of respiration, is an example of a metabolic chain

The Calvin cycle, a part of photosynthesis, is an example of a metabolic cycle

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8.1 Metabolism

Metabolic pathways: cycles or chains of enzyme catalysed reactions.

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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8.1 Metabolism

What is activation energy?

8.1.U2 Enzymes lower the activation energy of the chemical reactions that they catalyse.

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Enzymes benefit organisms by speeding up the rate at which reactions occur, they make them happen millions of times faster.

8.1 Metabolism

What is activation energy?

8.1.U2 Enzymes lower the activation energy of the chemical reactions that they catalyse.

Activation energy: the initial input of energy that is required to trigger a chemical reaction.

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When the substrate enters the active site the enzyme changes shape.

This puts pressure on the substrate molecule making it easier for bonds to break bringing substrate molecules closer together.

When the product is released the enzyme returns to its original shape.

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8.1 Metabolism

What is the induced fit model?

8.1.U1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

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Due to the formation of an enzyme-substrate complex the bonds in the substrate molecule are stressed/become less stable.

8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U2 Enzymes lower the activation energy of the chemical reactions that they catalyse.

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Inhibitor: a molecule that binds to an enzyme and slows down or stops the enzyme’s function.

8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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http://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swf

8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

https://www.youtube.com/watch?v=PILzvT3spCQ&feature=emb_logo

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8.1 Metabolism

Define the following

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

  • Enzymes can be inhibited by other molecules
  • Inhibition can be competitive or non-competitive

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  • Inhibitors are chemicals that reduce the rate of enzyme controlled reactions
  • The are usually specific and they work at low concentrations
  • They block the enzyme but they do not usually destroy it
  • Many drugs and poisons are inhibitors of enzymes in the nervous system

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8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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  • Compete with the substrate molecules for the active site
  • Resembles the substrate’s structure closely
  • The inhibitor’s action is proportional to its concentration
  • An increase in the substrate concentration can reverse the effect of a competitive inhibitor

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8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Relenza competitively binds to the neuraminidase active site and prevents the cleavage of the docking protein. Consequently, virions are not released from infected cells, preventing the spread of the influenza virus

8.1 Metabolism

 Example of Competitive Enzyme Inhibitor

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Competitive Inhibitor Example

8.1 Metabolism

Competitive Enzyme Inhibitor Example

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Competitive Inhibitor Example

An enzyme called PDE5 degrades cGMP. As cGMP degrades, there is less blood flow.

So. What would happen if PDE5 was inhibited?

8.1 Metabolism

Competitive Enzyme Inhibitor Example

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Sildenafil (Viagra)

Nitric Oxide (NO) binds receptors in the smooth muscle cells of the penis. This results in increased levels of cyclic guanosine monophosphate (cGMP) which increases vasodilation. An enzyme called PDE5 degrades cGMP. Sildenafil fits into the same active site of PDE5 as cGMP, thus competitively inhibiting PDE5 from working. cGMP is not degraded so vasodilation continues.

8.1 Metabolism

Competitive Enzyme Inhibitor Example

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

Competitive Enzyme Inhibitor Example

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

 How do enzymes lower the activation energy of a reaction?

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

 Enzyme activity graph

8.1.S2 Distinguishing different types of inhibition from graphs at specified substrate concentration.

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8.1 Metabolism

 Enzyme activity graph

8.1.S2 Distinguishing different types of inhibition from graphs at specified substrate concentration.

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Examples of a Noncompetitive Inhibitor

Cyanide

Cyanide acts as irreversible noncompetitive inhibitor to the enzyme cytochrome c oxidase.

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This prevents cellular respiration from working, meaning that the cell can no longer produce ATP.

A cyanide is any chemical compound that consists of a carbon atom triple bonded to a nitrogen atom.

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By changing the shape of the active site, cytochrome oxidase can no longer pass electrons to the final acceptor (oxygen). Consequently, the electron transport chain cannot continue to function and ATP is not produced via aerobic respiration

8.1 Metabolism

 Example of Non-Competitive Enzyme Inhibitor

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Allosteric means “other site”

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Active site

Allosteric site

8.1 Metabolism

Allosteric Site

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Allosteric enzymes have two receptor sites

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One site fits the substrate like other enzymes

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The other site fits an inhibitor molecule

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Inhibitor molecule

Inhibitor fits into allosteric site

Substrate cannot fit into active site

8.1 Metabolism

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  • Non-competitive inhibitors bind to an allosteric site which changes the shape of the active site
  • As concentration of inhibitor increases the rate of reaction decreases.
  • This is because there are fewer functional active sites available for reaction

8.1 Metabolism

 

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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  • The inhibitor binds irreversibly to the enzyme but not at the active site
  • These are not influenced by the concentration of the substrate.

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8.1 Metabolism

 

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Negative feedback

End point or end product inhibition

Poisons

Snake bites, plant alkaloids and nerve gases

Medicine

Antibiotics, sulphonamides, sedatives and stimulants

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8.1 Metabolism

 Some uses of enzyme inhibitors

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

 Some uses of enzyme inhibitors

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Combine with the functional groups of the amino acids in the active site, irreversibly

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Examples: nerve gases and organophosphate pesticides combine with serine residues in the enzyme acetylcholine esterase

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8.1 Metabolism

 Some uses of enzyme inhibitors

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

 Some uses of enzyme inhibitors

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

Compare and contrast between competitive and non-competitive inhibition

8.1.S2 Distinguishing different types of inhibition from graphs at specified substrate concentration.

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http://highered.mheducation.com/sites/0072943696/student_view0/chapter2/animation__a_biochemical_pathway.html

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End product inhibition prevents a large build-up of products

8.1 Metabolism

Compare and contrast between competitive and non-competitive inhibition

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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8.1 Metabolism

Compare and contrast between competitive and non-competitive inhibition

8.1.U3 Enzyme inhibitors can be competitive or non-competitive.

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Conformational change

Substrate fits into active site

Allosteric site is empty

No inhibitor present

Inhibitor enters allosteric site

Active site changes shape

Substrate no longer fits active site

8.1 Metabolism

The allosteric site is the enzyme “on-off” switch

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8.1 Metabolism

8.1.A1 End-product inhibition of the pathway that converts threonine to isoleucine.

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  • The first reaction in the pathway from threonine to isoleucine is inhibited by the end product, isoleucine.
  • The end product, isoleucine, is an allosteric inhibitor of the first enzyme in the sequence.
  • This was one of the first examples of allosteric feedback inhibition to be discovered.

*Essential amino acids cannot be made by the body, therefore they must come from food.

8.1 Metabolism

8.1.A1 End-product inhibition of the pathway that converts threonine to isoleucine.

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  • Sometimes when a chemical binds to a target site, it can significantly alter metabolic activity.
  • Massive libraries of chemicals are tested individually on a range of related organisms.
  • For each organism a range of target sites are identified.
  • A range of chemicals which are known to work on those sites are tested.

Bioinformatics is an approach whereby multiple research groups can add information to a database enabling other groups to query the database.

Bioinformatics has facilitated research into metabolic pathways is referred to as Chemogenomics.

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.A2 Use of databases to identify potential new anti-malarial drugs

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  • The life cycle of the parasite requires both a human and mosquito host – hence the disease is transmitted via mosquito bites
  • The maturation and development of the parasite in both human and mosquito host is coordinated by specific enzymes
  • By targeting these enzymes for inhibition, new anti-malarial drugs and medications can be produced

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.A2 Use of databases to identify potential new anti-malarial drugs

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  • Scientists have sequenced the genome of infectious species of Plasmodium and used it to determine the parasite’s proteome

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  • From the proteome, enzymes involved in parasitic metabolism have been identified as potential targets for inhibition

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.A2 Use of databases to identify potential new anti-malarial drugs

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Analyse the data from an experiment on enzymes and inhibitors to try to find out if the inhibitors are competitive or non-competitive

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.A2 Use of databases to identify potential new anti-malarial drugs

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  • In one study, approx. 300,000 chemicals were screened against a chloroquine-sensitive 3D7 strain and the chloroquine-resistant K1 strain of P. falciparum.
  • Other related and unrelated organisms, including human cell lines, were also screened.
  • (19) new chemicals that inhibit the enzymes normally targeted by anti-malarial drugs were identified
  • Additionally (15) chemicals that bind to malarial proteins were identified - this can help in the location of P. falciparum
  • These results indicate possible new directions for drug research.

As bioinformatics involves the use of huge databases this approach only became practical with the development of modern computing and the internet.

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.A2 Use of databases to identify potential new anti-malarial drugs. AND Nature of science: Developments in scientific research follow improvements in computing - developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways. (3.8)

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The rate of reaction can be calculated using the formula:

 

Rate of reaction (s-1) = 1 / time taken (s)

 

Time taken in enzyme experiments this is commonly the time to reach a measurable end point or when a standard event, caused by the enzyme reaction, has come to pass. This is usually measured by the effects of the accumulation of product, but can as easily be measured by the disappearance of substrates.

Use the results from it or data from one of your enzyme inhibition labs to calculate the rate of reaction.

Enzyme inhibition can be investigated using these two outlines by Science & Plants for Schools:

8.1 Metabolism

Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

8.1.S1 Calculating and plotting rates of reaction from raw experimental results.

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TOOTHPICKASE: Introduction

Table tops are a cell.

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Toothpicks (50) are molecules in the cell that need to be hydrolyzed (broken apart).

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TOOTHPICKASE: Introduction

Roles:

  1. Time keeper: announce time to group at 15 second intervals
  2. Enzyme: break toothpicks, blindfolded, non-dominant hand
  3. Counter: count how many toothpicks are completely broken, announce at 15 second intervals
  4. Recorder: record the number of toothpicks broken as reported by the counter, post results to class data table

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TOOTHPICKASE: �Scenario #1: No enzyme

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Practice roles

Record data for 1 minute

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TOOTHPICKASE: �Scenario #1: No enzyme

Record class data for average and SD in a table

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Explain results using the following words:

    • Activation energy
    • Enzyme
    • Substrate
    • Product

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TOOTHPICKASE: �Scenario #2: Enzyme present

  • Start with 50 substrates in the cell
  • Blindfold enzyme
  • Enzyme active site is thumb and two fingers
  • Enzyme must completely break apart the substrate
  • Timer: run scenario for two minutes
  • Counter: count running total of toothpicks broken

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TOOTHPICKASE: �Scenario #2: Enzyme present

Record class data for average and SD in a table

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Explain results using the following words:

    • Activation energy
    • Enzyme
    • Substrate
    • Product
    • Active site
    • Induced fit

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TOOTHPICKASE: �Scenario #2: Enzyme present

Graph the class data for the average number of toothpicks metabolized over time for the two scenarios.

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Explain results:

    • Compare no enzyme present vs. enzyme present (refer to overlap of SD bars)
    • Trend of enzyme present line

Figure out the right type of graph to use! Include the standard deviation.

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TOOTHPICKASE: �Scenario #3: Feedback Inhibition

  • Rotate roles
  • Start with 50 substrates in the cell
  • Timer: run scenario for two minutes
  • Counter: count running total of toothpicks broken. After the enzyme has broken 15 toothpicks, tell the enzyme to STOP.
  • Time continues, recording continues, but enzyme stops.

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TOOTHPICKASE: �Scenario #3: Feedback Inhibition

Record class data for average and SD in a table

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Explain results using the following words:

    • Enzyme
    • Substrate
    • Product
    • Feedback inhibition

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TOOTHPICKASE: �Scenario #4: Allosteric Inhibitor

  • Inhibit the enzyme as shown
  • Rotate roles
  • Start with 50 substrates in the cell
  • Timer: run scenario for one minutes

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TOOTHPICKASE: �Scenario #4: Allosteric Inhibitor

Record class data for average and SD in a table

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Explain results using the following words:

    • Enzyme
    • Substrate
    • Product
    • Active site
    • Allosteric site
    • Allosteric inhibitor

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TOOTHPICKASE: �Scenario #5: Competitive Inhibitor

  • Competitively inhibit the enzyme as shown
  • Rotate roles
  • Start with 50 substrates in the cell
  • Timer: run scenario for one minutes

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TOOTHPICKASE: �Scenario #5: Competitive Inhibitor

Record class data for average and SD in a table

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Explain results using the following words:

    • Enzyme
    • Substrate
    • Product
    • Active site
    • Competitive inhibitor

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TOOTHPICKASE: �

Graph the class data for the average total number of toothpicks metabolized at 1 minute time for

    • No enzyme inhibition (scenario 2)
    • Allosteric inhibition (scenario 4)
    • Competitive inhibition (scenario 5)

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Figure out the right type of graph to use! Include standard deviations.

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TOOTHPICKASE: �Scenario #6: Effect of [Substrate]

Rotate roles

Vary the amount of substrate in the cell

    • 0 substrates
    • 20 substrates
    • 40 substrates
    • 60 substrates
    • 80 substrates

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Timer: run each for 1 minute, no need to announce intervals

Counter: count how many toothpicks are completely broken

Recorder: record the number of toothpicks broken

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TOOTHPICKASE: �Scenario #6: Effect of [Substrate]

Record class data for average in a table

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Find the average RATE of enzyme reaction for each amount of substrate

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RATE= # of toothpicks broken

second

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TOOTHPICKASE: �Scenario #6: Effect of [Substrate]

Graph the average rate of metabolism for each amount of substrate

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Explain results:

    • Why do the results have this trend?

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Figure out the right type of graph to use!

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TOOTHPICKASE: �Scenario #7: Effect of [enzyme]

Rotate roles

Vary the amount of enzymes in the cell

    • 0 enzymes
    • 1 enzyme
    • 2 enzymes
    • 3 enzymes
    • 4 enzymes

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Timer: your teacher will announce time (1 min)

Counter: count broken toothpicks at end

Recorder: record the number of toothpicks broken

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TOOTHPICKASE: �Scenario #7: Effect of [enzyme]

Record class data for average in a table

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Find the average RATE of enzyme reaction for each amount of enzyme

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RATE= # of toothpicks broken

second

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TOOTHPICKASE: �Scenario #7: Effect of [enzyme]

Graph the average rate of metabolism for each amount of enzyme

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Explain results:

    • Why do the results have this trend?

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Figure out the right type of graph to use!

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TOOTHPICKASE: �Scenario #8: Effect of temperature

  • Rotate roles
  • Use 50 toothpicks
  • Enzyme is cold
  • Determine # of toothpicks broken in 30 seconds

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TOOTHPICKASE: �Scenario #8: Effect of temperature

Record class data for average in a table

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Find the average RATE of enzyme reaction

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RATE= # of toothpicks broken

second

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TOOTHPICKASE: �Scenario #8: Effect of temperature

Find the average rate of enzyme action at room temperature (scenario #2, at 30 seconds).

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Create a graph to compare cold to room temperature enzymes reaction rates.

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Explain results:

    • Why do the results have this trend?

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Figure out the right type of graph to use!