unit 2 metabolism and survival sub topic 2.1: regulation ... · unit 2 metabolism and survival sub...

Unit 2 Metabolism and Survival

Sub Topic 2.1: Regulation of Metabolism and Enzymes

Higher Biology Pupil Course Notes

of 26 Duncanrig Secondary School CG 2015

At the end of this topic, you will be able to:

State that metabolism is all the sum total of all the enzyme controlled

chemical reactions occurring within a living cell.

State that anabolic pathways are synthesis reactions and require energy

input.

State that catabolic pathways are breakdown reactions and are energy

releasing.

State that metabolic pathways can have reversible and irreversible steps.

State that alternative routes can be taken to bypass steps in pathway.

State that membranes are a phospholipid bilayer with embedded and surface

proteins.

State that membranes form surfaces and compartments to localise metabolic

activity within the cell.

State that the folding of membranes and organelles increases the surface

area allowing high concentrations to accumulate and this can increase

reaction rates.

State that small compartments have a higher surface area to volume ratio

than larger compartments.

State that proteins in the membrane form pores, pumps and enzymes.

State that metabolic pathways are controlled by the presence or absence of

enzymes and the rate of activity of these key enzymes.

State that regulation of pathways can be controlled by intra and extra cellular

signal molecules.

State that the activity of enzymes depends on the depends on their shape,

and the ability of the substrate to bind to the active site.

Describe the induced fit model of enzyme action.

State that substrates have high affinity for the enzyme active site.

State that products have low affinity for the enzyme active site.

Describe the effect of enzymes on the activation energy.

Describe how the substrate and end product concentrations can affect the

direction and the rate of activity of the enzyme reaction.

State that metabolic reactions are reversible and the presence of a substrate

or removal of a product will drive a sequence of reactions in a particular

direction.

State that enzymes often act in groups or as multi enzyme complexes.

State that genes for some enzymes are continuously expressed.

Describe non competitive inhibition of enzyme action.

Describe competitive inhibition of enzyme action.

Describe how end product inhibition controls a metabolic pathway.



At the end of this topic you will have developed the following skills:

Demonstrating knowledge and understanding of biology by making

statements.

Describing information, providing explanations and integrating knowledge.

Applying knowledge of biology to new situations and analysing information.

Planning and designing experiments and practical investigations to test a

given hypothesis or to illustrate particular effects.

Carrying out experiments and practical investigations safely, recording

detailed observations and collecting data.

Selecting information from a variety of sources.

Presenting information appropriately in a variety of forms.

Processing information (using calculations and units, where appropriate).

Making predictions and generalisations from evidence or information.

Drawing valid conclusions and giving explanations supported by evidence or

justification.

Evaluating experiments and practical investigations and suggesting

improvements.

Communicating findings and information effectively.



Prior Learning: National 5 Biology

Unit 1 Cell Biology Sub Topic 2 Transport Across Cell

Membranes:

The cell membrane consists of phospholipid and protein molecules.

The cell membrane is selectively permeable.

Transport of materials across the membrane can be either passive or active.

Passive transport includes diffusion and osmosis and does not require energy.

Diffusion is the movement of molecules down a concentration gradient.

Active transport is the movement of molecules and ions against a concentration

gradient.

Active transport requires energy.

The energy for active transport comes from respiration.

Factors that affect the rate of respiration, will also affect the rate of active

transport.

Unit 1 Cell Biology Sub Topic 5 Proteins and Enzymes:

All proteins are made of chains of amino acid molecules.

The sequence of amino acids in a protein codes for and determines the protein’s

shape.

The shape of a protein determines it’s function.

Proteins provide a vital structural role in all cell membranes.

Enzymes function as biological catalysts because they speed up the rate of

all biochemical reactions in living organisms.

Enzymes are made inside living cells.

Although enzymes take part in a reaction they remain unchanged at the end of

it and can be used repeatedly.

The active site of an enzyme is the place on the enzyme's surface which

matches the shape of the substance that it works on (its substrate).

An enzyme is specific to its substrate and produces specific product(s),

working like a lock and a key.



Cell Metabolism

Metabolism is the sum total of all the enzyme controlled chemical reactions occurring

within a living cell.

There are two types of metabolic pathways:

Anabolic Pathways

Anabolic pathways are synthesis reactions and they require an input of energy.

Anabolic reaction (Energy In)

Catabolic Pathways:

Catabolic pathways are breakdown reactions and they release energy.

Catabolic reaction (Energy Out)

+ ENERGY

+ ENERGY



Summary of Metabolism

The diagram below that summarises catabolic and anabolic reactions in metabolism.

Add the following labels to the BOXES:

PROTEIN

ATP

ADP + Pi

GLUCOSE + OXYGEN

CARBON DIOXIDE+WATER

AMINO ACIDS

Add the following labels to the correct line:

CATABOLISM

ANABOLISM

ENERGY

TRANSFER

(aerobic respiration)

ENERGY ENERGY



Metabolic pathways consist of a series of enzyme controlled reactions. Each step in

this series of reactions may be reversible or irreversible allowing the process to

be kept under tight control. Metabolic pathways also contain alternative routes

where steps can be bypassed.

The diagram below shows the series of reactions involved in the breakdown of

glucose to pyruvate during glycolysis.

The conversion of intermediate 1 to intermediate 2 by enzyme B is reversible. If

more of intermediate 2 is formed than is needed, then it can be converted back into

intermediate 1 and used in the alternative pathway, for example, to build glycogen

in animal cells or starch in plant cells.

The conversion of intermediate 2 to intermediate 3 by enzyme C is irreversible and

is a key regulatory point in the pathway.

GLUCOSE

INTERMEDIATE

COMPOUND 1

INTERMEDIATE

COMPOUND 2

INTERMEDIATE

COMPOUND 3

PYRUVATE

GLYCOGEN (mammals)

STARCH

(plants)

ENZYME B

ENZYME A

MANY ENZYME CONTROLLED STEPS

ENZYME C

SORBITOL

ALTERNATIVE

ROUTE

SEVERAL

ENZYME

CONTROLLED

STEPS



Key Questions

Answer the following question in sentences.

1. Explain the meaning of the word metabolism.

____________________________________________________________________

____________________________________________________________________

____________________________________________________________________

2. Complete the following sentences by underlining the correct word in each bracket:

(a) Synthesis reactions are (anabolic / catabolic) and (require / produce)

energy.

(b) Breakdown reactions are (anabolic / catabolic) and (require / produce)

energy.

The answers can be checked using the PowerPoint that accompanies these

pupil course notes.



Toxic Effects of Poisons, Toxins and Venom on Metabolic Pathways

Poisons are substances that can disrupt metabolic pathways in cells following

absorption of the chemical through the skin, gut or lung lining.

Toxins are usually poisonous substances produced by a living organism.

Venom is a poisonous fluid secreted by certain snakes and scorpions.

Some examples and their effects on metabolic pathways are shown below (there are

more on the PowerPoint that accompanies the pupil course notes):

DEATH CAP MUSHROOMS

Death cap mushrooms are found widely in

Europe. When they are eaten, they inhibit

the enzyme RNA polymerase. The effects

are liver and kidney damage. Most

sufferers die within 6 – 10 days. There is

currently no known antidote.

CYANIDE

Once inhaled or ingested, cyanide inhibits

the enzymes located in the mitochondria

that are essential for producing ATP

during respiration. Hydrogen cyanide

was used in the gas chambers as a

method of execution.

BOTOX

Botulinum toxin kills its victims by causing

respiratory failure. It is a neurotoxin that

enters nerves and destroys vital proteins. It

is used as an anti wrinkle product. When

injected into the face it destroys the nerves

that cause frowning. The quantities used are

tiny - a few billionths of a gram.

ARSENIC

Arsenic oxides are tasteless, dissolve in

hot water and take less than a hundredth

of an ounce to kill. Yet in the 19th

Century, as a rat poison, it was cheap and

easily available. Arsenic trioxide has also

found a legitimate medical use, as an

anti-cancer agent.



Membranes

The cell membrane separates the internal contents of the cell from its external

surroundings. It controls the flow of materials into and out of the cell.

Membranes also surround organelles which compartmentalises functions within

the cell to either keep them close together or keep them apart. Some of these

organelles such as mitochondria and chloroplasts, have inner membranes which take

the form of folds or compartments.

The folding of membranes and organelles increases the surface area which allows

high concentrations of substances to accumulate and therefore increases

reaction rates. Small compartments like mitochondria and chloroplasts have a high

surface area to volume ratio.

inner folded membrane

outer smooth membrane

cristae

matrix

outer membrane

inner membrane

lamellae

stroma

granum



Structure of the Cell Membrane

The cell membrane consists of protein and phospholipid. The structure of the cell

membrane is described as a fluid mosaic model. This proposes that the

phospholipid bilayer component of the membrane is constantly moving. The patchy

arrangement of proteins that differ in size, structure and function throughout the

membrane are described as mosaic.

Add the following labels to the diagram of the fluid mosaic model of the cell

membrane.

LABELS: partially embedded protein surface protein pore

channel forming protein phospholipid

Role of Protein in the Cell Membrane

Pores

In order to transport larger molecules across the membrane, some proteins form

pores. They are described as channel forming proteins because they provide

channels for the diffusion of specific substances into or out of the cell.



Pumps

Active transport is the movement of molecules and ions across the cell membrane

against the concentration gradient, in other words, from low concentration to high

concentration. Active transport requires energy.

Certain proteins in the cell membrane act as carriers which can recognise specific

ions and transport them. These carriers are called pumps. Some of them play a

dual role exchanging one type of ion for another. An example of this is the

sodium/potassium pump (shown in the diagram below) where the same carrier

actively pumps sodium out of the cell and potassium into the cell each against its

own concentration gradient. This is important for the proper functioning of muscle

and nerve cells.

Protein pumps require energy. This is provided by respiration. As a result, factors

such as temperature, the availability of oxygen and food (respiratory substrate)

which affect the rate of respiration, will also affect the rate of active transport.

Enzymes

Some of the proteins embedded in the cell membrane are enzymes which control

the steps in a metabolic process essential to the cell. An example of this is ATP

synthase which catalyses the synthesis of ATP. ATP synthase is a protein found in

the membrane of mitochondria, chloroplasts and prokaryotes. Several enzymes can

also be arranged in the membrane as a multienzyme complex to promote a

series of related steps in a metabolic pathway.

INSIDE CELL

OUTSIDE CELL



Enzymes and Metabolism

Enzymes are biological catalysts that are responsible for speeding up chemical

reactions by lowering the activation energy. This is the energy needed to break

the chemical bonds in the reactants. The energy input in an uncatalysed reaction is

often in the form of heat meaning that the reaction will only proceed at a faster rate

if the temperature of the reactants is increased. In a catalysed reaction, the energy

input required to break the chemical bonds in the reactants is much lower. Because

of this, biochemical reactions can proceed relatively rapidly at much lower

temperatures.

Metabolic pathways rely on several enzymes that each control a single

step in a series of reactions. Therefore, metabolism is controlled by the

activity or inactivity of these key enzymes and the rate of metabolic

pathways is determined by the activity of each individual enzyme.

Progress of the Reaction

En

erg

y

Reactants

Products

Uncatalysed reaction

Catalysed reaction

higher activation energy required

lower activation energy required



Induced Fit

Enzymes have a groove or hollow on their surface that is called the active site.

Each enzyme acts on one type of substance – the substrate with the shape which

exactly fits into the enzyme’s active site. The theory that an enzyme and a substrate

fit together like a “lock and key” is not strictly true. A more accurate description of

the process would be that the enzyme’s active site is not a rigid structure, it is

flexible and dynamic. This means that the enzyme’s shape can alter to bind to the

substrate and then change back. The substrate induces the enzyme to change

shape and the enzyme has a high affinity for the substrate.

Here is an example:

The end products are released from the enzyme’s active site as the end products

have a low affinity for the active site.

A The two substrates enter the active

site of the enzyme because the

enzyme has a high affinity for them.

B Enzyme-Substrate Complex:

The enzyme changes shape forcing the

two substrates to combine.

(The dotted line indicates the original

shape of the enzyme)

C The enzyme has a low affinity for

the resulting product. Consequently,

the enzyme releases the product and

returns to its normal shape ready to

undergo more reactions.



Factors Affecting Enzyme Activity

Substrate Concentration: At low substrate concentrations, the reaction rate will

be slow as there are too few substrate molecules to make maximum use of all the

active sites of the enzymes. As the substrate concentration increases, the reaction

rate increases as more active sites are being used. A point is eventually reached

where a further increase in substrate concentration fails to cause an increase in

reaction rate because all active sites are occupied. Now, the enzyme’s

concentration has become the limiting factor. This effect is summarised in the

diagram below.

enzyme

(limited concentration) substrate

high concentration

medium concentration

very high concentration

+

+

+

+

enzyme-substrate complex

product produced (per unit of time)

low

medium

high

high

(limited due to the fact there are no more enzyme active sites available)

unused active sites

unused substrate

low concentration



Direction of Enzyme Action:

Metabolic pathways will usually involve a number of enzymes. A metabolic pathway

is shown below.

As the substrate becomes available, enzyme 1 will become active and convert the

substrate into metabolite A. In the presence of metabolite A, enzyme 2 becomes

active and converts A to B and so on. A continuous supply of substrate entering the

system will drive the sequence of reactions shown with the product of each

individual reaction acting as the substrate for the following reaction.

As mentioned before, most reactions are reversible; often one enzyme can catalyse

a reaction in both the forward and the reverse reaction. The direction will depend

on the concentrations of the reactant(s) and the product(s). In the example above,

if the concentration of C were to increase to an unusually high level, then enzyme 3

could go into reverse and convert C back into B until a more balanced state is

achieved.

ENZYME 5

ENZYME 6

ENZYME 4

ENZYME 1

ENZYME 2

ENZYME 3

SUBSTRATE(S)

METABOLITE B

METABOLITE A

METABOLITE C

END PRODUCT(S)

METABOLITE D



Use the diagram and the information on page 16 to answer the following questions

in sentences.

Key Questions

1) Which reaction in the metabolic pathway is reversible?

____________________________________________________________________

____________________________________________________________________

____________________________________________________________________

2) Metabolite C is toxic if it builds up, explain why this is not a problem.

____________________________________________________________________

____________________________________________________________________

____________________________________________________________________

3) If enzyme 3 is not produced, explain why metabolite B will not build up.

____________________________________________________________________

____________________________________________________________________

____________________________________________________________________

The answers can be checked using the PowerPoint that accompanies these

pupil course notes.

Enzyme Cofactors

Co-factors are molecules that are often needed to make the enzyme more

efficient. They can be inorganic such as iron, zinc, magnesium. They can also be

organic and are known as co-enzymes such as FAD and NAD (both involved in

respiration) and many vitamins.

Multi Enzyme Complexes

Some enzymes work in groups or in multi-enzyme complexes such as pyruvate

dehydrogenase complex. Pyruvate dehydrogenase has 3 enzymes that work together

to convert pyruvate into acetyl coA (a co-enzyme).



Control and Regulation of Enzymes and Metabolic Pathways

Regulation of enzyme activity can be controlled in several ways:

Enzyme Concentration – by controlling the concentration of the enzyme

present which is achieved by the switching “on” and “off” of the genes that

code for each enzyme as they are required.

Compartmentalisation – enzymes that are involved in the same metabolic

pathway are contained within the same cell organelle. For example, the

enzymes required for aerobic respiration are contained within the

mitochondria.

Enzyme Shape – by changing the enzyme shape, the efficiency of the

enzyme can be enhanced or reduced.



Lactose Metabolism in E.coli – the Lac operon

Some proteins are only required by a cell under certain circumstances. There is

evidence that, in such cases, genes that code for these proteins are switched on and

off as required. Two scientists called Jacob and Monod were the first to suggest this

idea of genes switching on and off after studying the bacterium Escherichia coli

(E.coli) this is known as the Jacob-Monod Hypothesis.

Lactose is a sugar found in milk. E.coli have the ability to synthesise an enzyme

called β-galactosidase that catalyses the breakdown of lactose into two types of

sugar (glucose and galactose):

lactose glucose + galactose

Jacob and Monod found that β-galactosidase is only manufactured when the E.coli

detects that there is lactose present, preventing the unnecessary wastage of

resources such as amino acids and energy. Therefore, the expression of the gene

for β-galactosidase is controlled. The process of switching on a gene only when the

enzyme is needed is called enzyme induction. How is this achieved?

An operon is made up of 2 separate genes;

Structural gene – codes for the enzyme in question (in this case, β-

galactosidase)

Operator gene – controls the structural gene

The activation of the operon is dependent on a third gene that is located nearby on

the DNA chain called the regulator gene. This codes for a repressor molecule.

It is the repressor that is responsible for controlling the operon depending on the

presence or absence of lactose. The diagrams on the next page summarise this.

β-galactosidase



The Lac Operon

ABSENCE OF LACTOSE

When lactose is absent, a repressor molecule (coded for by the regulator gene)

binds to the operator gene. This switches “off” the operator gene and prevents the

structural gene from switching “on” and being transcribed for the enzyme β-

galactosidase. Therefore, no β-galactosidase is made.

PRESENCE OF LACTOSE

When lactose is present, a repressor molecule (coded for by the regulator gene)

binds to lactose, the inducer instead of the operator. The operator gene now

switches on the structural gene, allowing the transcription of the code for the

enzyme β-galactosidase. The β-galactosidase is then made.

When all the lactose has been broken down, the repressor molecule no longer has

an inducer to bind to so now it binds to the operator gene, switching it off again.

regulator gene operator gene structural gene

regulator gene operator gene structural gene

switched on switched off switched off

REPRESSOR

MOLECULE

repressor molecule produced

repressor molecule

binds with operator no enzyme

X

switched on switched on switched on

repressor molecule produced

enzyme

produced repressor molecule

binds with the lactose

(the inducer)

LACTOSE

(INDUCER)

REPRESSOR

MOLECULE

REPRESSOR

MOLECULE

REPRESSOR

MOLECULE



Effect of Inhibitors on Enzyme Action An inhibitor is a substance that decreases the rate of an enzyme controlled reaction. There are two forms of inhibitor; competitive and non-competitive.

Competitive Inhibitors

A molecule of very similar shape to the substrate competes for the active site of the

enzyme, binding with it and therefore, reducing the overall concentration of the

enzyme that is available. This type of inhibition can be reversed by increasing the

concentration of the substrate. Competitive inhibition is summarised in the diagram

below.

Competitive inhibitor ABSENT:

Competitive inhibitor PRESENT:

+

enzyme

substrate

+

enzyme end products enzyme-substrate complex

showing induced fit

+

enzyme

substrate

+

enzyme-inhibitor complex unused

substrate

competitive

inhibitor



Non-competitive inhibitors

A non-competitive inhibitor does not directly bind with the enzyme’s active site.

Instead, it becomes attached to an non-active site called an allosteric site. This

interaction changes the shape of the enzyme’s active site indirectly and thus, the

enzyme cannot bind to the substrate. This is summarised in the diagram below.

Non-competitive inhibitor PRESENT:

Effect of Substrate Concentration

As the substrate concentration increases, the rate of reaction increases and then

becomes constant. This is linked to the number of available active sites as described

on page 14. Inhibitors will affect the rate of reaction in different ways and is

dependent on whether the inhibitor is competitive or non-competitive. The graph

below demonstrates this:

+

enzyme substrate

non-competitive

inhibitor

non-competitive inhibitor attached

to allosteric site on the enzyme

(NOT the active site) – causing a

change in the enzyme shape

+

substrate no longer

fits in the enzyme

active site

no inhibitor present: this is the point in the reaction

when all the active sites in the enzyme are occupied

substrate concentration

rate

of

rea

cti

on

competitive inhibitor present: increasing the substrate

concentration increases the rate of reaction gradually

because as the substrate molecules increase in number, they

outnumber those of the competitive inhibitor.

non competitive inhibitor present: increasing the

substrate concentration has no effect on the rate of

reaction. This is because the inhibitor has changed the

shape of the active site and it can no longer bind to the

substrate. Therefore, the rate of reaction remains low.



Feedback Inhibition by an End Product (End Product Inhibition)

End product inhibition is another way in which a metabolic pathway can be

regulated.

In the example above, as the concentration of the end product(s) increases, some of

the end product will bind to enzyme 1. This will slow down the conversion of the

substrate(s) to metabolite A. As the concentration of the end product(s) drops, the

effect it is having on enzyme 1 then decreases and therefore the pathway is under

constant regulation and fine tuning.

ENZYME 1

ENZYME 2

ENZYME 3

SUBSTRATE(S)

METABOLITE B

METABOLITE A

METABOLITE C

END PRODUCT(S)

METABOLITE D

ENZYME 4

ENZYME 5

ENZYME 6



An Example of End Product Inhibition: Phosphatase

Phosphatase is an enzyme that is found in a wide range of plant and animal

tissues (such as mung beans or beansprouts) where it reacts with a number of

different substrates to release phosphate groups. These phosphate groups are

important for the synthesis of ATP, phospholipids and nucleotides in living cells. An

artificial substrate called phenolphthalein phosphate (PPP) will react with

phosphatase to produce phenolphthalein (PP) and a free phosphate group (P).

This reaction is characterised by a colour change as the phenolphthalein is produced

from colourless to pink:

The more intense the pink colour, the more phenolphthalein is present. Therefore,

the more active the enzyme is, the more intense the pink colour. The intensity of

the pink colour produced can be measured and quantified using a colorimeter.

substrate enzyme products

phenolphthalein

phosphate (PPP)

phenolphthalein (PP) +

free phosphate (P)

phosphatase

COLOURLESS

PINK

(in alkaline conditions)



Sub topic 2.1 Regulation of Metabolism and Enzymes

How well do you rate your knowledge?

I am able to…….

State that metabolism is all the sum total of all the enzyme controlled chemical reactions occurring within a living cell.

State that anabolic pathways are synthesis reactions and require energy input.

State that catabolic pathways are breakdown reactions and are energy releasing.

State that metabolic pathways can have reversible and irreversible steps.

State that alternative routes can be taken to bypass steps in pathway.

State that membranes are a phospholipid bilayer with embedded and surface proteins.

State that membranes form surfaces and compartments to localise metabolic activity within the cell.

State that the folding of membranes and organelles increases the surface area which allows high concentrations to accumulate and this can increase reaction rates.

State that small compartments have a higher surface area to volume ratio than larger compartments.

State that proteins in the membrane form pores, pumps and enzymes.

State that metabolic pathways are controlled by the presence or absence of enzymes and the rate of activity of these key enzymes.

State that regulation of pathways can be controlled by intra and extra cellular signal molecules.

State that the activity of enzymes depends on their shape, and the ability of the substrate to bind to the active site.

Complete:

Column 1 – before your Unit assessment

Column 2 – before your Prelim

Column 3 – before your final exam



Describe the induced fit model of enzyme action.

State that substrates have a high affinity for the enzyme active site.

State that products have a low affinity for the enzyme active site.

Describe the effect of enzymes on the activation energy.

Describe how the substrate and end product concentrations can affect the direction and the rate of activity of the enzyme reaction.

State that metabolic reactions are reversible and the presence of a substrate or removal of a product will drive a sequence of reactions in a particular direction.

State that enzymes often act in groups or as multi enzyme complexes.

State that genes for some enzymes are continuously expressed.

Describe non competitive inhibition of enzyme action.

Describe competitive inhibition of enzyme action.

Describe how end product inhibition controls a metabolic pathway.

unit 2 metabolism and survival sub topic 2.1: regulation ... · unit 2 metabolism and survival sub...

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