C1.

1 Enzymes &
Metabolism
What is a Catalyst?

- It is a substance that decreases the time of chemical reaction

without being changed itself by this reaction. Accordingly,
catalysts can be recycled or re-used.
- Catalysts could be inorganic or organic (biological/ produced
by living things).
- Platinum is an example of inorganic catalysts used in engines
to make the burning process of fuel faster. Platinum is an
inorganic metal.
 What are Enzymes? Allosteric site

- **Biological (made by living things) **Catalysts (speed

up chemical reactions without being altered
themselves).Globular proteins with many shapes.
-
- If cells did not make enzymes, the chemical reactions on
which life is based would happen very slowly and
accordingly puts the cell’s life in specific and the whole
organism in general in fatal danger.
-
- Substances undergoing chemical reactions
(**SUBSTRATE) attach to specific parts of enzymes
(**ACTIVE SITE).
- Each Enzyme has a specific active site shape that fits
to a specific substrate. This is called
“Enzyme-Substrate specificity”. (Like Lock & Key)
- The result of this activity between an enzyme and its
substrate is the ** PRODUCT of the chemical reaction,
which is released from the enzyme active site freeing it
to catalyze another similar reaction
Role of Enzymes in Metabolism
- 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 .
- Enzymes’ specificity is a significant difference between
enzymes and other non biological catalysts.
- Each enzyme catalyses one specific reaction or a specific
group of reactions.
- Cells with complicated metabolism make thousands of
different enzymes, ex: Liver cell
- Enzymes not only they catalyze metabolic reactions, but
they also control it, it’s start, it’s end as well as it’s rate. Ex:
if a cell releases little enzymes a reaction goes slow, or if a
cell stops producing an enzyme a reaction may stop.
- In brief, enzymes give living organisms a considerable
control over their metabolism and thus over their activities
and chemical composition. Enzymes REGULATE metabolic
pathways.
Metabolism
- All chemical reactions that take place in an organism.
- It consists of pathways by which molecules are transformed into another.
- Might take place inside a cell in the cytoplasm, or extracellular like digestion of food in the intestine.
- Metabolic reactions in an organism are catalyzed by enzymes.
- There are global maps that show metabolic reactions in organisms and are very complex.
- The Kyoto Encyclopedia of Genes & Genome for instance show the complex map of how genes work.
- Metabolism has two types:
# Anabolism: (Formation of macromolecules from monomers by condensation reactions)
- When small molecules join together to build larger structure.
- Requires energy provided by ATP
- Ex: protein synthesis by ribosomes, DNA synthesis during replication, Photosynthesis, Anabolic
steroids and amino acids used for building muscles in GYm.
# Catabolism : (Hydrolysis of macromolecules into monomers by hydrolysis reactions)

- When large molecules are broken down into smaller molecules

- Releases energy that is captured in ATP, so formation of ATP as well
- Ex: Digestion & Cellular Respiration
How does an enzyme catalyze a chemical reaction? Ex: The breakdown of
Sucrose (disaccharide) into its monosaccharides (Fructose + Glucose)

Condensation reaction = H2O

Sucrose - 6 - Phosphate Synthase

enzyme
How does an enzyme catalyze a chemical reaction? Ex: The breakdown of
Sucrose into its monosaccharides
- Second: How does Sucrose break to give back fructose and Glucose??

Hydrolysis Reaction + H2O

in presence of SUCRASE
ENZYME
How does an enzyme catalyze a chemical reaction?
1- Specific substrate binds to specific active site of a specific enzyme. The
Active site is made of amino acids of different polypeptides that are brought
together due to the folding of the enzyme to form globular 3D shape of
enzymes (proteins). It is not amino acids within the same chain. Thus the, as
discussed earlier, the 3D shape of an enzyme as a protein is crucial

2- Once a substrate approaches the active site, which happens randomly as

the substrate is in random motion, the enzyme surface attracts the substrate
towards its active site.

3- The Substrate then binds with the enzyme’s active site, and both change
their shape and length, in a phenomenon known as “Induced-Fit Binding” .
The product of this is one bulky mass known as “Enzyme-Substrate
Complex”.

4- Changes that happen to the substrate structure makes it easier to break

bonds and form bonds converting the substrate into products.

5- Products then separate from the active site, and accordingly the active
site becomes free again and back to its original shape, making it available for
the next reaction round.

** This happens for both catabolic and anabolic reactions.

How does an enzyme catalyze a chemical reaction? (
- A substrate can only bind to its specific active site, if both get too close to one another.
And since all molecules of a matter are in continuous motion, especially if dissolved in
water , enzyme and substrate hit one another, a mechanism known as “Collision”. Thus
collision between enzyme and substrate occur as a result of random motion of
molecules.
- Collisions are not usually successful, since enzyme and substrate might hit each other
at the wrong angles for instance.
- Successful collision is the one that brings the active site and substrate to the
appropriate angle that allow for fitting to take place.
- The speed of motion depends on the size of molecules involved. Ex: if the substrate
Molecule is too big, we will find the enzyme doing most of the

Motion and vice versa.

How does an enzyme catalyze a chemical reaction?
- What an enzyme does in a chemical reaction is as
follows:
● Holds the substrate in position to expose it to Transition State
(products start to show)
other materials involved in a chemical reaction.
● Any chemical reaction needs some energy to
start up. Or in other words a substrate has to
reach a transition state at which it will start to
go through a chemical reaction and change
into a product. This energy needed to start up a
chemical reaction or to push the substrate to
its transition state, is known as “ACTIVATION
ENERGY” . An enzyme lowers the activation
energy of the chemical reaction.
 Factors affecting Enzyme Activity

- There are several factors that affect the

activity of an enzyme, meaning that a
change in those factors can either
increase or decrease the enzyme
activity, which in turn affect the rate at
which a reaction takes place. These
factors are:
➢ Temperature
➢ pH
➢ Substrate concentration
 Factors affecting Enzyme Activity - TEMPERATURE
- There is always one specific temperature at which an enzyme shows its
maximum activity, this is known as “OPTIMUM TEMPERATURE” and
differs from one enzyme to another, and also from one organism to
another. Ex: optimum temperature for human enzymes is 37॰ C.
- Temperature affect the enzyme activity in 2 ways:

1- Both enzymes and substrates are dissolved in water. Water is a liquid

when heated up its molecules move faster. This fast movement gives a
higher chance of collision between and enzyme and its substrate and thus
allow the chemical reaction to go on faster.

2- On the other hand, when enzymes are heated, bonds between enzyme
molecules vibrate more and become weaker, and may break. If bonds
between an enzyme molecule break, this changes the structure and
accordingly the shape of the active site of the enzyme, making it unable to
perform its function. This change is permanent and the enzyme is said to
be “DENATURED”. This definitely lowers the rate at which a chemical
reaction is taking place.
 Factors affecting Enzyme Activity - pH
- The pH scale (0-14)is used to measure the acidity or
alkalinity of a solution. The lower the pH the more
acidic is the solution, showing higher concentration
of H+ ions; and the higher the pH the more alkaline
it is, showing higher concentration of OH- ions. The
midpoint of the scale is “7” is the neutral point, at
which is solution is neither acidic nor alkaline, ex:
water. The pH scale of logarithmic, means that
shifting between one unit and the next means that
the solution has become ten times more acidic or
alkaline.
- Again each enzyme has an optimum pH at which its
activity is the max. Shifting away from this optimum
pH decreases the enzyme activity.
- At extreme pH the active site of the enzyme
becomes permanently altered and the enzyme loses
its function.
 Factors affecting Enzyme Activity - Substrate Concentration
- As the substrate concentration increases, the
probability of effective collisions between the
substrate and the enzyme also increases, thus
increasing the rate of the chemical reaction.
- However, also as the substrate concentration
increases, the available active sites of the
enzyme become occupied more often, making the
active site less available to bind with more and
more substrate. AT this point the enzyme activity
doesn’t increase and the rate of the reaction stays
at a specific point.

## When an enzyme denatures due to extreme

temperatures or pH, it might become insoluble in water
and forms a precipitate.
Intracellular and Extracellular Enzyme- catalyzed
reactions:
- Since enzymes are proteins, they are mainly synthesized by ribosomes.
- Enzymes used within the cell (intracellular) are produced by free ribosomes
while those used outside the cell (extracellular) are synthesized by bound
ribosomes. These are called EXOENZYMES.
- Some enzymes work within organelles, like for instance enzymes catalyzing
Kreb’s cycle (aerobic respiration) in the mitochondria.
- Many Exoenzymes catalyze the breakdown of macromolecules that can not
pass through the plasma membrane. Once broken down into smaller ones,
makes their absorption into the cell easier ex: small intestine - digestive
system.
Generation of heat energy by Metabolism

- The conversion of energy from one form to another is never 100% efficient.
During metabolism, some of the energy is converted into heat that either
accumulates in cells or lost to the surroundings (ex: sweating mechanism -
evaporative cooling). This is known as “Metabolic Heat”.
- Some organisms make use of this metabolic heat in keeping themselves
warm. Some other organism tend to convert some of the energy they
possess into heat energy for warmth as well (ex: Shivering mechanism -
muscle contraction - multiple mitochondria).
Cyclical and Linear pathways in metabolism

- In metabolism, major transformations

don’t occur in a jump, but takes place
through a series of steps.
- Steps that are linear and stop at one
point, are steps that belong to LINEAR
METABOLIC REACTIONS.
- Steps , where one product of a reaction
starts the next chemical reaction being
the substrate then, belong to CYCLICAL
METABOLIC REACTIONS.
Does an Enzyme keep working forever and the chemical reaction
keeps going forever??
● There are chemical substances that bind to enzymes and inhibit their
activity. These are known as “INHIBITORS”.
● There are two main types of inhibitors:
➔ Competitive Inhibitors:
- Compete with substrate as it binds to the active site of
the enzyme thus preventing the substrate from binding to
it.
- Here if we increase the concentration of a substrate it
might increase the activity a bit
➔ Non-Competitive Inhibitors:
- Bind to parts of the enzyme (allosteric site) other than the
active site, changing the enzyme’s shape and thus
making it unsuitable to bind to specific substrate.
- Sometime the end product of a metabolic pathway act
itself as a non competitive inhibitor. This is called “End
product inhibition - Negative Feedback Inhibition”. This
changes the shape of an enzyme however once the
inhibitor is removed the enzyme goes back to its original
shape.
- This is a very efficient method of regulating metabolic
pathway.
Effect of Enzymes Inhibitors
- Interpret this graph
 Effect of Enzymes Inhibitors
- Purple line is the effect on increasing substrate
concentration on the activity of an enzyme in absence of
inhibitors.
- Green line represents the effect of increasing substrate
concentration in presence of competitive inhibitors. Here
the maximum enzyme activity is reached at a higher
concentration compared to when in absence of inhibitors.
But basically reaching the same activity.
- The blue line represents the effect of increasing the
substrate concentration on the activity of an enzyme in
presence of non competitive inhibitor. Here the activity of
the enzyme is too low compared to the other conditions;
this is because the non competitive inhibitors alter the
shape of an enzyme, and thus the substrate can not bind
to it no matter what the substrate concentration is.
Mechanism - based inhibition as a consequence of
chemical changes to the active site caused by the
irreversible binding of an inhibitor.
- Examples of enzymes inhibition discussed so far are all types
of “reversible” type of inhibition.
- Enzyme inhibition could also be irreversible. Heavy metals are
non specific inhibitors that cause irreversible inhibition to
enzymes. They permanently bind to the active site of the
enzyme, by covalent bonds without being released later. The
product is a stable “Inhibitor- Enzyme complex” that will never
work as a catalyst again. This is known as
“mechanism-based” inhibition. It is in general harmful to
organisms.
- For this reason, heavy metals are considered toxic if they
enter the body of an organism.
- Some living organisms synthesize a mechanism based
enzyme inhibitor to kill another organism. Ex: penicillin that
kills gram positive bacteria.
 Lab Report
Amendments