Download P3- Biochemical Processes

P3Biochemical
Processes
Processes within cells
Key Knowledge
The nature of biochemical processes within cells
 Catabolic and anabolic reactions – reactions
releasing or requiring energy
 Role of enzymes as protein catalysts
 The role of ATP and ADP in energy
transformations
 Requirements for photosynthesis
 Requirements for aerobic and anaerobic
cellular respiration
Chemical reactions in cells
In the cell reactions happen in stepsA biochemical pathway.


This allows for management of energy
requirements.
Each step is controlled and facilitated by
protein catalysts and coenzymes.
Cellular Metabolism
 This
refers to the thousands of chemical reactions
that occur constantly in each living cell.
 Heat
is generated
by the activity of
cells as they break
down and build
molecules.
 All
metabolic reactions that occur in cells are
controlled and regulated to maintain cell functions
and to meet the energy needs of a cell.
 A biochemical pathway.
 Each step is controlled by an enzyme.
http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf



Key metabolic pathways include:
Photosynthesis
Cellular Respiration
It is important the products don’t build up in a cell as
it can inhibit the cells function:
 In
plants glucose from photosynthesis is converted
to starch which is stored by the plant.
 In
animals the products of cellular respiration diffuse
from cells and release into the atmosphere.
Types of reactions:
 Anabolic:
a reaction that builds up complex
molecules from more simple ones.
 Catabolic:
reactions, such as cellular respiration,
that involve the breakdown of complex molecules
to simpler products.
 Aerobic:
a reaction that requires oxygen.
 Anaerobic: a reaction that doesn’t require oxygen.
 Endergonic: an energy requiring chemical
reaction.
 Exergonic: a reaction that releases energy.

In endergonic reactions (reactions that absorb
energy) – total net amount of energy is absorbed and
locked up in the bonds of the products, which have
more stored energy than the reactants.

In exergonic reactions (reactions that release energy)
– total net amount of energy is released from the
bonds of the reactants and the products have less
energy than the reactants.
Types of reactions:
Anabolic
Catabolic
Endergonic
Exergonic
Photosynthesis
Cellular
respiration
The amount of energy needed for the reaction to
occur is known as activation energy.
The energy shuttle
 Cells
capture the chemical energy released from
exergonic reactions to fuel endergonic reactions.
 These
two reactions occur simultaneously in cells.
 In
this process some energy is lost as heat, which
escapes from the cells into the atmosphere.
 Reactions
don’t always occur in the same place
within the cell, energy needs to be transferred
between reactions.
ATP: Adenosine triphosphate


ATP is the universal primary source of free energy for all
living organisms.
ATP contains adenosine attached to a sugar group
(ribose), which is bound to a chain of three phosphate
groups.
ATP is a well designed
renewable energy
source. When a cell
requires energy to
drive an endergonic
reaction, the high
energy chemical bonds
attaching to the last
phosphate group is
broken, thus releasing
stored energy
ATP  ADP


The energy that was held in that bond (now broken) is
able to fuel a cellular reaction.
The remaining molecule now has only two phosphate
groups and is called ADP (adenosine diphosphate). This
reaction is sped up by the enzyme ATPase.
... and in reverse

Free energy obtained from
an exergonic reaction can
also be used to add a
phosphate group to ADP,
converting it to ATP. The
ATP-ADP cycle is the cells
way of shuttling energy
between reactions.

The addition of a phosphate
group to an organic
molecule of any sort is
called phosphorylation.
Definitions
 ATP:
a molecule
that released
energy for cellular
reactions when its
terminal phosphate
group is removed.
 ADP:
a compound
composed of
adenine and ribose
with two phosphate
groups attached; it
is converted to ATP
for energy storage
when it gains a
phosphate group
(phosphorylation).
Characteristics of enzymes
 Only
a small amount of enzyme is needed to
do a big job. They are not used up in the
reaction. Can be re-used over and over.
 An
enzyme doesn’t change the direction of the
reaction, but does speed up the reaction.
 Make
the reaction occur more easily by
reducing activation energy.
 An
enzyme won’t change the final amount of
product formed.
 Are
proteins
 Are
substrate specific
Enzymes Are Proteins
The enzyme binds to the substrates by its active site
The active site is a pocket formed by the folding of the protein
where the substrates bind.
How enzymes bind their substrates
 The
active site of an enzyme has a shape that
complements the shape of the binding site of the
substrate; that is, they ‘fit together’ like pieces of a
jigsaw puzzle.
 Two
models exist to describe the mechanism of an
enzyme binding with it’s substrate.
 These
are:
 Lock and key model
 Induced fit model has been refer red
Induced fit hypothesis
http://scholar.hw.ac.uk/site/biology/activity6.asp
Enzyme specificity is
at the heart of how
enzymes control
each step in a
biological pathway.
What allows proteins
to be so specific in
their function?
Enzymes
 Even
though enzymes are manufactured inside
cells, their site of function may be either within the
cell (intracellular) or outside the cell (extracellular).
 Intracellular
enzymes speed up and control
metabolic reactions inside the cell.
 Extracellular
enzymes are secreted from the cell
and catalyse reactions outside the cell. For
example, digestive enzymes are secreted from
specialised cells in the lining of the gut but act on
food in the gut.
Naming enzymes
 It
is usually easy to tell if a substance is an
enzyme, they often have the suffix – ase
eg: protease, lipase, amylase, nuclease,
ATPase etc.
 Unfortunately,
there is always an exception to
the rule
eg: pepsin and trypsin, found in the
mammalian gut and work on breaking
down protein.
Substrate
Enzyme
Product
Hydrogen
peroxide
Catalase
Oxygen and water
Starch
Amylase
Maltose
Maltose
Maltase
Glucose
Protein
Pepsin
Peptides
Peptides
Protease
Amino acids
Fats
Lipase
Fatty Acids and
Glycerol
Enzymes lower activation energy
Enzyme power

Adding ferric ions (Fe3+) to
hydrogen peroxide increases
rate of decomposition and
therefore make it less toxic.

Catalase – a catalytic protein,
one of the fastest, found in the
liver. It contains a Fe ions which
speed up decomposition of
hydrogen peroxide to water and
oxygen by 100million times,
making it less toxic.

This ability to lower the activation
energy needed is why enzymes
are so important.
Enzyme power

Enzymes generally work rapidly.

Catalase: one of the fastest acting enzymes.
It is found in several organs and tissues,
including the liver, where its job is to speed up
the decomposition of hydrogen peroxide
(H2O2) into oxygen and water.
2 H 2O2
2H2O + O2
Enzyme power
 Hydrogen
peroxide is a toxic by-product of
metabolism so it is essential that the cell removes
it quickly.
 Hydrogen
peroxide has a high activation energy,
which means that the energy needed to
decompose it to water and oxygen is high.
Enzymes – fast workers



Enzymes are large globular
proteins.
Earlier we looked at the
formation of proteins. At the
tertiary structure the protein
has its definitive shape.
During this stage in an
enzyme a pocket or groove
is formed (usually made by
a beta pleated sheet).
This groove or pocket can
accommodate one or more
specific substrate molecules
and is called the active site.
The active site is highly specific for a
particular substrate. This model of
enzyme action is known as the lock
and key model.
Enzymes – fast workers

The bonds that form
between an enzyme and
the substrate can also
modify the shape of the
enzyme so that the
substrate can be fully
accommodated.

This is knows as the induced
fit model of enzyme action.

It is important to note that
enzymes are generally
proteins, but not always eg:
ribozymes
http://www.youtube.co
m/watch?v=V4OPO6J
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Coenzymes & cofactors
The catalytic activity of many
enzymes also depends upon the
presence of metallic cations.
Cations that bind to an enzyme,
and increase the rate of
catalysis are called cofactors
Coenzymes assist catalysis by binding
to enzymes or by functioning as carriers
of electrons and protons. They may also
carry specific atoms or groups of atoms,
such as phosphate, that are required
for or produced by chemical reactions
 Cofactors:
small
 Coenzymes:
inorganic
substances (e.g.
zinc ions and
magnesium ions)
that need to be
present in addition
to an enzyme to
catalyse a certain
reaction
non-protein
organic substances that
are required for enzyme
activity.



Small molecules compared to
the enzyme
Major role in metabolic
pathways
Can function as a carrier,
donor or acceptor of a
substance involved in the
reaction and/or may bind
with an enzyme to activate it.
Important Coenzymes
ABBREVIATION
COENZYME
Loaded
form
Unloaded
form
FUNCTION
Adenosine triphosphate
ATP
ADP
Energy transfer
Nicotine adenine
dinucleotide
NADH
NAD+
Transfer of electrons and
protons
NADPH
NADP+
Transfer of electrons and
protons
FADH2
FAD
Transfer of electrons and
protons
(based on the vitamin niacin)
Nicotine adenine
dinucleotide phosphate
(based on the vitamin niacin)
Flavine adenine
dinucleotide
(based on the vitamin B12)
Key Knowledge

Cellular Metabolism: the
thousands of cellular reactions
that occur constantly in living cells.

Biological Pathway: series of steps
in a reaction where the product
from one step becomes the
reactant for the next, each step is
regulated by an enzyme.





ATPase releases the third
phosphate to turn ATP to ADP
and the process of
phosphorylation attaches a
third phosphte to ADP to
create ATP.

Activation energy: the amount
of energy needed for a
reaction to occur (enzymes are
so effective as they are able to
lower this activation energy to
get the reaction started
quicker).

Products need to be removed
from the cell so that they do
not build up and slow down
vital metabolic reactions.
Aerobic – in the presence of
oxygen
Anaerobic – in the absence of
oxygen
ATP: Endergonic = Catabolic : ADP
ADP: Exergonic = Anabolic : ATP
Key Knowledge

Enzymes are organic catalysts
(speed up reaction).

Generally proteins, however not
always eg: ribozymes.





Beta folded sheets created in
secondary stage of protein
production become the
enzymes active site.

The active site of the enzyme
binds with the substrate of the
reactant. Highly specific: lock
and key model.
When the active site and
substrate binds the enzyme can
change shape, this is knows as
the induced fit model.
Enzymes are recycled.
Intracellular enzymes: work within
the cell.
Extracellular enzymes: created in
a cell and then excreted to work
outside of the cell.
Enzymes generally end with the
suffix ‘ase’ eg: lipase, amylase.


Enzymes need help: cofactors
(inorganic substances eg:
zinc)and coenzymes (non
protein organic substances).
Factors that influence enzyme
activity
 Factors






that influence enzyme activity include:
pH
Temperature
Inhibitors
Enzyme concentration
Substrate concentration
Cofactors and coenzymes
Factors effecting enzyme capabilities

Enzymes are sensitive:

The optimum temperature
for an enzyme is that in
which they naturally occur
in.

For most of the enzymes
associated with plants
and animal metabolism,
there is little activity at low
temperatures – it slows
down the number of
collisions, but doesn’t
denature the enzyme.

As the temperature increases,
so does the enzyme activity.
This is because as the
temperature increases
molecules become more
excited and collide more often.
This increase in collisions
increases the opportunity for a
substrate to bump into its
enzymes active site.

However, if the point is reached
where the temperature is too
high and the enzyme structure
is damaged, the enzyme
ceases to function; this is called
enzyme or protein denaturation.
Factors effecting enzyme capabilities

Poisons often work by denaturing 
enzymes or occupying the
enzyme’s active site so that it does
not function.

Some enzymes will not function
without cofactors, such as vitamins
or trace elements.


A change in pH affects the amino
acid chain of a protein.

As a solution becomes more basic,
proteins tend to lose hydrogen ions.
In acidic solutions, proteins gain
hydrogen ions.
Buffered solution: weak acid,
are better solutions for
chemical reactions that water
(neutral) due to the H being
released from the acidic
solution, creates a buffer for H
or OH being released.
If the charges on the amino
acids in a protein are
changed, then the bonds that
maintain the three-dimensional
structure of a protein can be
changed.
For example...
 Pepsin
in the stomach
(pH1.5).
 Catalase
works in a
neutral environment of
cells in the liver (pH 7).
 Alkaline
Phosphatase in
bone (pH 9.5).
Effect of having more substrate...
 The
amount of substrate present in a reaction can
limit the amount of product produced.
 More substrate will result in more product until all
enzymes are working at their maximum capacity
(enzyme saturation)
Effect of having more enzyme...
 When
the amount of enzyme in a system is
increased, then the amount of product increases
until:
the product starts to inhibit enzyme action
the substrate is depleted.
 The
rate of reaction is proportional to the enzyme
concentration provided there is enough substrate
present.
pH affects enzyme activity
 The
pH scale is 1–14, where 1 is very acidic, 14 is very
basic, 7 is neutral.
 The
optimum pH for an enzyme is that at which the
enzyme shows maximal activity.
 Each
enzyme has an optimum pH (enzymes are very
sensitive to pH).
 Changing
pH affects enzyme function because
hydrogen bonds break, and therefore the 3D shape
of the enzyme changes.
pH affects enzyme activity

Different enzymes have different optimum pH values.

For example, in the stomach the enzyme pepsin has a low
optimum pH, so the stomach produces acid to maintain this low
pH. The enzymes of the pancreas need a higher pH to work.
Temperature affects enzyme activity
 Warming
increases the rate of most chemical
reactions, including enzyme catalysed reactions.
 Extra
heat energy is taken up by molecules so they
move faster. This increases the rate of interaction
between substrate and enzyme.
 Lower
temperatures meant that molecules move
more slowly. This decreases the rate of interaction
between substrate and enzyme.
 Although
temperatures either side of the optimum
temperature will decrease enzyme activity, extremes
of heat and cold have different effects.
Temperature affects enzyme activity

Most enzymes have an optimum temperature range, which is the
temperature at which the enzyme’s catalytic activity is
greatest.

Temperatures outside the optimum temperature range will
decrease enzyme activity.
Temperature affects enzyme activity


The rate of enzyme activity increases with increasing
temperature until the enzyme begins to denature or break
down.
The temperature at which denaturation begins is referred
to as the critical temperature of an enzyme.

Denaturation means that the tertiary structure of the
protein is permanently changed and cooling it back down
again won’t restore the enzyme’s function.

In contrast, enzymes are not denatured when it is too cold.
Enzymes that are inactivated because of low
temperatures become active again when the
temperature is returned to normal.

Different types of inhibitors
 Competitive
inhibitors
 Inhibitory molecule competes with the substrate for
the active site.
 Slow down enzyme activity by blocking substrate
binding to active site.
 Non-competitive
inhibitors
 Allow the substrate to bind to the active site.
 Slow down enzyme activity by binding elsewhere to
enzyme.

Inhibitors
 An
inhibitor is any chemical that changes the shape
of the active site of the enzyme so that it has a lower
affinity for substrate.
 Inhibitors
may be reversible or irreversible.
 Reversible
inhibitors are used to control enzyme
activity as they only temporarily deactivate enzymes.
 Heavy
metals such as lead, mercury and arsenic are
toxic because they are irreversible inhibitors of
enzymes.
 Inhibition
may be competitive, non-competitive or
allosteric.
Regulating enzyme affinity
 Affinity
refers to the ease with which
the enzyme binds with a substrate.
 Cells do this by attaching other
molecules to the enzyme to
change the shape of its active site.
 This allows cells to increase or
decrease the rate of reaction in
particular circumstances.
Enzyme concentration

The rate of enzyme activity
increases with increasing
enzyme concentration.

Increased enzyme
concentration will increase
the rate of reaction.

Increased enzyme
concentration will not
increase the amount of
product formed.
Substrate concentration

Increased substrate
concentration will
increase the amount of
product formed.

Increased substrate
concentration will
increase the rate of
reaction up to the point
when the enzyme is
saturated with
substrate.
Enzymes and disease



Several inherited diseases involve an inability to manufacture a
particular enzyme required to break down substances that are
normally part of the diet.
Examples include: galactosaemia, lactose intolerance and
phenylketonuria.
Galactosaemia





due to an error (mutation) in the gene responsible for
producing one of the enzymes needed to convert galactose
to glucose-1-phosphate.
Galactose accumulates in the blood and present in their
urine. The liver becomes enlarged, cataracts form, growth is
slow and mental development is retarded.
Sufferers who are left untreated do not often live beyond
infancy.
The treatment for galactosaemia is simple and largely
successful if it is commenced soon enough.
All foods containing galactose, chiefly milk and milk pro ducts,
must be excluded from the diet.
Two very important chemical
reactions

The importance of enzymes, and the linkage between
endergonic and exergonic reactions is highlighted when we
study photosynthesis and cellular respiration.

Photosynthesis is an endergonic reaction.

Cellular respiration is an exergonic reaction.
Enzyme regulation

Enzyme concentrations are
regulated in response to the
need of the cells.
The regulation is achieved by:
 controlling the production
 breaking down the enzyme
 inactivating the enzyme

For example: pepsinogen is
the dormant form or pepsin
(enzyme that breaks down
protein), it only becomes
pepsin when it is introduced
into the acidic stomach
environment.
Enzyme regulation
An enzyme can have
more than one active
site if they are
composed of more
than one polypeptide
chain – therefore they
can catalyse more
than one reaction =
increased efficiency.
Inhibiting the work of enzymes

Some enzymes have two or
more active binding sites.

Activity of almost every
enzyme in a cell is regulated
by feedback inhibition
where the product of the
reaction can inhibit enzyme
activity.

Inhibitor binds to enzyme 
active site or allosteric site
changing shape, therefore
cannot bind to substrate.

http://highered.mcgrawhill.com/olc/dl/120070/bio10.swf
http://www.youtube.c
om/watch?v=cbZsXjgP
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Inhibitors

Non-competitive inhibitor:
a molecule that binds to
an enzyme at a site other
than the active site which
changes the shape of the
enzyme so that the
substrate can no longer
bind to the active site.

Competitive inhibitor: a
substance that competes
with a substrate for an
enzyme’s active site.
Examples: poisons whereby the inhibitor binds to the active site
preventing the enzyme from catalysing reactions and overtime this
concentration of enzyme reduces and the reactions stop.
Photosynthesis



Occurs in the chloroplast.
Two stages
Light dependent (occurs in
the thylakoid membrane –
grana)
Light independent (occurs
in the stroma)
Light dependent
 Light
energy is absorbed by chlorophyll.
 The
energy absorbed energises the electrons in the
water molecules, which breaks the water
molecules apart.
Each water molecule is broken up into:
 2 H+ (protons)
 2e1O
Light dependent
• Oxygen is released
• Electrons make an electron transport chain, which
creates the energy (ATP).
• Phosphorylation occurs so ADP + Pi changes to ATP,
this is also shuttled off to the light dependent stage.
• Hydrogen ions and electrons are picked up by
carrier molecule NADP to create NADPH and
shuttles the hydrogen ions to the light independent
stage that occurs in the stroma
Light dependent
Light dependent summary
Inputs
Output
Light energy (absorbed by
chlorophyll)
Oxygen gas
Water
NADPH
ATP
Light independent









Could not occur without the light dependent as it relies on NADPH
and ATP.
Occurs in the stroma.
Calvin-Benson cycle – ATP from light dependent stage is used to
drive this process.
CO2 is joined (carbon fixation) to a 5 carbon molecule circulating in
the cycle (ribulose biphosphate RuBP), rubisco aids this process.
A 6 carbon molecule is formed, but is unstable.
6 carbon molecule is split into two 3 carbon molecules (PGA stable).
NADPH donates H+ to form 3 carbon phosphate molecule (PGAL).
Some 3 carbon phosphate molecules exit the cycle, join with
another 3 carbon phosphate molecule = hexose, which builds
glucose.
Some 3 carbon phosphate molecules remain in the cycle to
regenerate RuBP.
Light independent
Light independent
Light independent
Light independent
Light independent
Light independent
Light independent
Light dependent
Inputs
Outputs
NADPH (light dependent)
NADP
ATP
ADP + Pi
CO2
Glucose
Water
Factors affecting photosynthesis
 CO2
 Light
intensity
 Temperature
 Oxygen (reduces
carbon dioxide
fixation)
 Water (reduced water
causes stomata to
close, therefore less
CO2 can come in)
 Amount of chlorophyll.
Cellular Respiration
 Cellular
respiration is the process in which
an organism breaks down an energy rich
molecule (glucose) to release the energy
in the usable form (ATP).
 Aerobic
respiration requires O2 (efficient)
 Anaerobic
respiration doesn’t require O2
(inefficient)
Aerobic Respiration
 Occurs
in three stages
 Glycolysis - cytoplasm
 Kreb’s cycle – matrix of the mitochondrion
 Electron Transport Chain – cristae of the
mitochondrion
Glycolysis

Occurs in the cytoplasm.

Glucose enters

It is broken down into two
pyruvate/pyruvic acid.

2 ATP molecules are produced


2 NADH molecules are
produced
Doesn’t require O2
Glucose
Glycolysis
2 NADH
2 ATP
2 pyruvate
(pyruvic acid)
In between

Occurs in the matrix of the mitochondria.

2 pyruvate molecules (from glycolysis) enter the
mitochondrion.

Pyruvate undergoes a reaction that results in the
formation of a compound called acetyl CoA.

CO2 is produced as a by product of this reaction.
Loaded NADH carriers are also created.

2 pyruvate
2 Carbon Dioxide

2 Acetyl co A
2 NADH
The reaction that occurs now is called the Krebs cycle.
Kreb’s cycle

Occurs in the
mitochondrial matrix

O2 required

Net yield of 2 ATP per
glucose molecule (per 2
acetyl CoA)

Net yield of 6 NADH and
2 FADH2 (FAD serves the
same purpose as NAD)
Electron Transport Chain

Occurs in the cristae of the mitochondria

Electrons are released from NADH and
from FADH2 and are passed along a series
of enzymes.

Electrons are transported via cytochromes
(series of compounds).

H+ ions are actively transported across the
inner mitochondrial membrane.

The H+ ions then flow back through special
pores in the membrane, a process that is
thought to drive the process of ATP
synthesis.

Net yield of 32 ATP per glucose molecule

6 H2O are formed when the electrons unite
with O2 (electron acceptor) at the end of
electron transport chain and then bind
with 2H to form water.
Aerobic respiration in a nutshell
Anaerobic respiration
Putting it all together