ENERGY, CATALYSIS, and BIOSYNTHESIS
Chapter 3 p83-115
The living cell is a chemical industry in miniature, where thousands of reactions
occur within a microscopic space. Metabolism is an emergent property of life that
arises from specific interactions between molecules within the orderly environment
of the cell. Sugars are converted into amino acids, and vice versa. Small molecules
are assembled into polymers, which may later be hydrolyzed as the needs of cell
change.
Two Laws of Thermodynamics
According to the first law of thermodynamics, the energy of universe is constant.
Energy can be transferred and transformed, but it cannot be created or destroyed.
This is also known as conservation energy.
The second law of thermodynamics can be stated in several ways. Every energy
transfer or transformation makes universe more disordered. There is a quantitative
measure of disorder, called entropy, whose value increases as disorder increases.
Therefore, second law of thermodynamics states that every energy transfer or
transformation makes universe more disordered.
One of the unique property living things is to create and maintain the order. In order to
create and maintain order cells perform many different chemical reactions, which are
small organic molecules like sugars, fatty acids, nucleotides are taken up and modified
within cells by chemical reactions through a series of reactions.
The chemical reactions occur in every cells require boost in reactivity and precise
chemical control. These are achieved by specialized protein called enzymes. Each
enzyme accelerates or catalyzes a specific reaction. Enzyme-catalyzed reactions are
usually under connected in a series, so that the product of one reaction becomes the
starting material or substrate for the next.
How a set of enzyme-catalyzed reactions generates a metabolic pathway.
Each enzyme catalyzes a particular chemical reaction, leaving the enzyme unchanged.
In this example, a set of enzymes acting in series converts molecule A to molecule F,
forming a metabolic pathway.
As a whole, metabolism is concerned with managing the material and energy
resources of the cell.
Some metabolic pathways release energy by breaking down
complex molecules into simpler compounds. These degradative processes are called
catabolic pathways. A major example of catabolism is cellular respiration, in which
sugar glucose and other and other organic fuels are broken down to carbon dioxide
and water.
There are also anabolic pathways or biosynthesis, which consumes
energy to build complicated molecules from simpler ones. An example of anabolism
is the synthesis of protein from amino acids.
Schematic representation of the relationship between catabolic and anabolic
pathways in metabolism.
As suggested here, since a major portion of the energy stored in the chemical bonds
of food molecules is dissipated as heat, the mass of food required by any organism
that derives all of its energy from catabolism is much greater than the mass of the
molecules that can be produced by anabolism.
The Metabolic Map
Metabolism is the totality of an organism’s chemical processes. We can think of a
cell’s metabolism as an elaborate road map of the thousands of reactions in that cell.
These longer linear reaction pathways, or metabolic pathways, are in turn linked to
one another, forming a complex web interconnected reactions that enable to the cell
to survive, grow, and reproduce
Some of the metabolic pathways and
their interconnections in a typical cell.
About 500 common metabolic reactions are
shown diagrammatically, with each molecule
in a metabolic pathway
represented by a filled circle
Biological Order Is Made Possible by the Release of Heat Energy from Cells
Living cells-by surviving, growing, and forming complex organisms-are generating order
and thus might appear to defy the second low of thermodynamics. But this is not the
case. A cell is not isolated system. It takes energy form as food or photons from the
sun and it then use this energy to generate order within itself. In the course of performing
the chemical reactions that generate order, chemical and bond energy is converted into
heat.
A simple thermodynamic analysis of a living cell.
In the diagram on the left the molecules of both the cell and the rest of the
universe (the sea of matter) are depicted in a relatively disordered state.
In the diagram on the right the cell has taken in energy from food molecules
and released heat by a reaction that orders the molecules the cell contains.
Because the heat increases the disorder in the environment around the cell
(depicted by the jagged arrows and distorted molecules, indicating increased
molecular motions), the second law of thermodynamics, which states that the
amount of disorder in the universe must always increase, is satisfied as the cell
grows and divides.
Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules
All animals live on energy stored in the chemical bonds of organic molecules
made by other organisms.
Solar energy enters the living world through photosynthesis carried out by plants and
photosynthetic bacteria. Photosynthesis allows the electromagnetic energy in sunlight
to be converted into chemical energy into cell. Plants needs inorganic source to make
its food
Carbon dioxide from atmosphere
Oxygen and hydrogen from water
Nitrogen from ammonia and nitrates
And other elements from the soil
The reactions of photosynthesis take place in two stages
1. Light -dependent stage: in this stage light captured and transiently stored as
chemical bond energy in specialized small molecules that carry energy in their reactive
chemical group.
2. Carbon fixation: in this stage, sugars are formed from carbon dioxide and oxygen.
The net result of the entire process of photosynthesis
Light energy+ CO2+H2O ------ Sugars +O2 + heat energy
Cells Obtain Energy by the Oxidation of Organic Compound
All animal and plant cells are powered by chemical energy stored in the chemical
bonds organic molecules.
Sugars+ O2 ------ CO2+H2O
This process is known as cellular respiration.
Photosynthesis and respiration are complementary processes
Oxidation and Reduction Involve Electron Transfer
In oxidation reaction electrons are transferred to from one atom to another. Oxidation,
in this sense, refers to removal of electrons. However, in reduction reaction addition
of electrons occurs Oxidation and reduction reactions always occur simultaneously: i.e. if
one molecule gains an electron in a reaction (reduction), second molecules loses the
electron (oxidation).
When molecule in a cell picks up an electron, it often picks up a proton H+ at the
same time. The net effect in this case is to add a hydrogen atom to the molecule.
Although a proton plus electron is involved, such hydrogenation reactions are
reductions, and the reverse, dehydrogenation reactions, are oxidants. Reduction
is occurring if its number of C-H increases, whereas oxidation is occurring if its number
of C-H bonds decreases.
Enzymes Lower the Barriers That Block Chemical Reactions
A chemical reaction involves bond breaking and bond forming. When a reaction
rearranges the atoms of molecules, existing bonds in the reactants must be broken
and the new bonds of products formed. These processes require exchanges of energy
between the mixture of molecules and surrounding environment. The reactant
molecules must absorb energy for their bonds to break, and energy is released when
the bonds of product molecules are formed.
The initial investment of energy for starting of a reaction –the energy required to
break bonds in the reactant molecules- is known as activation energy or free energy
of activation.
The success of living organisms is attributable to the cell’s ability to make enzymes of
many types, each with precisely specified properties. Each enzyme has unique shape
containing an active site where a particular substrate will fit.
The Free-Energy Change for a Reaction Determines Whether It Can Occur
Although enzymes speed up reactions, they cannot by themselves force
energetically unfavorable reactions to occur. According to the second law of
thermodynamics, a chemical reaction can proceed only if it results in net increase
in disorder of the universe. Disorder is increased when useful energy that could
be harnessed to do work is dissipated as heat. This disorder can be measured by
free energy, G, of a system.
Energetically favorable reactions are those create disorder by decreasing the
free energy of system to which they belong, in other words, they have negative ΔG.
On the other hand, energetically unfavorable reactions which have positive ΔG create
order in the universe.
Rapid diffusion Allows Enzymes to Find Their Substrates
Rapid binding of an enzyme to its substrate is possible because motions are
enormously fast at molecular level. Because of heat energy, molecules are in constant
motion and consequently will explore the space inside cell very efficiently by wandering
randomly through it-a process called diffusion. In this way, every molecule in a cell
collides with a huge number of molecules every second.
Vmax and Km Measure Enzyme Performance
To catalyze a reaction, an enzyme first binds its substrate. The substrate then
undergoes a reaction to form a product, which initially remains bound to the enzyme.
Finally, the product is released and diffuses away, leaving the enzyme free to bind to
another substrate molecule and catalyze another reaction.
The rates of these different steps vary widely from one enzyme to another, and they
can be measured by mixing purified enzymes and substrate under the defined conditions.
Enzyme molecules become occupied by substrate until very high concentration of
substrate reaches a maximum value, termed Vmax. At this point all active sites of all
enzymes are occupied with substrate. And product formation will depend on how fast
enzymes are.
The concentration of substrate needed to make an enzyme work efficiently is often
measured by Michaelis constant, Km. An enzyme’s Km is the concentration of substrate
at which enzymes works at half of its maximum speed.
Enzyme
Substrate
Km (mM)
Catalase
H2 O2
1,100
Chymotrypsin
Gly-Tyr-Gly
108
Carbonic anhydrase
CO2
12
beta-galactosidase
D-lactose
4
Acetylcholinesterase
acetylcholine
(ACh)
0.09
beta-lactamase
benzylpenicillin
0.02
Activated Carrier Molecules and Biosynthesis
The energy is released during break down of food into small molecules. This energy
is usually stored as a chemical bond in small sets of activated “carrier molecules”.
These molecules rapidly diffuse within the cell and moves to sites where energy is
required.
Activated carriers store energy in an easily exchangeable form. The most important
activated carriers are ATP, NADH, and NADPH.
ATP Is the Most Widely Used Activated Carrier Molecule
The most important and versatile of the activated carriers in cells is ATP.
ATP serves as a convenient and versatile store, or currency, of energy to drive a
variety of chemical reactions in the cell
The energetically favorable reaction of ATP hydrolysis is coupled to many other
unfavorable reactions through which other molecules are synthesized. Hydrolysis
reaction often involve the transfer of a phosphate group to a molecule is termed a
phosphorylation.
Phosphorylation reactions are involved in many important cellular functions:
-activation of substrate
-facilitate the exchange of chemical energy
-help to control of the cell signaling process
ATP is used for many important cellular processes:
1.to supply energy for many of the pumps
2.to power molecular motors
3.transport of organelles or vesicle
Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together
A frequent type of reaction that is needed for biosynthesis (anabolic) is one in which
two molecules, A and B, are joined together to produce A-B in the energetically
unfavorable condensation reaction.
NADH and NAPDH Are Important Electron Carriers
There are other important activated carriers involved in biosynthesis of molecules.
These activated carriers are involved in oxidation-reduction reactions and involved in
coupling reactions. The most important of these carriers are NAD+ (nicotinamide
adenine dinucleotide) and closely related molecule NADP+ (nicotinamide adenine
dinucleotide phosphate).
NADPH is produced in the reactions in which two hydrogen atoms are removed from
substarte. Oxidized form of NADP+ receives one hydrogen atom plus an electron,
and the proton (H+) from other H atom is released into the solution. Because
NADPH holds it hydride ion in a high-energy linkage, the added hydride ion can
easily be transferred to other molecules.