Explain how enzymes work, explaining the four major types of metabolic reactions enzymes perform. Include: (Metabolism, catabolism, anabolism, substrate product, active site, induced fit, competative and non competative inhibitors, allosteric regulation, cofactors and coenzymes, hydrolysis and dehydration reactions, Redox Reactions, NADH, FADH2, phosphorylation, exergonic/ endergonic reactions, ATP, isomerization reactions, feedback inhibition) Solution Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism. Substrate binding[edit] Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic/hydrophobic characteristics to the substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective, regioselective and stereospecific. Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome. Some of these enzymes have \"proof-reading\" mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.:5.3.1 Similar proofreading mechanisms are also found in RNA polymerase, aminoacyl tRNA synthetases and ribosomes. Conversely, some enzymes display enzyme promiscuity, having broad specificity and acting on a range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally), which may be the starting point for the evolutionary selection of a new function. Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N, 2E2Q) \"Lock and key\" model To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.This is often referred to as \"the lock and key\" model:8.3.2 This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve. Induced fit model In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is conti.

1. Explain how enzymes work, explaining the four major types of metabolic reactions enzymes
perform. Include: (Metabolism, catabolism, anabolism, substrate product, active site, induced fit,
competative and non competative inhibitors, allosteric regulation, cofactors and coenzymes,
hydrolysis and dehydration reactions, Redox Reactions, NADH, FADH2, phosphorylation,
exergonic/ endergonic reactions, ATP, isomerization reactions, feedback inhibition)
Solution
Enzymes are biological molecules (typically proteins) that significantly speed up the rate of
virtually all of the chemical reactions that take place within cells.
They are vital for life and serve a wide range of important functions in the body, such as aiding
in digestion and metabolism. Substrate binding[edit]
Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are
usually very specific as to what substrates they bind and then the chemical reaction catalysed.
Specificity is achieved by binding pockets with complementary shape, charge and
hydrophilic/hydrophobic characteristics to the substrates. Enzymes can therefore distinguish
between very similar substrate molecules to be chemoselective, regioselective and stereospecific.
Some of the enzymes showing the highest specificity and accuracy are involved in the copying
and expression of the genome. Some of these enzymes have "proof-reading" mechanisms.
Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks
that the product is correct in a second step. This two-step process results in average error rates of
less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.:5.3.1 Similar
proofreading mechanisms are also found in RNA polymerase, aminoacyl tRNA synthetases and
ribosomes.
Conversely, some enzymes display enzyme promiscuity, having broad specificity and acting on a
range of different physiologically relevant substrates. Many enzymes possess small side
activities which arose fortuitously (i.e. neutrally), which may be the starting point for the
evolutionary selection of a new function.
Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex.
Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate
and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N,
2E2Q)
"Lock and key" model
To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the
enzyme and the substrate possess specific complementary geometric shapes that fit exactly into

2. one another.This is often referred to as "the lock and key" model:8.3.2 This early model
explains enzyme specificity, but fails to explain the stabilization of the transition state that
enzymes achieve.
Induced fit model
In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are
rather flexible structures, the active site is continuously reshaped by interactions with the
substrate as the substrate interacts with the enzyme.As a result, the substrate does not simply
bind to a rigid active site; the amino acid side-chains that make up the active site are molded into
the precise positions that enable the enzyme to perform its catalytic function. In some cases, such
as glycosidases, the substrate molecule also changes shape slightly as it enters the active site.
The active site continues to change until the substrate is completely bound, at which point the
final shape and charge distribution is determined.Induced fit may enhance the fidelity of
molecular recognition in the presence of competition and noise via the conformational proof
reading mechanism.
Four major reactions are:-
Catabolic pathway (catabolism)
A catabolic pathway is a series of reactions that bring about a net release of energy in the form of
a high energy phosphate bond formed with the energy carriers Adenosine Diphosphate (ADP)
and Guanosine Diphosphate (GDP) to produce Adenosine Triphosphate (ATP) and Guanosine
Triphosphate (GTP), respectively. The net reaction is, therefore, thermodynamically favorable,
for it results in a lower free energy for the final products. A catabolic pathway is an exergonic
system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc.
from energy containing sources such as carbohydrates, fats, and proteins. The end products are
often carbon dioxide, water, and ammonia. Coupled with an endergonic reaction of anabolism,
the cell can synthesize new macromolecules using the original precursors of the anabolic
pathway. An example of a coupled reaction is the phosphorylation of fructose-6-phosphate to
form the intermediate fructose-1,6-bisphosphate by the enzyme phsophofructokinase
accompanied by the hydrolysis of ATP in the pathway of glycolysis. The resulting chemical
reaction within the metabolic pathway is highly thermodynamically favorable and, as a result,
irreversible in the cell.
{ Fructose-6-Phosphate+ATP Fructose-1,6-Bisphosphate+ADP}
Cellular respiration
A core set of energy-producing catabolic pathways occur within all living organisms in some
form. These pathways transfer the energy released by breakdown of nutrients into ATP and other
small molecules used for energy (e.g. GTP, NADPH, FADH). All cells can perform anaerobic
respiration by glycolysis. Additionally, most organisms can perform more efficient aerobic

3. respiration through the citric acid cycle and oxidative phosphorylation. Additionally plants, algae
and cyanobacteria are able to use sunlight to anabolically synthesize compounds from non-living
matter by photosynthesis.
Anabolic pathway (anabolism)
In contrast to catabolic pathways, anabolic pathways require an energy input to construct
macromolecules such as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. The
isolated reaction of anabolism is unfavorable in a cell due to a positive Gibbs Free Energy (+G).
Thus, an input of chemical energy through a coupling with an exergonic reaction is necessary.
The coupled reaction of the catabolic pathway affects the thermodynamics of the reaction by
lowering the overall activation energy of an anabolic pathway and allowing the reaction to take
place. Otherwise, an endergonic reaction is non-spontaneous.
An anabolic pathway is a biosynthetic pathway, meaning that it combines smaller molecules to
form larger and more complex ones. An example is the reversed pathway of glycolysis,
otherwise known as gluconeogenesis, which occurs in the liver and sometimes in the kidney to
maintain proper glucose concentration in the blood and supply the brain and muscle tissues with
adequate amount of glucose. Although gluconeogenesis is similar to the reverse pathway of
glycolysis, it contains three distinct enzymes from glycolysis that allow the pathway to occur
spontaneously. An example of the pathway for gluconeogenesis is illustrated in the image titled
"Gluconeogenesis Mechanism".
Amphibolic pathway
An amphibolic pathway is one that can be either catabolic or anabolic based on the availability of
or the need for energy. The currency of energy in a biological cell is adenosine triphosphate
(ATP), which stores its energy in the phosphoanhydride bonds. The energy is utilized to conduct
biosynthesis, facilitate movement, and regulate active transport inside of the cell. Examples of
amphibolic pathways are the citric acid cycle and the glyoxylate cycle. These sets of chemical
reactions contain both energy producing and utilizing pathways. To the right is an illustration of
the amphibolic properties of the TCA cycle.
The glyoxylate shunt pathway is an alternative to the tricarboxylic acid (TCA) cycle, for it
redirects the pathway of TCA to prevent full oxidation of carbon compounds, and to preserve
high energy carbon sources as future energy sources. This pathway occurs only in plants and
bacteria and transpires in the absence of glucose molecules.