catabolic-pathway

Metabolism Pathways-Examples, Diagrams, and Overview

Introduction

Metabolic pathways are biochemical pathways that involve the transformation of chemical substances. These biochemical pathways can occur in multi-cellular organisms, such as humans, animals, plants, and single-celled organisms, such as bacteria and archaea.

The metabolic pathways in these organisms can vary in size. Some involve few reactions, while others are complex connections with multiple chemical reactions. The basis of Metabolism is found in the cell and involves the transformation of molecules into energy.

Figure: Metabolic pathways-flow chart

Metabolism Overview

Metabolism is the total process of converting food to energy, including the breakdown and synthesis of nutrients. During Metabolism, an organism takes in food and oxygen. Nutrients are broken down to provide energy for the cell, with some excess nutrients excreted as urine.

Depending on what the organisms eat, Metabolism can also create various byproducts that are eventually discharged. One example of this process is lipid metabolism, the creation of body fat from food.

Lipid metabolism can also be chemically divided into ketone and lipid metabolism. Ketone metabolism refers to the breakdown of fatty acids for energy in animals, while lipid metabolism is the creation of lipids.

In humans and most animals, food is metabolized by two processes. The first process involves mechanical and chemical digestion, where the body breaks down large molecules into smaller ones that cells can use. For example, during digestion, the food we eat is first chewed by our teeth and mechanically ripped apart by our gastrointestinal tract.

Figure: Gastrointestinal tract

The second process involves chemical digestion, where enzymes break down food into its parts. Each of these processes is essential for proper nutrition and energy production.

The human body requires energy to carry out essential life functions and is dependent on food for this energy. Nutrients are consumed through food, and the human body needs specific nutrients to survive. These nutrients are used as a source of energy for bodily functions such as growth, maintenance, and repair of tissues.

Biochemical Reactions Interdependence

Metabolism is a chain of biochemical reactions that are closely interrelated and interdependent. One reaction leads to another, and the products of each reaction form the substrates for the next.

For example, in lipid metabolism, the hydrolysis of triglycerides leads to fatty acid and glycerol. The products of this reaction are substrates for the subsequent reaction, which is esterification. Esterification condenses a fatty acid with glycerol to form a triglyceride

Another illustration is the production of glucose from a food source such as cereal. To produce glucose, the food must be broken down into its components first. This process is done in two different steps.

First, food is broken down into its parts. In the next step, these foods are converted into component parts of glucose. The products of these reactions are substrates for the next reaction, which is decarboxylation. Decarboxylation adds a carboxylic acid group to a molecule.

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Metabolic Pathways

Figure: An illustration of the two main metabolic pathways

A metabolic pathway is a series of biochemical reactions that take place within cells. These chemical reactions are the basis for all of a cell’s activities. Metabolic pathways can be utilized by individual cells or by the body as a whole.

Metabolic pathways are essential for regulating energy and intermediates, and they also provide a variety of molecules needed for cell growth. These pathways are metabolic and involve the transformation of chemicals, energy, and molecules.

The primary function of these pathways is to provide intermediates used in biosynthesis. Metabolic intermediates are molecules in the process of being transformed from one substance to another.

All metabolic pathways share the same components, including enzymes and coenzymes that help speed up reactions in the pathway. Enzymes are specialized proteins needed for these pathways to occur. Coenzymes help by speeding up the processes to achieve the desired results faster.

Metabolic pathways are also classified by their chemical nature. These pathways are usually catalyzed, which means that enzymes and coenzymes act as catalysts to help speed up the reactions.

The Two Main Types of Metabolic Pathways

Metabolic pathways can be divided into two categories: catabolic and anabolic. Anabolic reactions are those that build up molecules through the addition of carbon-containing groups. In contrast, catabolic reactions are those that break down molecules by removing carbon-containing groups.

Catabolic pathway

Figure: Catabolic pathway

A catabolic pathway is a series of reactions that breaks down complex molecules into simpler ones. These catabolic pathways are essential to the process of releasing energy from food for cells to use.

This pathway also contributes to the process of cellular respiration. The catabolic pathway breaks down sugars and fats in food into carbon dioxide, water, and energy.

An example of a catabolic pathway is the Metabolism of glucose to carbon dioxide and water, which occurs during cellular respiration. During this process, glucose is broken down and converted to energy.

Glucose breakdown process

During the breakdown of glucose, energy is released, and carbon dioxide, water, heat, and energy are produced. This process occurs in the cell’s mitochondria.

Cellular respiration begins when the molecule glucose is broken down into carbon dioxide and water. It also involves a series of chemical reactions that break down food into energy for the cell to use. The energy produced helps cells to function. The chemical formula for the breakdown of glucose is:

C6H12O6 + 6O2 –> 6CO2 + 6H2O (carbon dioxide) + energy

The pathway begins with oxygen atoms to carbon atoms, forming two-carbon molecules called acetyl coenzyme A (acetyl CoA). This process of adding oxygen atoms is known as oxidation. These acetyl coenzymes are further oxidized and broken down to produce carbon dioxide and water. The equation for this process is acetyl-coenzyme A –> acetate + coenzyme A + energy.

Steps of Cellular Respiration

Figure: The steps of cellular respiration

The main steps in cellular respiration are respiration, glycolysis, the citric acid (Krebs) cycle, and oxidative phosphorylation. These pathways are also called the “citric acid” or “Krebs” cycle and the respiratory chain.

In glycolysis, glucose is broken down into smaller molecules called pyruvate. Glycolysis is the first step in the breakdown of glucose that provides cells with energy. The equation for glycolysis is:

1 glucose + 2 ATP –> 2 pyruvate + 2 ATP

During glycolysis, some of the energy produced is used to make the cell’s energy carrier molecule. Energy is also stored in this compound for later use by the cell. The equation for the buildup of the energy-carrying molecule is:

2 pyruvate + 2 NAD+ –> acetyl coenzyme A + CO2

The citric acid cycle is known as the Krebs cycle, after Hans Adolf Krebs. This process uses some of the energy released from glucose breakdown to make ATP.

Figure: The Krebs Cycle

The citric acid cycle also makes carbon dioxide and releases energy. Glycolysis, the citric acid cycle, and oxidative phosphorylation occur in the cell’s mitochondria during cellular respiration.

The difference between glycolysis and the citric acid cycle is that; glycolysis breaks down one molecule of glucose, producing two pyruvate molecules. In contrast, the citric acid cycle breaks down multiple glucose molecules and produces one molecule of pyruvate.

Anabolic Pathway

Figure: Anabolic pathway

An anabolic pathway is a series of reactions that builds up molecules by adding carbon-containing groups. These pathways are essential to the growth and repair of complex molecules.

Anabolic pathways also produce energy and aid in forming bone, tissues, proteins, and other essential compounds for cell survival.

An example of an anabolic pathway is glucose production from non-carbohydrate molecules, such as amino acids and glycerol. This process occurs during the production of proteins from amino acids.

Production of Glucose from amino acid molecules

This process is an example of an anabolic pathway. It involves breaking amino acid molecules, such as alanine and proline to release energy-rich ammonium groups. This process releases the chemical energy from the amino acid molecules.

An essential step in this process is removing one carbon atom, which releases a molecule consisting of two carbons, ammonia. This process is called transamination.

A nitrogen-containing amino acid, alanine, is converted to a molecule with one fewer carbon atom during transamination. The oxygen in the amino acid is linked to the carbon from the carbons in a molecule.

Oxygen + NH2 (amine) –> H+ and NH3 + CO2

The ammonia molecule is converted into glucose by adding oxygen to form a ring with four carbons. This step in the process is called deamination. This process occurs in two steps when oxygen is added to the ammonia molecule, and then another nitrogen group is added to form a ring.

OR

NH3 + O –> HO2- + NH2 (amine) HO2- –> H+ + O2

Figure: Deamination of amino acids

The next step in the process is phosphorylation, which occurs when ATP adds a phosphate group to an amino acid. The addition of the phosphate group creates adenosine diphosphate (ADP). Also, a molecule of water is released during this process.

Diphosphate –> diphosphate + H2O

Another molecule of ATP is added to the amino acid, and then a third molecule is added. This process makes adenosine triphosphate (ATP), which stores energy in its phosphate group. The ATP is used to add another phosphate group to make adenosine monophosphate (AMP). ATP has a phosphate group, and ADP has a diphosphate group.

ADP + phosphate –> AMP + PPi

Production of Glucose from Glycerol

The formation of glucose from glycerol is another example of an anabolic pathway. It involves the breakdown of glycerol molecules into two three-carbon sugar molecules, called glycerol 3-phosphate or glyceraldehyde. These reactions release energy to the cell.

Several reactions happen, leading to the production of triglycerides, which are stored energy molecules in cells. Fatty acids are synthesized from acetyl groups and carbon dioxide, which are removed from the glycerol. They form triglyceride molecules.

Triglycerides are broken down to form ketone bodies, which are the primary energy source for most cells. The breakdown of glycerol by the organism can be used to provide energy for the organism. This process is known as gluconeogenesis and occurs in animals and plants.

Figure: Glucogenesis of glycerol

The glycerol molecules come from the process that breaks down fats during digestion, called lipolysis. During this process, glycerol is split into two one-carbon molecules, called glycerol 1-phosphate. This process involves the removal of a phosphate group from glycerol.

Glycerol –> Glycerol 1-phosphate + H2O

The glycerol 1-phosphate is converted to two three-carbon sugar molecules by adding a phosphate group and hydrogen.

NH2OH –> Glycerol 3-phosphate + H2O + H+

Producing Glucose From Fructose 1,6-biphosphate and glyceraldehyde-3-P

This process is another example of an anabolic pathway. The equation for this process is: glucose-6-phosphate + fructose-6-phosphate + glyceraldehyde 3-phosphate –> glucose-1-phosphate + fructose 6-phosphate + dihydroxyacetone phosphate

The process occurs in a series of steps. Step one involves the addition of a phosphate group to fructose-6-phosphate by ATP and phosphoenolpyruvate. This step creates fructose-1,6-biphosphate.

Figure: Glucogenesis of fructose-1,6-biposphate

Fructose 6-phosphate and dihydroxyacetone phosphate are produced in the last step.

Glucose-6-phosphate –> glucose-1-phosphate + fructose 6-phosphate + dihydroxyacetone-phosphate

Examples of anabolic pathways in plants are photosynthesis and the Calvin cycle.

Photosynthesis

During photosynthesis, plants convert carbon dioxide (CO2) into glucose and other compounds using light energy. This process requires chlorophyll and involves CO2, water (H2O), and light energy.

The light energy is harvested to produce reduced nicotinamide adenine dinucleotide (NADH). This compound has a hydrogen atom. It transfers the hydrogen to water, producing oxygen (O2) and NADPH.

The Calvin Cycle
Figure: The Calvin Cycle

The Calvin cycle uses the energy of sunlight to convert carbon dioxide (CO2) into glucose. This process is still not fully understood by scientists, but it is facilitated by the Calvin Cycle enzyme RuBP carboxylase.

During the cycle, carbon dioxide is fixed to RuBP by using light energy and ATP. This process creates two molecules of glucose, which can be used to produce energy.

Other Metabolic Pathways

Apart from the major metabolic pathways, others follow similar patterns but not as popular. Some are subsets of the main pathways but are usually treated differently. Below are other metabolic pathways applicable to living organisms:

Anaerobic Bacteria Pathways

Figure: Anaerobic bacteria pathway

Anaerobic bacteria produce energy without oxygen, and they produce ATP molecules through a process called fermentation. The equation for this pathway is: glucose + H2O –> 2 pyruvate + H2 + energy

This process occurs in the absence of oxygen. The glucose is converted into two pyruvate molecules, which leave the cell. In the absence of oxygen, H2 is produced and can be used to produce energy for the cell.

Amphibolic Pathway

The amphibolic pathway can either be anabolic or catabolic. The classification depends on whether the process needs energy input or not. If it needs energy, the pathway is anabolic. In this case, the organism will use energy to convert NAD+ into NADH.

This process can also be catabolic, and the cell will use this pathway to generate ATP molecules without using energy. An example of an amphibolic pathway is the glyoxylate cycle. This process occurs in plants and some microorganisms such as algae.

Figure: Glyoxylate cycle

The equation for this pathway is: oxaloacetate + glyceraldehyde-3-phosphate –> glycerate + phosphoenolpyruvate + CO2

Stages: This pathway occurs in three stages. The first is when glyoxylate combines with α-ketoglutarate in the mitochondria to form 5-hydroxy-2-oxohexanoate.

In the second stage, 5-hydroxy-2-oxohexanoate is converted into malate by changing its carrier molecule.

In the third stage, malate combines with NAD+ and oxaloacetate to form the carrier molecule, which transports it into the cytoplasm.

In the cytoplasm, the carrier molecule is converted to CO2 and transported back into the mitochondria. It’s important to note that this reaction only occurs in the absence of oxygen.

The Conjugate Pathway (Catabolic)

This pathway occurs when the cell needs to produce NAD+ or NADP+. In other words, it occurs when the cell needs to produce energy. This pathway can be catabolic because it can produce ATP molecules without inputting energy.

This pathway can also be used to synthesize glucose in plants and microorganisms.

The equation for this pathway is: glyceraldehyde-3-phosphate –> dihydroxyacetone phosphate + phosphoenolpyruvate

Enzymes Used in Metabolic Pathways

Metabolic pathways occur in cells. Cells have an intracellular environment that is very different from the extracellular environment. This means that most enzymes in these pathways need to be changed to function in their new environment.

Another reason for this is that they function better in different temperatures and pH levels than what is found outside of the cell.

The following is a list of some enzymes used in metabolic pathways.

Figure: Glycogenolysis
  • (ADPRase) (glycolysis)- breaks down diphosphate to ribose.
  • Convertase (glycogenolysis)- phosphorylates glucosyl units, which allows for glycogen breakdown.
  • Glyceraldehyde-3-phosphate dehydrogenase (gluconeogenesis)- converts glyceraldehyde-3-phosphate into a 1,3-diphosphoglycerate.
  • Glucose 6-phosphate dehydrogenase (gluconeogenesis)- converts glucose 6-phosphate into a ribulose 1,5-bisphosphate. This process occurs to make G6P and inorganic phosphate.
  • GLYCTK: glycogen synthase kinase (glycogenolysis)- phosphorylates glucosyl units, which allows for glycogen breakdown.
  • Pyruvate carboxylase (pyruvate metabolism)- converts pyruvate to oxaloacetate.
  • Pyruvate dehydrogenase (pyruvate metabolism)- converts pyruvate to acetyl CoA. This enzyme requires thiamine pyrophosphate and a lipoamide cofactor.
  • Pyruvate dehydrogenase complex (pyruvate metabolism)- converts pyruvate to acetyl CoA. This enzyme requires thiamine pyrophosphate and lipoamide cofactor.
  • Pyruvate kinase (pyruvate metabolism)- transfers phosphate groups from phosphoenolpyruvate to pyruvate. This enzyme requires ATP and magnesium.
  • Valine, leucine, and isoleucine degradation (valine)- is a two-part process. First, it converts valine to propionyl-CoA and acetyl-CoA. Then it transforms the propanoyl-CoA into isobutyryl-CoA.

What Does Free Energy mean in Metabolism?

Free energy is a measurement of how efficiently a reaction takes place. It is the amount of energy produced if 1 mole of glucose was wholly oxidized to CO2.

The idea is that a reaction with a higher amount of free energy will occur more readily than one with a lower amount of free energy. This difference is because the cell will want to save its high-energy molecules to use them for other reactions. Scientists express this value in kilojoules per mole (kJ/mol).

No Free Energy Change (NFE) is the measurement of free energy if a reaction occurs in the same environment as it is taking place.

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Different Free Energy Change (FEC) Measurements

The following are various measurements of free energy changes when different processes occur:

Removal of a compound from a solution

The measurement of free energy if a compound is removed from the solution and placed in its standard state. This means that it would have half of the concentration in the solution.

It would also be added to an equal volume of a standard buffer solution with a pH of 7. The standard state of a compound is when it has left the solution, and its concentration has been reduced by half.

Product formation

It refers to the measurement of free energy if a compound is formed from its decomposition reaction. An example of this would be inorganic phosphate being converted to phosphoenolpyruvate.

Chemical reaction

It would be the measurement of free energy if that reaction were to occur in a biological cell. An example of this would be glyceraldehyde 3-phosphate being converted into 1,3-diphosphoglycerate.

Formation of NADH or NADPH

It refers to the measurement of free energy if 1 NADH or NADPH is formed. An example of this would be when glyceraldehyde 3-phosphate is converted into 1,3-diphosphoglycerate.

ATP formation

Free Energy Change when 1 ATP is formed is the measurement of free energy if 1 ATP is formed. In this example, the free energy change when 1 ATP is formed would be the same as the free energy change when 1 NADH or NADPH is formed.

Inorganic phosphate formation

Free Energy Change for inorganic phosphate formation would be the measurement of free energy if one molecule of inorganic phosphate were formed. It would be the same as inorganic phosphate being converted into phosphoenolpyruvate.

These values are the same no matter what reaction is taking place. The energy change will be less than or equal to zero. It may even be negative to go from a more stable compound to one that is less stable.

For example, the energy change for glyceraldehyde 3-phosphate is -26.5 kJ/mol when it is converted to 1,3-diphosphoglycerate. This is because, in this reaction, glyceraldehyde 3-phosphate has been converted into something more stable.

The overall free energy change for a reaction is the sum of the individual parts. When a reaction takes place, there will be two different energy changes. The enthalpy change is for the forward reaction, and the entropy change is for the reverse reaction.

What is Activation Energy (AE)?

Figure: Activation energy

Activation energy is the minimum amount of energy required for a reaction to occur. It allows it to overcome the activation barriers that are set up in the reaction.

The activation energy for a reaction will be less than or equal to the standard free energy change for that reaction. It is expressed in kilojoules per mole (kJ/mol). This means that the energy of activation will be slightly less positive than the standard free energy change.

An example of activation energy will be if 2,3-diphosphoglycerate is converted into 3-phosphoglycerate. The standard free energy change is -99 kJ/mol. The AE would be -98 kJ/mol to ensure that there are enough bonds for the reaction to occur.

Activation energy is different from the activation barrier. The AE is the minimum amount of energy needed to be overcome for a reaction to occur. The activation barrier is the minimum amount of energy needed for a reaction to overcome the barrier. It usually involves an elementary step that needs to occur.

The activation energy can also be seen as being the difference in energy between reactants and products.  

Shuttle Mechanisms and Bridge Mechanisms

Shuttle Mechanism – An activation energy is needed for the reaction to be able to take place. If two different compounds react together and are separated from one another, the activation energy will be needed to form bonds. The result is that they will still need each other for one to react with the other.

Bridge mechanism-It takes the place of one compound that may be needed for the reaction. An example would be if an enzyme were created using a cofactor instead of an ion.

When a “shuttle mechanism” is used in relation to coenzymes, it also involves phosphorylation and dephosphorylation. A coenzyme is a non-protein structure that helps transfer chemical groups from one enzyme to another. This also includes activating and deactivating them in the process.

The two compounds that are represented by the reaction could be a substrate and an enzyme. It is beneficial when one of the compounds needs to be made more reactive for it to take place.

A “bridge mechanism” is a way for one compound to substitute for the other. It allows for the reaction to take place without one of the compounds.

An example would be if a hydroperoxide were able to substitute for water in the hydrogen peroxide reaction. The process would become more reactive than it was before.

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Summary

Metabolism is the sum of all chemical reactions in a cell that result in energy production and storage. Knowing how to identify metabolic pathways can help you understand Metabolism better and what types of food your body needs for optimal functioning.

Metabolic pathways are a vital component of all living organisms. They are divided into two broad categories: catabolic and anabolic. Catabolic pathways break complex molecules into simpler ones, while anabolic pathways build complex molecules from simple ones.

The pathways provide the chemical reactions for Metabolism. The latter is the process by which energy-yielding compounds in food and oxygen convert into adenosine triphosphate (ATP) that provides us with fuel to run our bodies.

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