What are Biochemical Pathways?
Biochemical or metabolic pathways can be explained as a step by step series of interconnected biochemical reactions and each step is catalysed by a specific enzyme. Whilst these chemical reactions are carried out by a specific enzyme, the substrate is converted to a product which acts as a substrate for subsequent reactions. Thus substrates are being continuously converted into metabolic intermediates eventually producing a final product. An important function of these pathways is to maintain homeostasis of the organism and to keep it alive.
Approximately 1300 enzymes are found in the human cell and these enzymes are coded by a different gene. Metabolism takes place when these enzymes work synchronously resulting in chemical reactions taking place at the rate of 37000 billion times billion per second in the human body. These biochemical catalysts (enzymes) play a critical role as they are the only ones who are capable of making small minute changes to a molecular layer by either breaking a bond or making a bond.
The Role of Enzymes in Metabolic Pathways
Below are various enzymatic control of metabolic pathways are:
Regulation of Glycolysis: Glycolysis is regulated at three enzymes:
Hexokinase: It is hindered by glucose-6-Phosphate
Phosphofructokinase: It is hindered by citrate and ATP
Pyruvate Kinase: This is hindered by ATP, alanine, free fatty acids and acetyl-CoA.
Regulation of Gluconeogenesis: The regulation of flow in gluconeogenesis/ gluconeogenesis is by Pyruvate carboxylase. It activated by acetyl-CoA, which signals the abundance of citric acid cycle intermediates, i.e., a decreased need for glucose
Regulation of Citric Acid Cycle: The primary enzyme that regulates the Krebs or the citric acid cycle is Pyruvate dehydrogenase. It is hindered by its products, NADH and acetyl-CoA.
Citrate Synthase: Hindered by its product, citrate. It is also restrained by intermediates of the TCA cycle at a high level such as succinyl-CoA and NADH.
Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase such as citrate synthase, are inhibited by NADH and succinyl-CoA.
Regulation of the urea acid cycle.
Regulation of fatty acid metabolism.
Regulation of pentose phosphate pathway.
Arrangement of Metabolic Pathways can be Any of the Following:
Linear Pathways – It involves the conversion of one compound through a series of intermediates to another compound. An example would be glycolysis, where glucose is converted to pyruvate.
Branched Divergent Pathway – It is a type of pathway in which an intermediate can enter several linear pathways to different end products. Biosynthesis of purines and of some amino acids are examples of divergent pathways. A certain amount of regulation happens at this point. Branched Convergent as in several precursors which can give rise to a common intermediate. The conversion of various carbohydrates into the glycolytic pathway would be an example of convergent pathways.
Cyclic Pathway forms a closed loop. In the Citric acid cycle, an acetyl group is oxidised via a reaction that regenerates the intermediates in the cycle is a pathway resulting in some intermediates acting catalytically. The TCA is an example of a cyclic pathway.
Spiral pathway- The same set of enzymes catalyse a progressive lengthening of an acetyl chain.
Being multistep, these pathways allow regulation mechanisms to activate one pathway while inhibiting another. The regulation of the metabolites is necessary depending on the needs of the cell and the availability of the substrate. The end product of a pathway can be used immediately, can be used to initiate another metabolic pathway or it may be stored for use later.
Classification of Metabolic Pathways:
Metabolic pathways can be primarily classified into three types:
Anabolic pathways
Catabolic pathways
Amphibolic pathways
Anabolic Pathways
In this type of biochemical pathway, energy is required to form bonds. The reactants, intermediates and products utilised in the reaction are jointly called metabolites. The chemical reactions carried out are concerned with building up or production of complex macromolecules from simpler micro molecules.
A typical example is the synthesis of sugar (glucose from H2O and CO2). Other examples include the synthesis of fatty acids from acetyl CoA, synthesis of larger proteins from amino acids and synthesis of new DNA strands from nucleotides. These reactions are energy demanding which is provided by ATP and other high energy molecules such as NADH and NADPH. The energy that is taken up will be stored in the C-C bond of larger molecules.
List of Examples for Major Anabolic Pathways:
Photosynthesis
Gluconeogenesis
Protein biosynthesis
Fatty synthesis
Pentose phosphate pathway
Catabolic Pathways
These types of catabolic pathways have chemical reactions involving the breaking down of complex macromolecules into micro molecules and hence the release of a large amount of bond energy. An example is the breakdown of sugar. When these reactions occur, energy stored in covalent bonds such as C-C bonds will get released.
Examples of Catabolic Pathways:
Glycolysis
TCA cycle
Oxidative phosphorylation
Beta oxidation of fatty acid
Urea cycle
Glycogenolysis
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Amphibolic Pathways
Amphibolic pathways are either circular or linear. The intermediate in the pathway can be the starting point of another pathway. As an example, the breakdown of respiratory substrates such as proteins, glucose and fatty acids.
When glucose acts as a respiratory substrate, it is oxidised to pyruvate and then to acetyl CoA. Also, beta-oxidation of fatty acid results in the formation of acetyl-CoA. When protein undergoes degradation, it forms either pyruvate or acetyl-CoA. However, when the cell needs to prepare glucose or fatty acid or protein, either acetyl CoA or pyruvate can be withdrawn from the catabolic pathway and diverted for the synthesis of glucose or fatty acids or amino acid.
Hence, there is always an existence of a link between the anabolic and the catabolic process, it would be considered the respiratory pathway is amphibolic.
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Feedback Mechanism
The feedback mechanism is important as it is the only way it can avoid wasting energy in making end-products that are already in plenty.
The process is carried out when the final product of a pathway controls the rate of its synthesis through inhibition of its first step.
Enzyme inhibition starts when an inhibitor fixes itself to the active site of the enzyme and the substrate cannot bind to the enzyme. This stalls the sequence of the metabolic pathway.
The inhibitor denatures the enzyme so that it cannot work anymore, but the binding is temporary. As soon as the inhibitor disengages the enzymes go back to its active shape and continue to work on this substrate and the pathways open up once again.
It is this way, homeostasis is maintained concerning the amount of end product that is produced.
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FAQs on Biochemical Pathways
1. What is a biochemical pathway?
A biochemical pathway, also known as a metabolic pathway, is a sequence of connected chemical reactions occurring within a cell. In this series, the product of one reaction serves as the substrate (starting material) for the next. Each step is precisely catalysed by a specific enzyme, ensuring the efficient conversion of molecules to meet the cell's needs.
2. What are the main types of biochemical pathways?
Biochemical pathways are primarily classified into three types based on their overall function and energy flow:
- Anabolic Pathways: These pathways build complex molecules from simpler ones and require an input of energy. An example is the synthesis of proteins from amino acids.
- Catabolic Pathways: These pathways break down complex molecules into simpler units, releasing energy in the process. A key example is glycolysis, the breakdown of glucose.
- Amphibolic Pathways: These pathways can function as both anabolic and catabolic, serving as a link between breakdown and synthesis processes. The Krebs cycle is a prime example.
3. What are some key examples of biochemical pathways in living organisms?
Some of the most important biochemical pathways essential for life include:
- Glycolysis: The breakdown of a glucose molecule into two pyruvate molecules.
- Krebs Cycle (Citric Acid Cycle): A central pathway that oxidises acetyl-CoA to produce energy carriers like ATP, NADH, and FADH2.
- Oxidative Phosphorylation: The process where energy from electron carriers is used to generate a large amount of ATP.
- Photosynthesis: The process in plants and some other organisms to convert light energy into chemical energy.
- Urea Cycle: A pathway to remove toxic ammonia from the body by converting it into urea.
4. What is the importance of enzymes in a biochemical pathway?
Enzymes are vital biological catalysts that make biochemical pathways possible. Their importance lies in their ability to dramatically speed up the rate of specific reactions without being consumed. Each enzyme has a unique active site that binds to a specific substrate, ensuring that the correct reaction occurs at the right time. Without enzymes, metabolic reactions would proceed too slowly to sustain life.
5. How are anabolic and catabolic pathways different?
The main difference between anabolic and catabolic pathways lies in their purpose and energy relationship. Catabolic pathways are degradative; they break down large, complex molecules to release energy (exergonic processes). In contrast, anabolic pathways are synthetic; they use this energy to build complex molecules from smaller ones (endergonic processes). Essentially, catabolism provides the energy that anabolism consumes.
6. Why is the regulation of biochemical pathways essential for a cell?
The regulation of biochemical pathways is critical for maintaining homeostasis, the stable internal environment of a cell. It allows the cell to respond to changing conditions and prevents the wasteful overproduction of molecules or excessive energy expenditure. By controlling key enzymes in a pathway, often through mechanisms like feedback inhibition, the cell can ensure that products are synthesized only when and in the amount they are needed.
7. What is an amphibolic pathway, with an example?
An amphibolic pathway is a metabolic pathway that has a dual function, participating in both catabolism (breakdown) and anabolism (synthesis). Intermediates within the pathway can be either further broken down to release energy or withdrawn to serve as precursors for building other molecules. The most common example is the Krebs cycle. While it catabolises acetyl-CoA to produce energy, its intermediates (like α-ketoglutarate and oxaloacetate) can be used to synthesise amino acids.
8. How can a single gene mutation disrupt an entire metabolic pathway?
A gene contains the instructions for making a specific enzyme. A mutation in that gene can lead to the production of a malformed or non-functional enzyme. Since each step of a metabolic pathway relies on a specific functional enzyme, the absence of just one can create a bottleneck. The substrate for the missing enzyme accumulates, and the subsequent products cannot be formed, effectively halting the entire pathway and potentially causing a metabolic disorder.
9. What does it mean for a biochemical pathway to be linear, cyclic, or branched?
These terms describe the overall structure and flow of reactions in a pathway:
- Linear Pathway: Follows a straight sequence where a starting substrate is converted through a series of intermediates to a final product. Glycolysis is a prime example.
- Cyclic Pathway: Forms a closed loop where an intermediate from the end of the pathway is regenerated to begin the cycle again. The Krebs cycle is the classic example.
- Branched Pathway: An intermediate compound can act as a branch point, entering several different pathways to yield different end products. The synthesis of various amino acids often follows branched pathways.
10. What is the concept of feedback inhibition in the context of metabolic pathways?
Feedback inhibition is a common and efficient form of metabolic regulation. It occurs when the final product of a pathway binds to an enzyme that functions early in the sequence, inhibiting its activity. This self-regulating mechanism prevents the cell from wasting energy and resources by making more of a product that is already abundant. When the product's concentration decreases, it detaches from the enzyme, allowing the pathway to become active again.
