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Enzymes Bioenergetics

Enzymes Bioenergetics

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Enzymes are like superheroes in our bodies. They are natural substances that help to speed up chemical reactions that occur in all living things. These reactions take place inside cells and involve changing one molecule into another. Enzymes are special because they are not consumed or 'used up' during these reactions. This means they can be reused over and over again to help with many different reactions.

Most enzymes are proteins, specifically globular proteins. These are functional proteins that perform metabolic functions such as acting as enzymes, carriers, hormones, receptors, and more. A more recent discovery, ribozymes, are RNA molecules with enzymatic capabilities. This means that they function as enzymes, even though they are made of a different molecule than most enzymes.

One example of an enzyme is alpha-amylase, found in human saliva. It is a type of protein with a unique 3-D structure made up of regions coiled in α-helix and β-sheets. To learn more about protein structure, check out our article on Protein Structure.

Overall, enzymes are essential for our bodies to function properly. Understanding more about enzymes and their role in bioenergetics can help us appreciate the complexities of our bodies and the importance of proper nutrition.

Ribbon diagram of the enzyme salivary alpha-amylase
Ribbon diagram of the enzyme salivary alpha-amylase

Where do enzymes get their names?

You may have noticed that all enzyme names end in -ase. Enzymes get their names from the substrate or the chemical reaction they catalyse. Have a look at the table below. Reactions involving various substrates such as lactose and starch, and chemical reactions such as oxidation/reduction reactions, are catalysed by enzymes.

Examples of enzymes, their substrates and functions
Examples of enzymes, their substrates and functions

Glucose oxidase (sometimes written in the shorter form GOx or GOD) exhibits antibacterial activities. We find it in honey, serving as a natural preservative (i.e., it kills microbes). Female honey bees produce glucose oxidase and do not reproduce (unlike queen bees, they are called worker bees).

The structure of enzymes

Enzymes have a unique shape that helps them function properly. They are like tiny spheres made up of twisted and folded chains of amino acids. This three-dimensional shape is essential for their function.

Each enzyme has a specific area called the active site, which is like a small dent on the surface of the enzyme. The active site has a few amino acids that can temporarily bond with other molecules. Only one active site exists on each enzyme, and the molecule that binds to it is called a substrate. When the substrate temporarily binds to the active site, an enzyme-substrate complex is created.

This interaction between the enzyme and substrate is crucial for chemical reactions to occur quickly and efficiently in the body. Without enzymes, many of these reactions would take too long to happen, and our bodies wouldn't be able to function properly.

How does an enzyme-substrate complex form?

Let's break down the process of how enzymes and substrates work together to create chemical reactions:

  1. A substrate collides with the enzyme and binds to the active site, forming an enzyme-substrate complex. This requires a specific orientation and speed.
  2. The enzyme catalyzes the reaction, causing the substrate to convert into one or more products. This forms an enzyme-product complex.
  3. The products detach from the enzyme, leaving the enzyme free to be used again.

It's essential to understand the difference between enzymes, substrates, and products. In some, there be multiple substrates and products involved. Check out the image below to see how both enzyme-substrate and enzyme-product complexes form.

By understanding how enzymes and substrates work together, we can better appreciate the role these molecules play in our bodies and how they help keep us healthy.

A substrate binding to an enzyme forms the enzyme-substrate complex, followed by the enzyme-product complex
A substrate binding to an enzyme forms the enzyme-substrate complex, followed by the enzyme-product complex

This is an interesting question and one that scientists have been trying to answer for a long time. The relationship between genes and enzymes is a critical aspect of molecular biology, and understanding how it developed is crucial to our understanding of life itself.

To answer your question, it's important to note that genes and enzymes are both essential components of life. Genes are the instructions for making proteins, including enzymes. Enzymes, on the other hand, are the catalysts that facilitate the chemical reactions necessary for life.

It's believed that enzymes came first in the evolution of life. These enzymes were simple in structure and had broad functions, catalyzing a variety of chemical reactions. Over time, as organisms became more complex, new enzymes with more specific functions evolved through the process of gene duplication and mutation.

Eventually, genes evolved to encode for specific enzymes, which allowed for even greater control over cellular processes. This evolution of genes and enzymes is believed to be a crucial step in the development of complex life as we know it.

While we don't fully understand the origin of this relationship between genes and enzymes, it's clear that they both play essential roles in the development and function of all living organisms.

The induced-fit model of enzyme action

There is a clear difference the active sites and the general shapes of enzymes and substrates in Figures 2 and 3. In Figure 2, the lock-and-key model, the active site and substrate are depicted as rigid, geometric shapes that together perfectly like a key in a lock suggests that the enzyme's active site is a fixed shape, and the substrate must have a complementary shape for it to bind and catalyze the reaction.

However, in Figure 3, the induced-fit model, the active site is depicted as a flexible structure that changes shape when the substrate binds to it. This model suggests that the active site is not fixed but adapts to the shape of the substrate. The conformational changes that occur when the substrate binds to the enzyme's active site maximize the enzyme's ability to catalyze the reaction.

The induced-fit model is a more accurate representation of how enzymes and substrates interact in chemical reactions. It explains how enzymes can be specific to certain reactions while still being able to catalyze a wide range of reactions. The conformational changes that occur in the active site when the substrate binds allow for a more precise fit and efficient catalysis of the reaction.

Overall, the induced-fit model provides a better understanding of how enzymes work and how their structure and function are closely intertwined.

 

The active site changes shape when a substrate binds to it, followed by the formation of the enzyme-substrate complex
The active site changes shape when a substrate binds to it, followed by the formation of the enzyme-substrate complex

That's correct! Cofactors play a crucial role in enzyme function and can be inorganic or organic molecules that bind to the enzyme's active site or other specific sites to facilitate catalysis. Inorganic cofactors, such as metal ions, often help stabilize the enzyme's structure or participate directly in the reaction. Organic cofactors, also known as coenzymes, are typically derived from vitamins and often participate in redox reactions, such as the transfer of electrons.

One such coenzyme is NADPH, which is important in cellular respiration and photosynthesis. NADPH is a critical molecule in the production of ATP, which is the primary energy source used by cells. NADPH is involved in the process of electron transport, which helps generate a proton gradient across the mitochondrial membrane, driving ATP synthesis.

Overall, the role of cofactors such as NADPH in enzyme function cannot be overstated. These molecules play an essential role in facilitating the biochemical reactions necessary for life and are crucial to many metabolic processes.

The function of enzymes

That's absolutely correct!es lower the activation energy required for a reaction to occur, which allows the reaction to proceed more quickly and efficiently. By lowering the activation energy, enzymes make it easier for the reactants to overcome the energy barrier and form the products.

Enzymes achieve this by providing an alternative pathway for the reaction to occur, one that has a lower energy barrier than the uncatalyzed reaction. This alternative pathway involves the formation of an enzyme-substrate complex that is more stable than the transition state, which is the high-energy intermediate that must be formed for the reaction to proceed. By stabilizing the transition state, enzymes lower the activation energy needed to reach it, making the reaction faster and more efficient.

As you noted, enzymes also allow reactions to occur at lower temperatures than would typically be required. This is because they lower the activation energy, allowing the reaction to proceed at a lower temperature. This is essential for living organisms, which must maintain a constant internal temperature to survive.

Overall, enzymes play a crucial role in biochemical reactions by lowering the activation energy and allowing reactions to occur more quickly and efficiently, even at lower temperatures.

The difference in activation energy between two reactions, only one of which is catalysed by an enzyme (the blue curve)
The difference in activation energy between two reactions, only one of which is catalysed by an enzyme (the blue curve)

Factors affecting enzyme activity

Enzymes are sensitive to certain conditions in the body. Can enzymes, these powerful little machines, ever be altered? Do substrates bind to altered enzymes? Several factors affect enzyme activity, including temperature, pH, enzyme and substrate concentrations, and competitive and non-competitive inhibitors. They can cause the denaturation of enzymes. Denaturation is the process in which external factors such as temperature or changes in acidity alter the molecular structure. Denaturation of proteins (and, therefore, enzymes) involves modifications of the complex 3-D protein structure to such an extent that they no longer function properly or even stop functioning altogether.

Changes in external factors such as heat (2) affect the protein's 3-D structure (1), causing it to unfold (3) (the protein denatures)
Changes in external factors such as heat (2) affect the protein's 3-D structure (1), causing it to unfold (3) (the protein denatures)

Temperature changes affect the kinetic energy required to carry out reactions, especially the collision of enzymes and substrates. Too low a temperature results in insufficient energy, while too high results in denaturation of the enzyme. Changes in pH affect the amino acids in the active site. These changes break the bonds between the amino acids, causing the active site to change shape, i.e. the enzyme denatures.

Enzyme and substrate concentration affect the number of collisions between enzymes and substrates. Competitive inhibitors bind to the active site and not to the substrates. In contrast, non-competitive inhibitors bind elsewhere on the enzyme, causing the active site to change shape and become non-functional (again, denaturation). When these conditions are optimal, the collision between enzymes and substrates is most significant. You can learn more about these factors in our article Factors Affecting Enzyme Activity. There are thousands of enzymes involved in different pathways, where they perform different roles. Next, we will discuss some of the functions of enzymes.

The function of enzymes in catabolism

Catabolic reactions involve the breakdown of complex molecules into simpler ones, releasing energy in the process. This energy can then be used by the cell to perform various functions. Enzymes accelerate these reactions by lowering the activation energy required for the reaction to occur.

As you mentioned, food digestion is a major example of a catabolic reaction. The enzymes responsible for breaking down carbohydrates, proteins, and lipids are essential for the process. Amylases break down carbohydrates into simple sugars, proteases break down proteins into amino acids, and lipases break down lipids fatty acids and glycerol.

colic process is cellular respiration, which involves the breakdown of glucose into ATP, the primary energy source used by cells. Enzymes such as ATP synthase play a crucial role in this process by catalyzing the formation of ATP through oxidative phosphorylation.

Overall, enzymes are essential for catabolic reactions, allowing cells to break down complex molecules and release energy that can be used for various cellular processes.

The function of enzymes in anabolism or biosynthesis

In anabolic reactions, simple molecules are joined together to form more complex molecules, requiring energy input. These reactions are essential for building up macromolecules such as carbohydrates, proteins, and nucleic acids.

As you mentioned, anabolic reactions involve the binding of two or more substrates to the enzyme's active site, where they are joined together to form a single product. Enzymes play a crucial role in these reactions by lowering the activation energy required for the reaction to occur, allowing the reaction to proceed more quickly and efficiently.

Protein synthesis is a key example of anabolic reactions. RNA polymerase is the central enzyme in the process of transcription, which involves the synthesis of RNA from a DNA template. DNA synthesis is also an anabolic reaction, with enzymes such as DNA helicase and DNA polymerase playing crucial roles in joining nucleotides together to form a new DNA strand.

Photosynthesis is another important anabolic reaction, in which the enzyme RUBISCO plays a central role. RUBISCO is responsible for fixing carbon dioxide from the atmosphere and incorporating it into organic molecules such as glucose.

Overall, anabolic reactions are essential for building up complex molecules from simple ones, and enzymes play a crucial role in catalyzing these reactions.

Enzymes in other roles

Great job summarizing the key takeaways about enzymes!

Enzymes are biological catalysts that accelerate chemical reactions and can be reused. The active site of an enzyme is a depression on its surface where substrates bind. When a substrate binds to the active site, an enzyme-substrate complex is formed, followed by an enzyme-product complex.

The induced-fit model suggests that the active site only forms when the substrate binds to the enzyme, and that the active site has a form complementary to the substrate. Enzymes lower the activation energy required to initiate a reaction, making it easier and faster for the reaction to occur.

Enzymes play a crucial role in both catabolic and anabolic reactions. Catabolic reactions involve the breakdown of complex molecules into simpler ones, such as in food digestion and cellular respiration. Anabolic reactions involve the synthesis of complex molecules from simpler ones, such as in protein synthesis and photosynthesis.

Enzymes also play important roles in other processes, such as protein kinase enzymes that affect transcription in response to chemical and physical signals, and ATPase enzymes that hydrolyze ATP to generate energy for muscle contraction. Reverse transcriptase is enzyme that plays role in DNA, such as in the replication of viruses.

Overall, enzymes are essential for many biological processes and have a wide range of functions in the body.

Enzymes

What are enzymes?

Enzymes are biological catalysts in biochemical reactions. They accelerate the rate of chemical reactions by lowering the activation energy.

What type of enzymes are not proteins?

All enzymes are proteins. However, ribozymes (ribonucleic acid enzymes) exist, which are RNA molecules with enzymatic abilities.

What are the most common enzymes?

Carbohydrases, lipases, and proteases.

How do enzymes function?

Enzymes catalyse (accelerate) chemical reactions by lowering the activation energy necessary for the reaction to start.

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