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3.1 Enzyme Structure

5 min readjanuary 11, 2023

Jed Quiaoit

Jed Quiaoit

Caroline Koffke

Caroline Koffke

Jed Quiaoit

Jed Quiaoit

Caroline Koffke

Caroline Koffke

One of the ways in which living systems maintain their highly complex organization is through the constant input of energy. This energy is typically obtained through , such as or , which involve the conversion of nutrients into usable energy. In addition to providing the energy needed to fuel cellular processes, this constant input of energy also helps to maintain the structural integrity of the cell. For these processes to occur, are required.

are a crucial component of the highly complex organization of living systems. These specialized proteins act as catalysts, speeding up chemical reactions within cells and enabling them to carry out the many functions necessary for life. are involved in a wide range of cellular processes, including metabolism, cell division, and gene expression, and they are essential for the proper functioning of cells. ⚡

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-lKEWcZ3OTxYS.png?alt=media&token=410147ee-efe6-4af8-909e-27fe1e818863

Source: Wikimedia Commons

Shape of Enzymes

It is important to understand the structure of and how it relates to their function as are the workhorses of the cell, catalyzing the chemical reactions necessary for metabolism, growth, and reproduction. The structure of plays a critical role in their ability to carry out these functions. ⚪

are composed of one or more , which are long chains of . The specific sequence of in an enzyme determines its . The is the linear sequence of in a polypeptide or protein. However, alone cannot account for the complexity and diversity of enzyme function, this is where the higher levels of structure come into play. 🐜

The specific arrangement of the amino acid residues in space determines the enzyme's three-dimensional structure, which is crucial for its function. The three-dimensional structure of can be divided into several levels:

  • Secondary structure, which refers to the local patterning of the , such as the formation of alpha-helices or beta-sheets.

  • Tertiary structure, which refers to the overall three-dimensional conformation of the enzyme, including the location of the and other functional groups.

  • Quaternary structure, which refers to the spatial relationship between the subunits in multimeric (Multimeric refers to a complex of multiple identical or non-identical subunits).

function by binding to substrate molecules and catalyzing specific chemical reactions. The of an enzyme is the region of the enzyme where the substrate binds and the reaction takes place. The three-dimensional structure of the enzyme, including the , must be complementary to the substrate in order for the enzyme to bind to it and catalyze the reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2FEnzyme_mechanism_1.jpg?alt=media&token=266c6c0c-10a0-49be-9008-e4479081ca10

Source: WikiMedia Commons.

Furthermore, are dynamic molecules that can change shape upon binding to substrate or other molecules, this is known as the induced fit mechanism. This conformational change can enhance the specificity and efficiency of the enzyme-substrate interaction, thus increasing the rate of the chemical reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F648px-Induced_fit_diagram.png?alt=media&token=c2a83e87-c8d0-43f6-8e3f-a2b6b873de81

Source: WikiMedia Commons.

Active Site

have a specific region called the , which is where the substrate(s) bind and the chemical reaction takes place. The is usually a depression or cleft on the surface of the enzyme and is often lined with specific that interact with the substrate. 🧑‍🤝‍🧑

are highly specific and only catalyze specific reactions. This specificity is due to the specific shape of the , which only fits the substrate for which it is intended.

In order for an enzyme-mediated chemical reaction to occur, the substrate must first bind to the of the enzyme. The is a specific region on the surface of the enzyme that is designed to interact with the substrate.

The shape and charge of the substrate must be compatible with the of the enzyme in order for the substrate to bind effectively. This is because the is specifically shaped to fit the substrate, and the that make up the often have specific charges that interact with the substrate.

If the shape or charge of the substrate is not compatible with the of the enzyme, the substrate will not bind effectively, and the chemical reaction will not occur.

Likewise, can be regulated to control the rate of a reaction. This can be done by several mechanisms, including allosteric regulation, where a molecule binds to a specific site on the enzyme (called an allosteric site) and changes the shape of the , causing the enzyme to either become more or less active. can also be regulated by the concentration of substrate or the presence of an inhibitor. 👎

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-ZcOnoxHa5dET.webp?alt=media&token=10074443-02b5-47f0-bc46-b8eacbd4548a

Source: Jack Westin

Induced Fit

Induced fit is a mechanism (model) of enzyme in which the enzyme changes its conformation or shape upon binding to the substrate, resulting in a tighter and more specific binding of the enzyme and substrate, and ultimately, a more efficient catalytic reaction. 🧤

In induced fit, the enzyme's is not a rigid, pre-formed structure that exactly matches the substrate's shape (think of a glove snugly fitting into your hand), but rather a flexible structure that adjusts its conformation upon binding to the substrate. As the substrate enters the , the enzyme's amino acid residues in the move slightly to adjust their positions, resulting in a tighter fit between the enzyme and substrate. This tighter fit allows for more efficient formation of the , which is the high-energy intermediate between the substrate and the products, and hence increases the rate of the reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-564dwr519UIO.webp?alt=media&token=aa0357a1-0568-4fce-9595-2588a37a873b

Source: Biology Dictionary

This mechanism of enzyme can also play a role in . When the enzyme's is flexible, it can adjust its conformation to fit a variety of different substrates. However, the adjustments it makes to bind different substrates may be different, and only the substrate that fits the the best will be catalyzed with the highest efficiency.

In addition, induced fit can also contribute to the regulation of enzyme activity by controlling the rate of substrate binding and product release. Some can tightly bind the substrate only in certain conditions such as the presence of a or a specific environment, in these cases the is more relevant for the regulation of the enzyme activity than for .

Key Terms to Review (18)

Active Site

: The active site is the region on an enzyme where substrate molecules bind and undergo chemical reaction.

Allosteric Regulation

: Allosteric regulation is a process that can increase or decrease the activity of an enzyme by binding to a protein at a site other than its active site.

Amino Acids

: Amino acids are organic compounds that combine to form proteins. They are the building blocks of life and are vital for a number of functions in the body.

Catalysis

: Catalysis is the process by which catalysts speed up chemical reactions without being consumed or altered themselves.

Cofactor

: A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity.

Enzymes

: Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process.

Induced Fit Mechanism

: The induced fit mechanism is a process that occurs when an enzyme changes its shape slightly to accommodate the binding of a specific substrate.

Metabolic Processes

: Metabolic processes are all the chemical reactions that occur within an organism to maintain life, including both breaking down substances for energy (catabolism) and building new cells and tissues (anabolism).

Photosynthesis

: Photosynthesis is the process by which green plants, algae, and some bacteria use sunlight to synthesize foods with the help of chlorophyll pigments. They convert carbon dioxide and water into glucose (a type of sugar) and oxygen.

Polypeptide Chains

: Polypeptide chains are long sequences of amino acids linked by peptide bonds. They fold into specific shapes to form proteins.

Primary Structure

: The primary structure of a protein refers to the sequence of amino acids that make up the protein. It's like the unique order of letters in a sentence.

Quaternary Structure

: The quaternary structure of a protein refers to the way in which multiple polypeptide chains (proteins) come together and interact. It's the highest level of organization in a protein.

Respiration

: Respiration is the process by which cells break down simple food molecules such as glucose and release the energy they contain.

Secondary Structure

: The secondary structure refers to how those sequences or strings (primary structures) fold upon themselves due to hydrogen bonding between backbone elements. Common forms include alpha-helices and beta-sheets.

Substrate Molecules

: Substrate molecules are reactants upon which enzymes act during biochemical reactions. They bind at an enzyme's active site and get converted into products through chemical reactions.

Substrate Specificity

: Substrate specificity refers to how particular enzymes can only catalyze certain substrates due their unique active site shapes and properties.

Tertiary Structure

: The tertiary structure of a protein is its three-dimensional shape, formed by further folding and bending of the secondary structures into a complex shape due to interactions between side chains of amino acids.

Transition State

: The transition state refers to the highest-energy state of a reaction, where old bonds are breaking and new ones are forming.

3.1 Enzyme Structure

5 min readjanuary 11, 2023

Jed Quiaoit

Jed Quiaoit

Caroline Koffke

Caroline Koffke

Jed Quiaoit

Jed Quiaoit

Caroline Koffke

Caroline Koffke

One of the ways in which living systems maintain their highly complex organization is through the constant input of energy. This energy is typically obtained through , such as or , which involve the conversion of nutrients into usable energy. In addition to providing the energy needed to fuel cellular processes, this constant input of energy also helps to maintain the structural integrity of the cell. For these processes to occur, are required.

are a crucial component of the highly complex organization of living systems. These specialized proteins act as catalysts, speeding up chemical reactions within cells and enabling them to carry out the many functions necessary for life. are involved in a wide range of cellular processes, including metabolism, cell division, and gene expression, and they are essential for the proper functioning of cells. ⚡

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-lKEWcZ3OTxYS.png?alt=media&token=410147ee-efe6-4af8-909e-27fe1e818863

Source: Wikimedia Commons

Shape of Enzymes

It is important to understand the structure of and how it relates to their function as are the workhorses of the cell, catalyzing the chemical reactions necessary for metabolism, growth, and reproduction. The structure of plays a critical role in their ability to carry out these functions. ⚪

are composed of one or more , which are long chains of . The specific sequence of in an enzyme determines its . The is the linear sequence of in a polypeptide or protein. However, alone cannot account for the complexity and diversity of enzyme function, this is where the higher levels of structure come into play. 🐜

The specific arrangement of the amino acid residues in space determines the enzyme's three-dimensional structure, which is crucial for its function. The three-dimensional structure of can be divided into several levels:

  • Secondary structure, which refers to the local patterning of the , such as the formation of alpha-helices or beta-sheets.

  • Tertiary structure, which refers to the overall three-dimensional conformation of the enzyme, including the location of the and other functional groups.

  • Quaternary structure, which refers to the spatial relationship between the subunits in multimeric (Multimeric refers to a complex of multiple identical or non-identical subunits).

function by binding to substrate molecules and catalyzing specific chemical reactions. The of an enzyme is the region of the enzyme where the substrate binds and the reaction takes place. The three-dimensional structure of the enzyme, including the , must be complementary to the substrate in order for the enzyme to bind to it and catalyze the reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2FEnzyme_mechanism_1.jpg?alt=media&token=266c6c0c-10a0-49be-9008-e4479081ca10

Source: WikiMedia Commons.

Furthermore, are dynamic molecules that can change shape upon binding to substrate or other molecules, this is known as the induced fit mechanism. This conformational change can enhance the specificity and efficiency of the enzyme-substrate interaction, thus increasing the rate of the chemical reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F648px-Induced_fit_diagram.png?alt=media&token=c2a83e87-c8d0-43f6-8e3f-a2b6b873de81

Source: WikiMedia Commons.

Active Site

have a specific region called the , which is where the substrate(s) bind and the chemical reaction takes place. The is usually a depression or cleft on the surface of the enzyme and is often lined with specific that interact with the substrate. 🧑‍🤝‍🧑

are highly specific and only catalyze specific reactions. This specificity is due to the specific shape of the , which only fits the substrate for which it is intended.

In order for an enzyme-mediated chemical reaction to occur, the substrate must first bind to the of the enzyme. The is a specific region on the surface of the enzyme that is designed to interact with the substrate.

The shape and charge of the substrate must be compatible with the of the enzyme in order for the substrate to bind effectively. This is because the is specifically shaped to fit the substrate, and the that make up the often have specific charges that interact with the substrate.

If the shape or charge of the substrate is not compatible with the of the enzyme, the substrate will not bind effectively, and the chemical reaction will not occur.

Likewise, can be regulated to control the rate of a reaction. This can be done by several mechanisms, including allosteric regulation, where a molecule binds to a specific site on the enzyme (called an allosteric site) and changes the shape of the , causing the enzyme to either become more or less active. can also be regulated by the concentration of substrate or the presence of an inhibitor. 👎

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-ZcOnoxHa5dET.webp?alt=media&token=10074443-02b5-47f0-bc46-b8eacbd4548a

Source: Jack Westin

Induced Fit

Induced fit is a mechanism (model) of enzyme in which the enzyme changes its conformation or shape upon binding to the substrate, resulting in a tighter and more specific binding of the enzyme and substrate, and ultimately, a more efficient catalytic reaction. 🧤

In induced fit, the enzyme's is not a rigid, pre-formed structure that exactly matches the substrate's shape (think of a glove snugly fitting into your hand), but rather a flexible structure that adjusts its conformation upon binding to the substrate. As the substrate enters the , the enzyme's amino acid residues in the move slightly to adjust their positions, resulting in a tighter fit between the enzyme and substrate. This tighter fit allows for more efficient formation of the , which is the high-energy intermediate between the substrate and the products, and hence increases the rate of the reaction.

https://firebasestorage.googleapis.com/v0/b/fiveable-92889.appspot.com/o/images%2F-564dwr519UIO.webp?alt=media&token=aa0357a1-0568-4fce-9595-2588a37a873b

Source: Biology Dictionary

This mechanism of enzyme can also play a role in . When the enzyme's is flexible, it can adjust its conformation to fit a variety of different substrates. However, the adjustments it makes to bind different substrates may be different, and only the substrate that fits the the best will be catalyzed with the highest efficiency.

In addition, induced fit can also contribute to the regulation of enzyme activity by controlling the rate of substrate binding and product release. Some can tightly bind the substrate only in certain conditions such as the presence of a or a specific environment, in these cases the is more relevant for the regulation of the enzyme activity than for .

Key Terms to Review (18)

Active Site

: The active site is the region on an enzyme where substrate molecules bind and undergo chemical reaction.

Allosteric Regulation

: Allosteric regulation is a process that can increase or decrease the activity of an enzyme by binding to a protein at a site other than its active site.

Amino Acids

: Amino acids are organic compounds that combine to form proteins. They are the building blocks of life and are vital for a number of functions in the body.

Catalysis

: Catalysis is the process by which catalysts speed up chemical reactions without being consumed or altered themselves.

Cofactor

: A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity.

Enzymes

: Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process.

Induced Fit Mechanism

: The induced fit mechanism is a process that occurs when an enzyme changes its shape slightly to accommodate the binding of a specific substrate.

Metabolic Processes

: Metabolic processes are all the chemical reactions that occur within an organism to maintain life, including both breaking down substances for energy (catabolism) and building new cells and tissues (anabolism).

Photosynthesis

: Photosynthesis is the process by which green plants, algae, and some bacteria use sunlight to synthesize foods with the help of chlorophyll pigments. They convert carbon dioxide and water into glucose (a type of sugar) and oxygen.

Polypeptide Chains

: Polypeptide chains are long sequences of amino acids linked by peptide bonds. They fold into specific shapes to form proteins.

Primary Structure

: The primary structure of a protein refers to the sequence of amino acids that make up the protein. It's like the unique order of letters in a sentence.

Quaternary Structure

: The quaternary structure of a protein refers to the way in which multiple polypeptide chains (proteins) come together and interact. It's the highest level of organization in a protein.

Respiration

: Respiration is the process by which cells break down simple food molecules such as glucose and release the energy they contain.

Secondary Structure

: The secondary structure refers to how those sequences or strings (primary structures) fold upon themselves due to hydrogen bonding between backbone elements. Common forms include alpha-helices and beta-sheets.

Substrate Molecules

: Substrate molecules are reactants upon which enzymes act during biochemical reactions. They bind at an enzyme's active site and get converted into products through chemical reactions.

Substrate Specificity

: Substrate specificity refers to how particular enzymes can only catalyze certain substrates due their unique active site shapes and properties.

Tertiary Structure

: The tertiary structure of a protein is its three-dimensional shape, formed by further folding and bending of the secondary structures into a complex shape due to interactions between side chains of amino acids.

Transition State

: The transition state refers to the highest-energy state of a reaction, where old bonds are breaking and new ones are forming.


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© 2024 Fiveable Inc. All rights reserved.

AP® and SAT® are trademarks registered by the College Board, which is not affiliated with, and does not endorse this website.