Study Notes on Catalysts and Enzymes
Catalysts and Enzymes
Catalysts
Definition: Catalysts are substances that speed up chemical reactions.
Function:
They lower the activation energy required for a reaction to occur.
Result: Because less energy is needed to start the reaction, the rate of the reaction increases.
Characteristics:
Catalysts remain unchanged after the reaction.
They do not alter the initial and final energy levels of the reactants and products.
Activation Energy
Definition: Activation energy is the minimum energy required for a reaction to occur.
Explanation:
An analogy is made comparing the process of pushing a rock over a hill: the rock (reaction) cannot quickly be pushed (occur) unless it possesses sufficient energy (activation energy).
If the height of the hill (activation energy) were lower, the rock (reaction) could be pushed over more quickly, demonstrating how lower activation energy speeds up reactions.
Energy of Life
Living organisms require energy for survival, which is obtained through chemical reactions.
These reactions must occur rapidly for life processes to function efficiently.
Enzymes: Biological Catalysts
Definition: Enzymes are specialized catalysts produced by living organisms, primarily proteins.
Discovery: In 1982, researchers Sidney Altman and Thomas Cech discovered that certain RNA molecules, known as ribozymes, can also act as enzymes. Currently, RNA catalyzes over 100 cellular reactions.
Function of Enzymes:
Like catalysts, enzymes decrease activation energies and thus speed up chemical reactions within living organisms.
How Enzymes Work
Mechanism:
Enzymes increase the reaction speed by decreasing the activation energy, yet they do not change the Gibbs free energy (ΔG) of the reaction, meaning that the energy of the reactants and products remains unchanged.
Naming Enzymes
Suffix: Many enzymes tend to have names that end with the suffix “ase.”
Examples: Some examples include lactase, amylase, and peptidase, which are discussed in detail later.
Common Enzymes
Lactase:
Function: Helps in the digestion of dairy products.
Activity: Lactase breaks down lactose (a disaccharide found in dairy) into two monosaccharides.
Lactose Intolerance:
Condition where individuals have trouble digesting dairy due to decreased lactase production in adulthood.
Solution: Lactaid pills can be taken which contain lactase for individuals who cannot produce it.
Amylase:
Location: Found in human saliva.
Function: Initiates carbohydrate digestion by breaking down starchy foods into maltose (a disaccharide).
Process: Amylase acts on starch (found in potatoes) during chewing, converting it into smaller sugar molecules (maltose).
Peptidases:
Definition: A family of enzymes that breaks down proteins into polypeptides and amino acids by catalyzing hydrolysis reactions that break peptide bonds.
Example: Peptidase 1, an allergen from dust mite feces, may cause human allergies.
How do Enzymes Decrease Activation Energy?
Active Site:
Enzymes create an active site, which is a specific space for substrates (reactants) to bind. This arrangement helps lower the activation energy by positioning substrates optimally to break and form new bonds, allowing reactions to occur more rapidly than in a random environment.
Transition States
Definition: A transition state is an unstable intermediate molecule that exists between reactants and products during a reaction.
Characteristics:
Transition states have higher energy than either the reactants or products, making them unstable.
The enzyme's active site provides a conducive chemical environment to stabilize transition states, thereby lowering their energy and expediting the reaction.
Induced Fit Model
Description: Each enzyme has a specific shape that allows it to interact optimally with particular substrates.
Mechanism:
When substrates approach the active site, the enzyme's shape slightly changes to better accommodate the substrates, a phenomenon known as induced fit.
Enzyme-Substrate Complex
Definition: The interaction where substrates fit into the enzyme is known as the enzyme-substrate complex.
Process:
Once the substrates bind, the reaction proceeds, creating products that are released from the enzyme.
Another View of Enzyme Function
The active site becomes available for a molecule of substrate (e.g., sucrose).
The substrate binds to the enzyme.
The substrate undergoes conversion into products.
The products are released from the enzyme, completing the cycle.
Amino Acids and Enzyme Functionality
Importance:
The specific types of amino acids that constitute enzymes are crucial for their shape and functional properties.
Classification of Amino Acids:
Amino acids can be categorized as:
Non-polar
Positively charged
Negatively charged
Function of Charges:
The electric charge of the amino acids at the active site must oppose the charge of the substrate, facilitating interaction (opposites attract; like charges repel).
Biomolecule Shapes and Chemical Interactions
Structural Importance:
The various shapes of biomolecules, including those of enzymes, result from the interaction of chemical groups within their structures.
Conformation Changes:
In reactions, the interactions between enzyme chemical groups and substrate lead to significant shape changes, altering bonding patterns and creating new products.
Levels of Protein Structure in Enzymes
Primary Structure:
Unique sequence of amino acids in an enzyme, linked by peptide bonds, which dictates how the enzyme will fold.
Secondary Structure:
Maintained by hydrogen bonds between amine (N–H) and carbonyl (C=O) groups in the backbone, independent of side chain interactions.
Tertiary Structure:
Formed by interactions among R-groups, influenced by hydrophobic (water-repelling) and hydrophilic (water-attracting) forces as well as charge interactions.
Quaternary Structure:
Composed of multiple polypeptides associated together, sometimes stabilized by disulfide bridges, playing a crucial role in enzyme regulation and activity.
Dephosphorylation of Cyclic AMP
Example: An enzyme that removes phosphate groups from cyclic AMP demonstrates the quaternary conformation of the enzyme. The folding process involves R-groups that dictate the interactions in the active site.
Importance of R-Groups:
Specific R-groups at the active site create a suitable environment for substrate binding. Changes in the protein's folding can significantly alter the active site’s chemistry, affecting enzyme functionality.
Interactions with Cyclic AMP
Details on Active Site Binding: The active site contains several polar R-groups that bond with cyclic AMP, facilitating the cleavage of its phosphate group through hydrogen bonds and ionic interactions.
Induced Fit in Action: As the substrate binds, an induced fit occurs, altering the shape of the active site slightly to better accommodate cyclic AMP, leading to an easier cleavage of the phosphate group, forming the transition state.