enzymes Flashcards
Relate protein structures (conformation) to function and describe the four levels of structure.
- primary structure:
Description: this is the linear sequence of amino acids in the protein. It’s essentially the order in which amino acids are linked together by peptide bond (C-N)
Relation to function: A protein’s primary structure determines the sequence of amino acids, which influences the higher levels of structure. A single change in amino acid can drastically change the protein’s function, leading to sickle cell anemia. - secondary structure:
Description: This level involves localized folding patterns in a protein, primarily driven by hydrogen bonds between backbone atoms. Typical forms of secondary structures are alpha-helices and beta-sheets
relation to function: The secondary structure forms specific shapes that form a foundation for the protein’s three-dimensional structure. These patterns can be involved in creating channels, binding sites, or scaffolds for more complex structures. - tertiary structures:
Description: this refers to the overall three-dimensional shape of the entire protein molecule. It’s the result of interactions between the side chains (or R-groups) of the amino acids. Various types of bonds and interactions, including hydrogen bonds, ionic bonds, and hydrophobic interactions.
Relation to function: The tertiary structure creates a functional domain in proteins. It establishes the protein’s overall spatial orientation, creating areas for active sites (as in enzymes), ligand binding, and interaction with other proteins or molecules. The correct tertiary structure is vital for the proteins’ function - Quaternary structure:
Description: Not all proteins have his level of structure. It arises when multiple protein subunits (individual polypeptide chains) form a complex. Hemoglobin is an example.
Relation to function: The interaction of subunits in proteins with quaternary structure can create specific sites for molecule binding or alter the protein’s activity. In hemoglobin, the binding of oxygen to one subunit influences the ability of the other subunits to bind oxygen, an example of cooperative binding.
Protein Conformation and Function:
The conformation of a protein – its specific three-dimensional shape – is what enables it to perform its function. Enzymes, for instance, adhere to the “lock and key” model, where the substrate fits into the enzyme’s active site just as a key fits into a lock. If the protein’s conformation is altered (due to factors like pH, temperature, or mutations), its function can be compromised or lost.
In essence, the structure of a protein, from its primary sequence of amino acids to its complex 3D shape, dictates its function in the cell. Misfolded or improperly formed proteins can lead to numerous diseases and cellular dysfunctions.
Explain how enzymes alter a reaction pathway by reducing the activation energy required for a reaction by inducing the transition state.
- Activation Energy and Transition State:
For any reaction to occur, a certain amount of energy, called activation energy (Ea), must be provided to convert reactants into products. This energy is required to overcome the energy barrier between reactants and products. At the peak of this energy barrier is a high-energy, transient state called the transition state. It’s not a stable molecule but rather an unstable configuration of atoms that exists momentarily during the reaction. - Enzyme-Substrate Binding:
Enzymes recognize and bind to specific substrates with high specificity, forming an enzyme-substrate complex. The region on the enzyme where substrate binding occurs is called the active site. The precise fit between the enzyme’s active site and its substrate is often likened to a “lock and key” or, more accurately, an “induced fit” model where the enzyme undergoes a slight conformational change upon substrate binding.
- free energy doesn’t change when you use an enzyme, and when you don’t
- reactants and products don’t change when and when not using enzyme - Activation Energy:
The energy needed to get a reaction started is like the effort needed to push the boulder up the hill. In science, we call this the “activation energy.” - Enzymes’ Role:
Enzymes act like that ramp or gentler hill. They make it easier for reactions to happen by reducing the amount of energy you need to start the reaction. - How Enzymes Work:
Binding: Enzymes have a special pocket called the “active site” where they grab onto certain molecules (like a hand grabbing a ball).
Making Things Easier: Once the molecule is in the enzyme’s grip, the enzyme might hold it in a particular way or give it a little squeeze, making it easier for the molecule to react and change.
Helping the Reaction: The enzyme helps the reaction along and then releases the changed molecule, all set to go about its business.
Explain the role of the active site in forming the transition state and the properties of the active site that allow it to play this role.
The active site is a specific region on an enzyme where the substrate binds. Think of it as a docking station on the enzyme.
2. Active Site and the Transition State:
When a substrate binds to the enzyme’s active site, the enzyme slightly changes its shape to fit the substrate snugly. This shape change, often referred to as an “induced fit,” helps the substrate get to the transition state more easily. The transition state is a temporary and high-energy state that substrates must go through to be converted into products.
3. Properties of the Active Site:
Shape and Size: The active site has a unique shape and size that matches its specific substrate, kind of like how a key fits into a specific lock.
Charge Distribution: The active site can have areas of positive or negative charge that attract or repel parts of the substrate, helping it achieve the transition state.
Flexible: The active site is not rigid. It can change its shape a bit to fit better the substrate, which aids in reaching the transition state.
Chemical Environment: The active site might have acidic or basic parts that can donate or accept protons, or other groups that can temporarily interact with the substrate. These interactions can help the substrate reach the transition state faster.
Catalytic Residues: Within the active site, some specific amino acids, called catalytic residues, directly participate in the making and breaking of bonds, speeding up the reaction.
In simple terms, the active site is like a helpful assistant that holds onto a substrate, puts it in the right position, and gives it a nudge, making it easier for the substrate to undergo the chemical change it needs to. This “nudging” helps the substrate overcome the energy barrier and be transformed into the product.
Draw an illustration of activation energy.
Draw induced fit
The change in the shape of the active site of an enzyme so that it binds more snugly to the substrate is induced by the entry of the substrate.
draw catalysis
The acceleration of a reaction rate by a molecule that is unchanged by participating in the reaction
Describe how denaturation affects protein function
Denaturation refers to the process where the structure of the protein is altered due to various factors, such as heat, pH, or chemical agents.
- they can be either partial or complete denaturaton
pH: alterning the Ph can disrupt he ionic bonds within the protein
Heat: Increases in temperature can lead to increased molecular motion, breaking weak interaction ( like hydrogen bonds) that stabilize the protein’s structure
Chemicals: some chemicals, like urea or detergents, can interfere with the bonds and interactions that stabilize the proteins structure
mechanical agitation: vigorous shaking or stirring can lead to denaturation in some cases
For enzymes, denaturation often leads to loss of catalytic activity since their activity relies on the orecise geometry of their active sites
What are the various forms of enzyme inhibition and regulation?
Enzyme inhibition:
Competitive Inhibition: Inhibitors bind to the active site of the enzyme, preventing substrate binding. This type of inhibition can be overcome by increasing the concentration of the substrate.REVERSIBLE
Non-competitive Inhibition: The inhibitor binds to a site other than the active site (allosteric site). This binding causes the enzyme to change shape, rendering the active site less effective or non-functional. Increasing substrate concentration doesn’t overcome this inhibition. REVERSIBLE
Uncompetitive Inhibition: The inhibitor binds only to the enzyme-substrate complex, locking the substrate in the enzyme and preventing the reaction from proceeding.
Enzyme regulation:
Allosteric Regulation: Enzymes have allosteric sites where specific molecules can bind, inducing a conformational change that can either activate or inhibit enzyme activity.
