20 short questions with answers on Proteins & Enzymes for a graduation-level biology course
Proteins:
1.Describe the primary, secondary, and tertiary levels of protein structure. Briefly explain the forces that stabilize each level.
Answer- Primary structure refers to the linear sequence of amino acids held together by peptide bonds. Secondary structure involves localized folding of the polypeptide chain into regular structures like α-helices (stabilized by hydrogen bonds between backbone carbonyl and amide groups four residues apart) and β-sheets (stabilized by hydrogen bonds between backbone carbonyl and amide groups of adjacent polypeptide strands). Tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by various interactions between amino acid side chains, including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulphide bridges.
2.What are the common types of secondary structures found in proteins? Briefly describe their characteristics.
Answer- The common types of secondary structures are α-helices and β-sheets. α-helices are coiled structures with amino acid side chains extending outward. β-sheets are formed by aligned polypeptide strands that can be parallel or antiparallel, with side chains extending above and below the plane of the sheet.
3.Explain the significance of the amino acid sequence in determining the final three-dimensional structure of a protein.
Answers-The amino acid sequence (primary structure) dictates the final three-dimensional structure (tertiary structure) of a protein. The specific order and chemical properties of the amino acid side chains determine how the polypeptide chain will fold to achieve its most thermodynamically stable conformation through various intramolecular interactions. This unique 3D structure is crucial for the protein's specific function.
4.What is protein denaturation? List three factors that can cause protein denaturation and explain their effects.
Answers-Protein denaturation is the loss of a protein's native three-dimensional structure, leading to a loss of function. Three factors that can cause denaturation are:
Heat: Increased kinetic energy disrupts weak interactions like hydrogen bonds and hydrophobic interactions, causing the protein to unfold.
Extreme pH: Changes in pH disrupt ionic bonds and hydrogen bonds by altering the ionization state of amino acid side chains.
Detergents: These amphipathic molecules can disrupt hydrophobic interactions within the protein core, leading to unfolding.
5.Describe the role of chaperones in protein folding. Why are they important in a cellular environment?
Answers- Chaperones are proteins that assist in the proper folding of other proteins. They prevent aggregation of unfolded or partially folded polypeptide chains, providing a protected environment for correct folding to occur. They are important in a cellular environment because the high concentration of macromolecules increases the risk of improper interactions and aggregation, which can lead to non-functional proteins and cellular damage.
6.Distinguish between globular and fibrous proteins, providing one example of each and their primary function.
Answers- Globular proteins are typically compact, spherical, and water-soluble. An example is hemoglobin, whose primary function is oxygen transport in the blood. Fibrous proteins are elongated, insoluble, and often have a structural role. An example is collagen, which provides tensile strength in connective tissues.
7.Explain the concept of a protein domain. How does the presence of multiple domains contribute to protein function?
Answers- A protein domain is a distinct structural and functional unit within a protein. It often folds independently of other parts of the protein and has a specific function. The presence of multiple domains allows a single protein to have multiple functionalities or to perform complex tasks by integrating the activities of its individual domains. For example, a protein might have a DNA-binding domain and a catalytic domain.
8.What are intrinsically disordered proteins? How do they differ from globular proteins in terms of structure and function?
Answers- Intrinsically disordered proteins (IDPs) lack a fixed or ordered three-dimensional structure under physiological conditions. Unlike globular proteins with well-defined structures, IDPs exist as dynamic ensembles of conformations. Their flexibility allows them to interact with multiple partners and participate in diverse cellular processes, often involving signaling and regulation.
9.Briefly describe two common post-translational modifications of proteins and their potential impact on protein function.
Answers- Two common post-translational modifications are:
Phosphorylation: The addition of a phosphate group, often to serine, threonine, or tyrosine residues. This can alter the protein's charge and conformation, affecting its activity, interactions, or localization.
Glycosylation: The attachment of carbohydrate chains to specific amino acid residues. This can affect protein folding, stability, cell-cell recognition, and immune responses.
10.What is a protein motif? Give an example and explain its significance.
Answers- A protein motif (or structural motif) is a recurring combination of a few secondary structure elements arranged in a specific geometric pattern. For example, the helix-turn-helix motif is a common DNA-binding motif found in many regulatory proteins. While a motif doesn't usually fold independently like a domain, it plays a specific functional role within the larger protein structure.
Enzymes:
11.Define the terms "enzyme," "substrate," and "active site." Explain the interaction between an enzyme and its substrate.
Answer- An enzyme is a biological catalyst that speeds up the rate of biochemical reactions without being consumed in the process. A substrate is the specific molecule upon which an enzyme acts. The active site is a specific region on the enzyme that binds the substrate and where catalysis occurs. The enzyme and substrate interact through weak, non-covalent bonds (e.g., hydrogen bonds, hydrophobic interactions, ionic bonds) to form an enzyme-substrate complex. This interaction is highly specific due to the complementary shape and chemical properties of the active site and the substrate.
12.Describe the lock-and-key and induced-fit models of enzyme-substrate interaction. Which model is considered more accurate?
Answers- The lock-and-key model proposes that the active site of an enzyme has a rigid shape that is perfectly complementary to the shape of the substrate, like a key fitting into a lock. The induced-fit model suggests that the active site is more flexible and changes its conformation upon substrate binding to achieve a tighter fit, optimizing the interaction and facilitating catalysis. The induced-fit model is considered more accurate as it accounts for the dynamic nature of enzyme-substrate interactions.
13.Explain how enzymes increase the rate of biochemical reactions. Include the concept of activation energy in your explanation.
Answers- Enzymes increase the rate of biochemical reactions by lowering the activation energy (Ea), which is the minimum energy required for a reaction to proceed. Enzymes achieve this by providing an alternative reaction pathway with a lower energy barrier. By binding to the substrate and forming the enzyme-substrate complex, the enzyme stabilizes the transition state, the high-energy intermediate of the reaction, thus reducing the energy needed to reach it and accelerating the reaction.
14.What are cofactors and coenzymes? Provide one example of each and their role in enzyme activity.
Answers- Cofactors are non-protein chemical compounds that are required for the activity of certain enzymes. They can be inorganic ions (e.g., Mg2+, Zn2+) or complex organic molecules (coenzymes). Coenzymes are organic cofactors that often carry chemical groups or electrons during the catalytic process. An example of a cofactor is Mg2+, which is required by many enzymes involved in phosphate transfer. An example of a coenzyme is NAD$^+$ (nicotinamide adenine dinucleotide), which acts as an electron carrier in redox reactions.
15.Distinguish between competitive and non-competitive enzyme inhibition. How do they affect the enzyme's kinetics?
Answers-Competitive inhibition occurs when an inhibitor molecule binds to the active site of an enzyme, competing directly with the substrate for binding. This increases the apparent Km (decreases the enzyme's affinity for the substrate) but does not affect Vmax if the substrate concentration is high enough to outcompete the inhibitor. Non-competitive inhibition occurs when an inhibitor binds to a site on the enzyme other than the active site (an allosteric site). This binding changes the enzyme's conformation, reducing its catalytic activity and decreasing the Vmax without affecting the Km.
16.Explain the concept of enzyme specificity. What factors contribute to the high specificity of enzymes?
Answers-Enzyme specificity refers to the ability of an enzyme to bind to and catalyze a reaction with only one or a very limited number of substrates. This high specificity arises from the unique three-dimensional structure of the active site, which is complementary in shape, charge, and hydrophobicity to the substrate. Specific interactions between amino acid residues in the active site and functional groups on the substrate ensure precise binding and orientation for catalysis.
17.How do changes in pH and temperature affect enzyme activity? Explain the underlying reasons for these effects.
Answers- Changes in pH and temperature can significantly affect enzyme activity. Each enzyme has an optimal pH at which its activity is maximal. Deviations from this optimum can alter the ionization state of amino acid residues in the active site, disrupting substrate binding and catalysis. Similarly, each enzyme has an optimal temperature. Increasing temperature generally increases reaction rates up to a point. Beyond the optimum temperature, the enzyme's structure can be disrupted due to increased thermal energy, leading to denaturation and a rapid loss of activity.
18.What are allosteric enzymes? How does the binding of regulatory molecules affect their activity?
Answers-Allosteric enzymes are enzymes whose activity is regulated by the binding of effector molecules (activators or inhibitors) at a site distinct from the active site, called the allosteric site. The binding of a regulatory molecule induces a conformational change in the enzyme, which can either increase (activation) or decrease (inhibition) its affinity for the substrate or its catalytic efficiency. These enzymes often exhibit sigmoidal kinetics in response to substrate concentration.
19.Briefly describe the role of enzyme regulation in metabolic pathways. Why is it important for cellular homeostasis?
Answers- Enzyme regulation plays a crucial role in controlling the flow of metabolites through metabolic pathways. By regulating the activity of key enzymes, cells can adjust the rates of different metabolic reactions in response to changing cellular conditions and needs. This ensures that metabolic pathways operate efficiently, preventing the accumulation of unnecessary intermediates and conserving energy. Such regulation is essential for maintaining cellular homeostasis, the stable internal environment of the cell.
20.Explain the concept of enzyme kinetics and the significance of the Michaelis-Menten constant (Km) and maximum velocity (Vmax).
Answers- Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions and the factors that influence them. The Michaelis-Menten constant (Km) is the substrate concentration at which the reaction rate is half of the maximum velocity (Vmax). It provides an indication of the enzyme's affinity for its substrate; a lower Km indicates higher affinity. The maximum velocity (Vmax) is the theoretical maximum rate of the reaction when the enzyme is saturated with substrate. These kinetic parameters are crucial for understanding how enzymes function and how their activity can be affected by different factors, including inhibitors and activators.
