Unit 5 - Practice Quiz

Enzymes are biological catalysts, and the vast majority of them are proteins, folded into specific three-dimensional structures that determine their function.

Enzymes act as catalysts by lowering the activation energy required for a reaction to proceed, thereby speeding up the rate of the reaction without being consumed.

The active site is a unique pocket or cleft in the enzyme's structure that is complementary in shape and chemistry to the substrate, allowing for specific binding.

A substrate is the molecule that binds to the enzyme's active site and is converted into a product during the enzymatic reaction.

Hydrolases are a class of enzymes that use water to cleave chemical bonds, a process known as hydrolysis. Digestive enzymes are a common example.

Dehydrogenases are a type of oxidoreductase. These enzymes catalyze oxidation-reduction reactions, involving the transfer of electrons from one molecule to another.

A cofactor is a general term for a non-protein 'helper molecule' that binds to an enzyme and is necessary for its function. It can be an inorganic ion or an organic molecule (coenzyme).

An apoenzyme is the protein component of an enzyme that is catalytically inactive until its specific cofactor or coenzyme is bound to it.

Amylase, found in saliva and the pancreas, begins the digestion of complex carbohydrates like starch by breaking them down into simpler sugars.

Rennin is a protease that causes the milk protein casein to coagulate, or curdle, which is the first step in separating the solid curds from the liquid whey to make cheese.

The lock-and-key model is an early hypothesis that describes the enzyme's active site as a rigid 'lock' and the substrate as a specific 'key' that fits perfectly into it.

The holoenzyme is the entire active complex. It is formed when the inactive apoenzyme (protein part) combines with its necessary cofactor (non-protein part).

Proteases break down protein stains (like blood or grass), and lipases break down fat and oil stains (like grease or lipstick), making detergents more effective.

DNA Polymerase is a crucial enzyme in DNA replication, where it reads an existing DNA strand and synthesizes a new, complementary strand.

By convention, many enzymes are named by adding the suffix '-ase' to the name of their substrate (e.g., lactase acts on lactose) or the reaction they catalyze (e.g., polymerase).

When the substrate binds to the active site of the enzyme, they form the enzyme-substrate complex, which is a transient intermediate stage before the product is formed and released.

Isomerases facilitate the conversion of a molecule into one of its isomers, changing its structure without altering its overall chemical formula.

Unlike coenzymes that bind transiently, a prosthetic group is a non-protein component that is tightly or covalently bonded to the enzyme and is essential for its function, like the heme group in hemoglobin.

Pectinase breaks down pectin, a substance that makes plant cell walls rigid. In juice production, this helps to break down the fruit pulp and clarify the juice, increasing the yield and making it less cloudy.

Hydrogen peroxide is a harmful byproduct of metabolism. Catalase is an extremely efficient enzyme that protects cells by rapidly converting hydrogen peroxide into harmless water and oxygen gas.

Enzymes are biological catalysts that speed up reactions by providing an alternative reaction pathway with a lower activation energy (). They do not alter the thermodynamics of the reaction, meaning the starting energy of the reactants and the final energy of the products, and thus the overall free energy change (), are unaffected.

The induced-fit model is an enhancement of the older lock-and-key model. It proposes that the initial binding of the substrate to the enzyme induces a change in the enzyme's conformation, resulting in an active site that fits the substrate more precisely and optimally positions catalytic groups for the reaction.

This enzyme, hexokinase, is a transferase because it catalyzes the transfer of a functional group (a phosphate group) from one molecule (ATP) to another (glucose). Hydrolases use water to break bonds, lyases break bonds without water, and isomerases rearrange atoms within a molecule.

A prosthetic group is a type of co-factor that is tightly or covalently bound to its apoenzyme. Co-enzymes are organic co-factors that bind transiently. A co-factor is a general term for any non-protein chemical helper. A holoenzyme is the complete, active enzyme complex (apoenzyme + co-factor).

A competitive inhibitor competes with the substrate for the active site. This increases the apparent (more substrate is needed to reach half ). However, if the substrate concentration is high enough, it can outcompete the inhibitor, so the maximum velocity () can still be reached.

The first step, breaking down starch (a polymer) into glucose (a monomer), is a hydrolysis reaction catalyzed by enzymes like amylase (a hydrolase). The second step, converting glucose to its isomer fructose, is catalyzed by glucose isomerase (an isomerase).

Catalase catalyzes a redox reaction where one molecule of hydrogen peroxide is reduced to water and another is oxidized to oxygen. Enzymes that catalyze oxidation-reduction reactions belong to the class Oxidoreductase. Specifically, it's a peroxidase.

Feedback inhibition is a form of allosteric regulation where the end product of a metabolic pathway binds to a site other than the active site (an allosteric site) of an early enzyme in the pathway. This binding changes the enzyme's shape and reduces its activity, effectively shutting down the pathway when enough product has been made.

A non-competitive inhibitor binds to a site other than the active site and reduces the enzyme's efficiency. This lowers the effective enzyme concentration, decreasing . On a Lineweaver-Burk plot, a decrease in leads to an increase in the y-intercept (). Since it doesn't affect substrate binding, remains unchanged, and so does the x-intercept ().

The term apoenzyme refers specifically to the polypeptide (protein) portion of an enzyme. It is catalytically inactive until it binds with its required non-protein co-factor (like a co-enzyme or metal ion) to form the active holoenzyme.

Ligases (EC 6) are enzymes that catalyze the joining (ligation) of two large molecules by forming a new chemical bond, typically coupled with the hydrolysis of a small chemical group on one of the larger molecules or the molecule supplying the energy (e.g., ATP). DNA ligase is a classic example. Polymerase is a type of transferase.

PCR involves cycles of heating to high temperatures (around 95°C) to denature (separate) the DNA strands. Taq polymerase is isolated from the thermophilic bacterium Thermus aquaticus and is stable at these high temperatures, allowing it to function through many cycles without being destroyed.

Every enzyme has an optimal pH at which it functions most effectively. For pepsin, this optimum is very low (pH 1.5-2.5). A drastic change to an alkaline pH will disrupt the ionic bonds and hydrogen bonds that maintain the enzyme's specific three-dimensional structure, causing it to denature and lose its catalytic activity.

NAD⁺ is a classic example of a co-enzyme. It is an organic, non-protein molecule that binds transiently to oxidoreductase enzymes and acts as an electron acceptor (getting reduced to NADH) during catabolic reactions. It is then recycled by donating its electrons elsewhere.

Enzyme specificity arises from the unique geometry and arrangement of amino acid residues in the active site. This creates a specific chemical environment that is complementary to the enzyme's specific substrate(s), allowing for precise binding and catalysis. While other factors affect activity, specificity is a direct consequence of the active site's structure.

The Michaelis-Menten equation is . We are given and mM. Substituting these in gives: . Canceling and solving for [S] gives: mM.

Cellulase is a hydrolase that breaks down cellulose, a complex polysaccharide made of glucose units, into simpler sugars like glucose. In textiles, this partially degrades the surface of cotton fibers to soften the fabric and give a 'stone-washed' look. In biofuels, this process releases glucose which can then be fermented into ethanol.

Isomerases (EC 5) are enzymes that catalyze structural rearrangements of isomers. Since L-alanine and D-alanine are stereoisomers (enantiomers) of each other, the enzyme that facilitates their interconversion is classified as an isomerase, specifically a racemase.

Zymogens are inactive enzyme precursors. Synthesizing powerful digestive enzymes like trypsin in an inactive form (trypsinogen) prevents them from damaging the cells of the pancreas where they are made. They are only activated (e.g., by cleavage of a small peptide) once they reach their target location, such as the small intestine, where they are needed for digestion.

For metalloenzymes, the metal ion is an essential co-factor required for maintaining the structure of the active site or for participating directly in catalysis. Removing this ion with a chelating agent leaves only the inactive apoenzyme, thus abolishing the enzyme's catalytic activity.

A Lineweaver-Burk plot shows 1/V vs 1/[S]. The y-intercept represents 1/ and the x-intercept represents -1/. Intersection on the y-axis means that is unchanged, which is the hallmark of competitive inhibition. The inhibitor competes with the substrate for the active site, increasing the apparent but not affecting the maximum velocity at saturating substrate concentrations.

The EC number system is hierarchical. EC 2 denotes transferases. EC 2.7 denotes transfer of phosphorus-containing groups. EC 2.7.1 denotes phosphotransferases with an alcohol group as acceptor. The fourth digit is a serial number specifying the exact substrate (donor and acceptor). Since the phosphate donor has changed from ATP to GTP, the specific reaction is different, warranting a change in the fourth digit.

The catalytic and structural role of a metal ion cofactor depends critically on its size, charge, and preferred coordination geometry. Zn²⁺ (ionic radius ~74 pm) and Co²⁺ (~72 pm) are similar in size and can adopt similar geometries. Ca²⁺ is much larger (~100 pm) and prefers a different coordination number and geometry, which would disrupt the precise architecture of the active site, thus abolishing activity.

Enzymes accelerate reactions by lowering the activation energy (). According to transition state theory, they achieve this by stabilizing the high-energy transition state more than they stabilize the ground-state substrate. This preferential binding to the transition state effectively reduces the energy barrier that must be overcome. Enzymes do not alter the thermodynamics of the reaction ().

In immobilized enzyme systems, the overall rate can be limited by catalysis or mass transfer. When the limitation is the diffusion of substrate from the bulk fluid to the external surface of the support particle, it is called external mass transfer limitation. This is distinct from internal mass transfer limitation (diffusion within the pores). At high substrate concentrations, the enzyme's catalytic sites are not saturated because diffusion cannot supply substrate fast enough.

Protein synthesis is a relatively slow process. By storing enzymes as inactive zymogens, a cell can build up a large reservoir. Upon receiving a signal, these zymogens can be activated almost instantaneously by cleavage, providing a rapid and powerful response that would be impossible if the cell had to synthesize the enzymes from scratch. It also prevents self-digestion of the synthesizing cell.

Parallel lines on a Lineweaver-Burk plot are the defining characteristic of uncompetitive inhibition. An uncompetitive inhibitor binds only to the enzyme-substrate (ES) complex. This binding reduces the concentration of effective ES complex, which decreases the apparent . This binding also sequesters ES complex, which by Le Châtelier's principle, increases the apparent affinity of the enzyme for the substrate, thus decreasing the apparent . The ratio of (the slope) remains constant, resulting in parallel lines.

The isoalloxazine ring of FAD can accept one electron and one proton to form a relatively stable neutral radical, the semiquinone (FADH•). It can then accept a second electron and proton to form the fully reduced FADH₂. This ability to form a stable one-electron intermediate allows flavoenzymes to mediate reactions between two-electron donors and one-electron acceptors, a feat NAD⁺ cannot perform as it only undergoes two-electron (hydride) transfers.

This reaction is a classic transamination. The enzyme, Alanine Transaminase (ALT), transfers an amino group (-NH₂) from L-Alanine to 2-Oxoglutarate. The transfer of a functional group from a donor to an acceptor molecule is the defining characteristic of the Transferase class (EC 2). Specifically, it belongs to subclass EC 2.6 (transferring nitrogenous groups).

The Michaelis constant is defined as . The dissociation constant for the ES complex is . If the catalytic step is very slow compared to the dissociation of the substrate from the enzyme (i.e., ), then the term in the equation becomes negligible. Under this 'rapid equilibrium' assumption, , meaning reflects the true binding affinity.

The key to PLP's versatility is the electron-withdrawing power of its protonated pyridine ring. When a carbanionic intermediate is formed by removing a group from the -carbon of the amino acid substrate, the resulting negative charge is delocalized into the conjugated -system of the PLP cofactor. The positively charged nitrogen in the ring acts as an excellent electron sink, stabilizing this high-energy intermediate and lowering the activation energy for various reactions.

Allosteric activators bind to a site other than the active site and stabilize the high-affinity "R" (relaxed) state of the enzyme. This lowers the substrate concentration required for half-maximal velocity (decreasing apparent , shifting the curve left) and reduces the cooperativity, making the sigmoidal curve less pronounced and more like a hyperbolic Michaelis-Menten curve.

The primary advantage of immobilization in large-scale processes like HFCS production is economic and logistical. Enzymes are expensive. Immobilizing them in a reactor column allows the glucose solution to be continuously passed over them. The product flows out, while the enzyme remains, allowing for reuse which drastically reduces costs and simplifies downstream purification by preventing enzyme contamination of the product.

By inhibiting the very first enzyme that commits substrates to a specific pathway, the cell avoids wasting energy and resources on synthesizing a series of intermediates that are no longer needed once the final product has accumulated. If a later enzyme were inhibited, all the intermediates before it would continue to be produced and accumulate, which is metabolically wasteful. Regulating the first committed step is the most efficient control point.

The defining characteristic of the Ligase class (EC 6) is the catalysis of the joining (ligation) of two molecules. This process is energetically unfavorable and must be coupled to the hydrolysis of a high-energy phosphate bond in a nucleotide like ATP. DNA ligase perfectly fits this description: it joins two DNA molecules and the reaction is powered by ATP hydrolysis.

Cofactors like Mg²⁺ are typically loosely, non-covalently bound. Dialysis against a chelator (EDTA) will strip the Mg²⁺ from Enzyme A, converting it to an inactive apoenzyme. Prosthetic groups, by definition, are tightly bound, often covalently. The heme group in Enzyme B is deeply embedded and strongly attached, so it cannot be removed by simple dialysis or chelation. Therefore, Enzyme B would retain its activity.

The Michaelis-Menten equation is . When [S] << , the equation simplifies to . In this case, the reaction rate is directly proportional to the second-order rate constant . This specificity constant reflects how efficiently the enzyme converts substrate to product at low substrate concentrations, a common cellular condition.

Mixed inhibition involves the inhibitor binding to both E and ES. The special case where the inhibitor has equal affinity for both forms () is called pure non-competitive inhibition. The inhibitor effectively removes a fraction of the enzyme from being active, which decreases the apparent . Since it binds E and ES equally well, it does not alter the enzyme's apparent affinity for the substrate, so remains unchanged. On a Lineweaver-Burk plot, this results in lines that intersect on the x-axis.

Heart muscle operates aerobically. When pyruvate levels are high, it's more efficient to direct it into the Krebs cycle for maximal ATP production. Pyruvate inhibiting the heart's H-form of LDH achieves this. In contrast, skeletal muscle often works anaerobically, where it must rapidly convert pyruvate to lactate to regenerate NAD⁺ for glycolysis. The M-form of LDH is not inhibited by pyruvate, allowing it to perform this function effectively.

Many biotin-dependent carboxylases have two distinct active sites. The first site carboxylates the biotin. The long, flexible lysine-biotin linker then acts as a swinging arm, translocating the carboxylated biotin to the second active site. Here, the carboxyl group is transferred to the acceptor substrate. This mechanism allows two separate but coupled reactions to occur on a single enzyme polypeptide.