Enzymes: Comprehensive Notes – Practice Flashcards

A set of 50 question-and-answer flashcards reviewing key concepts in enzymology, enzyme kinetics, regulation, isoenzymes, clinical markers, and therapeutic/industrial applications.

What is the primary and fundamental role of enzymes in biological systems, and how do they achieve this without being consumed or altering the final balance of the reaction?

Enzymes act as highly specific biological catalysts, significantly accelerating the rates of biochemical reactions by lowering the activation energy. Crucially, they achieve this without being consumed in the process or shifting the equilibrium point of the reaction, only the speed at which equilibrium is reached.

In the context of enzyme catalysis, what precisely is a 'substrate', and what happens to it during the enzymatic reaction?

A substrate is the specific reactant molecule or molecules that an enzyme binds to at its active site. The enzyme then chemically transforms the substrate into one or more new molecules, referred to as product(s), through a catalyzed reaction.

Beyond their catalytic function, what are two fundamental physical characteristics that define the majority of enzymes?

Virtually all enzymes are complex globular proteins, meaning they possess a specific three-dimensional structure crucial for their function. Consequently, they are typically heat-labile, easily undergoing denaturation (loss of their specific 3D structure and thus activity) at elevated temperatures.

Alcohol dehydrogenase, an enzyme crucial in metabolism, is classified under which of the six major IUBMB (International Union of Biochemistry and Molecular Biology) enzyme classes, and what general type of reaction does this class catalyze?

Alcohol dehydrogenase belongs to Class 1: Oxidoreductases. This class of enzymes catalyzes oxidation-reduction reactions, involving the transfer of electrons, hydrogen atoms, or hydride ions between substrates. Alcohol dehydrogenase specifically catalyzes the interconversion of alcohols and aldehydes/ketones with the concomitant reduction or oxidation of NAD⁺/NADH.

Identify the IUBMB enzyme class responsible for catalyzing the transfer of specific chemical groups (excluding hydrogen) from one molecule (donor) to another molecule (acceptor). Provide an illustrative example.

The enzyme class that catalyzes the transfer of functional groups like methyl, acyl, amino, or phosphate groups from one substrate to another (but not hydrogen or electrons) is Class 2: Transferases. A common example is kinase enzymes, which transfer phosphate groups, often from ATP to another molecule.

Into which IUBMB enzyme class are nearly all digestive enzymes categorized, and what defines the type of reaction catalyzed by this class?

Almost all digestive enzymes fall under Class 3: Hydrolases. These enzymes catalyze hydrolysis reactions, which involve the breaking of a chemical bond by the addition of a water molecule, typically splitting a larger molecule into two smaller ones. Examples include lipases, proteases, and amylases.

What is the main catalytic function of lyases (Class 4), and how do their mechanisms differ from hydrolases?

Lyases catalyze the cleavage of C-C, C-O, C-N, and other bonds by elimination, leaving behind double bonds or rings, or conversely, adding groups to double bonds. Their key characteristic is that they break bonds without involving hydrolysis or oxidation-reduction reactions. For instance, decarboxylases remove CO_2 and aldolases break C-C bonds.

Clarify the distinction between 'synthetases' and 'synthases' regarding their involvement with ATP in biosynthetic reactions.

The key distinction lies in energy coupling: Synthetases are ligases (Class 6) that catalyze the formation of new bonds by coupling the reaction with the hydrolysis of a high-energy phosphate bond (e.g., ATP or GTP) to provide the necessary energy. Synthases are lyases (Class 4) that catalyze anabolic reactions (synthesis of molecules) but do not directly require ATP hydrolysis for their function.

What is the protein component of a holoenzyme called?

The protein component of a holoenzyme, which is the complete and catalytically active enzyme, is called the apoenzyme. The apoenzyme requires a non-protein component (a cofactor) to become functional.

Many crucial coenzymes, essential for various enzyme activities, are structurally derived from which specific group of vitamins?

Most coenzymes are organic molecules that act as transient carriers of specific functional groups or electrons. A large number of these vital coenzymes, such as NAD⁺, FAD, Coenzyme A, and Thiamine pyrophosphate (TPP), are derivatives of B-complex vitamins (e.g., niacin, riboflavin, pantothenic acid, thiamine).

Which coenzyme pair is involved in converting lactate to pyruvate, a process crucial in cellular metabolism, especially under anaerobic conditions?

The coenzyme pair involved in the interconversion of lactate and pyruvate, catalyzed by lactate dehydrogenase, is NAD⁺/NADH. NAD⁺ acts as an electron acceptor to oxidize lactate to pyruvate, becoming reduced to NADH; conversely, NADH can donate electrons to reduce pyruvate back to lactate.

Name the essential coenzyme that functions as the primary carrier of acyl groups (e.g., acetyl groups) in numerous metabolic pathways, including the citric acid cycle and fatty acid metabolism.

Coenzyme A (CoA) is the principal coenzyme responsible for the transfer of acyl groups, forming highly energetic thioester bonds (e.g., acetyl-CoA). It plays a central role in energy metabolism, including the oxidation of pyruvate and fatty acids, and in various biosynthetic pathways.

What specific term is used to describe an enzyme that absolutely requires a tightly bound metal ion (like Cu^{2+} in tyrosinase or Zn^{2+} in carbonic anhydrase) within its structure to exhibit catalytic activity?

An enzyme that contains a tightly bound metal ion, which is an intrinsic part of its active site and essential for its catalytic function, is known as a metalloenzyme. These metal ions often participate directly in catalysis (e.g., by acting as Lewis acids) or help stabilize the enzyme's structure.

What is the overarching collective term used to describe all non-protein chemical components, whether organic molecules (like vitamins) or inorganic ions (like metal ions), that are required for an enzyme to exhibit its full catalytic activity?

Cofactors is the collective term that encompasses all non-protein chemical components essential for enzyme activity. This includes both organic molecules called coenzymes (often derived from vitamins, e.g., FAD, NAD⁺) and inorganic metal ions (e.g., Zn^{2+}, Mg^{2+}, Fe^{2+}) that assist in catalysis.

Explain how enzymes, according to the activation-energy concept, manage to significantly speed up the rate of biochemical reactions.

Enzymes accelerate reaction rates by providing an alternative reaction pathway with a significantly lower activation energy (E_a). They achieve this by stabilizing the transition state, the high-energy intermediate form that molecules must pass through to convert from reactants to products, making it easier and faster for the reaction to proceed.

Describe the enzyme catalytic mechanism where specific amino acid residues within the enzyme's active site directly participate in the reaction by donating or accepting protons.

The catalytic mechanism where amino acid residues of the enzyme (e.g., Aspartate, Glutamate, Histidine, Lysine, Cysteine, Tyrosine) act as general acid-base catalysts by reversibly donating or accepting protons to or from the substrate is called acid-base catalysis. This often stabilizes charged intermediates or promotes nucleophilic/electrophilic attack.

Which classic enzyme-substrate interaction theory, proposed by Emil Fischer, posits that the active site of the enzyme and the substrate possess perfectly complementary, rigid structures, much like a specific key fitting into a specific lock?

The classic theory that describes the enzyme-substrate interaction as a highly specific, static fit where the enzyme's active site is pre-formed and rigid, perfectly matching the substrate, is known as Fischer’s template (lock-and-key) theory (1894).

Building upon earlier models, what crucial dynamic concept did Daniel Koshland Jr.'s induced-fit theory introduce regarding the interaction between an enzyme and its substrate?

Koshland's induced-fit theory (1958) refined the lock-and-key model by proposing that the active site of an enzyme is not rigid but flexible. Upon substrate binding, the enzyme undergoes significant conformational changes (a 'fit') that optimize the interaction, further molding the active site to precisely accommodate the substrate, leading to enhanced catalytic efficiency and sometimes facilitating the correct alignment of catalytic residues.

Within an enzyme's three-dimensional structure, what is the critically important, typically small region where specific substrate molecules bind and undergo chemical transformation, and what are its key features?

The small, distinct three-dimensional cleft or pocket on the enzyme's surface where substrate binding occurs and the actual catalytic reaction takes place is called the active site (or active center). It's characterized by its unique shape and specific arrangement of amino acid residues that facilitate substrate recognition and catalysis.

How many and which specific amino acid residues form the highly conserved 'catalytic triad' essential for the hydrolytic activity of serine proteases like chymotrypsin?

The catalytic triad of chymotrypsin and other serine proteases (such as trypsin and elastase) consists of Serine 195, Histidine 57, and Aspartate 102. These residues are precisely positioned in the active site to cooperatively facilitate the nucleophilic attack on the peptide bond, enabling efficient proteolysis.

Considering its physiological environment, at what approximate pH range does the digestive enzyme Pepsin, found in the stomach, exhibit its maximal catalytic activity?

Pepsin, a protease secreted in the stomach, is optimally active in an extremely acidic environment, typically showing maximal activity around pH 1.5 – 2.0. This low pH is crucial for its function in breaking down proteins in the gastric lumen and also helps in denaturing dietary proteins.

Which specific divalent metal ion (Me^{2+}) is absolutely essential for the catalytic activity of alcohol dehydrogenase, acting as a cofactor in its active site?

The metal ion essential for the activity of alcohol dehydrogenase is Zinc (Zn^{2+}). It is typically found in the enzyme's active site, where it plays a crucial role in coordinating with the substrate and facilitating the transfer of hydride ions (H^-) during the oxidation/reduction reaction.

In thermodynamics, what term describes a chemical reaction that releases free energy into its surroundings and proceeds spontaneously in the forward direction, often making it effectively irreversible under physiological conditions?

A reaction that releases free energy (\Delta G < 0) and can proceed spontaneously is termed an exergonic reaction. If the energy is released as heat, it's specifically called an exothermic reaction. These reactions tend to be irreversible because a significant amount of energy must be supplied to drive the reverse reaction.

In Michaelis-Menten enzyme kinetics, define V_{max} and explain the condition under which it is achieved.

V_{max} represents the maximum initial reaction velocity or rate that an enzyme-catalyzed reaction can achieve. It occurs when the enzyme's active sites are completely saturated with substrate, meaning that increasing the substrate concentration further will not increase the reaction rate, as all enzyme molecules are constantly busy converting substrate to product.

Define the Michaelis constant (K_m) in enzyme kinetics and explain its significance in relation to enzyme activity.

The Michaelis constant (Km) is defined as the substrate concentration [S] at which the initial reaction velocity (Vo) is exactly half of the maximum velocity (V{max}). It provides an inverse measure of the enzyme's affinity for its substrate: a low Km indicates high affinity, while a high K_m suggests low affinity.

What does a particularly low value for the Michaelis constant (K_m) imply about an enzyme's affinity for its substrate, and how does this relate to its catalytic efficiency at low substrate concentrations?

A low Km value indicates a high affinity of the enzyme for its substrate. This means that the enzyme can achieve half of its maximum reaction velocity (V{max}/2) at a relatively low substrate concentration, suggesting that the enzyme binds efficiently and catalyzes the reaction effectively even when substrate availability is limited.

Assuming substrate concentration is not a limiting factor (i.e., substrate is in excess), how does increasing the concentration of the enzyme impact the overall reaction velocity?

When the substrate is in saturating amounts, the reaction velocity is directly proportional to the enzyme concentration. This is because adding more enzyme molecules means more active sites are available to bind and convert substrate into product, leading to a proportional increase in the overall reaction velocity.

Explain the physiological reason why enzyme activity initially increases with temperature but then sharply declines beyond an optimal temperature.

Enzyme activity generally increases with temperature up to an optimum point due to increased kinetic energy and more frequent collisions. However, beyond this optimum temperature, the enzyme's activity drops sharply because it undergoes denaturation. Denaturation is the irreversible loss of the enzyme's specific three-dimensional structure (especially its active site), which is crucial for its catalytic function, rendering it inactive.

Provide a well-known example of a human enzyme that functions optimally in a highly acidic environment, specifying its approximate optimal pH range.

A prominent example is Pepsin, a proteolytic enzyme found in the human stomach. Its optimal pH for activity is remarkably low, approximately pH 1.5 – 2.0, which is well-suited for the highly acidic conditions of the gastric lumen where it initiates protein digestion.

In competitive inhibition, what is the principal effect observed on the Michaelis constant (K_m), and how does this impact the enzyme's apparent affinity for its substrate?

In competitive inhibition, where an inhibitor structurally resembles the substrate and competes for binding to the active site, the apparent Km increases. This means that a higher concentration of the substrate is now required to achieve half of the maximum velocity (V{max}/2), effectively reducing the enzyme's apparent affinity for its substrate, although V_{max} remains unchanged.

How does non-competitive inhibition kinetically affect the reaction parameters V{max} and Km?

In non-competitive inhibition, the inhibitor binds to a site other than the active site (allosteric site) on either the free enzyme or the enzyme-substrate complex, typically causing a conformational change that reduces the enzyme's catalytic efficiency. This type of inhibition decreases V{max} (because fewer functional enzyme molecules are available or their turnover rate is lowered), but it does not change Km (as the binding affinity for the substrate at the active site is unaffected).

What are the kinetic consequences of uncompetitive inhibition on the Michaelis constant (Km) and maximal velocity (V{max})?

In uncompetitive inhibition, the inhibitor exclusively binds to the enzyme-substrate (ES) complex, not the free enzyme. This binding effectively removes ES complex from the equilibrium, which in turn leads to a decrease in the apparent concentration of functional ES complex. As a result, both the apparent Km and V{max} decrease proportionally.

Identify the classical competitive inhibitor that structurally resembles succinate and specifically inhibits the enzyme succinate dehydrogenase in the citric acid cycle.

Malonate is a classical competitive inhibitor of succinate dehydrogenase (also known as Complex II in the electron transport chain). Its structure (a 3-carbon dicarboxylate) is very similar to that of the natural substrate, succinate (a 4-carbon dicarboxylate), allowing it to bind to the active site but preventing the catalytic conversion, thus blocking this step of the citric acid cycle.

Name the potent poison that exerts its toxic effects by irreversibly binding to and inhibiting cytochrome oxidase (Complex IV) in the mitochondrial electron transport chain, thereby effectively blocking cellular respiration and ATP production.

Cyanide is a highly toxic compound that irreversibly inhibits cytochrome oxidase (cytochrome c oxidase), also known as Complex IV. It binds to the ferric iron (Fe^{3+}) within the heme a_3 group of the enzyme, preventing the transfer of electrons to oxygen and thus halting the entire electron transport chain and aerobic ATP synthesis, leading to cellular anoxia.

Describe the type of enzyme regulation where the binding of a regulatory molecule (an 'effector') to a site distinct from the active site significantly alters the enzyme's activity, either enhancing or inhibiting it.

Allosteric regulation is a type of enzyme control where activator or inhibitor molecules (allosteric effectors) bind non-covalently to a specific regulatory site on the enzyme, called the allosteric site, which is separate from the active site. This binding induces a conformational change in the enzyme, which in turn affects the shape and activity of the active site, either increasing (allosteric activation) or decreasing (allosteric inhibition) its catalytic efficiency.

Which crucial regulatory enzyme in glycolysis has its activity allosterically inhibited by high cellular concentrations of ATP, serving as a feedback mechanism to slow down glucose breakdown when energy is abundant?

Phosphofructokinase-1 (PFK-1) is a key regulatory enzyme in glycolysis that catalyzes the committed step of the pathway (fructose-6-phosphate to fructose-1,6-bisphosphate). It is allosterically inhibited by high levels of ATP, signaling sufficient cellular energy. This feedback mechanism ensures that glucose is not excessively broken down when energy reserves are already high.

Which specific type of reversible covalent modification is primarily responsible for activating glycogen phosphorylase, an enzyme central to glycogen breakdown?

Activation of glycogen phosphorylase, the enzyme responsible for breaking down glycogen into glucose-1-phosphate, is primarily achieved by phosphorylation. The attachment of a phosphate group (typically provided by ATP, catalyzed by phosphorylase kinase) to specific serine residues on the enzyme induces a conformational change that shifts it from a less active 'b' form to a more active 'a' form.

The process by which inactive precursor proteins like trypsinogen are converted into their active enzyme forms (e.g., trypsin) through specific proteolytic cleavage (such as by enterokinase) is an example of what important regulatory mechanism?

The conversion of an inactive enzyme precursor (known as a zymogen or proenzyme) into its active form by irreversible proteolytic cleavage (the breaking of peptide bonds) is an example of proteolytic activation (or zymogen activation). This mechanism, exemplified by trypsinogen to trypsin conversion by enteropeptidase (formerly enterokinase), allows for controlled, localized, and often irreversible activation of enzymes, particularly important for digestive enzymes and blood clotting factors.

The enzyme lactate dehydrogenase (LDH) exists in multiple isoenzymatic forms. Which two distinct types of protein subunits combine in various proportions to create these different LDH isoenzymes?

The different isoenzymes of lactate dehydrogenase (LDH), which vary in their tissue distribution and kinetic properties, are tetramers composed of combinations of two distinct types of subunits: H (heart) subunits and M (muscle) subunits. These subunits can combine in five different arrangements (e.g., H4, H3M1, H2M2, H1M3, M4), each with slightly different electrophoretic mobilities and catalytic characteristics.

Which specific LDH isoenzyme, consisting solely of H subunits, is predominantly found in cardiac muscle and erythrocytes, and whose elevated serum levels are a classic indicator of myocardial infarction (heart attack)?

The LDH isoenzyme that predominates in cardiac muscle and red blood cells is LDH1 (H_4), meaning it is composed of four 'heart' subunits. Elevated levels of LDH1 in serum are a significant diagnostic marker for myocardial infarction, indicating damage to heart tissue.

Creatine Kinase (CK) has several isoenzymes. A significant rise in the serum level of a specific isoenzyme, CK-MB, is a highly sensitive and specific indicator of damage to which particular tissue?

A rise in CK-MB (Creatine Kinase-MB) levels in serum is a highly specific and sensitive biochemical marker for myocardial (heart) tissue damage, particularly in the diagnosis of acute myocardial infarction. CK-MB is predominantly found in cardiac muscle, distinguishing it from CK-MM (muscle) and CK-BB (brain) isoenzymes.

When diagnostic tests reveal elevated serum levels of the bone isoenzyme of alkaline phosphatase (ALP), what specific type of bone cells does this typically indicate increased activity of?

Elevated levels of the bone isoenzyme of alkaline phosphatase (ALP) in serum are indicative of increased activity of osteoblasts. Osteoblasts are bone-forming cells responsible for synthesizing and mineralizing the bone matrix, and ALP is involved in the bone calcification process.

While both are used in diagnosis, which serum enzyme marker is generally considered more specific for diagnosing acute pancreatitis compared to amylase?

While serum amylase levels can also be elevated, serum lipase is considered a more specific and sensitive enzyme marker for the diagnosis of acute pancreatitis. Lipase elevation typically persists longer than amylase and is less commonly elevated in other non-pancreatic conditions.

Name a key therapeutic enzyme often administered as a thrombolytic agent to dissolve blood clots (thrombi) and restore blood flow during acute myocardial infarction or ischemic stroke.

Streptokinase is a well-known therapeutic enzyme, derived from bacteria, used as a fibrinolytic (thrombolytic) agent. It catalyzes the conversion of plasminogen to plasmin, which then breaks down fibrin clots, thereby helping to clear obstructed blood vessels during conditions like myocardial infarction and pulmonary embolism.

Which specific enzyme is employed as a chemotherapeutic agent in the treatment of certain cancers, particularly acute lymphoblastic leukemia (ALL)?

Asparaginase is a therapeutic enzyme used in the treatment of acute lymphoblastic leukemia (ALL) and some other malignancies. It works by hydrolyzing the amino acid asparagine into aspartate and ammonia. Since many leukemia cells lack the ability to synthesize asparagine, they are dependent on exogenous sources, and asparaginase effectively depletes the circulating asparagine, selectively starving and killing the cancerous cells.

Describe the common diagnostic technique that utilizes antibodies conjugated or 'linked' to an enzyme to detect and quantify specific antigens or antibodies in a sample, producing a measurable colorimetric or fluorescent signal.

ELISA (Enzyme-Linked Immunosorbent Assay) is a widely used biochemical diagnostic technique that detects and quantifies specific proteins (antigens) or antibodies in a sample. It employs antibodies that are chemically linked to an enzyme (e.g., horseradish peroxidase or alkaline phosphatase). When the enzyme substrate is added, it reacts with the enzyme to produce a measurable signal, typically a color change, allowing for the detection of the target molecule.

From an industrial perspective, what is considered a primary practical advantage of using immobilized enzymes over soluble enzymes in large-scale bioprocesses?

A major practical advantage of using immobilized enzymes (enzymes physically confined or localized to a support material) in industrial applications is that they can be easily recovered and reused after the reaction is complete. This significantly reduces enzyme consumption costs, simplifies downstream product purification, and allows for continuous processing, contributing to overall economic efficiency.

Identify the enzyme immobilization technique where the enzyme molecules are chemically bound to an insoluble solid support material through the formation of covalent bonds.

Covalent bonding immobilization is a technique where enzymes are chemically attached to a solid, insoluble support matrix (e.g., beads, membranes) via stable covalent bonds between specific amino acid residues on the enzyme and reactive groups on the support. This method typically results in very stable immobilized enzymes and minimal leakage from the support.

In the industrial production of high-fructose corn syrup (HFCS), which specific enzyme is extensively used in its immobilized form to catalyze the conversion of glucose to fructose?

The industrial production of high-fructose corn syrup (HFCS), which is widely used as a sweetener, heavily relies on the immobilized form of the enzyme glucose isomerase (also known as xylose isomerase). This enzyme reversibly catalyzes the isomerization (conversion) of glucose into fructose, a sweeter sugar.

For glucose biosensors, widely used in diabetes management to measure blood glucose levels, which specific enzyme is most commonly employed to catalyze the oxidation of glucose and generate a measurable signal?

In glucose biosensors (e.g., glucometers for diabetes management), the enzyme most commonly used for glucose detection is glucose oxidase. This enzyme catalyzes the oxidation of glucose to gluconolactone while simultaneously producing hydrogen peroxide (H2O2), which can then be electrochemically detected or coupled with other reactions to generate a measurable signal proportional to the glucose concentration.