C1.1 Enzymes and metabolism

Enzymes are biological catalysts that increase reaction rate without being consumed.

They provide an alternative pathway with lower activation energy, so more substrate molecules can react at a given temperature. The enzyme is regenerated after products leave its active site.

For a catalyst claim, check:

• reaction rate increases
• activation energy decreases
• enzyme is not used up
• equilibrium position is unchanged

Adding catalase to hydrogen peroxide makes oxygen bubbles appear faster, but the catalase remains available for further reactions.

An enzyme changes kinetics, not the overall energy difference or equilibrium constant.

Metabolism is the complex network of interdependent and interacting chemical reactions occurring in a living organism; each step is catalysed by a specific enzyme.

Enzyme specificity requires many different enzymes, because each active site catalyses only a limited reaction. Linking enzyme-controlled steps lets the products of one reaction become substrates for another.

Cells control metabolic flux by changing enzyme synthesis, activity, location or access to substrate. Regulation at one key step can alter the output of an entire pathway while other pathways continue independently.

In a pathway A → B → C, one enzyme catalyses A → B and a different enzyme catalyses B → C; inhibiting the first step reduces both B formation and downstream C production.

Metabolism is not one reaction or only energy release: it includes all interacting anabolic and catabolic reactions and the controls acting through their enzymes.

Anabolic reactions build larger molecules from smaller units and require energy; catabolic reactions break down or oxidize molecules and often release usable energy.

Anabolism commonly joins monomers by condensation, forming covalent bonds and releasing water. Catabolism includes hydrolysis of macromolecules in digestion and oxidation of respiratory substrates.

Catabolic respiration can supply ATP and reducing power that drive anabolic protein or glycogen synthesis, linking the two parts of metabolism.

Energy input or release is a typical consequence, not the sole classification rule: identify whether the cellular pathway constructs or breaks/oxidizes material.

Most enzymes are globular proteins whose overall three-dimensional fold creates a small active-site pocket for substrate binding and catalysis.

Only a few amino-acid residues directly form the active site, but interactions among many residues elsewhere—hydrogen bonds, ionic attractions, hydrophobic effects and sometimes disulfide bonds—position those catalytic residues correctly.

The active site binds substrate to form an enzyme–substrate complex and presents chemical groups with the charge, polarity and geometry needed to stabilize the transition state and promote reaction.

Changing a residue far from the pocket can disrupt the protein fold and reposition an active-site residue, reducing catalysis even though that altered residue never contacts substrate.

The active site is only a small part of the enzyme, but it depends on the entire globular conformation; a matching outline alone is not enough for catalytic chemistry.

In induced-fit binding, initial substrate contact changes the conformation of both the enzyme active site and the substrate, producing a catalytically effective fit.

Enzyme side chains move to align catalytic groups, while the substrate can be bent, strained or have bonds polarized. These changes make the transition state easier to reach.

Sequence: initial recognition → enzyme–substrate complex → reciprocal conformational change → transition-state stabilization → products form and leave → enzyme returns to a reusable state.

Hexokinase closes around glucose and ATP, aligning them and excluding water; after phosphate transfer, the differently shaped products have weaker interactions and are released.

Induced fit is not a rigid lock-and-key event and does not mean the enzyme permanently changes. Specificity remains because only suitable substrates trigger productive interactions.

Enzyme catalysis requires random molecular motion to bring a substrate into a productive collision with an active site.

Higher kinetic energy increases motion and collision frequency up to the point where enzyme structure becomes unstable. A collision must also have suitable orientation and enough energy for binding and reaction.

Sometimes a large substrate is effectively immobilized, so enzyme molecules diffuse to exposed sites. In other systems the enzyme is immobilized in a membrane, and moving substrate molecules collide with its fixed active sites.

A membrane-embedded enzyme remains in one location while dissolved substrate diffuses through the membrane environment and collides with the active site.

Immobilized does not mean inactive, and faster motion alone cannot guarantee catalysis: molecular complementarity, orientation and enzyme conformation still matter.

Substrate specificity depends on the three-dimensional arrangement and chemistry of amino acids in the active site; denaturation disrupts that arrangement and lowers activity.

A suitable substrate forms complementary shape, charge, polarity and hydrogen-bond interactions. Temperature extremes or unsuitable pH can disrupt bonds maintaining tertiary structure, changing the active site's geometry.

Trace the relationship: amino-acid interactions maintain fold → fold positions active-site residues → substrate binds specifically → catalysis occurs. Denaturation breaks this chain without normally hydrolysing peptide bonds.

If heating moves a charged catalytic residue away from the substrate-binding position, fewer enzyme–substrate complexes form and the reaction rate falls even after the solution is cooled.

Denaturation is a structural loss, not simply temporary active-site occupancy. The protein may remain present and its peptide sequence intact while its function is lost.

Enzyme activity depends on temperature, pH, substrate concentration and enzyme concentration within an appropriate range.

Warming usually increases collisions until bonds in the protein are disrupted; pH changes alter ionization and active-site interactions. More substrate or enzyme increases rate only while another factor is not limiting.

Interpret a rate curve by locating:

• optimum region
• limiting factor
• denaturation or inhibition
• plateau from saturated active sites

Increasing substrate raises rate until every active site is occupied; further substrate then produces little additional increase.

The optimum is not a universal constant: it depends on the enzyme’s structure and cellular environment.

An enzyme reaction rate is measured from the change in substrate or product concentration per unit time.

Choose a signal proportional to concentration, keep conditions controlled and use the initial linear section before substrate depletion or product inhibition changes the rate.

A sound measurement includes:

• dependent signal and calibration
• controlled temperature and pH
• initial-rate interval
• repeats and uncertainty

A colorimeter can track product colour every ten seconds; the slope of absorbance against time estimates the initial rate.

A final product amount alone cannot distinguish a fast reaction from a slow reaction allowed to run longer.

Enzymes lower activation energy by providing an alternative reaction pathway that stabilizes the transition state; reactant and product energy levels remain unchanged.

Energy must be supplied to distort or break bonds in substrate before new product bonds can form. Bond formation then releases energy; the balance between starting and ending states determines the overall energy change.

On an energy profile, catalysed and uncatalysed curves begin and end at the same levels, but the catalysed curve has a lower peak. More molecules can reach that lower transition-state barrier at the same temperature.

Read the vertical gap from reactants to the peak as activation energy: the enzyme reduces this gap but does not alter the vertical difference between reactants and products.

An enzyme does not remove the barrier, add net energy or make an endergonic reaction exergonic. It changes rate, not the equilibrium position.

Intracellular enzyme reactions occur inside cells, whereas extracellular enzymes are secreted and catalyse reactions outside the cell that produced them.

Glycolysis in the cytoplasm and the Krebs cycle in the mitochondrial matrix are intracellular pathways. Digestive enzymes secreted into the gut lumen catalyse extracellular chemical digestion.

Location matches access to substrate and conditions. Extracellular products must often be small enough for absorption, while intracellular products can feed directly into other compartmentalized pathways.

Pancreatic amylase is secreted into the small intestine and hydrolyses starch outside cells; absorbed sugars can then enter intracellular metabolic reactions.

Extracellular means outside the producing cell, not outside the organism. An enzyme enclosed in a cytoplasmic organelle is still intracellular.

Metabolic reactions transfer energy, and some of the released energy appears as heat rather than being captured in ATP or products.

Cells use coupled reactions and ATP to conserve part of the energy, but inefficiency and thermodynamic constraints produce heat. Heat generation can help endotherms maintain body temperature but must be regulated.

Trace energy allocation:

• chemical energy in substrate
• captured work or ATP
• unavoidable heat release
• heat loss or regulation

During respiration, not all glucose energy becomes ATP; some warms tissues and must be dissipated or used for thermoregulation.

Heat is an energy transfer, not a separate metabolic substance or proof that ATP production stopped.

A linear metabolic pathway converts an initial substrate through a sequence to a terminal product; a cyclical pathway regenerates an acceptor needed for the next turn.

Glycolysis is linear: glucose passes through intermediates and ends as pyruvate. The Krebs cycle regenerates oxaloacetate, and the Calvin cycle regenerates ribulose bisphosphate while processing new carbon input.

Identify pathway form by tracing carbon or the acceptor: if a starting acceptor is re-formed, the pathway is cyclical; if intermediates lead to a different terminal product without regeneration, it is linear.

Each Krebs-cycle turn combines an acetyl group with oxaloacetate and later regenerates oxaloacetate, allowing another acetyl group to enter when substrates and cofactors are available.

A cycle is not self-sustaining perpetual motion: it requires new inputs and energy transfers. A linear pathway can also contain reversible steps without becoming a cycle.

An allosteric site is a specific regulatory binding site separate from the active site; reversible inhibitor binding there can produce non-competitive inhibition.

Only molecules with suitable interactions bind the allosteric site. Binding changes interactions within the enzyme and causes a conformational change that alters the active site enough to prevent or reduce catalysis.

Because the inhibitor does not compete for the active site, adding more substrate does not fully restore activity. When the inhibitor dissociates, the enzyme can return to its active conformation.

If maximum rate remains lower at high substrate concentration in the presence of a reversible allosteric inhibitor, the pattern is consistent with non-competitive inhibition.

Non-competitive does not mean irreversible or nonspecific. The inhibitor binds a specific separate site and affects activity through conformation.

A competitive inhibitor binds reversibly to the enzyme's active site and prevents substrate binding while it occupies that site.

The inhibitor often resembles part of the substrate. Increasing substrate concentration raises the chance that substrate rather than inhibitor occupies the active site, so the inhibition can be reduced.

Statins competitively inhibit an active site in the cholesterol-synthesis pathway, reducing pathway flux. In the ideal kinetic model, more substrate raises the apparent substrate requirement while the original maximum rate remains reachable.

If a reaction recovers its uninhibited maximum rate at sufficiently high substrate concentration, reversible active-site competition is a plausible mechanism.

Competitive inhibition does not permanently destroy enzyme. Contrast it with reversible allosteric inhibition, whose effect is not overcome simply by adding substrate.

Feedback inhibition regulates a metabolic pathway when its end product reversibly inhibits an enzyme near the beginning of that pathway.

As end product accumulates, binding to a regulatory site lowers early-pathway activity and prevents unnecessary substrate and energy use. When product concentration falls, inhibition decreases and flux resumes.

In isoleucine synthesis, accumulated isoleucine inhibits an early enzyme in its own pathway. This negative-feedback loop matches production to demand without reversing the intervening reactions.

High isoleucine → early enzyme inhibited → fewer downstream intermediates → isoleucine production slows; use by the cell lowers isoleucine → inhibition eases → production increases.

The end product is a regulator, not a substrate for the inhibited step, and feedback inhibition controls pathway flux rather than proving that the pathway runs backwards.

A mechanism-based inhibitor undergoes enzyme-catalysed chemistry and then binds irreversibly or causes an irreversible active-site change, disabling that enzyme molecule.

Penicillin acts on bacterial transpeptidase involved in peptidoglycan cross-linking. Interaction at the active site forms a stable covalent complex, preventing further wall cross-link formation.

Without effective cross-linking, growing bacterial walls are weakened. Resistance can arise when a transpeptidase changes so penicillin binds or reacts less effectively while the enzyme still performs its normal function.

Unlike a reversible competitive inhibitor, increasing the normal substrate cannot reactivate a transpeptidase molecule already irreversibly modified by penicillin; new functional enzyme is required.

Mechanism-based inhibition is not merely temporary active-site competition. Penicillin targets bacterial wall synthesis; it does not directly inhibit an equivalent human cell-wall pathway.