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.