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.

Enzymes make metabolism feasible by controlling the rates and sequence of reactions in cells.

Different enzymes recognize particular substrates and conditions, allowing pathways to run in compartments and at regulated rates. Without catalysts, many reactions would be too slow at cell temperature.

Think of enzyme control at three levels:

• substrate recognition
• reaction rate
• pathway regulation

A cell can increase a digestive enzyme when food is present while keeping unrelated pathways slower, conserving resources.

Metabolism is not one reaction; it is a network whose steps require different enzymes.

Anabolic reactions build larger molecules from smaller units, whereas catabolic reactions break molecules down and often release usable energy.

Cells couple the two: catabolism supplies ATP or reducing power, while anabolism uses energy and building blocks for growth and repair. Both directions require enzymes and regulation.

Classify the reaction by its flow:

• small to large: anabolic
• large to small: catabolic
• energy input or release is a consequence, not the definition

Protein synthesis is anabolic; digestion of a protein into amino acids is catabolic.

A reaction can be chemically reversible, but the pathway context determines whether the cell uses it for building or breakdown.

Most enzymes are globular proteins whose folded three-dimensional shape creates a specific active site.

Hydrophobic interactions, hydrogen bonds, ionic attractions and disulfide bonds stabilize the fold. The active site presents chemical groups in a geometry that binds substrates and promotes the transition state.

Connect structure to function:

• amino-acid sequence
• folding and active-site shape
• substrate binding
• catalytic chemistry

Changing one amino acid near an active site can alter its shape and reduce activity even if the rest of the protein remains folded.

An enzyme’s function depends on its three-dimensional conformation, not only its amino-acid list.

In the induced-fit model, substrate binding causes a small active-site shape change that positions reactants and catalytic groups.

The flexible fit stabilizes the transition state and can strain bonds or exclude water. Binding is therefore more than a rigid lock-and-key match.

A useful induced-fit explanation includes:

• initial recognition
• conformational change
• transition-state stabilization
• product release

When substrate enters an enzyme pocket, side chains can rotate into a catalytic arrangement; products then leave because their interactions are weaker.

Induced fit does not mean every substrate binds equally well or that the enzyme permanently changes shape.

Molecules move randomly, and enzyme reactions depend on collisions that have enough energy and the correct orientation.

Temperature changes average kinetic energy and collision frequency. Diffusion brings substrate and enzyme together, while the active site filters collisions by shape and chemistry.

For a collision explanation, include:

• random motion and diffusion
• collision frequency
• orientation
• activation energy

At low substrate concentration, adding more substrate increases productive collisions until most active sites are occupied.

Faster motion alone does not guarantee reaction; collisions still need a suitable orientation and energy.

Enzyme function depends on the relationship between amino-acid sequence, three-dimensional shape and active-site chemistry.

A mutation, pH shift or temperature change can alter bonds maintaining the fold. If substrate contacts or catalytic residues move, binding and reaction rate change even when the protein is still present.

Trace a structure–function effect:

• structural change
• active-site geometry
• substrate binding
• rate or specificity

Replacing a charged residue in an active site with a non-polar one can remove an ionic interaction and lower catalytic activity.

A smaller enzyme band or unchanged concentration does not prove that its active site still works.

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 the activation energy needed to reach the transition state, increasing the fraction of successful collisions.

They bind substrates and orient reactive groups, strain bonds or create a favorable local environment. The energy difference between reactants and products is unchanged.

Compare catalysed and uncatalysed paths:

• same reactants and products
• lower peak for the enzyme pathway
• faster forward and reverse rates
• unchanged equilibrium position

On an energy profile, the catalysed curve has a lower peak while its starting and ending energy levels match the uncatalysed curve.

Lower activation energy does not mean the reaction becomes more exergonic.

Intracellular enzymes act inside cells, while extracellular enzymes are secreted and act outside the producing cell.

Location matches the task: lysosomal enzymes digest material in a compartment, whereas digestive enzymes such as amylase act in the gut lumen after secretion. Secretion requires targeting and transport.

Distinguish the locations:

• substrate inside the cytoplasm or organelle
• substrate outside the cell
• secretion or vesicle pathway
• local pH and conditions

A fungus secretes cellulase into its surroundings, breaks cellulose into sugars, then absorbs the products.

Extracellular does not mean non-biological; it describes where the enzyme acts.

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 pathway passes through a sequence of intermediates, whereas a cyclic pathway regenerates a starting acceptor so the sequence can repeat.

Pathway shape affects regulation and flux. Linear pathways can end in a product; cycles can process repeated inputs while conserving key carriers or accepting molecules.

Identify pathway structure by asking:

• is the starting acceptor regenerated?
• is there one terminal product?
• where are branch points?
• which step controls flux?

The Krebs cycle regenerates oxaloacetate after acetyl groups are processed, allowing another turn when substrates and electron acceptors are available.

A cycle is not perpetual motion; it still needs inputs, energy and conditions that sustain each step.

An allosteric site is a regulatory binding site separate from the active site; binding there changes enzyme conformation and activity.

A non-competitive inhibitor can reduce activity by stabilizing a shape that binds substrate poorly or catalyses slowly. Increasing substrate cannot fully overcome inhibition when the active-site enzyme population is altered.

Diagnose allosteric inhibition:

• inhibitor binds away from active site
• conformation changes
• maximum rate decreases
• substrate increase has limited effect

If an inhibitor lowers the maximum rate at every substrate concentration, it is consistent with non-competitive effects on functional enzyme molecules.

Non-competitive does not mean the inhibitor never affects substrate binding; the key is the separate site and altered activity.

A competitive inhibitor resembles the substrate and competes for the active site, reducing reaction rate at a given substrate concentration.

Because the competition is reversible, increasing substrate can outcompete the inhibitor in the ideal model. The apparent substrate concentration needed for a given rate rises, while maximum rate can remain reachable.

Look for the competitive pattern:

• same active site
• substrate-like molecule
• reversible competition
• effect reduced by excess substrate

If adding more substrate restores the original maximum rate, active-site competition is a plausible explanation.

A competitive inhibitor does not permanently destroy the enzyme; it changes access to the active site.

Feedback inhibition occurs when a pathway’s end product inhibits an earlier enzyme, preventing unnecessary accumulation.

The product binds a regulatory site or otherwise reduces flux at a committed step. When product concentration falls, inhibition eases and pathway activity can resume.

Trace the control loop:

• pathway produces end product
• product concentration rises
• early enzyme is inhibited
• flux falls until demand returns

If amino-acid synthesis slows when the amino acid accumulates, the product is acting as a signal that the pathway’s output is sufficient.

Feedback inhibition is regulation, not evidence that the pathway’s reactions have reversed.

A mechanism-based inhibitor is processed by an enzyme into a reactive product that binds or modifies the enzyme’s catalytic machinery.

Because the enzyme’s own chemistry activates the inhibitor, the inhibition can be highly specific and effectively irreversible until new enzyme is made. It differs from simple reversible competition.

Identify the mechanism:

• inhibitor resembles substrate
• enzyme begins normal catalysis
• reactive intermediate forms
• active site is modified or blocked

An inhibitor designed for one enzyme may be harmless until that enzyme converts it into a reactive species that covalently modifies a catalytic residue.

Specific activation does not make the inhibitor harmless; it can permanently reduce functional enzyme concentration.