Metabolism, Respiration, and Photosynthesis

This is Unit Three of Biology, Part Two: enzymes, and the first pathway. Part One established that a catalyst lowers activation energy without changing whether a reaction runs. This part is about the catalysts cells actually use, and then the first pathway that puts them to work. Enzymes recognise their substrates by shape and chemistry rather than by general affinity, and the model for that recognition was revised rather than replaced. Induced fit is not lock-and-key restated — it says both partners shift shape as they bind, which the earlier rigid picture did not allow. Two inhibitors then get distinguished by a single test. Add more substrate: if the inhibition weakens, it was competitive, because the two were contesting the same site. If it does not weaken, the inhibitor was never at that site. Then redox, which is the accounting the rest of the unit depends on. Oxidation and reduction never happen alone — an electron lost by one molecule is always gained by another, so the two are one reaction described from two ends. The part closes on glycolysis, which every cell runs and which needs no oxygen at all. By the end you will be able to do five things. One: say what an enzyme changes. Two: say what specificity comes from. Three: tell the two inhibitions apart. Four: say why redox is always paired. Five: say what glycolysis nets.

Three entries. The first applies Part One's catalyst rule to proteins, the second locates where recognition happens, and the third corrects a model most readers already carry — and it is a correction rather than a synonym.

A protein catalyst.

Bio 0514 Enzymes as Catalysts

An enzyme is a protein catalyst that lowers a specific reaction's activation energy without being consumed. Like any catalyst it changes a reaction's speed, never whether that reaction is exergonic or endergonic.

Where it binds.

Bio 0516 The Active Site and Substrate Specificity

An enzyme's active site is the region where its substrate binds, its amino acid arrangement shaped to fit one substrate or a narrow set. Specificity comes from the site's precise shape and chemistry, not from a general stickiness to organic molecules.

Both shift.

Bio 0518 Induced Fit

Induced fit describes an enzyme and substrate each shifting shape slightly as they bind, refining an earlier model that pictured a rigid fit. It expands lock-and-key into a dynamic, mutual-adjustment view — it is not lock-and-key restated.

Two entries. An enzyme has conditions it works best in, and past that optimum more heat makes things worse rather than better. The second entry names what happens at the extreme, and is careful about what does and does not change.

An optimum.

Bio 0520 Temperature, pH, and Enzyme Activity

Each enzyme has an optimal temperature and p H at which its active site binds substrate most effectively, with activity falling off either side. Raising temperature speeds a reaction only up to the optimum — beyond it, activity drops.

Losing the shape.

Bio 0522 Enzyme Denaturation

Denaturation is a change to an enzyme's natural shape, usually from extreme heat or p H, that disrupts the active site and destroys function. It changes the enzyme's structure, not its amino acid sequence — the underlying protein chain is not broken apart.

Two entries, and one experiment distinguishes them. Add more substrate. If the inhibition eases, the inhibitor was competing for the active site. If nothing changes, it was bound somewhere else entirely.

At the active site.

Bio 0524 Competitive Inhibition

A competitive inhibitor resembles an enzyme's substrate closely enough to bind the active site, blocking the true substrate. Its effect weakens as substrate concentration rises, because substrate and inhibitor are competing for the same place.

Somewhere else.

Bio 0526 Noncompetitive and Allosteric Inhibition

A noncompetitive inhibitor binds an enzyme away from the active site, at an allosteric site, changing the enzyme's shape so the active site no longer works. Because it binds elsewhere, its effect does not weaken as substrate concentration rises.

Three entries. Some enzymes need something besides themselves, and where that something comes from connects this material to diet. Then two ways a cell controls enzymes without changing the enzymes at all.

Inorganic, or organic.

Bio 0528 Cofactors and Coenzymes

A cofactor is an inorganic ion an enzyme needs to function; a coenzyme is a small organic helper molecule, often sourced from a dietary vitamin. Some vitamins, like B3, are only coenzyme precursors — others, like vitamin C, act as coenzymes themselves.

Control by location.

Bio 0530 Enzyme Compartmentalization

Compartmentalising enzymes inside specific organelles restricts where and when they act on their substrates. It controls substrate access rather than intrinsic activity — the same enzyme would still function if relocated.

Control by product.

Bio 0532 Feedback Inhibition

Feedback inhibition is a pathway's end product binding back to inhibit an earlier enzyme in its own production, slowing the pathway as product accumulates. It targets the pathway's regulatory enzyme, usually the first committed step, not every enzyme along the way.

Two entries supplying the accounting the rest of the unit runs on. An electron lost by one molecule is gained by another, always — so oxidation and reduction are one reaction seen from two sides rather than two events.

Lost, and gained.

Bio 0534 Redox Reactions

A redox reaction pairs oxidation, the loss of an electron, with reduction, the gain of one, since a lost electron always transfers to something. Oxidation and reduction always occur together — neither happens to a molecule in isolation.

The ferries.

Bio 0536 Electron Carriers: NAD+ and FAD

N A D plus and F A D are electron-carrier molecules, derived from B vitamins, that accept high-energy electrons to become N A D H and F A D H two. The reduced form, marked by the added H, holds the energy — the oxidised form must be regenerated.

Three entries to close. The simpler of the two ways a cell makes A T P, then the pathway every cell runs — and the entry that walks its ten steps has a number worth watching, because the gross yield is not the yield.

Straight across.

Bio 0538 Substrate-Level Phosphorylation

Substrate-level phosphorylation makes A T P directly, transferring a phosphate group from a reaction intermediate straight onto A D P. It is direct and immediate — it does not depend on the multi-step chemiosmotic process covered later.

Glucose, split.

Bio 0540 Glycolysis, Overview

Glycolysis splits one six-carbon glucose molecule into two three-carbon pyruvate molecules in the cytoplasm. It needs no oxygen and is not anaerobic respiration — it is the pathway every cell runs before oxygen becomes relevant at all.

Ten steps, two phases.

Bio 0542 The Steps of Glycolysis

Glycolysis proceeds through an energy-investment phase and an energy-payoff phase, ten enzyme-catalysed steps carrying one glucose to two pyruvate. The arithmetic is the point: the pathway pays back its own two-A T P investment before it profits, so four gross A T P nets down to two.

Five things to carry out of Part Two. An enzyme is a protein catalyst. Like every catalyst it lowers activation energy and changes how fast a reaction runs, and it never changes whether the reaction is exergonic or endergonic. That rule came from Part One and it does not bend for proteins. Specificity comes from the active site's shape and chemistry rather than from general stickiness. Induced fit revised the older rigid picture: enzyme and substrate each shift as they bind, which is a different claim from lock-and-key rather than a rewording of it. Competitive and noncompetitive inhibition are told apart by one test. Adding substrate weakens a competitive inhibitor, because both are contesting the active site. It does nothing for a noncompetitive one, which binds at an allosteric site and changes the enzyme's shape. Oxidation and reduction always happen together, because an electron lost by one molecule is gained by another. The carriers N A D plus and F A D accept those electrons to become N A D H and F A D H two, and the added H is what marks the form holding the energy. And glycolysis splits one glucose into two pyruvate in the cytoplasm, with no oxygen involved. It produces four A T P gross and nets two, because the pathway spends two of its own before the payoff phase begins. Part Three follows the pyruvate into the mitochondrion.