Metabolism, Respiration, and Photosynthesis

This is Unit Three of Biology, Part One: energy, and the rules it obeys. Nothing in this part is a process. It is the accounting system the next three parts spend — what energy is, which reactions run on their own, and what a cell uses to pay for the ones that do not. The organising fact arrives in the fourth entry. Glucose stores energy and A T P spends it, and cells never spend glucose directly. Every use of stored energy passes through A T P first, which is why the rest of the unit keeps returning to one molecule. Two words then need care. A spontaneous reaction is one that needs no outside energy — it says nothing about speed, and a spontaneous reaction can take years. And a closed system is not an isolated one: matter stays in, energy still moves freely. The second law says every transfer loses usable energy as heat and raises entropy. A cell looks like an exception and is not — it stays ordered locally only by exporting disorder outward, and the total still rises. By the end you will be able to do five things. One: tell anabolic from catabolic pathways. Two: tell exergonic from endergonic. Three: say what a catalyst changes. Four: state the two laws. Five: say how energy coupling works.

Four entries. The first names the whole of a cell's chemistry rather than any part of it, the next two give its directions and its organisation, and the fourth sets up the distinction the entire unit runs on.

All of it, at once.

Bio 0481 Metabolism and Bioenergetics

A cell's metabolism is the sum of every chemical reaction taking place inside it; bioenergetics is the study of how energy flows through those reactions. Metabolism names every reaction together, not any single reaction or pathway alone.

Two directions.

Bio 0483 Anabolic and Catabolic Pathways

An anabolic pathway builds complex molecules from simpler ones and requires energy; a catabolic pathway breaks complex molecules down and releases it. The two are opposite directions on one chemical relationship, not two unrelated processes.

How reactions are organised.

Bio 0485 The Metabolic Pathway

A metabolic pathway is a series of interconnected reactions, each catalysed by its own enzyme, converting a starting substrate into a product. A pathway's intermediates are not waste — many feed directly into other pathways elsewhere in the cell.

Storage, and currency.

Bio 0487 ATP versus Glucose: Currency and Storage

Glucose stores energy long-term in its bonds; A T P is the unstable, short-term currency cells spend to do immediate work. Cells do not spend glucose directly — every use of stored energy passes through A T P first.

Two entries. The first distinguishes energy in motion from energy held in position, and the second locates the kind this course cares about — in bonds. The warning on the second is the one most often skipped.

Motion, or position.

Bio 0489 Kinetic and Potential Energy

Kinetic energy is the energy of an object in motion; potential energy is the energy an object holds because of its position or structure. An object at rest is not without energy — its potential energy has not yet been released.

Held in bonds.

Bio 0491 Chemical Energy

Chemical energy is potential energy stored in a molecule's chemical bonds, released when those bonds break. Breaking a bond releases energy only when that bond stored more energy than the bonds replacing it — breaking alone does not release anything.

Three entries. The first supplies the criterion, the second is a misconception entry about a word that sounds like it describes speed and does not, and the third explains why a living cell must never reach the state a sealed flask settles into.

Usable energy.

Bio 0493 Gibbs Free Energy and Exergonic/Endergonic Reactions

Gibbs free energy is a reaction's usable energy. An exergonic reaction releases free energy and proceeds unaided; an endergonic one absorbs it and does not. A negative free-energy change marks exergonic and a positive one endergonic — the sign decides, not the size.

The standing error.

Bio 0494 "Spontaneous Means Instantaneous"

A spontaneous reaction is one that releases energy and needs no outside energy source to proceed — and it says nothing about how fast that happens. Confusing spontaneous with instant misreads a claim about energy direction as a claim about reaction speed.

Why a cell never settles.

Bio 0496 Chemical Equilibrium in an Open System

A sealed flask's reactions drift toward chemical equilibrium, its lowest free-energy state; a living cell, constantly trading matter with its surroundings, never arrives there. Reaching equilibrium would leave a cell with no free energy for life's work.

Two entries. Even a reaction that releases energy has to be pushed to start, and the entry that follows is careful about what lowering that barrier does — and what it leaves entirely alone.

The input to start.

Bio 0498 Activation Energy

Activation energy is the input every reaction needs to reach its unstable transition state, even one that releases energy overall. It is not part of the reaction's net free-energy change — it is recovered once the transition state resolves.

Lowering the barrier.

Bio 0500 Catalysis Lowers Activation Energy

A catalyst speeds a reaction by lowering its activation energy, without being consumed and without changing the reaction's overall free-energy change. Lowering activation energy changes how fast a reaction proceeds, never whether it is exergonic or endergonic.

Three entries. The first defines what a system is, and its warning matters — closed does not mean sealed off from everything. Then the two laws that govern every energy transfer for the rest of the course.

What is under study.

Bio 0502 Systems: Open and Closed

A system is the matter and energy under study. An open system exchanges both matter and energy with its surroundings; a closed one exchanges energy only. A closed system is not isolated — energy still moves freely, and only matter stays sealed in.

Energy is conserved.

Bio 0504 The First Law of Thermodynamics

The first law of thermodynamics holds the universe's total energy constant — energy transfers and transforms but is never created or destroyed. The law governs transformation and transfer only, and says nothing about how efficiently a transfer proceeds.

And degraded.

Bio 0506 The Second Law of Thermodynamics and Entropy

The second law holds that every energy transfer loses usable energy as heat, raising the universe's entropy. A cell stays low-entropy locally only by exporting disorder outward — the total still rises, so life is not an exception to the law.

Three entries to close. What makes two of A T P's bonds worth spending, what its breakdown produces, and then the mechanism that gets that energy into a reaction which could not otherwise run.

Three phosphates.

Bio 0508 ATP Structure

A T P, adenosine triphosphate, is a nucleoside bound to three phosphate groups, its two outer phosphate bonds high-energy because of how their charges repel. Not every bond in A T P is high-energy — only the two linking the outer phosphates qualify.

Splitting the last one.

Bio 0510 ATP Hydrolysis

A T P hydrolysis splits off the terminal phosphate, producing A D P and an inorganic phosphate ion while releasing free energy the cell can use. The reaction is reversible — regenerating A T P from A D P costs exactly the energy hydrolysis released.

Getting it to the reaction.

Bio 0512 Energy Coupling and Phosphorylation

Energy coupling pairs A T P hydrolysis with an endergonic reaction, often by phosphorylation — transferring A T P's terminal phosphate to another molecule. The energy does not leap between reactions; phosphorylation physically links the two.

Five things to carry out of Part One. Anabolic pathways build and consume energy; catabolic pathways break down and release it. They are two directions on one relationship. And a cell never spends glucose directly — glucose is storage, A T P is currency, and every use of stored energy passes through A T P first. A negative free-energy change marks an exergonic reaction, which proceeds unaided; a positive one marks endergonic, which does not. The sign decides, not the size. And spontaneous means no outside energy is required — it makes no claim about speed, so a spontaneous reaction can take years. Every reaction needs activation energy to reach its transition state, even one that releases energy overall. A catalyst lowers that barrier without being consumed, changing how fast a reaction goes and never whether it goes. The first law says energy is conserved through every transfer and transformation. The second says every transfer loses usable energy as heat and raises entropy. A cell stays ordered locally by exporting disorder, so it obeys the second law rather than escaping it. And A T P carries two high-energy bonds, not three. Hydrolysis splits off the terminal phosphate to release usable energy, and coupling delivers that energy by physically transferring the phosphate to the molecule that needs it. Part Two turns to the enzymes that make these reactions run fast enough to matter.