Skip to ContentGo to accessibility pageKeyboard shortcuts menu
OpenStax Logo
Organic Chemistry

29.1 An Overview of Metabolism and Biochemical Energy

Organic Chemistry29.1 An Overview of Metabolism and Biochemical Energy

29.1 • An Overview of Metabolism and Biochemical Energy

The many reactions that occur in the cells of living organisms are collectively called metabolism. The pathways that break down larger molecules into smaller ones are called catabolism, and the pathways that synthesize larger biomolecules from smaller ones are known as anabolism. Catabolic reaction pathways are usually exergonic and release energy, while anabolic pathways are often endergonic and absorb energy. Catabolism can be divided into the four stages shown in Figure 29.2.

The production of adenosine triphosphate and water from fats, carbohydrates and proteins involves four stages. Acetyl coenzyme A formed in second stage undergoes citric acid cycle and electron-transport chain.
Figure 29.2 An overview of catabolic pathways for the degradation of food and the production of biochemical energy. The ultimate products of food catabolism are CO2 and H2O, with the energy released in the citric acid cycle used to drive the endergonic synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) plus hydrogen phosphate ion, HOPO32–.

In the first catabolic stage, commonly called digestion, food is broken down in the mouth, stomach, and small intestine by hydrolysis of ester, acetal (glycoside), and amide (peptide) bonds to yield fatty acids, simple sugars, and amino acids. These smaller molecules are then absorbed and further degraded in the second stage of catabolism to yield acetyl groups attached by a thioester bond to the large carrier molecule, coenzyme A. The resultant compound, acetyl coenzyme A (acetyl CoA), is a key substance in the metabolism of food molecules and in many other biological pathways. As noted in Section 21.8, the acetyl group in acetyl CoA is linked to the sulfur atom of phosphopantetheine, which is itself linked to adenosine 3',5'-bisphosphate.

The structure of acetyl Co A, a thioester. It comprises of a C H 3 C O linked to a phosphopantetheinyl adenosine bisphosphate.

Acetyl groups are oxidized inside cellular mitochondria in the third stage of catabolism, the citric acid cycle, to yield CO2. (We’ll see the details of the process in Section 29.7.) Like most oxidations, this stage releases a large amount of energy, which is used in the fourth stage, the electron-transport chain, to accomplish the endergonic phosphorylation of adenosine diphosphate (ADP) with hydrogen phosphate ion (HOPO32–, abbreviated Pi) to give adenosine triphosphate (ATP).

As the final result of food catabolism, ATP has been called the “energy currency” of the cell. Catabolic reactions “buy” ATP with the energy they release to synthesize it from ADP and hydrogen phosphate ion. Anabolic reactions then spend the ATP by transferring a phosphate group to another molecule, thereby regenerating ADP. Energy production and use in living organisms thus revolves around the ATP ADP interconversion.

The reversible reaction of adenosine diphosphate with phosphate and hydrogen ions. The removal of water leads to the product named adenosine triphosphate. Diphosphate and triphosphate groups in structures are labeled.

ADP and ATP are both phosphoric acid anhydrides, which contain Phosphoric acid anhydride with two phosphorus atoms connected to oxygen via a single bond and each phosphorus atom  double bonded to an oxygen atom. linkages analogous to the Carboxylic acid anhydride with two carbon atoms connected to oxygen via a single bond, and each carbon atom  double bonded to an oxygen atom. linkage in carboxylic acid anhydrides. Just as carboxylic acid anhydrides react with alcohols by breaking a C–O bond and forming a carboxylic ester, ROCOR' (Section 21.5), phosphoric acid anhydrides react with alcohols by breaking a P–O bond and forming a phosphate ester, ROPO32–. The reaction is, in effect, a nucleophilic acyl substitution at phosphorus. Note that phosphorylation reactions with ATP generally require the presence of a divalent metal cation in the enzyme, usually Mg2+, to form a Lewis acid–base complex with the phosphate oxygen atoms and to neutralize negative charge.

The reaction shows an alcohol reacting with adenosine triphosphate to form an intermediate, which decomposes to form a phosphate ester, adenosine diphosphate, and magnesium cation.

How does the body use ATP? Recall from Section 6.7 that the free-energy change ΔG must be negative and energy must be released for a reaction to be energetically favorable and occur spontaneously. If ΔG is positive, the reaction is energetically unfavorable and the process can’t occur spontaneously.

For an energetically unfavorable reaction to occur, it must be “coupled” to an energetically favorable reaction so that the overall free-energy change for the two reactions together is favorable. To understand what it means for reactions to be coupled, imagine that reaction 1 does not occur to any reasonable extent because it has a small equilibrium constant and is energetically unfavorable; that is, the reaction has ΔG > 0.

A reversible reaction where A reacts with m to form B and n. The value of delta G is greater than zero.

where A and B are the biochemically “important” substances while m and n are enzyme cofactors, H2O, or other small molecules.

Imagine also that product n can react with substance o to yield p and q in a second, highly favorable reaction that has a large equilibrium constant and ΔG << 0.

A reversible reaction where n reacts with o to form p and q. The value of delta G is much less than zero.

Taking the two reactions together, they share, or are coupled through, the common intermediate n, which is a product in the first reaction and a reactant in the second. When even a tiny amount of n is formed in reaction 1, it undergoes essentially complete conversion in reaction 2, thereby removing it from the first equilibrium and forcing reaction 1 to continually replenish n until reactant A is gone. That is, the two reactions added together have a favorable ΔG < 0, and we say that the favorable reaction 2 “drives” the unfavorable reaction 1. Because the two reactions are coupled through n, the transformation of A to B becomes favorable.

Two reversible reactions are combined to give a net overall reversible reaction, A plus m plus give B plus p plus q. The delta G is less than zero.

For an example of two reactions that are coupled, look at the phosphorylation reaction of glucose to yield glucose 6-phosphate plus water, an important step in the breakdown of dietary carbohydrates.

Glucose reacts reversibly with phosphate ion to give glucose-6-phosphate and water. The standard G value is equal to plus 13 point 8 kilojoules.

The reaction of glucose with HOPO32– does not occur spontaneously because it is energetically unfavorable, with ΔG°' = 13.8 kJ/mol. (The standard free-energy change for a biological reaction is denoted ΔG°' and refers to a process in which reactants and products have a concentration of 1.0 M in a solution with pH = 7.) At the same time, however, the reaction of water with ATP to yield ADP plus HOPO32– is strongly favorable, with ΔG°' = –30.5 kJ/mol. When the two reactions are coupled, glucose reacts with ATP to yield glucose 6-phosphate plus ADP in a reaction that is favorable by about 16.7 kJ/mol (4.0 kcal/mol). That is, ATP drives the phosphorylation reaction of glucose.

Two reactions combine to form net reaction where glucose combines with adenosine triphosphate to give glucose-6-phosphate, adenosine diphosphate and hydrogen positive ion. The overall  delta G is less than zero.

It’s this ability to drive otherwise unfavorable phosphorylation reactions that makes ATP so useful. The resultant phosphates are much more reactive as leaving groups in nucleophilic substitutions and eliminations than the alcohols they’re derived from and are therefore more chemically useful.

Problem 29-1
One of the steps in fat metabolism is the reaction of glycerol (1,2,3-propanetriol) with ATP to yield glycerol 1-phosphate. Write the reaction, and draw the structure of glycerol 1-phosphate.
Order a print copy

As an Amazon Associate we earn from qualifying purchases.


This book may not be used in the training of large language models or otherwise be ingested into large language models or generative AI offerings without OpenStax's permission.

Want to cite, share, or modify this book? This book uses the Creative Commons Attribution-NonCommercial-ShareAlike License and you must attribute OpenStax.

Attribution information
  • If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:
    Access for free at
  • If you are redistributing all or part of this book in a digital format, then you must include on every digital page view the following attribution:
    Access for free at
Citation information

© Jan 9, 2024 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike License . The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.