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Basic Energy Concepts
Types of Catabolism
Feremented Foods
Catabolism of Fats
Catabolism of Proteins
Amazing Respirations
Membranes and
Energy Generation

Anaerobic Respiration
Summary of Catabolism
Collecting Elements
Synthesizing Monomers
Carbon Assimilation
Nitrogen Assimulation
Other Assimilation
Formation of
Amino Acids

Lipid Synthesis
Nucleotide Synthesis
Making Polymers
Structural Assembly
Amphibolic Pathways

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Basic Energy Concepts

©2000 Timothy Paustian, University of Wisconsin-Madison

Before we dive into bacterial metabolism I want to present some over arching ideas that you should keep in mind as we explore how bacteria make their energy and what they use it for.

First let me impress on you an important idea. Thousands of years ago, human tribes worshiped the sun. The light and heat of the sun was pivotal to their survival. Life on earth is possible because of the energy generated by the sun and almost all life depends upon it. (OK, OK, organisms living at deep sea ocean vents don't need the sun.)

This ultimate source of energy is transformed into living matter. To start getting comfortable with this idea, let's look at thermodynamics, which is concerned with the storage, transformation and dissipation of energy. Cells store energy, they transform it and they dissipate it to drive unfavorable reactions. Here we introduce the laws of thermodynamics because they govern everything a cell does.

The first law of thermodynamics

Energy can neither be created nor destroyed in the universe.

For living organisms this means they must collect and convert existing energy into a form suitable for biological processes from the surrounding environment. Usually this means grabbing it from the sun or breaking down large molecules and releasing the energy in them.

  • Plants and photosynthetic microbes convert light from the sun into high energy compounds that help to build cell material.

    Fig1SuntoPlant picture

    Figure 1 - Energy from the sun.

  • When you eat a bagel, your stomach and intestines break down the compounds that make up the bagel and convert this into high energy compounds for you to use..

    Fig2BagelToYou picture

    Figure 2 - Energy from a bagel.

The second law of thermodynamics

In all processes or reactions, some of the energy involved irreversibly loses its ability to do work.


In any reaction the amount of molecular disorder always increases

Living systems are ordered, while the natural tendency of the universe is to move toward systems of disorder with unavailable energy (increasing entropy). A cell is a protest against the second law of thermodynamics! Organisms are in a constant battle with entropy and when they finally lose the war, they die. Ah the futility of existence....

Free Energy (delta G)

All chemical reactions can be describe by the following equation.

  • H is the total energy of a reaction.
  • S is the amount of energy that is lost to disordering the system and is not available for work (entropy).
  • G is the amount of free energy available to do work

This equation can be rearranged as follows


Think about this for a moment. Increasing DS (entropy) results in a disordering of the system, giving a negative DG. So things that result in a large amount of disorder, like breaking starch (a polymer of sugar) into carbon dioxide and water, are favorable and result in a negative DG value. The take home message - negative DG (free energy) is good and is available to do work in the cell.

<img src="images/starchdegrade.gif" height="200" width="496" alt="starchdegrade picture" border="0">

Figure 3 - A favorable reaction - the degradation of starch by amylase. Note how the system becomes more disorganized by the action of amylase.

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get_shockwave picture

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A decrease in entropy results from an ordering of a system and a positive DG. For example, building a cell wall orders a system. This is an unfavorable reaction and will not occur spontaneously. But cells have to build cell walls, how do they do it? To get these reaction to go, you have to add energy. This energy usually increases the entropy of the universe by breaking down ATP into ADP + "Pi" or degrading some other phosphate containing compound. The increase in molecular disorder from breaking apart ATP compensates for the ordering of the cell wall assembly and enables the reaction to proceed..

<img src="images/peptidoassem.jpg" height="200" width="496" alt="peptidoassem picture" border="0">

Figure 4 - A unfavorable reaction. Synthesis of peptidoglycan by peptidoglycan synthase. This decreases the ordering the peptidoglycan, but is offset by the large amount of phosphate bond hydrolysis.

Oxidation-Reduction Reactions (Redox reactions)

Much of the energy that cells extract from the universe comes from oxidation-reduction reactions. It is critical to have a basic understanding of these if you are going to have any idea about how metabolism works.

All molecules contain electrons as part of the atoms that make them up. Each molecule has a potential to donate and accept electrons from another molecule. In chemistry this is written as a redox reaction.

NAD(P)+ + 2H+ + 2e- arrow picture NAD(P)H + H+

Figure 5 - An example of redox reaction

The potential of a redox reaction to donate electrons can be measured. Scientists of a previous age spent some time sitting around in lab and determined the redox potential at "standard conditions" (E´o) for almost every chemical reaction imaginable. They arbitrarily designated a hydrogen electrode as the standard and everything else is determined from it. The table below lists some common redox reactions found in the cell)

Redox Coupleo
2H++ 2e- arrow picture H2-0.42
ferredoxin(Fe+3) + e- arrow picture ferredoxin(Fe+2)-0.42
NAD(P)+ + 2H+ + 2e- arrow picture NAD(P)H + H+-0.32
S + 2H+ + 2e- arrow picture H2S-0.274
SO4-2 + 8H+ + 8e- arrow picture H2S-0.22
pyruvate + 2H+ + 2e- arrow picture lactate-2-0.185
FAD + 2H+ + 2e- arrow picture FADH + H+-0.18
cytochrome b(Fe3+) + e- arrow picture cytochrome b(Fe+2)0.075
ubiquinone + 2H+ + 2e- arrow picture ubiquinone H20.10
cytochrome c(Fe+3) + e- arrow picture cytochrome c(Fe+2)0.254
NO3- + 2H+ + 2e- arrow picture NO2- + H2O0.421
NO2- 8H+ + 6e- arrow picture NH40.44
Fe+3 + e- arrow picture Fe+20.771
O2 + 4H+ + 4e- arrow picture 2H2O0.815

Redox reactions with more negative reduction potentials will donate electrons to redox reactions with more positive potentials. For example.

NAD(P)+ + 2H+ + 2e- arrow picture NAD(P)H + H+-0.32
O2 + 4H+ + 4e- arrow picture 2H2O0.815
2 NAD(P)H+ 2 H+ + 4e- + O2 + arrow picture 2NAD+ + 2H2O1.135

Notice that to get the reaction to work, you have to reverse the first redox reaction -

NAD(P)+ + 2H+ + 2e- arrow picture NAD(P)H + H+ becomes

2NAD(P)H + 2H + arrow picture 2NAD(P)+ + 4H+ + 4e-.

There are many oxidation reduction reactions in the cell, during both catabolism and Anabolism. Much of the energy for the cell is captured by running redox reactions as you will see when we talk about respiration.

Energy Requirements

To summarize what we have learned so far, cells get their energy from the universe to drive energy requiring (thermodynamically unfavorable) reactions. Many of their reactions involve oxidation/reduction couples.

So the cell has energy. What do they use it for?

Three main activities

  1. Chemical energy - synthesis of complex biological molecules. In other words, to make more of themselves.

  2. Transport - Cells often live in dilute environments. They are sitting in a lake and they need some amino acid, the concentration of that nutrient is very low in the environment. Cells have to expend energy to transport that nutrient into the cell.

  3. Mechanical Energy - Cells may be able to change their physical location and all cells need to move structures within them. This requires energy.

Energy Carriers

Cells can get energy and now we know generally what they do with it, but how do you get from the sun to a cell wall? Photons from the sun don't directly get put into the chemical bonds of the cell wall, there has to be intermediate "high energy" carriers to store this energy until the cell is ready to use it. There are two main carriers of energy in living cells, Adenosine TriPhosphate (ATP) and Nicotinamide Adenine Dinucleotide (NAD+).

ATP picture

Figure 6 - The structure of ATP

NAD picture

Figure 7 - The structure of NAD+. The oxidized form is on the left and the reduced form is on the right. After reduction, NAD can carry two protons and two electrons.

ATP is a carrier of chemical energy in the form of high energy phosphate bonds. (The anhydride links between the phosphate groups in the figure above.) NAD+ is a carrier of hydrogen and electrons and is involved in many oxidation-reduction reactions in the cell. It can pick up and transport 2e- and 2H+ when loaded. You can think of NAD+ and ATP as little trucks that transport energy around the cell.

Another common metaphor for them is money. NAD+ and ATP are the energy currency for the cell. Money is a medium of exchange. People assign work for us to do, we receive money for doing it, and we convert that money into things we want or need. The cell takes its energy source, converts it into NADH and ATP, and then uses them to perform needed tasks in the cell.

NAD+ and ATP are not the only carriers of energy, but they are the major ones. It is amazing to consider that given the diversity of life on this planet that we all use the same energy carriers.


An important player in many forms of catabolism is the hydrogen ion (H+). Hydrogen is the smallest element. It has one proton in its nucleus and one electron orbiting it. If you remove that electron, you have a hydrogen ion, which is also called a proton since that is all that's left. Protons play a major role in respiration and many enzymatic reactions.

To pull it all together, the energy in chemicals or light is extracted by running a series of reactions that eventually deposit bond energy and high energy electrons in ATP and NADH. This stored up energy then drives other reactions that help the cell grow and reproduce. Great, but what catalyzes, controls and coordinates all these reactions? Enzymes!

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