Metabolism

Metabolism is the word we use for the management of material and energy resources. Energy can be gained by breaking down complex molecules (catabolism) or energy can be used to build complex molecules (anabolism). Anabolic and catabolic processes are often combined in such a way that energy derived from anabolism can be applied to catabolism.

A few words about energy:

Energy can be transferred. It can't be created. Transfer of energy is always inefficient-some energy is always lost as heat. Free energy is the energy available to do work. There are two types of chemical reactions. Exergonic reactions proceed with a net release of free energy. Endergonic reactions absorb free energy.

I know I told you that you would not be responsible for the terms exergonic and endergonic but it still helps for you to know them so you can read the rest of these notes.

Another way to think of these reactions is to consider the relative potential energy of the products and the reactants (5.3 pg 74). Endergonic reactions require energy input to take simple, low energy reactants and build complex, high energy products. Exergonic reactions release the energy bound up in the reactants and yield simpler, low energy products. A key strategy in driving the endergonic reactions is to couple them to exergonic reactions through an energy shuttle called ATP.

What do we need this energy for? A cell does three kinds of work:

1. Mechanical work. Examples: Beating of cilia, muscle contractions, intracellular movement.

2. Transport work. Examples: Pumping substances across gradients.

3. Chemical work. Examples: synthesis of polymers from monomers.

 The immediate source of energy for this work, this so called energy shuttle, is ATP, adenosine triphosphate.

 ATP

 ATP is a nucleoside triphosphate consisting of adenine bonded to ribose which is connected to three phosphate groups (5.4a, pg 75).

When a phosphate group is broken off the tail of an ATP molecule (by hydrolysis) the molecule becomes ADP (adenosine diphosphate). That hydrolysis is an exergonic reaction and it yields energy. The bonds holding the phosphate onto ATP are weak. They are known as high energy bonds but not because they are strong (if they were strong it would require alot of energy to break them. Think of the ATP as a spring loaded molecule with that last phosphate just jammed onto the end).

When the phosphate is removed from ATP it gets added to a molecule that is part of the endergonic reaction that we're interested in driving. Now that molecule is unstable (ie. more reactive) thus some energy has been made available for the endergonic reaction. That molecule that has had the phosphate group added to it is called a phosphorylated intermediate.

ATP is regenerated via cellular respiration in which the energy of glucose gets used to phosphorylate ADP to form ATP. Plants can also use the energy available in light to produce ATP.

Cellular Respiration

Living is work. Cells are always doing work, building molecules, pumping ions, moving, etc. In order to do that work cells need energy from outside sources. Energy enters (most) ecosystems as solar energy, plants then turn it into chemical energy. All the rest of the organisms get their energy from food, which can be traced back to those plants.

Cells release the energy bound up in food by the systematic degradation of food molecules into simple, low energy waste products. Some of the chemical energy gets used to do work, some of it gets lost as heat. Breakdown pathways are called catabolic pathways. One such catabolic pathway is fermentation (no oxygen). A more prevalent pathway that is more efficient is called cellular respiration. Oxygen is combined with organic molecules to release energy.

Organic compounds + Oxygen º CO2 + Water + Energy

All types of macromolecules can be broken down and used as fuel. Typically we study the degradation of glucose:

C6H12O6 +6 O2 º 6 CO2 + 6 H2O + Energy (ATP + Heat)

We tend to ingest proteins, carbohydrates and fats within our diets. If we use tose types of molecules for their energy content (as opposed to using them for their Aspare parts@ to build some new molecules) the molecules are broken into intermediary molecules that enter into the respiratory pathway of glucose somewere along the line.

Cellular respiration does not directly move flagella, pump solutes or do any of the cellular work. Cellular respiration generates ATP, which is in turn expended by the cell to do work. Remember that ATP is like a loaded spring. Phosphates are jammed on to the end of ADP to form ATP. That process is called phosphorylation.

There are three stages to respiration: Glycolysis, the Krebs Cycle, and the Electron Transport System. You should read modules 6.1 and 6.2 in your textbook. They cover pretty much what I have said in class about cellular respiration. Notice that even though we consider cellular respiration to be an efficient way to convert the energy in glucose to ATP (a usable form), we still don=t get all of it. (Where does the rest of the energy go?)

6.3 talks about how much energy we use for various activities. This may be of interest to you. Note they use the term AK-cal@ or Akilocalorie@. This is the equivalent of what we refer to in everyday language as a Calorie.

Enzymes

Enzymes are catalysts. Catalysts are chemical agents that change the rate of a reaction without being consumed by the reaction. These are what regulate the various reactions of metabolism.

Even though many reactions are exergonic they still require some energy to get them going. This extra boost is called the activation energy. Enzymes function to lower the activation energy necessary to start reactions. They do not affect the net energy change of the equation. (5.5a&b, pg 76)

The reactant an enzyme works on is called its substrate. Enzymes are very substrate specific. They are usually proteins. Recall that proteins have specific shapes. There is a region of the enzyme called the active site where the substrate molecule(s) fit. The catalyst (enzyme) can do a number of things to facilitate the reaction. It can twist the molecules promoting bond breaking, it can serve as a template to bring to substrate molecules into proper position, it can provide a "microenvironment" conducive to promoting the reaction (eg. pH). (5.6, pg 77)

Many things effect the action of enzymes. Most enzymes function in a specific optimal range of temperature and pH. Many enzymes require the aid of cofactors. Enzyme inhibitors may interfere with the action of the enzyme by binding (either permanently or temporarily) to a site on the enzyme. The inhibitor may attach to the active site, blocking substrates (called a competitive inhibitor), or it may attach elsewhere causing a change in the shape (therefore function) of the enzyme (a noncompetitive inhibitor)(5.8, pg 78). The production of enzymes, cofactors, inhibitors, etc. is the means by which an organism controls metabolism.