5.1 Catabolic and Anabolic Reaction

Metabolism refers to the sum of all chemical reactions within a living organism.
Catabolism is the breakdown of complex organic compounds into simpler ones.
Anabolism is the building of complex organic molecules from simpler ones.

5.2 Enzymes

The collision theory explains how chemical reactions occur and how certain factors affect the rates of those reactions.
- The basis of the collision theory is that all atoms, ions, and molecules are continuously moving and colliding with one another.
The collision energy required for a chemical reaction is its activation energy, which is the amount of energy needed to disrupt the stable electronic configuration of any specific molecule so that the electrons can be rearranged.
The reaction rate—the frequency of collisions containing sufficient energy to bring about a reaction—depends on the number of reactant molecules at or above the activation energy level.
Substances that can speed up a chemical reaction without being permanently altered themselves are called catalysts.
In living cells, enzymes serve as biological catalysts.
As catalysts, each enzyme acts on a specific substance, called the enzyme’s substrate (or substrates, when there are two or more reactants), and each catalyzes only one reaction.
Although some enzymes consist entirely of proteins, most consist of both a protein portion, called an apoenzyme, and a nonprotein component, called a cofactor.
- If the cofactor is an organic molecule, it is called a coenzyme.
- Together, the apoenzyme and cofactor form a holoenzyme, or whole, active enzyme.
The rate of reaction declines beyond the optimal temperature because of the enzyme’s denaturation, the loss of its characteristic three-dimensional structure.
- Denaturation of an enzyme changes the arrangement of the amino acids in the active site, altering its shape and causing the enzyme to lose its catalytic ability.
Saturation is when an enzyme’s active site is always occupied by substrate or product molecules, and it’s catalyzing a specific reaction at its maximum rate.
Competitive inhibitors fill the active site of an enzyme and compete with the normal substrate for the active site.
Noncompetitive inhibitors do not compete with the substrate for the enzyme’s active site; instead, they interact with another part of the enzyme.
In this process, called allosteric (“other space”) inhibition, the inhibitor binds to a site on the enzyme other than the substrate’s binding site, called the allosteric site.
Noncompetitive, or allosteric, inhibitors play a role in a type of biochemical control called feedback inhibition, or end-product inhibition.
- In some metabolic reactions, several steps are required for the synthesis of a particular chemical compound, called the end-product.

5.3 Energy Production

Oxidation is the removal of electrons (e−) from an atom or molecule, a reaction that often produces energy.
Reduction means the molecule has gained one or more electrons.
In substrate-level phosphorylation, ATP is usually generated when a high-energy is directly transferred from a phosphorylated compound (a substrate) to ADP.
In oxidative phosphorylation, electrons are transferred from organic compounds to one group of electron carriers (usually to NAD+ and FAD).
The sequence of electron carriers used in oxidative phosphorylation is called an electron transport chain (system).
The third mechanism of phosphorylation, photophosphorylation, occurs only in photosynthetic cells, which contain light-trapping pigments such as chlorophylls.

5.4 Carbohydrates Catabolism

Carbohydrate catabolism, the break- down of carbohydrate molecules to produce energy, is therefore of great importance in cell metabolism.
Glycolysis is the oxidation of glucose to pyruvic acid, and is usually the first stage in carbohydrate catabolism.
The pentose phosphate pathway (or hexose monophosphate shunt) operates simultaneously with glycolysis and provides a means for the breakdown of five-carbon sugars (pentoses) as well as glucose.
From each molecule of glucose, the Entner-Doudoroff pathway produces one NADPH, one NADH, and one ATP for use in cellular biosynthetic reactions.
Cellular respiration, or simply respiration, is defined as an ATP-generating process in which molecules are oxidized and the final electron acceptor comes from outside the cell and is (almost always) an inorganic molecule.
There are two types of respiration, depending on whether an organism is an aerobe, which uses oxygen, or an anaerobe, which does not use oxygen and may even be killed by it.
- In aerobic respiration, the final electron acceptor is O2; in anaerobic respiration, the final electron acceptor is an inorganic molecule other than O2 or, rarely, an organic molecule.
The Krebs cycle, also called the tricarboxylic acid (TCA) cycle or citric acid cycle, is a series of biochemical reactions in which the large amount of potential chemical energy stored in acetyl CoA is released step by step.
An electron transport chain (electron transport system) consists of a sequence of carrier molecules that are capable of oxidation and reduction.
Flavoproteins contain flavin, a coenzyme derived from riboflavin (vitamin B2), and are capable of performing alternating oxidations and reductions.
Cytochromes are proteins with an iron-containing group (heme) capable of existing alternately as a reduced form (Fe2+) and an oxidized form (Fe3+).
Fermentation is defined as a process that:
- releases energy from sugars or other organic molecules;
- does not require oxygen (but can occur in its presence);
- does not require the use of the Krebs cycle or an electron transport chain;
- uses an organic molecule synthesized in the cell as the final electron acceptor.
During glycolysis, which is the first phase of lactic acid fermentation, a molecule of glucose is oxidized to two molecules of pyruvic acid.
Because these microbes produce only lactic acid, they are referred to as homolactic.
Alcohol fermentation also begins with the glycolysis of a molecule of glucose to yield two molecules of pyruvic acid and two molecules of ATP.

5.7 Photosynthesis

The major mechanism for such synthesis is a process called photosynthesis, which is carried out by plants and many microbes.
This synthesis of sugars by using carbon atoms from CO2 gas is also called carbon fixation.
Photosynthesis takes place in two stages. In the first stage, called the light-dependent (light) reactions, light energy is used to convert ADP and to ATP.
- In the second stage, the light-independent (dark) reactions, these electrons are used along with energy
- from ATP to reduce CO2 to sugar.
Photophosphorylation is one of the three ways ATP is formed, and it occurs only in photosynthetic cells.
- In this mechanism, light energy is absorbed by chlorophyll molecules in the photosynthetic cell, exciting some of the molecules’ electrons.
Chlorophyll and other pigments are packed into thylakoids of chloroplasts and are called photosystems.
In cyclic photophosphorylation, the electrons released from chlorophyll in the photosystem 1 eventually return to chlorophyll.
In noncyclic photo- phosphorylation, which is used in oxygenic organisms, both photosystems are required.

5.9 Metabolic Diversity among Organisms

Phototrophs use light as their primary energy source, whereas chemotrophs depend on oxidation-reduction reactions of inorganic or organic compounds for energy.
For their principal carbon source, autotrophs (self-feeders) use carbon dioxide, and heterotrophs (feeders on others) require an organic carbon source.
Photoautotrophs use light as a source of energy and carbon dioxide as their chief source of carbon.
- Because this photosynthetic process produces O2 it is sometimes called oxygenic.
- Consequently, their photosynthetic process does not produce O2 and is called anoxygenic.
- The green sulfur bacteria, such as Chlorobium, use sulfur, sulfur compounds (such as hydrogen sulfide, H2S), or hydrogen gas (H2) to reduce carbon dioxide and form organic compounds.
- The purple sulfur bacteria, such as Chromatium, also use sulfur, sulfur compounds, or hydrogen gas to reduce carbon dioxide.
Photoheterotrophs use light as a source of energy but cannot convert carbon dioxide to sugar; rather, they use organic compounds, such as alcohols, fatty acids, other organic acids, and carbohydrates, as sources of carbon.
Chemoautotrophs use the electrons from reduced inorganic compounds as a source of energy, and they use CO2 as their principal source of carbon.
Chemoheterotrophs specifically use the electrons from hydrogen atoms in organic compounds as their energy source.
Saprophytes live on dead organic matter, and parasites derive nutrients from a living host.

5.11 The Integration of Metabolism

Metabolic pathways that function in both anabolism and catabolism are called amphibolic pathways, meaning that they are dual-purpose.

Chapter 5: Microbial Metabolism

5.1 Catabolic and Anabolic Reaction

Metabolism refers to the sum of all chemical reactions within a living organism.
Catabolism is the breakdown of complex organic compounds into simpler ones.
Anabolism is the building of complex organic molecules from simpler ones.

5.2 Enzymes

The collision theory explains how chemical reactions occur and how certain factors affect the rates of those reactions.
- The basis of the collision theory is that all atoms, ions, and molecules are continuously moving and colliding with one another.
The collision energy required for a chemical reaction is its activation energy, which is the amount of energy needed to disrupt the stable electronic configuration of any specific molecule so that the electrons can be rearranged.
The reaction rate—the frequency of collisions containing sufficient energy to bring about a reaction—depends on the number of reactant molecules at or above the activation energy level.
Substances that can speed up a chemical reaction without being permanently altered themselves are called catalysts.
In living cells, enzymes serve as biological catalysts.
As catalysts, each enzyme acts on a specific substance, called the enzyme’s substrate (or substrates, when there are two or more reactants), and each catalyzes only one reaction.
Although some enzymes consist entirely of proteins, most consist of both a protein portion, called an apoenzyme, and a nonprotein component, called a cofactor.
- If the cofactor is an organic molecule, it is called a coenzyme.
- Together, the apoenzyme and cofactor form a holoenzyme, or whole, active enzyme.
The rate of reaction declines beyond the optimal temperature because of the enzyme’s denaturation, the loss of its characteristic three-dimensional structure.
- Denaturation of an enzyme changes the arrangement of the amino acids in the active site, altering its shape and causing the enzyme to lose its catalytic ability.
Saturation is when an enzyme’s active site is always occupied by substrate or product molecules, and it’s catalyzing a specific reaction at its maximum rate.
Competitive inhibitors fill the active site of an enzyme and compete with the normal substrate for the active site.
Noncompetitive inhibitors do not compete with the substrate for the enzyme’s active site; instead, they interact with another part of the enzyme.
In this process, called allosteric (“other space”) inhibition, the inhibitor binds to a site on the enzyme other than the substrate’s binding site, called the allosteric site.
Noncompetitive, or allosteric, inhibitors play a role in a type of biochemical control called feedback inhibition, or end-product inhibition.
- In some metabolic reactions, several steps are required for the synthesis of a particular chemical compound, called the end-product.

5.3 Energy Production

Oxidation is the removal of electrons (e−) from an atom or molecule, a reaction that often produces energy.
Reduction means the molecule has gained one or more electrons.
In substrate-level phosphorylation, ATP is usually generated when a high-energy is directly transferred from a phosphorylated compound (a substrate) to ADP.
In oxidative phosphorylation, electrons are transferred from organic compounds to one group of electron carriers (usually to NAD+ and FAD).
The sequence of electron carriers used in oxidative phosphorylation is called an electron transport chain (system).
The third mechanism of phosphorylation, photophosphorylation, occurs only in photosynthetic cells, which contain light-trapping pigments such as chlorophylls.

5.4 Carbohydrates Catabolism

Carbohydrate catabolism, the break- down of carbohydrate molecules to produce energy, is therefore of great importance in cell metabolism.
Glycolysis is the oxidation of glucose to pyruvic acid, and is usually the first stage in carbohydrate catabolism.
The pentose phosphate pathway (or hexose monophosphate shunt) operates simultaneously with glycolysis and provides a means for the breakdown of five-carbon sugars (pentoses) as well as glucose.
From each molecule of glucose, the Entner-Doudoroff pathway produces one NADPH, one NADH, and one ATP for use in cellular biosynthetic reactions.
Cellular respiration, or simply respiration, is defined as an ATP-generating process in which molecules are oxidized and the final electron acceptor comes from outside the cell and is (almost always) an inorganic molecule.
There are two types of respiration, depending on whether an organism is an aerobe, which uses oxygen, or an anaerobe, which does not use oxygen and may even be killed by it.
- In aerobic respiration, the final electron acceptor is O2; in anaerobic respiration, the final electron acceptor is an inorganic molecule other than O2 or, rarely, an organic molecule.
The Krebs cycle, also called the tricarboxylic acid (TCA) cycle or citric acid cycle, is a series of biochemical reactions in which the large amount of potential chemical energy stored in acetyl CoA is released step by step.
An electron transport chain (electron transport system) consists of a sequence of carrier molecules that are capable of oxidation and reduction.
Flavoproteins contain flavin, a coenzyme derived from riboflavin (vitamin B2), and are capable of performing alternating oxidations and reductions.
Cytochromes are proteins with an iron-containing group (heme) capable of existing alternately as a reduced form (Fe2+) and an oxidized form (Fe3+).
Fermentation is defined as a process that:
- releases energy from sugars or other organic molecules;
- does not require oxygen (but can occur in its presence);
- does not require the use of the Krebs cycle or an electron transport chain;
- uses an organic molecule synthesized in the cell as the final electron acceptor.
During glycolysis, which is the first phase of lactic acid fermentation, a molecule of glucose is oxidized to two molecules of pyruvic acid.
Because these microbes produce only lactic acid, they are referred to as homolactic.
Alcohol fermentation also begins with the glycolysis of a molecule of glucose to yield two molecules of pyruvic acid and two molecules of ATP.

5.7 Photosynthesis

The major mechanism for such synthesis is a process called photosynthesis, which is carried out by plants and many microbes.
This synthesis of sugars by using carbon atoms from CO2 gas is also called carbon fixation.
Photosynthesis takes place in two stages. In the first stage, called the light-dependent (light) reactions, light energy is used to convert ADP and to ATP.
- In the second stage, the light-independent (dark) reactions, these electrons are used along with energy
- from ATP to reduce CO2 to sugar.
Photophosphorylation is one of the three ways ATP is formed, and it occurs only in photosynthetic cells.
- In this mechanism, light energy is absorbed by chlorophyll molecules in the photosynthetic cell, exciting some of the molecules’ electrons.
Chlorophyll and other pigments are packed into thylakoids of chloroplasts and are called photosystems.
In cyclic photophosphorylation, the electrons released from chlorophyll in the photosystem 1 eventually return to chlorophyll.
In noncyclic photo- phosphorylation, which is used in oxygenic organisms, both photosystems are required.

5.9 Metabolic Diversity among Organisms

Phototrophs use light as their primary energy source, whereas chemotrophs depend on oxidation-reduction reactions of inorganic or organic compounds for energy.
For their principal carbon source, autotrophs (self-feeders) use carbon dioxide, and heterotrophs (feeders on others) require an organic carbon source.
Photoautotrophs use light as a source of energy and carbon dioxide as their chief source of carbon.
- Because this photosynthetic process produces O2 it is sometimes called oxygenic.
- Consequently, their photosynthetic process does not produce O2 and is called anoxygenic.
- The green sulfur bacteria, such as Chlorobium, use sulfur, sulfur compounds (such as hydrogen sulfide, H2S), or hydrogen gas (H2) to reduce carbon dioxide and form organic compounds.
- The purple sulfur bacteria, such as Chromatium, also use sulfur, sulfur compounds, or hydrogen gas to reduce carbon dioxide.
Photoheterotrophs use light as a source of energy but cannot convert carbon dioxide to sugar; rather, they use organic compounds, such as alcohols, fatty acids, other organic acids, and carbohydrates, as sources of carbon.
Chemoautotrophs use the electrons from reduced inorganic compounds as a source of energy, and they use CO2 as their principal source of carbon.
Chemoheterotrophs specifically use the electrons from hydrogen atoms in organic compounds as their energy source.
Saprophytes live on dead organic matter, and parasites derive nutrients from a living host.

5.11 The Integration of Metabolism

Metabolic pathways that function in both anabolism and catabolism are called amphibolic pathways, meaning that they are dual-purpose.