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7.4: Prokaryote Metabolism - Biology

7.4: Prokaryote Metabolism - Biology


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What do bacteria need to grow?

Like most everything else, they need food. Given the right conditions, bacteria can grow from just a few cells to millions or billions overnight.

Prokaryote Metabolism

Like all living things, prokaryotes need energy and carbon. They meet these needs in a variety of ways. In fact, prokaryotes have just about every possible type of metabolism. They may get energy from light (photo) or chemical compounds (chemo). They may get carbon from carbon dioxide (autotroph) or other living things (heterotroph). Most prokaryotes are chemoheterotrophs. They depend on other organisms for both energy and carbon. Many break down organic wastes and the remains of dead organisms. They play vital roles as decomposers and help recycle carbon and nitrogen. Photoautotrophs are important producers. They are especially important in aquatic ecosystems.

Classification of Prokaryotes Based on Metabolism

Two major nutritional needs can be used to group prokaryotes. These are (1) carbon metabolism, their source of carbon for building organic molecules within the cells, and (2) energy metabolism, their source of energy used for growth.

In terms of carbon metabolism, prokaryotes are classified as either heterotrophic or autotrophic:

  • Heterotrophic organisms use organic compounds, usually from other organisms, as carbon sources.
  • Autotrophic organisms use carbon dioxide (CO2) as their only source or their main source of carbon. Many autotrophic bacteria are photosynthetic, and get their carbon from the carbon dioxide in the atmosphere.

Energy metabolism in prokaryotes is classified as one of the following:

  • Phototrophic organisms capture light energy from the sun and convert it into chemical energy inside their cells.
  • Chemotrophic organisms break down either organic or inorganic molecules to supply energy for the cell. Some chemotrophic organisms can also use their organic energy-supplying molecules as a carbon supply, which would make them chemoheterotrophs.
  • Photoheterotrophs are organisms that capture light energy to convert to chemical energy in the cells, but they get carbon from organic sources (other organisms). Examples are purple non-sulfur bacteria, green non-sulfur bacteria and heliobacteria.
  • Chemoheterotrophs are organisms that get their energy source and carbon source from organic sources. Chemoheterotrophs must consume organic building blocks that they are unable to make themselves. Most get their energy from organic molecules such as sugars. This nutritional mode is very common among eukaryotes, including humans.
  • Photoautotrophs are cells that capture light energy, and use carbon dioxide as their carbon source. There are many photoautotrophic prokaryotes, which include cyanobacteria. Photoautotrophic prokaryotes use similar compounds to those of plants to trap light energy.
  • Chemoautotrophs are cells that break down inorganic molecules to supply energy for the cell, and use carbon dioxide as a carbon source. Chemoautotrophs include prokaryotes that break down hydrogen sulfide (H2S the “rotten egg” smelling gas), and ammonia (NH4).Nitrosomonas, a species of soil bacterium, oxidizes NH4+ to nitrite (NO2-). This reaction releases energy that the bacteria use. Many chemoautotrophs also live in extreme environments such as deep sea vents.

This flowchart helps to determine if a species is an autotroph or a heterotroph, a phototroph or a chemotroph. For example, “Obtain carbon elsewhere?” asks if the source of carbon is another organism. If the answer is “yes”, the organism is heterotrophic. If the answer is “no,” the organisms is autotrophic.

Summary

  • Prokaryotes fulfill their carbon and energy needs in various ways. They may be photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs.

Review

  1. Describe metabolism of most prokaryotes.
  2. Define phototrophic and chemotrophic organisms.
  3. What are photoautotrophs?
  4. What are photoheterotrophs?

Resources


7.4 Oxidative Phosphorylation

In this section, you will explore the following questions:

  • How do electrons move through the electron transport chain and what happens to their energy levels?
  • How is a proton (H + ) gradient established and maintained by the electron transport chain and how many ATP molecules are produced by chemiosmosis?

Connection for AP ® Courses

The electron transport chain (ETC) is the stage of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed during glucose metabolism in glycolysis and the citric acid cycle. The ETC is located in membrane of the mitochondrial cristae, an area with many folds that increase the surface area available for chemical reactions. Electrons carried by NADH and FADH2 are delivered to electron acceptor proteins embedded in the membrane as they move toward the final electron acceptor, O2, forming water. The electrons pass through a series of redox reactions, using free energy at three points to transport hydrogen ions across the membrane. This process contributes to the formation of the H + gradient used in chemiosmosis. As the protons are driven down their concentration gradient through ATP synthase, ATP is generated from ADP and inorganic phosphate. Under aerobic conditions, the stages of cellular respiration can generate 36-38 ATP.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 2 of the AP ® Biology Curriculum Framework, as shown in the table. As shown in the table, concepts covered in this section also align to the Learning Objectives listed in the Curriculum Framework that provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.
Enduring Understanding 2.A Growth, reproduction and maintenance of living systems require free energy and matter.
Essential Knowledge 2.A.1 All living systems require constant input of free energy.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Science Practice 3.1 The student can pose scientific questions.
Learning Objective 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy.
Essential Knowledge 2.A.1 All living systems require constant input of free energy.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store, or use free energy.

Teacher Support

Introduce oxidative phosphorylation using visuals such as this video.

Have students create a visual representation that shows an overview of glycolysis and the citric acid cycle and how the cycles relate to one another.

An example is illustrated here.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 2.5][APLO 2.15][APLO 2.18][APLO 2.22]

You have just read about two pathways Introduce glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it is derived from a process that begins with moving electrons through a series of electron transporters that undergo redox reactions. This causes hydrogen ions to accumulate within the intermembranous space. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the intermembranous space into the mitochondrial matrix by passing through ATP synthase. The current of hydrogen ions powers the catalytic action of ATP synthase, which phosphorylates ADP, producing ATP.

Electron Transport Chain

The electron transport chain (Figure 7.11) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants in animals, it enters the body through the respiratory system. Electron transport is a series of redox reactions that resemble a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen, producing water. There are four complexes composed of proteins, labeled I through IV in Figure 7.11, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes.

Complex I

To start, two electrons are carried to the first complex aboard NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2, also called riboflavin, is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is composed of 44 separate polypeptide chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.

Q and Complex II

Complex II directly receives FADH2, which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced, (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I, and the electrons derived from FADH2 from complex II. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane.

Complex III

The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins this complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe ++ (reduced) and Fe +++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes (cytochrome c is the acceptor of electrons from Q however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time).

Complex IV

The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the two cytochromes, a, and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient used in the process of chemiosmosis.

Chemiosmosis

In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the membrane. The uneven distribution of H + ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.

If the membrane were open to diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by their electrochemical gradient. Recall that many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through an integral membrane protein called ATP synthase (Figure 7.12). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of parts of this molecular machine facilitates the addition of a phosphate to ADP, forming ATP, using the potential energy of the hydrogen ion gradient.

Visual Connection

  1. DNP dissipates the proton gradient in the matrix, preventing the production of ATP. The body then increases its metabolic rate, leading to weight loss.
  2. DNP decreases the proton gradient in the inner mitochondrial space, leading to rapid consumption of acetyl-CoA, which causes weight loss.
  3. DNP blocks the movement of protons through the ATP synthase, halting ATP production. The stored energy dissipates as heat, causing weight loss.
  4. DNP uncouples the production of ATP by increasing the proton gradient in the matrix. The stored energy dissipates as heat, causing weight loss.

Chemiosmosis (Figure 7.13) is used to generate 90 percent of the ATP made during aerobic glucose catabolism it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed.

Visual Connection

  1. The proton concentration of the intermembrane space would decrease, stopping the production of ATP.
  2. The proton concentration of the intermembrane space would increase, leading to ATP formation.
  3. The hydrogen ion concentration of the intermembrane space would decrease, causing a high production of ATP.
  4. The proton concentration of the intermembrane space would increase, causing production of ATP in large amounts.

ATP Yield

The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD + or FAD + . As you have learned earlier, these FAD + molecules can transport fewer ions consequently, fewer ATP molecules are generated when FAD + acts as a carrier. NAD + is used as the electron transporter in the liver and FAD + acts in the brain.

Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Moreover, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.

Science Practice Connection for AP® Courses

Activity

Use construction paper and other art materials to create your own diagram of the electron transport chain (ETC). Be sure to include all parts of the electron transport chain, as well as the electrons themselves, NAD+ and NADH, and oxygen. On your diagram, label all parts of the ETC that transfers the free energy from electrons to another form. Then, use your model to make predictions about each of the following. Then, share your answers with the class.


Needs of Prokaryotes

The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, oxygen availability, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and environmental conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.

Macronutrients

Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients . When prokaryotes grow in nature, they must obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)

Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. In contrast, nitrogen represents only 12 percent of the total dry weight of a typical cell. Nitrogen is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain microorganisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.

Micronutrients

In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.

The Ways in Which Prokaryotes Obtain Energy

Prokaryotes are classified both by the way they obtain energy, and by the carbon source they use for producing organic molecules. These categories are summarized in (Figure). Prokaryotes can use different sources of energy to generate the ATP needed for biosynthesis and other cellular activities. Phototrophs (or phototrophic organisms) obtain their energy from sunlight. Phototrophs trap the energy of light using chlorophylls, or in a few cases, bacterial rhodopsin. (Rhodopsin-using phototrophs, oddly, are phototrophic, but not photosynthetic, since they do not fix carbon.) Chemotrophs (or chemosynthetic organisms) obtain their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called chemoorganotrophs. Those that can use inorganic compounds, like sulfur or iron compounds, as energy sources are called chemolithotrophs.

Energy-producing pathways may be either aerobic , using oxygen as the terminal electron acceptor, or anaerobic, using either simple inorganic compounds or organic molecules as the terminal electron acceptor. Since prokaryotes lived on Earth for nearly a billion years before photosynthesis produced significant amounts of oxygen for aerobic respiration, many species of both Bacteria and Archaea are anaerobic and their metabolic activities are important in the carbon and nitrogen cycles discussed below.

The Ways in Which Prokaryotes Obtain Carbon

Prokaryotes not only can use different sources of energy, but also different sources of carbon compounds. Autotrophic prokaryotes synthesize organic molecules from carbon dioxide. In contrast, heterotrophic prokaryotes obtain carbon from organic compounds. To make the picture more complex, the terms that describe how prokaryotes obtain energy and carbon can be combined. Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain both energy and carbon from an organic chemical source. Chemolithoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. Finally, prokaryotes that get their energy from light, but their carbon from organic compounds, are photoheterotrophs. The table below ((Figure)) summarizes carbon and energy sources in prokaryotes.

Energy Sources in Prokaryotes

  • Light
    • Chemicals
    • Chemotrophs
      • Organic Chemicals
      • Inorganic Chemicals
      • Chemo-organotrophs
      • Chemoliphotrophs

      Carbon Sources in Prokaryotes


      Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle ([link]). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.

      A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers , carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus) that undergo respiration.

      In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH4). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.



      Prokaryotic Metabolism

      Prokaryotes are metabolically diverse organisms. There are many different environments on Earth with various energy and carbon sources, and variable conditions. Prokaryotes have been able to live in every environment by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as nitrogen and carbon cycles, decomposing dead organisms, and thriving inside living organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.

      Needs of Prokaryotes

      The diverse environments and ecosystems on Earth have a wide range of conditions in terms of temperature, available nutrients, acidity, salinity, and energy sources. Prokaryotes are very well equipped to make their living out of a vast array of nutrients and conditions. To live, prokaryotes need a source of energy, a source of carbon, and some additional nutrients.

      Macronutrients

      Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)

      Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.

      Micronutrients

      In addition to these macronutrients, prokaryotes require various metallic elements in small amounts. These are referred to as micronutrients or trace elements. For example, iron is necessary for the function of the cytochromes involved in electron-transport reactions. Some prokaryotes require other elements—such as boron (B), chromium (Cr), and manganese (Mn)—primarily as enzyme cofactors.

      The Ways in Which Prokaryotes Obtain Energy

      Prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs (or phototrophic organisms) obtain their energy from sunlight. Chemotrophs (or chemosynthetic organisms) obtain their energy from chemical compounds. Chemotrophs that can use organic compounds as energy sources are called chemoorganotrophs. Those that can also use inorganic compounds as energy sources are called chemolitotrophs.

      The Ways in Which Prokaryotes Obtain Carbon

      Prokaryotes not only can use different sources of energy but also different sources of carbon compounds. Recall that organisms that are able to fix inorganic carbon are called autotrophs. Autotrophic prokaryotes synthesize organic molecules from carbon dioxide. In contrast, heterotrophic prokaryotes obtain carbon from organic compounds. To make the picture more complex, the terms that describe how prokaryotes obtain energy and carbon can be combined. Thus, photoautotrophs use energy from sunlight, and carbon from carbon dioxide and water, whereas chemoheterotrophs obtain energy and carbon from an organic chemical source. Chemolitoautotrophs obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide. The table below ([link]) summarizes carbon and energy sources in prokaryotes.

      Carbon and Energy Sources in Prokaryotes
      Energy Sources Carbon Sources
      Light Chemicals Carbon dioxide Organic compounds
      Phototrophs Chemotrophs Autotrophs Heterotrophs
      Organic chemicals Inorganic chemicals
      Chemo-organotrophs Chemolithotrophs

      Role of Prokaryotes in Ecosystems

      Prokaryotes are ubiquitous: There is no niche or ecosystem in which they are not present. Prokaryotes play many roles in the environments they occupy. The roles they play in the carbon and nitrogen cycles are vital to life on Earth.

      Prokaryotes and the Carbon Cycle

      Carbon is one of the most important macronutrients, and prokaryotes play an important role in the carbon cycle ([link]). Carbon is cycled through Earth’s major reservoirs: land, the atmosphere, aquatic environments, sediments and rocks, and biomass. The movement of carbon is via carbon dioxide, which is removed from the atmosphere by land plants and marine prokaryotes, and is returned to the atmosphere via the respiration of chemoorganotrophic organisms, including prokaryotes, fungi, and animals. Although the largest carbon reservoir in terrestrial ecosystems is in rocks and sediments, that carbon is not readily available.

      A large amount of available carbon is found in land plants. Plants, which are producers, use carbon dioxide from the air to synthesize carbon compounds. Related to this, one very significant source of carbon compounds is humus, which is a mixture of organic materials from dead plants and prokaryotes that have resisted decomposition. Consumers such as animals use organic compounds generated by producers and release carbon dioxide to the atmosphere. Then, bacteria and fungi, collectively called decomposers, carry out the breakdown (decomposition) of plants and animals and their organic compounds. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material (dead animals, plants, and humus) that undergo respiration.

      In aqueous environments and their anoxic sediments, there is another carbon cycle taking place. In this case, the cycle is based on one-carbon compounds. In anoxic sediments, prokaryotes, mostly archaea, produce methane (CH4). This methane moves into the zone above the sediment, which is richer in oxygen and supports bacteria called methane oxidizers that oxidize methane to carbon dioxide, which then returns to the atmosphere.

      Prokaryotes and the Nitrogen Cycle

      Nitrogen is a very important element for life because it is part of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds to ammonia, ammonium ions, nitrate, nitrite, and nitrogen gas by myriad processes, many of which are carried out only by prokaryotes. As illustrated in [link], prokaryotes are key to the nitrogen cycle. The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen from the air, but this nitrogen is not usable by plants, which are primary producers. Gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia through the process of nitrogen fixation. Ammonia can be used by plants or converted to other forms.

      Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. Ammonia released to the atmosphere, however, represents only 15 percent of the total nitrogen released the rest is as N2 and N2O. Ammonia is catabolized anaerobically by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium to nitrite and nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. The bacteria performs the reverse process, the reduction of nitrate from the soils to gaseous compounds such as N2O, NO, and N2, a process called denitrification.

      Which of the following statements about the nitrogen cycle is false?

      1. Nitrogen fixing bacteria exist on the root nodules of legumes and in the soil.
      2. Denitrifying bacteria convert nitrates (NO3 - ) into nitrogen gas (N2).
      3. Ammonification is the process by which ammonium ion (NH4 + ) is released from decomposing organic compounds.
      4. Nitrification is the process by which nitrites (NO2 - ) are converted to ammonium ion (NH4 + ).

      Section Summary

      Prokaryotes are the most metabolically diverse organisms they flourish in many different environments with various carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds.

      Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N2 as the final product. Nitrification is the conversion of ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N2O, NO, and N2.

      Art Connections

      [link] Which of the following statements about the nitrogen cycle is false?


      Prokaryotic Metabolism

      Prokaryotes are metabolically diverse organisms. In many cases, a prokaryote may be placed into a species clade by its defining metabolic features: Can it metabolize lactose? Can it grow on citrate? Does it produce H2S? Does it ferment carbohydrates to produce acid and gas? Can it grow under anaerobic conditions? Since metabolism and metabolites are the product of enzyme pathways, and enzymes are encoded in genes, the metabolic capabilities of a prokaryote are a reflection of its genome. There are many different environments on Earth with various energy and carbon sources, and variable conditions to which prokaryotes may be able to adapt. Prokaryotes have been able to live in every environment from deep-water volcanic vents to Antarctic ice by using whatever energy and carbon sources are available. Prokaryotes fill many niches on Earth, including involvement in nitrogen and carbon cycles, photosynthetic production of oxygen, decomposition of dead organisms, and thriving as parasitic, commensal, or mutualistic organisms inside multicellular organisms, including humans. The very broad range of environments that prokaryotes occupy is possible because they have diverse metabolic processes.


      Cells are essentially a well-organized assemblage of macromolecules and water. Recall that macromolecules are produced by the polymerization of smaller units called monomers. For cells to build all of the molecules required to sustain life, they need certain substances, collectively called nutrients. When prokaryotes grow in nature, they obtain their nutrients from the environment. Nutrients that are required in large amounts are called macronutrients, whereas those required in smaller or trace amounts are called micronutrients. Just a handful of elements are considered macronutrients—carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (A mnemonic for remembering these elements is the acronym CHONPS.)

      Why are these macronutrients needed in large amounts? They are the components of organic compounds in cells, including water. Carbon is the major element in all macromolecules: carbohydrates, proteins, nucleic acids, lipids, and many other compounds. Carbon accounts for about 50 percent of the composition of the cell. Nitrogen represents 12 percent of the total dry weight of a typical cell and is a component of proteins, nucleic acids, and other cell constituents. Most of the nitrogen available in nature is either atmospheric nitrogen (N2) or another inorganic form. Diatomic (N2) nitrogen, however, can be converted into an organic form only by certain organisms, called nitrogen-fixing organisms. Both hydrogen and oxygen are part of many organic compounds and of water. Phosphorus is required by all organisms for the synthesis of nucleotides and phospholipids. Sulfur is part of the structure of some amino acids such as cysteine and methionine, and is also present in several vitamins and coenzymes. Other important macronutrients are potassium (K), magnesium (Mg), calcium (Ca), and sodium (Na). Although these elements are required in smaller amounts, they are very important for the structure and function of the prokaryotic cell.


      7.4: Prokaryote Metabolism - Biology

      The living cell is either building molecules, which is referred to as anabolism or it is tearing molecules down called catabolism. The process of catabolism, that is the breakdown of molecules, is for energy generation or to create molecules used as building blocks for macromolecules. In catabolism molecules such as proteins, fats and carbohydrates are metabolized to yield energy storage molecules such as ATP, or precursor molecules for use in cell growth and homeostasis.

      In anabolism the energy rich molecules are utilized along with precursor molecules to build macromolecules required by the cell for survival and replication. These macromolecules include DNA, enzymes and cell wall components. Catabolism and anabolism are processes that work in synchrony to optimize the cells ability to survive.

      • Step by step description of energy generating pathways.
      • Detailed description of substrate level phosphorylation.
      • Electron transport in cell membranes and mitochondria for ATP generation.
      • Concept map showing inter-connections of new concepts in this tutorial.
      • Definition slides introduce terms as they are needed.
      • Visual representation of concepts.
      • Step by step animated examples of catabolic processes.
      • Practice quiz on major concepts of the tutorial.

      Microbial metabolism may be summed up as a balance between catabolic and anabolic pathways.
      Catabolic pathways generate energy by utilizing: carbohydrates, proteins and fats in metabolic cycles.
      Anabolic pathways use the energy created in catabolic processes and precursor molecules to generate complex macromolecules. These molecules include: polysaccharides, lipids, amino acids, proteins and nucleotides.
      Many pathways can be “forced” to run in reverse. Therefore pathways that are typically catabolic in reverse may function as an anabolic pathway.

      See all 24 lessons in Anatomy and Physiology, including concept tutorials, problem drills and cheat sheets: Teach Yourself Microbiology Visually in 24 Hours


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