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22.3: Prokaryotic Metabolism - Biology

22.3: Prokaryotic Metabolism - Biology


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Skills to Develop

  • Identify the macronutrients needed by prokaryotes, and explain their importance
  • Describe the ways in which prokaryotes get energy and carbon for life processes
  • Describe the roles of prokaryotes in the carbon and nitrogen cycles

Prokaryotes are metabolically diverse organisms. 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. Table (PageIndex{1}) summarizes carbon and energy sources in prokaryotes.

Table (PageIndex{1}): Carbon and Energy Sources in Prokaryotes
Energy SourcesCarbon Sources
LightChemicalsCarbon dioxideOrganic compounds
PhototrophsChemotrophsAutotrophsHeterotrophs
Organic chemicalsInorganic chemicals
Chemo-organotrophsChemolithotrophs

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 (Figure (PageIndex{1})). 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 Figure (PageIndex{2}), 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.

Art Connection

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 ((NO_3^-)) into nitrogen gas ((N_2)).
  3. Ammonification is the process by which ammonium ion ((NH_4^+)) is released from decomposing organic compounds.
  4. Nitrification is the process by which nitrites ((NO_2^-)) are converted to ammonium ion ((NH_4^+)).

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?

  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+).

[link] D

Glossary

ammonification
process by which ammonia is released during the decomposition of nitrogen-containing organic compounds
chemotroph
organism that obtains energy from chemical compounds
decomposer
organism that carries out the decomposition of dead organisms
denitrification
transformation of nitrate from soil to gaseous nitrogen compounds such as N2O, NO and N2
nitrification
conversion of ammonium into nitrite and nitrate in soils
nitrogen fixation
process by which gaseous nitrogen is transformed, or “fixed” into more readily available forms such as ammonia

The most fundamental feature of life is the presence of a cell. In other words, a cell is the simplest functional unit of a life. Bacteria are unicellular, prokaryotic organisms that have some of the least complex life processes in place however, prokaryotes such as bacteria do not contain membrane-bound vacuoles. The cells of microorganisms like bacteria, protozoa, and fungi are bound by cell membranes and use them to interact with the environment. Some cells, including some leucocytes in humans, are able to engulf food by endocytosis—the formation of vesicles by involution of the cell membrane within the cells. The same vesicles are able to interact and exchange metabolites with the intracellular environment. In some unicellular eukaryotic organisms such as the amoeba, shown in Figure 22.9, cellular wastes and excess water are excreted by exocytosis, when the contractile vacuoles merge with the cell membrane and expel wastes into the environment. Contractile vacuoles (CV) should not be confused with vacuoles, which store food or water.

Figure 22.9. Some unicellular organisms, such as the amoeba, ingest food by endocytosis. The food vesicle fuses with a lysosome, which digests the food. Waste is excreted by exocytosis.


22.3: Prokaryotic Metabolism - Biology

PART II. CORNERSTONES: CHEMISTRY, CELLS, AND METABOLISM

4. Cell Structure and Function

4.8. Prokaryotic and Eukaryotic Cells Revisited

Now that you have an idea of how cells are constructed, we can look at the great diversity of the kinds of cells that exist. You already know that there are significant differences between prokaryotic and eukaryotic cells.

Because prokaryotic (noneukaryotic) and eukaryotic cells are so different and prokaryotic cells show up in the fossil records much earlier, the differences between the two kinds of cells are used to classify organisms. Thus, biologists have classified organisms into three large categories, called domains. The following diagram illustrates how living things are classified:

The Domain Bacteria contains most of the microorganisms and can be found in a wide variety of environments. The Domain Archaea contains many kinds of microorganisms that have significant biochemical differences from the Bacteria. Many of the Archaea have special metabolic abilities and live in extreme environments of high temperature or extreme saltiness. Although only a few thousand Bacteria and only about 200 Archaea have been described, recent DNA studies of seawater and soil suggest that there are millions of undescribed species. In all likelihood, these noneukaryotic organisms far outnumber all the species of eukaryotic organisms combined. All other living things are comprised of eukaryotic cells.

Prokaryotic Cell Structure

Prokaryotic cells, the Bacteria and Archaea, do not have a typical nucleus bound by a nuclear membrane, nor do they contain mitochondria, chloroplasts, Golgi, or extensive networks of endoplasmic reticula. However, prokaryotic cells contain DNA and enzymes and are able to reproduce and engage in metabolism. They perform all of the basic functions of living things with fewer and simpler organelles. Although some Eubacteria have a type of green photosynthetic pigment and carry on photosynthesis, they do so without chloroplasts and use somewhat different chemical reactions.

Most Bacteria are surrounded by a capsule, or slime layer, which is composed of a variety of compounds. In certain bacteria, this layer is responsible for their ability to stick to surfaces, forming biofilms (e.g., the film of bacteria on teeth), and to resist phagocytosis. Many bacteria also have fimbriae, hairlike protein structures, which help the cell stick to objects. Those with flagella are capable of propelling themselves through the environment. Below the capsule is the rigid cell wall, comprised of a unique protein/carbohydrate complex called peptidoglycan. This gives the cell the strength to resist osmotic pressure changes and gives it shape. Just beneath the wall is the plasma membrane. Thinner and with a slightly different chemical composition from that of eukaryotes, the plasma membrane carries out the same functions as the plasma membrane in eukaryotes. Most bacteria are either rod-shaped (bacilli), spherical (cocci), corkscrew-shaped (spirilla), or comma-shaped (vibrio). The genetic material within the cytoplasm is DNA in the form of a loop.

The Archaea share many characteristics with the Bacteria. Many have a rod or spherical shape, although some are square or triangular. Some have flagella and have cell walls, but the cell walls are made of a different material than that of bacteria.

One significant difference between the cells of Bacteria and Archaea is in the chemical makeup of their ribosomes. The ribosomes of Bacteria contain different proteins from those found in the cells of Eucarya or Archaea. Bacterial ribosomes are also smaller. This discovery was important to medicine, because many cellular forms of life that cause common diseases are bacterial. As soon as differences in the ribosomes were noted, researchers began to look for ways in which to interfere with the bacterial ribosome’s function, but not interfere with the ribosomes of eukaryotic cells. Antibiotics, such as streptomycin, are the result of this research. This drug combines with bacterial ribosomes and causes bacteria to die because it prevents production of the proteins essential to survival of bacteria. Because eukaryotic ribosomes differ from bacterial ribosomes, streptomycin does not interfere with the normal function of the ribosomes in human cells.

Eukaryotic Cell Structure

Eukaryotic cells contain a true nucleus and most of the membranous organelles described earlier. Eukaryotic organisms can be further divided into several categories, based on the specific combination of organelles they contain. The cells of plants, fungi, protozoa and algae, and animals are all eukaryotic. The most obvious characteristic that sets plants and algae apart from other organisms is their green color, which indicates that the cells contain chlorophyll in chloroplasts. Chlorophyll is necessary for photosynthesis—the conversion of light energy into chemical-bond energy in food molecules. Another distinguishing characteristic of plant and algal cells is that their cell walls are made of cellulose (table 4.2).

The fungi are a distinct group of organisms that lack chloroplasts but have a cell wall. However, the cell wall is made from a polysaccharide, called chitin, rather than cellulose. Organisms that belong in this category of eukaryotic cells include yeasts, molds, mushrooms, and the fungi that cause such human diseases as athlete’s foot, jungle rot, and ringworm.

Eukaryotic organisms that lack cell walls and chloroplasts are placed in separate groups. Organisms that consist of only one cell are called protozoans—examples are Amoeba and Paramecium. They have all the cellular organelles described in this chapter except the chloroplast therefore, protozoans must consume food as do fungi and multicellular animals.

TABLE 4.2. Comparison of Various Kinds of Cells

Note: Viruses are not included in this classification system, because viruses are not composed of the basic cellular structural components. They are composed of a core of nucleic acid (DNA or RNA, never both) and a surrounding coat, or capsid, composed of protein. For this reason, viruses are called acellular or noncellular.

The Cell—The Basic Unit of Life

Although the differences in these groups of organisms may seem to set them worlds apart, their similarity in cellular structure is one of the central themes unifying the field of biology. One can obtain a better understanding of how cells operate in general by studying specific examples. Because the organelles have the same general structure and function, regardless of the kind of cell in which they are found, we can learn more about how mitochondria function in plants by studying how mitochondria function in animals. There is a commonality among all living things with regard to their cellular structure and function. The fact that all eukaryotic organisms have the same cellular structures is strong evidence that they all evolved from a common ancestor.

17. List five differences in structure between prokaryotic and eukaryotic cells.

18. What two types of organisms have prokaryotic cell structure?

The concept of the cell has developed over a number of years. Initially, only two regions, the cytoplasm and the nucleus, could be identified. At present, numerous organelles are recognized as essential components of both noneukaryotic and eukaryotic cell types. The structure and function of some of these organelles are compared in table 4.3. This table also indicates whether the organelle is unique to noneukaryotic or eukaryotic cells or is found in both.

The cell is the common unit of life. Individual cells and their structures are studied to discover how they function as individual living organisms and as parts of many-celled beings. Knowing how prokaryotic and eukaryotic organisms resemble each other and differ from each other helps physicians control some organisms dangerous to humans.

There are several ways in which materials enter or leave cells. These include diffusion and osmosis, which involve the net movement of molecules from an area of high to low concentration. In addition, there are several processes that involve activities on the part of the cell to move things across the membrane. These include facilitated diffusion, which uses carrier molecules to diffuse across the membrane active transport, which uses energy from the cell to move materials from low to high concentration and endocytosis and exocytosis, in which membrane-enclosed packets are formed.

TABLE 4.3. Summary of the Structure and Function of the Cellular Organelles


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 Table. 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.


Summary

This tutorial presented the diversity of prokaryotic carbon sources. Bacteria can use simple sugars, as well as complex sources of carbon. Some bacteria can live off oil, and some can decompose cellulose. The ability to breakdown complex carbon sources has been utilized for a variety of purposes. The field of bioremediation is based, to a large extent, on the use of bacteria that can breakdown harmful compounds that have been introduced into the environment from various industrial and agricultural sources. For example, bacteria are capable of breaking down TNT and PCBs.

A great deal of life on the planet depends on prokaryotes, either directly or indirectly. The saprophytes degrade material from dead organic matter, and in doing so make nitrogen and carbon available to other life forms. Without them, nutrients would quickly be tied up in the carcasses of dead organisms and unavailable for other organisms in the ecosystem.

Nitrogen is necessary for the synthesis of amino acids. As with carbon, bacteria obtain their nitrogen from various sources. Some bacteria can convert ammonia into a more useful form of nitrogen (like nitrates and nitrites). Saprophytic bacteria obtain their nitrogen from decaying organic matter, whereas nitrogen-fixing bacteria obtain their nitrogen from molecular nitrogen (N2) found in the atmosphere.

Cyanobacteria not only fix their own nitrogen from the air, but they also synthesize their own sugars from carbon dioxide, using sunlight as an energy source. They may be the most efficient form of life on the planet. Indeed, the ancestors of blue-green algae played an important role in the history of the planet because their photosynthetic activity converted our planet's early anaerobic environment into one that is oxygen rich.

We also examined the relationships between oxygen and metabolism, and in the next few tutorials we will explore, in more detail, the relationship between energy and metabolic processes.


Watch the video: Prokaryotic Cells - Introduction and Structure - Post 16 Biology A Level, Pre-U, IB, AP Bio (November 2022).