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Pathways and metabolites of microbial cells
KINDLY REDUCE IT TO PATHWAYS AND METABOLITES
Inside every cell, including the smallest bacterium, there is a constant whirl of metabolic activity as the cell uses
nutrients to form cellular energy and build cell structures. In this chapter we will discuss metabolism in microbial cells.
We'll focus on five key areas: a definition of metabolism, the role of enzymes in metabolism, energy production in the
cell, metabolic pathways in microbial cells, and the metabolic diversity of microorganisms.,
Let's start with a definition of metabolism. You've heard people talk about having a fast metabolism or a slow
metabolism. In biology, when we talk about metabolism, we are referring to the sum of all chemical reactions in the
cell. Metabolism can be divided into two components: catabolism and anabolism. Catabolic reactions break larger
molecules into smaller ones. For example, glucose is broken down releasing carbon dioxide and water. These
reactions release the energy stored in the chemical bonds of large molecules. The second component of metabolism
is anabolism, or biosynthesis. Anabolic reactions join smaller molecules to form large ones, such as joining
sugars and amino acids to form the bacterial cell wall.
We say that anabolism and catabolism are "coupled" or linked together because catabolic reactions release the
energy needed for anabolic reactions. Anabolism and catabolism are interrelated through the molecule ATP,
adenosine triphosphate. The high energy phosphate bonds of ATP stores energy captured in catabolism and
releases it later in anabolic reactions.
Okay, so now we know that metabolism is the sum of all chemical reactions in the cell and these are divided into
two components: catabolism and anabolism. Catabolic reactions break down larger molecules, releasing energy
that is used to form ATP. Anabolic reactions use the small molecules and ATP formed in catabolism to build large
molecules. Your textbook shows a diagram of the interrelated components of metabolism.
Now let's turn to our second topic, enzymes. Each of the thousands of metabolic reactions in the cell requires a
biological catalyst called an enzyme. Enzymes are proteins that catalyze, or speed up, chemical reactions. Each
enzyme acts upon a specific molecule, called a substrate molecule. By binding to and orienting substrate molecules,
enzymes increase the rate at which a substrate forms its reaction product, lowering its activation energy. The
region of the enzyme molecule where the substrate binds is called the enzyme's active site. The substrate fits into the
enzyme's active site, similar to the way a key fits into a lock. So, just like needing the right key to start your car, a
substrate must fit properly into the active site, or the chemical reaction will not "go". Enzymes are not consumed by
the reaction they catalyze, and so can perform the same reaction over and over again. They function best within
certain ranges of pH and temperature.
You can usually recognize an enzyme by its name. Enzymes are usually given names ending with "-ase".
"Hexokinase" and DNA ligase" are examples of enzyme names. The enzyme name sometimes indicates the type of
reaction that the enzyme catalyzes. For example, sucrase digests sucrose while maltase digests maltose.
Although enzymes are protein molecules, they may need nonprotein components, called cofactors, to be active.
Cofactors may be inorganic molecules, such as iron or magnesium, or organic molecules, like nucleotides. If the
cofactor is organic, then we call it a coenzyme. Two examples of coenzymes are NAD, nicotinamide adenine
dinucleotide, and FAD, flavin adenine dinucleotide. Both of these are derivatives of vitamin B and both are involved in
the transfer of electrons.
Okay, let's review the key properties of enzymes. Enzymes are protein molecules that catalyze reactions in the cell.
Each enzyme binds a specific substrate at a region on the enzyme molecule called the active site. Enzymes may
require inorganic or organic cofactors.
Now that we've learned about enzymes, let's discuss two general aspects of energy production in the cell-oxidationreduction and the mechanisms of ATP generation. We're very familiar with the use of energy to power our cars or
heat our homes. Just as we "burn" or oxidize fuel in our car engines or home furnaces, our cells use catabolism to
oxidize our food molecules. In everyday terms, the word oxidation often means corrosion, like the oxidation of
copper or iron. However, in chemical terms, oxidation is the removal of electrons. When electrons are removed, they
are transferred to electron acceptors. The chemical term for accepting electrons is reduction. In oxidation-reduction
reactions, when one substance is oxidized and loses electrons, the electrons are immediately picked up by another
substance, which is then reduced. These reactions are called "coupled" reactions-one cannot occur without the other.
So, oxidation is always coupled with reduction. Oxidation-reduction reactions in the cells frequently use the
coenzymes NAD or FAD to donate or accept electrons.
Pathways and metabolites of microbial cells
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As our food molecules are oxidized, the coenzymes NAD or FAD become reduced. The energy from our food is
now stored in the "reducing power" of the reduced coenzymes. The reducing power of these coenzymes is used
during the last stage of cellular respiration to power the electron transport chain and form ATP. ATP is formed
by adding a phosphate group onto an ADP (adenosine diphosphate) molecule.
So, why is it important to form ATP? Well, as we said earlier, ATP is needed for biosynthesis reactions. Both humans
and microbes need ATP to build cell structures like cell membranes and chromosomes. Also, the energy from ATP is
used for cellular movement. So, we use ATP to power our muscle cells, while some microbes use ATP to move their
flagella.
The reaction that forms ATP, also called a phosphorylation reaction, occurs in three ways: First, substrate-level
phosphorylation. Second, oxidative phosphorylation. And third, photophosphorylation. In the first method,
substrate-level phosphorylation, the phosphate group is transferred directly from a high-energy substrate to ADP,
forming ATP. The second method, oxidative phosphorylation, generates ATP by passing electrons from the
coenzymes NAD and FAD through an electron transport chain. Electrons passed along the electron transport chain
are ultimately picked up by oxygen, or another electron acceptor molecule. The energy released by this transfer
process is harnessed to form ATP. The third method of forming ATP, photophosphorylation, uses the energy from
sunlight to power ATP synthesis. Photophosphorylation occurs in photosynthesis.
Let's quickly summarize what we've learned about energy production. The oxidation, or removal of electrons, from
food molecules is used to reduce electron acceptor molecules. The reduced electron acceptors, such as reduced
NAD or FAD, then can be used to power ATP synthesis in oxidative phosphorylation. ATP can also be formed
through substrate-level phosphorylation or photophosphorylation.
Now that we've covered how energy is produced, we'll turn our attention to metabolic pathways. In this section, we
will discuss how cells capture energy from food molecules. A metabolic pathway is a sequence of enzyme-catalyzed
reactions.
Most microorganisms oxidize carbohydrates as their primary source of cellular energy, so let's look at the metabolic
pathways used in the catabolism of carbohydrates, starting with glucose. Microorganisms use two general
processes-cellular respiration and fermentation. Both processes begin with glycolysis. You can break this term
into two parts: "glyco" and "lysis" to remember that glycolysis splits glucose into two pieces.
The process of glycolysis begins with glucose and ends with two molecules of pyruvic acid. Glycolysis also
yields two molecules of ATP per glucose molecule. These ATP molecules are formed by substrate-level
phosphorylation steps that occur in glycolysis.
After glycolysis, pyruvic acid is then further oxidized through cellular respiration. Cellular respiration may
occur in two ways - it may be aerobic or anaerobic. Aerobic respiration takes the electrons from pyruvic acid
and passes them to oxygen. Anaerobic respiration uses inorganic molecules, such as sulfate or nitrate ions, as
electron acceptors. (Remember that the prefix "an" means without, so anaerobic respiration occurs without oxygen.)
In respiration, the pyruvic acid molecules from glycolysis lose a carboxyl group to form acetyl CoA. The acetyl
CoA then enters the Krebs cycle. In this cycle, the carbons from acetyl CoA are released as carbon dioxide.
The energy contained in the chemical bonds of acetyl CoA is harvested by forming reduced NAD and FAD
molecules.
From the Krebs cycle, respiration continues as NADH and FADH2 pass their electrons onto the electron
transport chain. The electron transporters are embedded in a membrane and are arranged from high to low affinity
for electrons. This high to low affinity arrangement causes electrons to "flow downhill". As electrons flow down the
electron transport chain, protons are pumped across the membrane. The pumping of protons across the membrane
creates an energy potential that is harvested by the enzyme ATP synthase. You can think of ATP synthase as an
ATP-forming "engine" that "runs" on proton flow to convert ADP to ATP. The process of ATP synthesis using proton
flow is known as chemiosmosis.
Cells can obtain a large amount of energy from glucose oxidation. The oxidation of a single glucose molecule
through the cellular respiration pathway in prokaryotes generates 38 ATP molecules. (In eukaryotes,
Pathways and metabolites of microbial cells
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approximately 36 ATP are obtained per glucose molecule. The reason for the slight difference is explained in
your text.)
Let's recap what we've learned about cellular respiration. Glucose enters glycolysis and is converted to pyruvic
acid. A small amount of ATP is made during glycolysis. Pyruvic acid is used to form acetyl CoA, which enters the
Krebs cycle. The Krebs cycle uses acetyl CoA to form carbon dioxide and reduced coenzymes. Again, a small
amount of ATP is made during the Krebs cycle. The reduced coenzymes from the Krebs cycle pass their
electrons onto the electron transport chain. The transport of electrons causes protons to be pumped across the
membrane. ATP is formed when the protons flow through ATP synthase. The majority of ATP made during
cellular respiration is made using the electron transport chain. In prokaryotes, the oxidation of one glucose
molecule generates approximately 38 ATP molecules.
In some organisms, the catabolism of glucose may follow a slightly different route. After glycolysis, pyruvate may
undergo fermentation. Fermentation pathways do not use the Krebs cycle or an electron transport chain. Some
organisms use fermentation when growing in anaerobic conditions. The end products of fermentation are
alcohols, like ethanol, or organic acids, like lactic acid. For example, yeast cells fermenting glucose produce
ethanol and carbon dioxide as their end products. The alcoholic fermentation pathway of yeast is used commercially
to produce beer and wine. Tests to detect fermentation end products are often used in the microbiology lab to
identify bacteria and other microbes. Animal muscle cells also undergo fermentation when not enough oxygen is
delivered to cells during intense exercise. In this case, the fermentation end product is lactic acid.
When cells use fermentation, they produce far less energy than cells using respiration. If glucose is fermented, only
two ATP molecules are produced per glucose molecule, compared with the 38 ATP that can be obtained through
respiration.
In our discussion of metabolic pathways, we have focused on the catabolism of carbohydrates through cellular
respiration and fermentation. Although we will not discuss them here, some microbes use other pathways for
carbohydrate catabolism, which are described in your textbook. You should also read the sections in your textbook
concerning photosynthesis and anabolism of macromolecules.
All organisms can be classified metabolically according to their nutritional pattern-their source of energy and their
source of carbon. In the last section we'll discuss the metabolic diversity of microorganisms and examine the various
sources of energy and carbon used by microbes. Microbes use one of two types of energy sources: chemical
energy or light energy. Organisms that use chemicals for energy are called chemotrophs. Microbes using light
energy are called phototrophs. (Remember that "troph" means feeding or eating. So, literally, phototrophs are "lighteaters".)
All organisms need a source of carbon to use in building their cellular molecules. There are two possible carbon
sources: organic carbon, like glucose, and inorganic carbon, like carbon dioxide. Organisms that use organic carbon
are called heterotrophs, while organisms that use inorganic carbon are called autotrophs.
The terms for energy and carbon sources can be combined, creating four categories. Thus, chemoheterotrophs use
chemicals for energy sources and organic carbon, while chemoautotrophs use chemical energy sources but
inorganic carbon. In the same way, photoheterotrophs use light energy sources and organic carbon, and
photoautotrophs use light energy and inorganic carbon.
That's the end of this section.