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8.11: Why It Matters- Metabolic Pathways - Biology

8.11: Why It Matters- Metabolic Pathways - Biology


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Why explain the metabolic pathways involved in the capture and release of energy in cells?

Every time you move—or even breathe—you’re using energy. Two of these ways are photosynthesis and cellular respiration.

Plants (and other autotrophs) undergo photosynthesis to create energy. Humans (and other heterotrophs) on the other hand must consume something that has energy (like plants or other animals)—we take this energy and convert it into a form our body can use. This process is known as cellular respiration.

Watch this 5 minute video for an overview of why even small changes in the global climate have the potential for big impacts on our daily lives through our food sources.

A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/biom1/?p=238

  • What role does farming play in giving us energy to use every day?
  • How do plants get energy to grow, and how do we then get our energy from them?

Ok, let’s see where we get all the energy to stay awake during biology class!

Learning Outcomes

  • Understand the role movement of electrons plays in energy exchanges in cells
  • Identify the basic components and steps of photosynthesis
  • Identify the reactants and products of cellular respiration and where these reactions occur in a cell
  • Illustrate the basic components and steps of fermentation

8.11: Why It Matters- Metabolic Pathways - Biology

Many cells are unable to carry out respiration because of one or more of the following circumstances:

  1. The cell lacks a sufficient amount of any appropriate, inorganic, final electron acceptor to carry out cellular respiration.
  2. The cell lacks genes to make appropriate complexes and electron carriers in the electron transport system.
  3. The cell lacks genes to make one or more enzymes in the Krebs cycle.

Whereas lack of an appropriate inorganic final electron acceptor is environmentally dependent, the other two conditions are genetically determined. Thus, many prokaryotes, including members of the clinically important genus Streptococcus, are permanently incapable of respiration, even in the presence of oxygen. Conversely, many prokaryotes are facultative, meaning that, should the environmental conditions change to provide an appropriate inorganic final electron acceptor for respiration, organisms containing all the genes required to do so will switch to cellular respiration for glucose metabolism because respiration allows for much greater ATP production per glucose molecule.

If respiration does not occur, NADH must be reoxidized to NAD + for reuse as an electron carrier for glycolysis, the cell’s only mechanism for producing any ATP, to continue. Some living systems use an organic molecule (commonly pyruvate) as a final electron acceptor through a process called fermentation. Fermentation does not involve an electron transport system and does not directly produce any additional ATP beyond that produced during glycolysis by substrate-level phosphorylation. Organisms carrying out fermentation, called fermenters, produce a maximum of two ATP molecules per glucose during glycolysis. Table 1 compares the final electron acceptors and methods of ATP synthesis in aerobic respiration, anaerobic respiration, and fermentation. Note that the number of ATP molecules shown for glycolysis assumes the Embden-Meyerhof-Parnas pathway. The number of ATP molecules made by substrate-level phosphorylation (SLP) versus oxidative phosphorylation (OP) are indicated.

Microbial fermentation processes have been manipulated by humans and are used extensively in the production of various foods and other commercial products, including pharmaceuticals. Microbial fermentation can also be useful for identifying microbes for diagnostic purposes.

Fermentation by some bacteria, like those in yogurt and other soured food products, and by animals in muscles during oxygen depletion, is lactic acid fermentation. The chemical reaction of lactic acid fermentation is as follows:

Bacteria of several gram-positive genera, including Lactobacillus, Leuconostoc, and Streptococcus, are collectively known as the lactic acid bacteria (LAB), and various strains are important in food production. During yogurt and cheese production, the highly acidic environment generated by lactic acid fermentation denatures proteins contained in milk, causing it to solidify. When lactic acid is the only fermentation product, the process is said to be homolactic fermentation such is the case for Lactobacillus delbrueckii and S. thermophiles used in yogurt production. However, many bacteria perform heterolactic fermentation, producing a mixture of lactic acid, ethanol and/or acetic acid, and CO2 as a result, because of their use of the branched pentose phosphate pathway instead of the EMP pathway for glycolysis. One important heterolactic fermenter is Leuconostoc mesenteroides, which is used for souring vegetables like cucumbers and cabbage, producing pickles and sauerkraut, respectively.

Lactic acid bacteria are also important medically. The production of low pH environments within the body inhibits the establishment and growth of pathogens in these areas. For example, the vaginal microbiota is composed largely of lactic acid bacteria, but when these bacteria are reduced, yeast can proliferate, causing a yeast infection. Additionally, lactic acid bacteria are important in maintaining the health of the gastrointestinal tract and, as such, are the primary component of probiotics.

Another familiar fermentation process is alcohol fermentation, which produces ethanol. The ethanol fermentation reaction is shown in Figure 1. In the first reaction, the enzyme pyruvate decarboxylase removes a carboxyl group from pyruvate, releasing CO2 gas while producing the two-carbon molecule acetaldehyde. The second reaction, catalyzed by the enzyme alcohol dehydrogenase, transfers an electron from NADH to acetaldehyde, producing ethanol and NAD + . The ethanol fermentation of pyruvate by the yeast Saccharomyces cerevisiae is used in the production of alcoholic beverages and also makes bread products rise due to CO2 production. Outside of the food industry, ethanol fermentation of plant products is important in biofuel production.

Figure 1. The chemical reactions of alcohol fermentation are shown here. Ethanol fermentation is important in the production of alcoholic beverages and bread.

Beyond lactic acid fermentation and alcohol fermentation, many other fermentation methods occur in prokaryotes, all for the purpose of ensuring an adequate supply of NAD + for glycolysis (Table 2). Without these pathways, glycolysis would not occur and no ATP would be harvested from the breakdown of glucose. It should be noted that most forms of fermentation besides homolactic fermentation produce gas, commonly CO2 and/or hydrogen gas. Many of these different types of fermentation pathways are also used in food production and each results in the production of different organic acids, contributing to the unique flavor of a particular fermented food product. The propionic acid produced during propionic acid fermentation contributes to the distinctive flavor of Swiss cheese, for example.

Several fermentation products are important commercially outside of the food industry. For example, chemical solvents such as acetone and butanol are produced during acetone-butanol-ethanol fermentation. Complex organic pharmaceutical compounds used in antibiotics (e.g., penicillin), vaccines, and vitamins are produced through mixed acid fermentation. Fermentation products are used in the laboratory to differentiate various bacteria for diagnostic purposes. For example, enteric bacteria are known for their ability to perform mixed acid fermentation, reducing the pH, which can be detected using a pH indicator. Similarly, the bacterial production of acetoin during butanediol fermentation can also be detected. Gas production from fermentation can also be seen in an inverted Durham tube that traps produced gas in a broth culture.

Microbes can also be differentiated according to the substrates they can ferment. For example, E. coli can ferment lactose, forming gas, whereas some of its close gram-negative relatives cannot. The ability to ferment the sugar alcohol sorbitol is used to identify the pathogenic enterohemorrhagic O157:H7 strain of E. coli because, unlike other E. coli strains, it is unable to ferment sorbitol. Last, mannitol fermentation differentiates the mannitol-fermenting Staphylococcus aureus from other non–mannitol-fermenting staphylococci.

Table 2. Common Fermentation Pathways
Pathway End Products Example Microbes Commercial Products
Acetone-butanol-ethanol Acetone, butanol, ethanol, CO2 Clostridium acetobutylicum Commercial solvents, gasoline alternative
Alcohol Ethanol, CO2 Candida, Saccharomyces Beer, bread
Butanediol Formic and lactic acid ethanol acetoin 2,3 butanediol CO2 hydrogen gas Klebsiella, Enterobacter Chardonnay wine
Butyric acid Butyric acid, CO2, hydrogen gas Clostridium butyricum Butter
Lactic acid Lactic acid Streptococcus, Lactobacillus Sauerkraut, yogurt, cheese
Mixed acid Acetic, formic, lactic, and succinic acids ethanol, CO2, hydrogen gas Escherichia, Shigella Vinegar, cosmetics, pharmaceuticals
Propionic acid Acetic acid, propionic acid, CO2 Propionibacterium, Bifidobacterium Swiss cheese

Think about It

  • When would a metabolically versatile microbe perform fermentation rather than cellular respiration?

Identifying Bacteria by Using API Test Panels

Identification of a microbial isolate is essential for the proper diagnosis and appropriate treatment of patients. Scientists have developed techniques that identify bacteria according to their biochemical characteristics. Typically, they either examine the use of specific carbon sources as substrates for fermentation or other metabolic reactions, or they identify fermentation products or specific enzymes present in reactions. In the past, microbiologists have used individual test tubes and plates to conduct biochemical testing. However, scientists, especially those in clinical laboratories, now more frequently use plastic, disposable, multitest panels that contain a number of miniature reaction tubes, each typically including a specific substrate and pH indicator. After inoculation of the test panel with a small sample of the microbe in question and incubation, scientists can compare the results to a database that includes the expected results for specific biochemical reactions for known microbes, thus enabling rapid identification of a sample microbe. These test panels have allowed scientists to reduce costs while improving efficiency and reproducibility by performing a larger number of tests simultaneously.

Many commercial, miniaturized biochemical test panels cover a number of clinically important groups of bacteria and yeasts. One of the earliest and most popular test panels is the Analytical Profile Index (API) panel invented in the 1970s. Once some basic laboratory characterization of a given strain has been performed, such as determining the strain’s Gram morphology, an appropriate test strip that contains 10 to 20 different biochemical tests for differentiating strains within that microbial group can be used. Currently, the various API strips can be used to quickly and easily identify more than 600 species of bacteria, both aerobic and anaerobic, and approximately 100 different types of yeasts. Based on the colors of the reactions when metabolic end products are present, due to the presence of pH indicators, a metabolic profile is created from the results (Figure 2). Microbiologists can then compare the sample’s profile to the database to identify the specific microbe.

Figure 2. The API 20NE test strip is used to identify specific strains of gram-negative bacteria outside the Enterobacteriaceae. Here is an API 20NE test strip result for Photobacterium damselae ssp. piscicida.

Clinical Focus: Alex, Part 2

This example continues Alex’s story that started in Energy Matter and Enzymes.

Many of Alex’s symptoms are consistent with several different infections, including influenza and pneumonia. However, his sluggish reflexes along with his light sensitivity and stiff neck suggest some possible involvement of the central nervous system, perhaps indicating meningitis. Meningitis is an infection of the cerebrospinal fluid (CSF) around the brain and spinal cord that causes inflammation of the meninges, the protective layers covering the brain. Meningitis can be caused by viruses, bacteria, or fungi. Although all forms of meningitis are serious, bacterial meningitis is particularly serious. Bacterial meningitis may be caused by several different bacteria, but the bacterium Neisseria meningitidis, a gram-negative, bean-shaped diplococcus, is a common cause and leads to death within 1 to 2 days in 5% to 10% of patients.

Given the potential seriousness of Alex’s conditions, his physician advised his parents to take him to the hospital in the Gambian capital of Banjul and there have him tested and treated for possible meningitis. After a 3-hour drive to the hospital, Alex was immediately admitted. Physicians took a blood sample and performed a lumbar puncture to test his CSF. They also immediately started him on a course of the antibiotic ceftriaxone, the drug of choice for treatment of meningitis caused by N. meningitidis, without waiting for laboratory test results.

  • How might biochemical testing be used to confirm the identity of N. meningitidis?
  • Why did Alex’s doctors decide to administer antibiotics without waiting for the test results?

We’ll return to Alex’s example in later pages.

Key Concepts and Summary

  • Fermentation uses an organic molecule as a final electron acceptor to regenerate NAD + from NADH so that glycolysis can continue.
  • Fermentation does not involve an electron transport system, and no ATP is made by the fermentation process directly. Fermenters make very little ATP—only two ATP molecules per glucose molecule during glycolysis.
  • Microbial fermentation processes have been used for the production of foods and pharmaceuticals, and for the identification of microbes.
  • During lactic acid fermentation, pyruvate accepts electrons from NADH and is reduced to lactic acid. Microbes performing homolactic fermentation produce only lactic acid as the fermentation product microbes performing heterolactic fermentation produce a mixture of lactic acid, ethanol and/or acetic acid, and CO2.
  • Lactic acid production by the normal microbiota prevents growth of pathogens in certain body regions and is important for the health of the gastrointestinal tract.
  • During ethanol fermentation, pyruvate is first decarboxylated (releasing CO2) to acetaldehyde, which then accepts electrons from NADH, reducing acetaldehyde to ethanol. Ethanol fermentation is used for the production of alcoholic beverages, for making bread products rise, and for biofuel production.
  • Fermentation products of pathways (e.g., propionic acid fermentation) provide distinctive flavors to food products. Fermentation is used to produce chemical solvents (acetone-butanol-ethanol fermentation) and pharmaceuticals (mixed acid fermentation).
  • Specific types of microbes may be distinguished by their fermentation pathways and products. Microbes may also be differentiated according to the substrates they are able to ferment.

Multiple Choice

Which of the following is the purpose of fermentation?

  1. to make ATP
  2. to make carbon molecule intermediates for anabolism
  3. to make NADH
  4. to make NAD +

Which molecule typically serves as the final electron acceptor during fermentation?

Which fermentation product is important for making bread rise?

Which of the following is not a commercially important fermentation product?

Fill in the Blank

The microbe responsible for ethanol fermentation for the purpose of producing alcoholic beverages is ________.

________ results in the production of a mixture of fermentation products, including lactic acid, ethanol and/or acetic acid, and CO2.

Fermenting organisms make ATP through the process of ________.

Matching

Match the fermentation pathway with the correct commercial product it is used to produce:


Dresden biologists make living sperm glow

How do female insects manage to keep the sperm fresh for months after mating? This is a central question of the sperm biologists of the Chair of Applied Zoology headed by Prof. Dr. Klaus Reinhardt. Now the scientists presented their first promising results in the journal Scientific Reports.

Dr. Cornelia Wetzker borrowed an innovative label-free technique from cancer research in order to investigate the metabolism of living biological tissues. This involves the measurement of the decay of the intrinsic fluorescence of the metabolic coenzyme NADH - a matter of nanoseconds, requiring a specialised microscope. This measure, also known as fluorescence lifetime, serves as a cell-specific signature and characterises the specific metabolic pathways of the tissue. Cancer cells have a shorter NADH fluorescence lifetime, are thus more glycolytic and can therefore be distinguished from healthy cells.

With this method, Dr. Cornelia Wetzker has now succeeded in examining the metabolism of intact tissues of the fruit fly outside the body. She analysed the metabolism of sperm in the storage organs of male and female animals as well as other tissues of the insect. The sperm were investigated in still intact closed organs, which in the male serve for storage before and in the females after mating. The team thus found that the sperm had a highly glycolytic metabolism similar to that of cancer cells. Other cells, such as intestinal, gland and fat cells, were in a much more oxidative state.

Using this method, the biologists found a first clue to their initial question of how the sperm remain fresh in the body of the insect females. They discovered that the fluorescence lifetime of another autofluorescent metabolic coenzyme called FAD differs between the sperm in the male and in the female body.

With regard to the clinical application of this technique, fluorescence lifetime imaging microscopy (FLIM) is proving to be highly promising. "The fluorescence lifetime signature analysis could even be automated with the help of neural networks", suspects Dr. Cornelia Wetzker. "And since the method is not dangerous, there is no reason why it should not be used on living humans or animals," adds Professor Klaus Reinhardt.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


Conclusion

During evolution, brown bears have adapted to a lifestyle comprising hyperphagia and obesity in the fall and immobilisation during up to half a year of hibernation in winter. Bears have developed a circular metabolic plasticity enabling these animals to avoid noncommunicable diseases such as metabolic syndrome, diabetes and cardiovascular disease, and they are not prone to osteoporosis or sarcopenia. It is likely that bears hold keys to gain insight into and perhaps treat lifestyle-related diseases in humans. Because hibernation is not genetically defined but likely confined to differently expressed proteins, a way forward is to screen for up- and downregulated peptides and proteins to identify biomarkers responsible for inducing and sustaining a healthy physiology during hibernation.


Watch the video: Metabolic pathways (January 2023).