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1.4.19.2: The Sulfur Cycle - Biology

1.4.19.2: The Sulfur Cycle - Biology


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Learning Outcomes

  • Discuss the sulfur cycle and sulfur’s role on Earth

Sulfur, an essential element for the macromolecules of living things, is released into the atmosphere by the burning of fossil fuels, such as coal. Atmospheric sulfur is found in the form of sulfur dioxide (SO2) and enters the atmosphere in three ways: from the decomposition of organic molecules, from volcanic activity and geothermal vents, and from the burning of fossil fuels by humans.

On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and geothermal vents (Figure 2). Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere, sulfur is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly from the atmosphere in a process called fallout. Also, the weathering of sulfur-containing rocks releases sulfur into the soil. These rocks originate from ocean sediments that are moved to land by the geologic uplifting of ocean sediments. Terrestrial ecosystems can then make use of these soil sulfates (SO4), and upon the death and decomposition of these organisms, release the sulfur back into the atmosphere as hydrogen sulfide (H2S) gas.

Sulfur enters the ocean via runoff from land, from atmospheric fallout, and from underwater geothermal vents. Some ecosystems rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine ecosystems in the form of sulfates.

Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large quantities of fossil fuels, especially from coal, releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls through this gas, it creates the phenomenon known as acid rain. Acid rain is corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid, which causes damage to aquatic ecosystems. Acid rain damages the natural environment by lowering the pH of lakes, which kills many of the resident fauna; it also affects the man-made environment through the chemical degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial in Washington, DC, have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects of human activities on our environment and the challenges that remain for our future.

Click this link to learn more about global climate change.

Biology:Sulfur cycle

The sulfur cycle is the collection of processes by which sulfur moves between rocks, waterways and living systems. Such biogeochemical cycles are important in geology because they affect many minerals. Biochemical cycles are also important for life because sulfur is an essential element, being a constituent of many proteins and cofactors, and sulfur compounds can be used as oxidants or reductants in microbial respiration. Ώ] The global sulfur cycle involves the transformations of sulfur species through different oxidation states, which play an important role in both geological and biological processes.

Steps of the sulfur cycle are:

  • Mineralization of organic sulfur into inorganic forms, such as hydrogen sulfide (H2S), elemental sulfur, as well as sulfide minerals.
  • Oxidation of hydrogen sulfide, sulfide, and elemental sulfur (S) to sulfate (SO4 2− ).
  • Reduction of sulfate to sulfide.
  • Incorporation of sulfide into organic compounds (including metal-containing derivatives).

These are often termed as follows:

Assimilative sulfate reduction (see also sulfur assimilation) in which sulfate (SO4 2− ) is reduced by plants, fungi and various prokaryotes. The oxidation states of sulfur are +6 in sulfate and –2 in R–SH. Desulfurization in which organic molecules containing sulfur can be desulfurized, producing hydrogen sulfide gas (H2S, oxidation state = –2). An analogous process for organic nitrogen compounds is deamination. Oxidation of hydrogen sulfide produces elemental sulfur (S8), oxidation state = 0. This reaction occurs in the photosynthetic green and purple sulfur bacteria and some chemolithotrophs. Often the elemental sulfur is stored as polysulfides. Oxidation in elemental sulfur by sulfur oxidizers produces sulfate. Dissimilative sulfur reduction in which elemental sulfur can be reduced to hydrogen sulfide. Dissimilative sulfate reduction in which sulfate reducers generate hydrogen sulfide from sulfate.


Background

When metal concentrations in the environment exceed the maximum tolerance of plants, it affects plant physiological and biochemical functions and further results in plant growth retardation and yield degradation [44]. Cadmium (Cd), as a non-nutritive heavy metal (HM), causes plant growth inhibition and affects nutrient uptake and homeostasis even in very small quantities [49, 26]. Prolonged Cd exposure adversely affects several metabolic processes and leads to phytotoxicity, which is caused by limited photosynthetic activity and enzyme activity and the generation of reactive oxygen species (ROS) such as superoxide radicals (O2• − ), hydroxyl (•OH), and hydrogen peroxide (H2O2) [2, 3, 47, 50, 52]. Moreover, high levels of ROS have damaging effects on plant cellular components, such as membranes, nucleic acids, and chloroplast pigments, which result in plant lipid peroxidation [54].

Plants, including Brassica juncea (L.) Czern., have evolved a series of protective and damage repair systems to react to and minimize the effect of oxidative stress. These defence systems are mainly antioxidants, such as glutathione (GSH) and ascorbic acid (AsA) [38, 50], and antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) [40]. Meanwhile, the genes encoding their respective antioxidants, such as GR, SOD, APX, and CAT, showed higher expression levels in response to Cd stress, acting as an adaptive response that could alleviate and minimize oxidative damage [15, 30, 39].

Phytoremediation is an eco-friendly method for pollutant removal that uses living plants to eliminate HMs and has been considered a highly promising technology for remediation of polluted sites ([46, 59]). However, in recent years, because of the lower biomass of hyperaccumulators and the phytotoxic effects of high HM concentrations on normal plants, improving phytoremediation efficiency has gained much attention [35]. With its characteristics of rapid growth, massive biomass and moderate accumulation of Cd, B. juncea has been considered one of the most promising plants for the phytoremediation of Cd-contaminated farmlands [22]. In addition, plant-microbe interactions in soil have led to the improvement of phytoextraction efficiency due to the potential role of microorganisms in eliminating the HM-induced toxicity and their positive effect on plant growth promotion in metal-contaminated soils [28, 34]. Previous studies have shown that plant growth-promoting bacteria (PGPB) not only reduce biotic or abiotic stress but also promote plant growth [33]. Bacillus spp. alleviated lead (Pb) and arsenic (As) stress in rice by reducing lipid peroxidation and increasing amylase and protease levels to promote plant growth in heavy metal-polluted soil ([43]). Several studies documented that endophytic bacteria associated with plant growth promotion, such as Bacillus licheniformis, enhanced copper (Cu), zinc (Zn), chromium (Cr), Cd and Pb accumulation and distribution in plants grown in heavy metal-contaminated soil, which led to reduced levels of toxic metals in the soil (Brunetti et al. 2012). The endophytic bacterium Pseudomonas fluorescens Sasm05 promoted Sedum alfredii Hance growth and enhanced Cd accumulation in response to Cd stress [13].

The PGPB Sphingomonas SaMR12, first isolated from the surface-sterilized root of a Chinese native Cd/Zn hyperaccumulator S. alfredii [60, 61], was shown to promote plant growth, protect S. alfredii roots from Cd damage and alleviate ROS damage by decreasing H2O2 and O2• − [11, 12, 63]. In a pot experiment, SaMR12 showed a positive effect on Brassica napus growth, plant Cd uptake and Cd translocation to the leaves [42]. However, the mechanisms of its promotion effect have not yet been elucidated. Therefore, we inoculated SaMR12 into B. juncea under hydroponic culture conditions and investigated its effects on 1) plant growth and Cd uptake at different Cd levels 2) the responses of antioxidant enzymes and the GSH-AsA cycle and 3) the expression levels of the responsive genes.


MCQ Biology 07: Biochemistry: Amino Acids – Part 3 for Life Science JRF/NET Examination, June 2015

(1). pH below pI amino acids will be___.
a. Anionic
b. Cationic
c. Net charge zero
d. No charge

(2). Naturally occurring proteins are usually polymers of _____.
a. D-amino acids
b. L-amino acids
c. A mixture of D and L amino acids
d. Either D amino acids or L- amino acids

(3). At zwitterionic form, an amino acid will act as_____.
a. Proton donor
b. Proton acceptor
c. Proton donor and acceptor
d. None of these

(4). Which of the following amino acid is more likely to occupy the interior of a globular protein?
a. Methionine
b. Aspartate
c. Lysine
d. Arginine
e. All of these

(5). Proteins absorb UV light at 280 nm and show a characteristic peak at this wavelength. Which amino acid residue in the protein is responsible for this absorption?

a. Methionine
b. Valine
c. Glutamic acid
d. Tryptophan

(6). Glycine is _____.
a. A stimulatory neurotransmitter
b. An inhibitory neurotransmitter
c. Not act acting as a neurotransmitter
d. Both (a) and (b)
e. Not a neurotransmitter

(7). Selenocysteine is a rare amino acid which contain ____-
a. Selenium
b. Selenium and Sulfur
c. Sulfur
d. Selenium and Nickel

(8). Which of the following amino acid contain a thioether group in the side chain?
a. Cysteine
b. Cystine
c. Glycine
d. Methionine

(9). An amino acid with a sulfhydryl group in the side chain:
a. Methionine
b. Cystine
c. Cysteine
d. All of these

(10). Which among the following is the largest amino acid?
a. Phenylalanine
b. Tyrosine
c. Tryptophan
d. Histidine

(11). Which of the following amino acid is completely non-polar?

a. Phenylalanine
b. Tyrosine
c. Tryptophan
d. All of these
e. None of these

(12). Which amino acid is known as “the 22nd amino acid”?

a. Selenocysteine
b. Pyrrolysine
c. N-formylmethionine
d. Selenomethionine

(13). Cystine is ___.

a. Highly polar
b. Highly non polar
c. Partially polar
d. Partially non polar

(14). The side chain of Histidine contain____.

a. Indole ring
b. Phenol group
c. Imidazole ring
d. Guanidino ring

(15). Taurine, the major constituent of bile, is derived from____.

a. Cysteine
b. Methionine
c. Tryptophan
d. Lysine

(16). Selenocysteine is a derived from _____.

a. Cysteine
b. Serine
c. Methionine
d. Cystine

(17). Example for selenocysteine containing protein:

a. Glutathione peroxidase
b. Thioredoxin reductase
c. Glycine reductase
d. All of these
e. None of these

(18). A fully protonated glycine (NH3+ – CH2 – COOH) can release ____ protons.

(19). ____ is the only amino acid which is optically inactive.

a. Valine
b. Glycine
c. Selenocysteine
d. Proline

(20). Selenocystein is coded by ________ codon.

Biology MCQ-6: Biology/Life Science Multiple Choice Questions (MCQ) / Model Questions with answers and explanations in Biochemistry: Amino Acids Part 2 for preparing CSIR JRF NET Life Science Examination and also for other competitive examinations in Life Science / Biological Science such as ICMR JRF Entrance, DBT JRF, GATE Life Science, GATE Biotechnology, ICAR, University PG Entrance Exam, JAM, GRE, Medical Entrance Examination etc. This set of practice questions for JRF/NET Life Science will help to build your confidence to face the real examination. A large quantum of questions in our practice MCQ is taken from previous year NET life science question papers. Please take advantage of our NET Lecture Notes , PPTs , Previous Year Questions and Mock Tests for you preparation. You can download these NET study material for free from our SLIDESHARE account (link given below).

Answers with explanations

1). Ans. (b). Cationic

At pH below pI, amino acid will be fully protonated with protonated – NH3+ and intact COOH, with a net positive charge and thus the amino acid will be cationic.

At pH above pI amino acid will be completely deprotonated with –NH2 and deprotonated COO-, with a net negative charge and thus the amino acid will be anionic.

At isoelectric pH (pI), the amino group will be protonated (NH3+) and the carboxylic group will be deprotonated (COO-) with net charge zero and the amino acid will be zwitterionic.

2). Ans. (b). L-amino acids

All amino acid except glycine has one chiral centre and thus can exist in two different optically active forms (enantiomers) designated as D and L amino acids. Naturally occurring proteins almost exclusively composed of L-amino acids because, during protein synthesis, the peptidyl transferase enzyme of ribosome can only recognize L-amino acids. D-amino acids do occur in nature and they usually exist as free amino acids or in short peptide sequences which are not synthesized by regular translation mechanism. Example: the peptide cross links of peptidoglycan cell wall of bacteria are rich in D-amino acids. In animals some D amino acids acts as neurotransmitters such as D-serine.

Enantiomers: Pair of stereoisomers that are non-superposable mirror images of each other. For example D and L Glyceraldehyde, D and L alanine

3). Ans. (c). Proton donor and acceptor

At zwitterionic form, the fully protonated amino group (NH3+) can act as proton donor whereas deprotonated carboxylic group (COO-) can act as proton acceptor.

4). Ans. (a). Methionine

Hydrophilic and hydrophobic interactions of amino acids play a crucial role in determining protein’s three dimensional conformations. In globular proteins, the hydrophobic residues occupy the interior portion whereas hydrophilic residues stay exterior and form a shell by interacting with water. This hydrophilic and hydrophobic interaction of amino acids with water assists the folding of polypeptide to globular manner in globular proteins.

5). Ans. (d). Tryptophan

Light wavelength used for protein quantification: 280 nm

Light wavelength used for DNA and RNA quantification: 260 nm

Tyrosine and phyenylalanine can also absorb light at 280 nm at a lesser extent.

A260/280 ratio: In laboratories a ratio of the absorption of 260/280 is used to assess the purity of extracted nucleic acid (DNA and RNA) from tissue samples. For a pure DNA, the ratio will be

1.8 and for pure RNA the ratio will be

2.0. Ratio values below 1.8 show protein contamination in the sample. As you know the reduced ratio is due to the higher values of denominator which is the absorption shown by protein in the sample.

6). Ans. (b). An inhibitory neurotransmitter

7). Ans. (a). Selenium

Selenocysteine contain selenium as selenol (SeH) same as thiol (Sulfhydril, SH) group in Cysteine. Both the selenol and thiol group are highly polar in nature.

8). Ans. (d). Methionine

Methionine (first amino acid in protein synthesis) is another sulfur containing amino acid. Sulfur in methionine is in the form of methyl thioether (C – S – C). Thioether group is highly non polar.

9). Ans. (c). Gysteine

10). Ans. (c). Tryptophan

11). Ans. (a). Phenylalanine

Among aromatic amino acids, phenylalanine is completely non polar. Tyrosine is slightly polar due to the hydroxyl group (-OH) in the side chain. Similarly Tryptophan is also shows some polarity due to the nitrogen in the indole ring.

12). Ans. (b). Pyrrolysine

Pyrrolysine biosynthesis: Two molecules of L-lysine condense together to form pyrrolysine. One molecule of lysine is first catalytically converted (3R)-3-Methyl-D-ornithine, which is then ligated to a second molecule of lysine. During this reaction an NH2 group is eliminated, followed by cyclization and dehydration to produce L-pyrrolysine.

13). Ans. (b). Highly non polar

Cystine is a dimeric amino acid of two cysteine molecules joined through Disulfide Bridge after oxidation. Sulfhydryl group (SH) in cysteine is highly polar however the disulfide bond is highly non polar making cysteine a nonpolar entity. Disulfide bond formation stabilizes the secondary and tertiary structures of protein.

14). Ans. (c). Imidazole ring

15). Ans. (a). Cysteine

Taurine (2-aminoethanesulfonic acid) is a major constituent of bile in human. It is very essential for proper cardiovascular functions, development and functions of skeletal muscles, retina and central nervous system.

16). Ans. (b). Serine

Selenocysteine synthesis: Selenocysteine is synthesized by a special mechanism in the cells only when they are required. Since selenocysteine is toxic to cells in higher concentration, unlike other amino acids, cell do not maintain the pool of this amino acid in the cytosol. Cells store selenium in the form of less reactive selenide (H2Se) to reduce the toxicity. Selenocysteine is synthesized on a specialized tRNA molecule and this special tRNA also does the duty of incorporation of selenocysteine in the growing polypeptide chain. The structure of selenocysteine-specific-tRNA differs from those of standard tRNA in many aspects.

During the biosynthesis of selenocysteine, the tRNA -Sec is charged by another amino acid serine with the help of an enzyme seryl-tRNA ligase. The elongation factors of prokaryotes and eukaryotes cannot recognize and incorporate Ser-tRNA -Sec in the polypeptide chain. Then the enzyme selenocysteine synthase act on the serine residue attached on tRNA -Sec and converted it to selenocysteine. Then this Sec-tRNA -Sec is incorporated into the growing polypeptide chain with the help of additional elongation factors in the cells.

17). Ans. (d). All of these

Selenocysteine containing proteins are called selenoproteins. So far about 25 selenoproteins are discovered in human cells.

One proton from – NH3+ and another form – COOH group

19). Ans. (b). Glycine

The side chain (R-group) of glycine is – H and thus it lacks a chiral centre. See the figure.

20). Ans. (c). UGA

UGA is a stop codon. Cell uses UGA codon to incorporate both selenocysteine and pyrrolysine (21st and 22nd amino acids) in the polypeptide by a special mechanism called translational recoding.

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Synthesis of 3-Pyrrolin-2-ones by Rhodium-Catalyzed Transannulation of 1-Sulfonyl-1,2,3-triazole with Ketene Silyl Acetal

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SCF Met30 and the cellular response to cadmium and arsenic

A first indication that SCF Met30 could play a significant role in regulating the response of yeast cells to exposure to the toxic heavy metal cadmium came from the observation that Met4 activation is important for cadmium resistance [26–29]. Recently, SCF Met30 and the fission yeast homolog SCF Pof1 were directly linked to the cellular response to cadmium ([12, 13, 30], for a recent review see [31]).

Met4 ubiquitination is blocked in response to cadmium leading to a rapid induction of Met4-dependent gene expression [12, 13]. Similar effects were observed in cells exposed to arsenic [12, 32], but not to other heavy metals [12, 13]. Intracellular cadmium and arsenic detoxification is primarily achieved by covalent sequestration by the tripeptide glutathione [33]. The rate-limiting step in glutathione biosynthesis is catalyzed by Gsh1 (γ-glutamyl-cysteine-synthase) (Fig. 1). Cadmium and arsenic block Met4 ubiquitination to induce a Met4-dependent transcription program, which includes induction of GSH1 expression [12, 13, 28, 29], and what has been described as the "sulfur sparing response" [28, 34]. Sulfur-sparing refers to the observation that upon cadmium stress, yeast cells repress expression of several glycolytic enzymes and instead strongly induce expression of isozymes with a significantly lower content of sulfur containing amino acids [28]. This isozyme switching has been proposed to help cells dedicate more of their sulfur resources to glutathione synthesis [28, 31, 34]. Isozyme switching could also make glycolysis less vulnerable to the toxic effects of cadmium because the induced isozymes have a markedly reduced number of sulfhydryl groups, which are the main targets for cadmium-induced protein damage [35, 36] (Fig. 3).

Cadmium-induced regulation of SCF Met30 . Cadmium leads to dissociation of Met30 from the SCF-core by preventing the Met30/Skp1 interaction and blocks Met4 ubiquitination. The resulting activation of Met4 induces synthesis of sulfur amino acids and glutathione as well as a process called isozyme switching, which is part of the sulfur sparing response. Cadmium also leads to activation of three independent cell cycle arrest pathways. The Met4/Met32-dependend and the Mec1/Rad53-dependent pathways, as well as one so far unidentified pathway, which was indicated by genetic results.

Cadmium also induces a complex cell cycle checkpoint response [12] (Fig. 3). Not all pathways that lead to the cadmium induced cell cycle arrest have been identified, but activation of the Met4/Met32 pathway via inhibition of SCF Met30 clearly plays an important role. In addition, cadmium (and arsenic) exposure activates the checkpoint kinases Mec1 and Rad53, which is likely to contribute to the G1 cell cycle arrest. In addition, the Mec1/Rad53 pathway is responsible for slow progression through S-phase when cells that have already initiated DNA replication experience cadmium stress [12]. Genetic experiments suggest at least one additional cadmium-induced cell cycle arrest mechanism that prevents entry into S-phase during cadmium stress conditions, because cadmium exposed mec1 met32 double mutants still arrest in G1 [12] (Fig. 3). Cell cycle arrest in response to cadmium stress is likely to be important to allow repair and replacement of damaged DNA, proteins and lipids.

Generally, ubiquitination by SCF-type ubiquitin ligases is regulated at the level of the interaction between substrates and the substrate-adapter subunit of the ligase (e.g. Met30/Met4 interaction) [8]. Remarkably, even though Met4 ubiquitination is blocked in response to cadmium stress, the interaction between Met30 and Met4 is unchanged [12, 13]. However, immunopurification experiments demonstrated that the interaction of Met30 with the SCF core component Skp1 is disrupted in cells exposed to cadmium, thus explaining inhibition of Met4 ubiquitination [12, 13] (Fig. 3). Cadmium stress most likely targets Met30 and not Skp1, because the interaction of Skp1 with the F-box protein Cdc4 is unaffected by cadmium [13]. Importantly, Met4 ubiquitination in vitro using a reconstituted system was unaffected by addition of cadmium [13]. Furthermore, addition of yeast cell lysates prepared from cadmium-exposed cells did not affect Met4 ubiquitination in this in vitro reaction [13]. Together these results suggest an indirect mechanism that requires active metabolism for cadmium-induced disassembly of SCF Met30 [13]. Interestingly, a similar regulation of the F-box protein/Skp1 interaction has been suggested for SCF Grr1 in response to changes in growth conditions [37]. More importantly, stress-induced disassembly of SCF-type ubiquitin ligases appears to be a conserved mechanism for regulation of the transcriptional response to stress conditions. In mammals, oxidative stress induces a transcription program that depends on activation of the transcription factor Nrf2 [38–40]. Similar to Met4 in budding yeast, Nrf2 regulates glutathione levels by inducing expression of the two subunits that form mammalian γ-glutamyl-cysteine-synthase [41]. Nrf2 protein abundance is regulated by ubiquitin-dependent degradation mediated by the Cul3-based ubiquitin ligase SCF3 Keap1 [42–45]. In striking similarity to the budding yeast SCF Met30 , it has been suggested that the mammalian ubiquitin ligase SCF3 Keap1 is disassembled during stress conditions [42]. Furthermore, immunopurification experiments indicate that the interaction between the substrate adapter Keap1 and its substrate Nrf2 is constitutive [42, 46], suggesting that stress-induced dissociation of Keap1 from SCF3 Keap1 controls Nrf2 ubiquitination. Despite the satisfying similarity in stress-mediated regulation of ubiquitin ligase integrity in budding yeast and mammals, the SCF3 Keap1 /Nrf2 results described above warrant a note of caution, because stress-induced dissociation of Keap1 from SCF3 Keap1 was not detected in other studies [43, 46]. Oxidation-induced conformational changes in Keap1 that lead to inhibition of the ubiquitin transfer to Nrf2 has been suggested as an alternative mechanism [46].

Cadmium clearly inactivates SCF Met30 by dissociation of Met30 [12, 13]. This raises the question of why cells choose to inactivate a ubiquitin ligase and thus prevent ubiquitination of all its substrates, rather than to block ubiquitination of specific substrates by regulating the ligase/substrate interaction. One can speculate that SCF Met30 ubiquitinates a set of proteins that are together important for coordination of the cellular response to cadmium stress. The dissociation of Met30 from the core SCF complex would be a direct way to simultaneously block ubiquitination of several SCF Met30 substrates. Alternatively, one can envision that Met30 has an additional SCF Met30 -independent function, which is activated in response to cadmium exposure and might involve the Met4/Met30 complex. It will be important to address these questions to understand the role of signal-induced disassembly of SCF-type ubiquitin ligases.

Cadmium-induced activation of Met4 not only requires inactivation of the ubiquitination reaction but also deubiquitination of the existing pool of ubiquitinated Met4 [13]. Surprisingly, Barbey and colleagues [13] demonstrated that cadmium-induced deubiquitination of Met4 is blocked in the temperature sensitive cdc53-1 strain, suggesting that Met4 deubiquitination depends on the cullin Cdc53. The deubiquitinating enzyme responsible for Met4 activation has not yet been identified, but clearly plays an important role in the cellular response to cadmium and arsenic stress.


Conclusion

In a nutshell, our kinetic models have demonstrated the importance of T[SH]2 in leishmanial cellular redox metabolism. Introducing the perturbation at the TryR reaction, our analyses suggests that the inhibition of TryR enzyme might be an important check point for disturbing the parasite's survival inside the host macrophages. By designing novel potent inhibitors against the TryR enzyme, inhibition of T[SH]2 reduction and thereby, the perturbation of activation and regulation of ISC proteins can be achieved. However, to prove this hypothesis, present kinetic models needs to be refined in order to reproduce longer oxidative stress conditions. Moreover, proper inhibition reactions should be incorporated in order to check which inhibition conditions suit the best to perturb the whole downstream metabolites production. This will require determination of experimental parameters solely in case of Leishmania major.


4.4 Fermentation

In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of the high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD + for reuse as an electron carrier for glycolysis to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD + from NADH are collectively referred to as fermentation . In contrast, some living systems use an inorganic molecule (other than oxygen) as a final electron acceptor to regenerate NAD + both methods are anaerobic (do not require oxygen) to achieve NAD + regeneration and enable organisms to convert energy for their use in the absence of oxygen.

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation (Figure 4.16). This occurs routinely in mammalian red blood cells and in skeletal muscle that has insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid produced by fermentation must be removed by the blood circulation and brought to the liver for further metabolism. The chemical reaction of lactic acid fermentation is the following:

The enzyme that catalyzes this reaction is lactate dehydrogenase. The reaction can proceed in either direction, but the left-to-right reaction is inhibited by acidic conditions. This lactic acid build-up causes muscle stiffness and fatigue. Once the lactic acid has been removed from the muscle and is circulated to the liver, it can be converted back to pyruvic acid and further catabolized for energy.

Visual Connection

Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat this plant, Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

Alcohol Fermentation

Another familiar fermentation process is alcohol fermentation (Figure 4.17), which produces ethanol, an alcohol. The alcohol fermentation reaction is the following:

In the first reaction, a carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the molecule by one carbon atom, making acetaldehyde. The second reaction removes an electron from NADH, forming NAD + and producing ethanol from the acetaldehyde, which accepts the electron. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages (Figure 4.18). If the carbon dioxide produced by the reaction is not vented from the fermentation chamber, for example in beer and sparkling wines, it remains dissolved in the medium until the pressure is released. Ethanol above 12 percent is toxic to yeast, so natural levels of alcohol in wine occur at a maximum of 12 percent.

Anaerobic Cellular Respiration

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic (Figure 4.19), reduce sulfate to hydrogen sulfide to regenerate NAD + from NADH.

Concepts in Action

Watch this video to see anaerobic cellular respiration in action.

Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia bacteria, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them upon exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. The various methods of fermentation are used by different organisms to ensure an adequate supply of NAD + for the sixth step in glycolysis. Without these pathways, that step would not occur, and no ATP would be harvested from the breakdown of glucose.

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    Modeling C4 Photosynthesis

    Susanne von Caemmerer , Robert T. Furbank , in C4 Plant Biology , 1999

    IV Summary

    A biochemical model of C4 photosynthesis is reviewed. The model is based on the assumption that CO2 fixation into C4 acids by phosphoenolpyruvate (PEP) carboxylase is a mechanism for concentrating CO2 in the bundle sheath, where Rubisco is located and CO2 is refixed via the C3 pathway. A steady-state balance is assumed between the transport of CO2 into the bundle sheath, its refixation by the C3 pathway, and the leakage of CO2 from the bundle sheath. Equations are developed that allow predictions of bundle-sheath CO2 and O2 concentrations. We show that model is able to explain key characteristics of the C4 photosynthetic pathway and use it to analyze the influence of PEP carboxylase activity, Rubisco activity, and bundle-sheath conductance on the CO2 assimilation rate. The model integrates current biochemical knowledge of C4 photosynthesis in a small number of equations. We test the output of the model using the response of both transgenic and wild-type plants to environmental parameters and address some of the common “What if?” questions posed about C4 plants. Hopefully, this approach will be valuable for integrating our current knowledge into a thesis of how C4 plants respond to their environment and the regulatory processes involved.


    Watch the video: Sulfur Cycle. Biogeochemical Cycles. ASRB NET. Ecology (July 2022).


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