Ch13
Provide an overview of the process of alcoholic fermentation, including examples of microbes that carry out this process.
Alcoholic fermentation results in the production of ethanol and carbon dioxide by catabolizingpyruvate into carbon dioxide and acetaldehyde. The acetaldehyde is then reduced to ethanol, which leaves the cell as waste. Although some bacteria usethe process of alcoholic fermentation, the pathway is mostly employed by yeast.
Differentiate between exergonic and endergonic reactions and identify their relative ΔGo′ values
An exergonic reaction is a chemical reaction that releases energy, as energy flows into a less ordered state. The relative ΔGo′ of an exergonic reaction is negative as energy is being released. An endergonic reaction is one that uses energy in the reaction, and its relative ΔGo′ value is positive.
Describe the process of assimilative sulfate reductions.
Assimilative sulfate reduction reduces sulfate (SO4−) to hydrogen sulfide (H2S) so it can be incorporated into cellular molecules. An ATP molecule is linked to sulfate with the release of two phosphate groups to make adenosine 5′-phosphosulfate, which is then phosphorylated by a second ATP molecule to make phosphoadenosine 5′-phosphosulfate. This molecule is reduced by NADPH to sulfite and finally to hydrogen sulfide, which can be incorporated into acetylserine to make organic sulfur compounds, like cysteine..
Describe the role of ATP synthase.
Chemolithotrophs use inorganic chemicals as an electron source, as opposed to the organic molecules used by chemoorganotrophs. Unlike chemoorganotrophs, which have to oxidize the organic molecules to obtain electrons and then use other molecules to transport these electrons through the electron transport chain to generate ATP, the inorganic substances used by chemolithotrophs directly donate electrons to the electron transport system and produce ATP through the proton motive force generated. Additionally, since the electron source in chemolithotrophs does not go through glycolytic or TCA pathways, there is no ATP generation by substrate-level phosphorylation.
Describe chemotrophs, phototrophs, organotrophs, lithotrophs, heterotrophs, and autotrophs.
Chemotrophs and phototrophs differ in the source of energy they use to produce ATP. Chemotrophs use chemicals found in nature as their source of energy while phototrophs obtain their energy from light. Organotrophs and lithotrophs use different electron sources; organotrophsremove electrons from organic molecules whereas lithotrophs remove electrons from inorganic molecules. Heterotrophs and autotrophs use different carbon sources. Heterotrophs obtain carbon from organic molecules, while autotrophs use inorganic sources of carbon, such as carbon dioxide.
Describe how enzymes enhance reaction rates.
Enzymes enhance reaction rates by *lowering the activation energy* (the amount of energy required to break and rearrange bonds in a reaction) of the reaction. This typically occurs when the enzyme binds to the substrate and modifies its structure to make it easier for the reaction to go to completion.
Describe how fatty acids are synthesized.
Fatty acids are long carbon chains linked to an acyl group. The precursor molecules, acetyl-CoA and a carboxyl group, are linked together using ATP to generate the three-carbon molecule malonyl-CoA. The CoA is displaced from malonyl-CoA and an acetyl-CoA by acyl carrier protein (ACP) to make malonyl-ACP and acetyl-ACP. Two of the three carbon groups frommalonyl-ACP combine with the two-carbon acetyl-CoA to form a four-carbon chain linked to ACP. This fatty acid can undergo successive reactions with malonyl-ACP, adding two carbon groups each time, to produce longer acyl chains linked to ACP. The fatty acid chain can then be transferred from the ACP to other molecules, such as glycerol 3-phosphate, to make lipids.
Differentiate between fermentation and cellular respiration.
Fermentation and cellular respiration are pathways used in cells to reset the levels of NAD+ so that catabolic pathways such as glycolysis can continue, ensuring ATP is made. In order to obtain NAD+, NADH has to donate its electrons. In fermentation, NADH donates its electrons to an organic molecule, such as pyruvate, bypassing the TCA cycle and the electron transport system. Cellular respiration occurs when NADH donates its electrons to the electron transport system, producing energy and NAD+.
Explain how glycolysis, the TCA cycle, and the electron transport system are involved in ATP generation in a cell.
Glycolysis catabolizes glucose into two molecules of pyruvate, producing two ATP by substrate-level phosphorylation. The pyruvates are then completely catabolized by the TCA cycle reactions, producing two more ATP by substrate-level phosphorylation. Through glycolysis and the TCA cycle, electrons are transferred to carrier molecules, such as NAD, that subsequently pass the electrons to the electron transport chain in the membrane. Here, a proton gradient is formed and a further 34 ATP are produced through oxidative phosphorylation using ATP synthase.
How are large polymers, including polysaccharides, proteins, lipids, and nucleic acids, utilized as nutrients by microbial cells?
Large polymers like polysaccharides, proteins, lipids, and nucleic acids cannot be transported into microbial cells, as they are too large for membrane transport systems. In order to use these polymers as nutrient sources, cells secrete enzymes such as proteases and nucleases that break the polymers down into smaller molecules that can enter the cell and be processed.
13.1Distinguish between the terms metabolism, catabolism, and anabolism.
Metabolism defines all the biochemical reactions happening in a living cell. Catabolism and anabolism are examples of metabolic events. Catabolism involves the breakdown of larger molecules to produce energy, whereas anabolism is the synthesis of large molecules, using energy.
Differentiate between dissimilative reduction and assimilative reduction.
Molecules are used in the cell for a number of different purposes. While nitrate is a source of nitrogen for the biochemical processes of the cell, it can also be used to generate energy by being an acceptor in the electron transport chain. When molecules are reduced to produce building blocks for metabolic processes in the cell, the process is defined as assimilative reduction. However, when molecules are reduced in the electron transfer chain by accepting electrons to produce energy, and the reduced products are discarded as waste, the process is defined as dissimilative reduction.
Describe the flow of electrons in the electron transport system of organisms using cellular aerobic respiration.
NADH and FADH2 produced from glycolysis and the TCA cycle transfer electrons to electron acceptors in the electron transport chain. The cofactors of these acceptors are usually directly involved in the transfer of electrons. The first electron acceptor in the chain is NADH dehydrogenase. The flavin mononucleotide (FMN) cofactor of NADH dehydrogenase accepts electrons from NADH. FMN then transfers the electrons to the iron-sulfur centers of iron-sulfur proteins. NADH dehydrogenase and the iron-sulfur proteins together make up Complex I of the electron transport chain. Electrons from FADH2 are donated to Complex II, which is associated with succinate dehydrogenase. Electrons from both Complex I and II are passed to the coenzyme Q (CoQ), which transfers them to Complex III. Complex III is composed of cytochrome oxidoreductases, and the electrons transferred to Complex III pass through two cytochrome boxidoreductases, an iron-sulfur center, a cytochrome coxidoreductase and finally to a cytochrome c that is attached to the external surface of the membrane. The final cytochrome c of Complex III passes the electron to Complex IV, where a cytochrome aenzyme (also called cytochrome c oxidase) catalyzes the transfer of the electrons to oxygen, which is the final electron acceptor. On accepting the electrons, oxygen gets reduced to make water.
13.7Why are nitrogen and sulfur necessary for cells?
Nitrogen and sulfur are important components of many organic molecules required by cells, such as the amine group in amino acids and the sulfur group in iron-sulfur centers which are required for the electron transfer system.
What is nitrogen fixation, and what role does nitrogenase play in the process?
Nitrogen fixation is the process of converting atmospheric nitrogen (N2) into nitrogen compounds that can be used by the cell. The enzyme nitrogenase catalyzes the conversion of N2 to ammonia, consuming ATP in the process.
Distinguish differences of oxidation and reduction.
Reduction and oxidation are chemical processes that involve the transfer of electrons between molecules. Reduction is the process of gaining an electron by a molecule, which is then called "reduced." Oxidation is the process of losing an electron by a molecule to become oxidized.
13.4 What are two main results or benefits of respiration?
Respiration, like fermentation, results in NADH and other electron carrier molecules being converted back to their oxidized forms (NAD+), which will be used for catabolic pathways such as glycolysis. In addition, respiration also results in the further oxidation of pyruvate, which produces large amounts of ATP.
13.2 Compare and contrast ATP generation by substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation.
Substrate level phosphorylation, oxidative phosphorylation and photophosphorylation all rely on highly exergonic reactions to provide the energy for ATP production via the phosphorylation of ADP. Substrate-level phosphorylation harnesses the high energy in the phosphate group of a phosphorylated molecule to make ATP by a direct chemical reaction. Oxidative phosphorylation couples ATP production to the flow of protons across a membrane. The enzyme ATP synthase catalyzes the phosphorylation of ADP by harnessing the energy of proton movement back across the membrane. The energy needed to form the proton gradient is generated by the transfer of electronsthrough a set ofmembrane carrier molecules. The electrons originate from the oxidation of chemical substrates taken up by the cell. Photophosphorylation also relies on a proton gradient and ATP synthase to generate ATP, but the electron transfer begins with absorption oflight energy, rather than oxidation of chemical substrates.
Differentiate between these two microbial pathways: GS-GOGAT pathway and GDH pathway
The GS-GOGAT and GDH pathways are commonly used by microbes to incorporate ammonium into glutamate or glutamine. The GS-GOGAT relies on two enzymes: glutamine synthetase and glutamate synthase for incorporation of ammonia, and consumes NADPH and ATP in the process. In contrast, the GDH pathway catalyzes the addition of ammonium to α-ketoglutarate to make glutamate, using only NADPH in the process. Although most microbes use both pathways, the GS-GOGAT pathway has a greater affinity for ammonium than GDH, and so it is preferentially used at low ammonium concentrations.
Describe how the following are involved in the TCA cycle: pyruvate, CO2, NADH, FADH2, and ATP.
The TCA cycle allows pyruvate produced by glycolysis to be further oxidized, and therefore produce more ATP and electron carriers that can donate electrons to the electron transport chain. Pyruvate is oxidized to a two-carbon acetyl group, to which coenzyme A (CoA) is linked. This acetyl-CoA enters the TCA and gets further oxidized and decarboxylated to finally produce CO2. The oxidation of acetyl-CoA is facilitated by NAD+ and FADH+, oxidized electron carriers that take electrons from the carbon intermediates in the TCA and become reduced to NADH and FADH2. The large amounts of NADH and FADH2 produced in the TCA cycle will go on to supply electrons to the electron transport chain. The TCA cycle also includes one substrate level phosphorylation step, when the loss of the CoA factor from succinyl-CoA produces energy to convert GDP to GTP. GTP, which is a molecule related to ATP, is then converted to ATP. Thus, the TCA uses pyruvate to produce CO2, high levels of NADH and FADH2 and, by substrate level phosphorylation, ATP.
How are amino acids typically broken down for use in the TCA cycle?
The amine group is removed from the amino acid (deamination), to produce molecules such as pyruvate that can enter the TCA cycle. However, this is only possible for amino acids with carbon backbones similar to pyruvate or one of the other molecules used in the TCA cycle.
What is the proton motive force, and what is it used for in a cell?
The proton motive force is the difference in potential energy across the cell membrane due to the pumping of protons out of the membrane during the electron transport process. This causes a proton concentration differential and a charge differential, which seeks to become equalized across the membrane. This "pushing" force allows protons to flow down the differential back across the membrane, through the enzyme ATP synthase, thus producing ATP or mechanical work, such as rotations of the flagella.
13.3Compare and contrast these three glycolytic pathways: Embden-Meyerhof-Parnas (EMP) pathway, Entner-Doudoroff pathway, and pentose phosphate pathway.
The three glycolytic pathways catalyze the breakdown of glucose to produce organic molecules such as pyruvate, as well as NADH and NADPH needed for biosynthetic pathways in cells. In all three pathways, glucose is initially phosphorylated to glucose6-phosphate, using ATP. The EMP pathway converts glucose to pyruvate through successive oxidation steps using electrons supplied by NADH. Thepathway results in two molecules of ATP formed by substrate-level phosphorylation for each molecule of glucose broken down. The Entner-Doudoroffpathway oxidizes the glucose6-phosphate intermediate produced in the EMP pathway, producing pyruvate and glyceraldehyde3-phosphate. The glyceraldehyde3-phosphate can be used in the EMP to produce more pyruvate and ATP. However, only one molecule of ATP is produced per molecule of glucose. The oxidizing agent in the Entner-Doudoroffpathway is NADP+ rather than NAD+ used in the EMP pathway, and so this pathway is useful for making NADPH, which is a common electron donor for various biosynthetic reactions. The Entner-Doudoroff pathway is also used for the breakdown of other carbohydrates that contain aldehyde groups that can't be catabolized by the EMP pathway. The pentose phosphate pathway works in conjunction with the EMP pathway. Like the Entner-Doudoroff pathway, it primarily produces NADPH. It also produces a number of five carbon intermediate products, which are useful in biosynthetic processes.
What is the role of ATP in a cell?
ATP supplies the cell with chemical energy that helps drive the endergonic biochemical reactions in the cell. It has two high-energy phosphoanhydride bonds that can be broken to release energy.
What is anaerobic respiration, and what can serve as terminal electron acceptors in this process?
Anaerobic respiration is the transfer of electrons using electron acceptors that are not oxygen. A number of inorganic molecules such as nitrate, nitrite, sulfate, sulfur, carbon dioxide, iron, and organic molecules such asfumarate can be used as terminal electron acceptors in the absence of oxygen.
Enzymes must obey the laws of thermodynamics. Describe the laws.
The first law of thermodynamics states that energy is conserved, which means it can never be created or destroyed, only converted from one form to another. The second law states that energy flows from a more ordered state to disorder (or entropy), so long as no energy enters or leaves the system.
What nitrogenous bases must cells be able to synthesize and why?
The five main nitrogenous bases used in cells are adenine, guanine, cytosine, thymine, and uracil. These are key components of nucleotides, molecules that are used to build DNA and RNA. The nucleotides ATP and GTP are also sources of chemical energy in cells.
13.8Cellular macromolecules are synthesized from a pool of precursors in the cell. Describe the sources of these precursors.
The precursor molecules required for production of amino acids, nucleotides, and fatty acids, and are typically obtained from catabolic pathways that produce small carbon molecules as intermediates. These include products from glycolytic pathways and the TCA cycle..
Describe the mathematical relationship between ΔEo′ and ΔGo′.
ΔE0′ is inversely related to free energy ΔGo′, such that a higher ΔE0′ results in a more negative ΔGo′ and therefore more free energy. The amount of free energy ΔGo′ for a particular ΔE0′ is determined by the number of electrons transferred and Faraday's constant.
What are cofactors and coenzymes and what are their roles in enzymatic reactions?
Cofactors are small chemicals that assist enzymes in their reactions by transferring functional groups. Coenzymes are organic cofactors.
Describe an overview of lactic acid fermentation, and provide examples of lactic acid fermenting bacteria.
Lactic acid fermentation occurs when the electrons donated to pyruvate by NADH are used by the enzyme lactate dehydrogenase to produce lactic acid, ATP, and sometimes ethanol. Lactic acid bacteria such as Streptococcus, Lactobacillus, and Bifidobacterium, use the EMP pathway to produce pyruvate, which is directly reducedto lactic acid.. The lactic acid is then lost from the cell as waste. Some lactic acid bacteria, such as Leuconostoc, produce a mix of lactic acid and ethanol. They use a more complicated pathway that is similar to the pentose phosphate pathway to generate ethanol and lactic acid from various five-carbon products.
What is the β-oxidation pathway, and how does it yield energy?
The β-oxidation pathway is the catabolic pathway microbes use to degrade fatty acids and release energy. Fatty acid chains, which are highly reduced, are obtained from the breakdown of phospholipids or triglycerides. They are oxidized by FADH and NAD+, producing large amounts of FADH2 and NADH. In addition, the smaller carbon products of the β-oxidation pathway can enter the TCA cycle, producing even more FADH2 and NADH. These carriers can donate their electrons to the electron transport chain, thus producing a large amount of ATP.
13.5Describe how sugars other than glucose are metabolized.
When microbes have to digest other simple sugars like fructose or more complex sugars, like lactose, they use enzymes that convert the sugar into glucose or one of the intermediate molecules of the glycolytic pathway, so they can be metabolized by glycolysis.