Chapter 6 Microbial Metabolism: Fueling cell growth

figure 6.16 pg 154, How many ATPs-total and net- are produced from breaking down one molecule of glucose in glycolysis?

4 ATP total but two are used in the investment phase.

figure 6.13 pg 150, why would an enzyme no longer function once it denature?

An enzyme no longer functions once it denatures because its chemical structure has been altered. The proteins denature.

figure 6.21 pg 161, Why is it difficult to calculate the actual maximum ATP yield of respiration in a prokaryotic cell?

It is difficult to calculate because we are only using theoretical numbers. The maximum energy yield assumes that for every pair of electrons donated to the electron transport chain, 3 ATP are synthesized; and for every pair of electrons donated by FADH2, 2 ATP are synthesized.

figure 6.2 pg140, what is energy?

It is the capacity to do work and it can exist as kinetic(motion) or potential(stored)

figure 6.22 pg 162, Why is it important for cells to have a mechanism to oxidize NADH?

NADH must be oxidized in order to regenerate NAD+. NAD+ is needed to accept electrons in the following of glycolysis, without it glycolysis would stop.

figure 6.7 pg 143, if Mn^2+ is used as anergy source, which two molecules on the chart in (a) could serve as terminal electron acceptors?

Nitrate

Distinguish between respiration and fermentation.

Respiration is when oxygen is used while fermentation is the alternative when oxygen is not an option.

Why does fermentation supply less energy than cellular respiration?

Fermentation only goes through glycolysis which only produces 2 ATP while in cellular respiration it goes through the ETC and it uses O2 as the electron acceptor

figure 6.19 pg 158, Which would be expected to generate more ATP per electron carried- NADH or FADH2?

NADH is expected to generate more ATP then FADH2 because NADH generates about 3 ATP each and FADH about 2 ATP each

Explain the function of a coenzyme.

A coenzymes are organic cofactors that functions as loosely carriers of molecules or electrons. They transfer substance from one compound to another. Coenzymes are recycled as they function and the same coenzyme can assist different enzymes.

figure 6.29 pg 171, Alpha-ketoglutarate tis produced in which central metabolic pathway?

In the TCA cycle

Describe allosteric regulation.

Enzymes that can be controlled are allosteric with an allosteric site and an active site. Allosteric regulation functions to regulate enzyme activity. If too much of a certain product is produced the pathway will be shut down until it is needed again.

figure 6.12 pg 149, What is the function of the coenzyme FAD?

FAD functions as a coenzyme which functions as loosely bound carriers of molecules or electrons.

Why is it important for a cell that allosteric inhibition be reversible?

If allosteric inhibition were not reversible the enzyme occupied by the inhibitor will change the shape of the enzyme, making it nonfunctional, so the inhibitor will poison the enzyme.

Who is the final electron acceptor for eukaryotic and Prokaryotic?

prokaryotic- aerobic or O2 and if the cell has the enzymes it can also use sulfate and nitrate as the electron acceptor. Eukaryotic- O2

Explain why sulfa drugs prevent bacterial growth without harming the human host.

Humans cannot synthesize folate, therefore, sulfa will have no effect on them. Humans must consume folate as folic acid in foods instead.

figure 6.14 pg 151, why would a cell need to regulate enzyme activity?

If a certain product is being produced and there is too much of it allosteric regulation will stop the production of this product and can begin again when it is needed. In the same way if there is not enough of a certain product, more of this product will be produced until it is no longer needed.

Compare and contrast competitive enzyme inhibition and non-competitive enzyme inhibition.

The site to which it binds to determines the wether it functions as a competitive or noncompetitive inhibitor. Competitive inhibition- the inhibitor competes with the substrate for the active site. Example includes the sulfa drugs. These inhibit an enzyme in the pathway bacteria use to synthesize the vitamin folate. Sulfa drugs have a similar structure as paraaminobenzoic acid(PABA), an intermediate in the bacterial pathway of folate synthesis. Because of this, they fit into the site of the enzyme where it normally uses PABA as a substrate. By doing so, they prevent the enzyme from binding PABA. One the sulfa is removed the enzyme functions properly with PABA. Noncompetitive inhibition- the inhibitor binds to a site other than the active site changing the shape of the enzyme so that the substrate can no longer bind. Allosteric inhibitors are noncompetitive inhibitors that have reversible reaction but all other noncompetitive inhibitor reactions are permanent. They leave the enzyme nonfunctional.

Describe the roles of the three central metabolic pathways.

The three central metabolic pathways are glycolysis, pentose phosphate pathway, and Tricarboxylic acid cycle. Pentose Phosphate:breaks down glucose, Glycolisis: converts 1 glucose to 2 pyruvate; yields Tricarboxylic acid cycle: CO2 is removed from pyruvate, electrons reduce NAD+ to N

Describe 3 central metabolic pathways. key outcomes

metabolic pathways contribute to ATP production. Glycolysis: converts glucose to pyruvate. Glycolysis has two phases: the investment phase and the pay-off phase. The investment phase uses energy(2 ATP molecules) to transfer a high energy phosphate group to the 6-carbon sugar. Then the 6-carbon sugar is split into two 3-carbon molecules each with a phosphate molecule. The pay-off phase oxidizes and rearranges the 3-carbon molecule, this generates 1 NADH and 2 ATP and a pyruvate is formed. The steps of this phase occur twice for each glucose molecule because in the investment phase the 6-carbon sugar was split into two 3-carbon molecules. RESULT: 1 glucose= 2NADH, 2 pyruvate, and 4 ATP(minus 2 that were used in the investment phase), six different precursor metabolites Pentose Phosphate Pathway: also used to break down glucose. It is important in biosynthesis of precursor metabolites: ribose-5-phosphate and erythrose-4-phosphate. This power generated reducing power as NADPH and the amount varies. Tricarboxylic Acid (TCA) cycle: it completes the oxidation of glucose. This cycle incorporates the acetyl groups from transition step, releasing two molecules of CO2 it is repeated twice to incorporate two acetyl groups. RESULT: 2 ATP by substrate level phosphorylation, 6 NADH+6H+, 2FADH2, and two different precursor metabolites

List two environmental factors that influence enzyme activity.

temperature- a 10 degree celsius rise will double the enzymatic reactions; until optimal activity is reached. However, if the temperature gets too high the enzyme will denature and lose function. PH and salt concentrations also influence enzyme activity.

figure 6.30 pg 171, The synthesis of aromatic amino acids requires precursor metabolites made in which central metabolic pathway?

Glycolysis and pentose phosphate pathway

What would happen if ribulose-1, 5-bisphophate (RuBP) where depleted in a cell?

In order for the calvin cycle to continue, RuBP must be continuously regenerated form G3P.

Which central metabolic pathway generates the the most reducing power?

The TCA cycle produces more reducing power with a 22 ATP gain from its reducing power while glycolysis only produces 6 ATP from reducing power and Pentose phosphate group varies in the number of reducing power it produces.

With a branched biochemical pathway, why would it be important for a cell to shut down the first step as well as branching steps?

The product from the step before the branch would accumulate.

Why is there no complex 3 in the electron transport chain in the prokaryotic cell?

because there is no mitochondrion releasing

What three general products of the central metabolic pathways does a cell require to carry out biosynthesis?

precursor metabolites, enzymes, and carrier proteins

figure 6.9 pg 145, what is the role of precursor metabolites in this process?

they are further oxidized to release energy.

figure 6.11 pg 149, Why are enzymes so specific with respect to the reaction they catalyze?

Enzymes are so specific because of the shape of the enzymes. Specific chemical interactions must induce fit as well.

In bacteria, what is the role of the molecule that serves as a source of vitamin K for humans?

Menaquinone serves as a source of vitamin K for humans. The role of this lipid soluble organic molecule is to transfer electrons between different protein complexes in the membrane.

figure 6.10 pg 146, what is the terminal electron acceptor in aerobic respiration?

O2

Describe the energy sources used by photosynthetic organisms and chemoorganoheterotrophs.

Photosynthetic organisms harvest the energy of the sunlight. Chemoorganoheterotrophs receive energy by degrading organic compounds and that some of that same energy is used to make other organic compounds. Chemoorganotrophs depend on the metabolic activities of photosynthetic organisms.

What is the role of rubisco?

Rubisco is an enzyme that joins carbon dioxide to RuBP or ribose-1, 5-bisphosphate

Describe the active site of an enzyme, and explain how it relates to the enzyme-substrate complex.

The active site of an enzyme is where a substrate binds. The binding of the substrate to the active site causes the shape of the enzyme to change slightly. This mutual interaction or induced fit results in the temporary intermediate called enzyme-substrate complex.

If there is not enough oxygen, what does the cell do when respiration is not an option?

The cell uses fermentation. Fermentation is used in anaerobic respiration. Also only 2 ATP is produced during fermentation.

How would cellulose-degrading bacteria in the rumen of a cow benefit the animal?

The cellulose-degrading bacteria allows the cow to eat grass as energy. Cellulase would help break down cellulose found in grass.

Compare and contrast the electron transport chains of eukaryotes and prokaryotes.

The eukaryotes ETC takes place in the inner mitochondrial membrane and it consists of 4 complexes. The electron carriers in eukaryotic ETC is ubiquinone and cytochrome c. The Prokaryotic ETC takes place in the cytoplasmic membrane and it only consists of three protein complexes called NADH dehydrogenase, succinate dehydrogenase, and ubiquinol oxidase. The ETC can be aerobic(O2 is final electron acceptor) or anaerobic( O2 cannot be used so nitrate or sulfate as terminal electron acceptor) in prokaryotes while in eukaryotes it is always aerobic(O2 terminal electron acceptor).

Explain the process used to degrade fatty acids.

The glycerol component is vonverted to the precursor metabolite dihydroxyacetone phosphate, which enters glycolysis. The fatty acid group is degraded by a series of reactions called B-oxidation, which are redox reactions. Each reaction transfers a 2-carbon unit from the end of the fatty acid to coenzyme A. forming acetyl-CoA, which enters the TCA cycle. Each B-oxidation generates 1 NADH+H+ and 1 FADH2

How do the methyl-red and Voges-Proskauer tests differentiate between certain members of the enterobacteriaceae?

The methyl-red tests serves to detect the low-pH resulting form acidic end products, distinguishing members that use this pathway. The Voges-Proskauer test detects acetoin, distinguishing members that use that pathway.

Why is the overall ATP yield in aerobic respiration only a theoretical number?

The overall ATP yield in aerobic respiration is only a theoretical number because it is not a straightforward comparison and the numbers were gathered from an experiment in rat mitochondria which only gave an approximate number.

Describe how a proton motive force is used to synthesize ATP and how the ATP yield of aerobic respiration is calculated.

The proton motive force is used to synthesize ATP by allowing the protons that were let out of the membrane during ETC back into the bacterial cell, slowly. The energy released is used to add a phosphate group to ADP. For every three protons one molecule of ATP is formed. ATP yield during aerobic respiration is calculated by adding up all the ATP produced from each metabolic pathway. Substrate-level phosphorylation produces 4 ATP total. Oxidative phosphorylation produced 6 ATP from reducing power in glycolysis, 6 ATP from reducing power in transition step, and 22 ATP from the reducing power in TCA cycle. For a total of 38 ATP gain.

Describe the components of metabolic pathways(enzymes, ATP, chemical energy sources and terminal electron receptors , and electron carriers) and the role of precursor metabolites.

The role of enzymes in metabolic pathways is to speed up the conversion of one substance, the substrate, to another, the product. Enzymes lower the activation energy and by doing this it speeds up the reaction. The role of ATP is to provides immediate free energy. The chemical energy source and the terminal electron acceptor help release energy. The Precursor metabolites are intermediate products produced during catabolism. They can later be used in anabolism or continues in catabolism.

Figure 6.1 pg 139, What subunits make up proteins? Which make up nucleic acids?

amino acids make up proteins. Nucleic acids are made up of a chain of nucleotides(phosphate group, sugar group, and a necleobase)

figure 6.8 pg 143, Why is hydrogenation a reduction?

cells remove electrons form the cell through a series or oxidation-reduction reactions. The removal of electrons from its biological molecule is often followed by the protons (H+). Hydrogenation is the addition of a hydrogen atom and this reaction is called a reduction.

Why are the central metabolic pathways called amphibolic?

in order to reflect their dual role. The pathways are catabolic, but the precursor metabolites and reducing power they generate can also be diverted for use in biosynthesis or anabolism.

Why would an oxidase also be called a reductase?

it is a Redox reaction. what you reduce an be oxidized and what is oxidized can be reduced.

figure 6.18 pg 157, O2 is serving as a terminal electron acceptor in this diagram; is it being oxidized, or reduced?

it is being reduced because it is receiving electrons.

figure 6.5 pg 142, what is activation energy?

it is the energy it takes to start a reaction.

figure 6.6 pg 142, what characteristic of the structure of ATP makes its phosphate bonds "high energy"?

The Adenosine diphosphate or ADP

figure 6.17 pg 155, Which generates more reducing power- glycolysis or the TCA cycle?

The TCA cycle produces more reducing power. Glycolysis podruces 2NADH while TCA cycle produces 6NADH+2H+ and 2FADH2

Compare and contrast cofactors and coenzymes.

cofactors are non-protein components. Coenzymes are organic cofactors that function as loosely bound carriers of molecules or electrons. Most coenzymes derive from certain B vitamins. Coenzymes are recycled as they function and the same coenzyme can assist different enzymes.

figure 6.15 pg 152, will the enzyme function if sulfa is removed?

competitive inhibitors leave the enzyme back to its original shape since it is very similar to the shape of its corresponding substrate. Therefore, once the sulfa is removed the PABA can bind again to the enzyme.

Why would a cell ferment rather than respire?

fermentation is only used when oxygen is not present, to respire means to be able to breathe. Fermentation is only for those organisms that cannot respire either because they don't have a suitable inorganic terminal electron acceptor or they lack a ETC.

Describe the role of fermentation and the importance of the common end products.

fermentation is used when an organism is missing a suitable terminal electron acceptor or lacks an ECT. The common end products are: (1) Lactic acid- when pyruvate acts as the final electron acceptor (2) Ethanol- Pathway that first removes CO2 from pyruvate, generating acetaldehyde, which then serves as the final electron acceptor. (3) Butyric acid- complex multistep pathway used by Clostridium species, which are obligate anaerobes. (4) Propionic acid- multistep pathway that first adds CO2 to pyruvate, generating a compound that can then be used as terminal electron acceptor. (5) Mixed acids- multistep branching pathway, generating a variety of fermentation products. The primary significance of this pathway is that it serves to differentiate members of the family enterobacteriaceae. (6) 2,3- Butanediol- multistep pathway that uses two molecules of pyruvate to generate acetone and two molecules of CO2. Acetoin is then used as terminal electron acceptor. It also helps differentiate members of the family Enterobacteria.

Explain why glutamate synthesis particularly important for a cell?

it is particularly important because it provides a mechanism for bacteria to incorporate nitrogen into organic material. Many bacteria use ammonium (NH4+) as their source of nitrogen; it primarily through glutamate that they do this.

figure 6.24 pg 164, which is more common- an organism that produces amylase or one that produces cellulase?

An oranism that produces amylase is more common than an organism that produces cellulase.

Compare and contrast catabolism and anabolism.

Both in catabolism and Anabolism is a set of chemical reactions. However, in catabolism the chemical reactions are used to degrade compounds that will release energy that will be used by the cell to make ATP. On the other hand, anabolism uses the set of chemical reactions to assemble and synthesize subunits of macromolecules. Catabolism helps produce ATP but anabolism uses the ATP produced in catabolism to assemble and synthesize the subunits of macromolecules.

Explain catabolism and anabolism(biosynthesis).

Catabolism is the process of a set of chemical reactions that degrade compounds releasing energy that is later used by the cell to make ATP- the energy currency of the cell. Anabolism or biosynthesis is a set of chemical reactions that cells use to synthesize and assemble subunits of macromolecules, it uses ATP for energy.

What is cellular respiration?

Cellular respiration uses electron transport chain to convert reducing power to proton motive force which an be used by ATP synthesis to produce ATP.

Describe cellular respiration and fermentation. Key outcomes

Cellular respiration uses the reducing power from glycolysis, the transition step, and TCA cycle to synthesize ATP. The Electron Transport Chain is embedded with electron carriers; it accepts electrons from NADH and FADH2 and passes those electrons from one carrier to the next. As the electrons are being passed along the transport chain it release protons across the membrane. At the end of the ETC the final complex passes the electrons to the terminal electron acceptor letting in the protons outside the membrane slowly which creates the proton motive force used by ATP synthase to make ATP. Fermentation is used when respiration is not an option either because they lack ETC or a suitable inorganic compound is not available. E.coli can use aerobic, anaerobic, and fermentation. Streptococcus pneumoniae only has the option of fermentation because it has no ETC. The key products of fermentation is lactic acid when pyruvate itself acts as the terminal electron acceptor, ethanol is produced when CO2 is removed from pyruvate, generating acetaldehyde, that will then serve as the terminal electron acceptor. Butyric acid is another end product which is produced by a complex multistep pathway by Clostridium species, which are obligate anaerobes. Proponic acid is generated in a multistep process that adds CO2 to pyruvate, generating a compound that is then used as terminal electron acceptor. Mixed acids are produced in a multistep pathway generating a different fermentation products. 2,3-Butanediol is a multistep pathway that uses two molecules of pyruvate to generate acetoin and two molecules of CO2 and acetoin will be used as the terminal electron acceptor.

Compare enzymatic inhibitions.

Competitive inhibition the inhibitor competes with the substrate for the active site while in noncompetitive inhibition occurs when the inhibitor binds to a site other than the active site. Noncompetitive inhibitors have a permanent effect on the enzyme changing its shape so that the substrate can no longer bind to the active site. In competitive inhibition, once the inhibitor is removed the enzyme can function properly with the substrate.

figure 6.20 pg 159, Succinate dehydrogenase is equivalent to which component of the mitochondrial electron transport chain?

Complex II

Fermentation is used as a means of preserving foods. Why would it slow spoilage?

Fermentation provides a oxygen free environment which will rapidly kill aerobic microbes.

Why do cells secrete hydrolytic enzymes?

In order to break down sugar, amino acid, and lipid subunits, cells synthesize hydrolytic enzymes, which break down bonds by adding water.

Explain how the electron transport chain contribute to generate ATP.

In order to generate ATP there needs to be an electro chemical gradient or proton motive force to drive the process. This is where ETC cooperates, during the ETC electrons are passed on through complexes. Every electron passed releases protons outside the membrane. Once the electrons reach the terminal electron acceptor, protons are brought back into the membrane slowly which results in the proton motive force that will be used by ATP synthase to produce ATP. The ATP will later be used in active transport or rotation of flagella.

Describe the three stages of the Calvin cycle.

In stage one carbon dioxide is joined to a 5-carbon compound, ribulose-1, and 5-bisphosphate by rubisco. The resulting compound hydrolyzes to produce two molecules of a 3-carbon compound, 3-phosphoglycerate. Stage two reducing power and ATP convert 3PG to G3P, which is also a precursor metabolite. G3P can have a variety of fates such as being used in photosynthesis, oxidized to make other precursor compounds, or converted to a six carbon sugar. RuBP must be regenerated from G3P in order for the cycle to continue. Stage three involves RuBP being regenerated so that the calvin cycle can continue.

How does the "investment phase" of glycolysis effect the net yield of ATP in that pathway?

In the investment phase 2 ATP are used for the transfer of a high energy phosphate group to a 6-carbon sugar. Therefore, the 2ATP from the investment phase is subtracted from the total ATP 4.

Describe the synthesis of lipids, amino acids, and nucleotides.

Lipid Synthesis- To produce fatty acids, the acetyl group from transition step is transferred to a carrier protein. The carrier protein holds the fatty acid chain as a 2-carbon atom and once it is long enough, it is released. The glycerol component is synthesized by dihydroxyacetone phosphate, which is generated in glycolysis. Amino acid Synthesis- Amino acids are grouped into structurally related families that share common pathways of biosynthesis. Glutamate provides a mechanism for bacteria to incorporate nitrogen into organic material. It is synthesized in one step, adding ammonia to the precursor metabolite a-ketoglutarate, produced in the TCA cycle. Synthesis of aromatic amino acids begins by joining to precursor metabolites- phosphoenolpyruvate(3-carbon) and erythrose-4-phophate- to form a 7-carbon compound. The 7-carbon compound is modified through a series of steps until they reach a brach point. One pathway they can take is to continue synthesis where tryptophan is produced which leads to the synthesis of other amino acids. In another direction, another branch point is reached and tyrosine or phenylalanine is produced leading to their synthesis. Nucleotide Synthesis- the starting compound for the synthesis of purine is ribose-5-phosphate a precursor metabolite. Then atoms from other sources are added to form the purine ring, which then can be converted to a purine nucleotide. To synthesize pyrimidine nucleotides the pyrimidine ring is made first and then is attached to the ribose-5-phosphate.

figure 6.23 pg163, How can end products of fermentation help identify a bacterium?

Mixed acids serves to differentiate certain members of the Enterobacteriaceae. The methyl-red test detects low pH resulting from the acid end products, distinguishing between those that use this pathway such as E.coli and those that don't such as Klebsiella and Enterobacter. 2.3-Butanediol serves to distinguish the members of the Enterobacteriaceae family. The Voges-Proskauer test detects acetoin distinguishing those that use this pathway from those that do not.

How does the fate of electrons carried by NADPH differ from the fate of electrons carried by NADH?

NADH transfer their electrons to the ETC where there energy will be used to generate a proton motive force that will drive the process to produce ATP. However, NADPH is used to reduce compounds during biosynthetic reactions.

figure 6.3 pg 140, How do chemoorganotrophs require the activities of photosynthetic organisms?

Photosynthetic organisms produce organic compounds that can be used by chemoorganotrophs to obtain energy.

Briefly describe how polysaccharides and disaccharides, lipids, and proteins are degraded and used by a cell.

Polysaccharides such as starch are degraded by the enzyme amylases while cellulose is degrade by the enzyme cellulases, which is produced by very few organisms. Disaccharides such as sucrose, lactose, and maltose is hydrolyzed by specific disaccharides. Fats are hydrolyzed by lipases. The glycerol is converted to precursor metabolite dihydroxyacetone phosphate, which will enter glycolysis. The fatty acid group is degraded by B-oxidation or a redox reaction. Proteins are hydrolyzed by proteases, which break peptide bonds between amino acid subunits. Remainig carbon skeletons are are converted into precursor metabolites while the amino group of the resulting amino acids is removed by deamination.

Describe the components of the electron transport chain and how they generate a proton motive force.

The Electron Transport Chain is composed of carriers grouped into several large protein complexes which are used as proton pumps or move electrons from one complex to the next. There are three notable electron carriers: (1) Quinones- lipid soluble organic molecules that move freely in the membrane. Can transfer electrons between different protein complexes in the membrane. The most common type is ubiquinone. (2) Cytochromes- are proteins that contain heme. Many cytochromes exist and are labeled by letters, for example, cytochrome c. (3) Flavoprotein- proteins to which a flavin is attached.