Chapter 8 - Quiz #3

Be able to calculate the change in free energy of a reaction when given the formation energies of each species.

(Products - reactants)

. How does oxidative phosphorylation differ from substrate-level phosphorylation?

-They differ in the number of ATP molecules made in each process. OP = 2nd mechanism that makes more ATP than SLP. Electrons are transferred from oxidizing NADH and FADH2. It uses those subsequent electrons and protons to form an electrochemical gradient. It harvests the potential energy stored within an electrochemical gradient. It regenerates ATP from ADP and Pi SLP= a phosphate group is removed from an organic molecule and transferred to a readily available ADP to form ATP. SLP will only occur if there is a reaction that releases sufficient energy to allow the direct phosphorylation of ADP.

Describe how ATP synthase generates ATP

ATP synthase is the integral membrane protein that harnesses the energy of the proton motive force by allowing hydrogen ions to diffuse down their electrochemical gradient (from a high concentration of protons to a lower concentration of protons). The turning parts of the ATP synthase regenerates ATP from ADP and Pi.

. What is the general strategy used by microbes for the degradation of macromolecules?

All catabolic pathways for about all molecules eventually connect into glycolysis and the Krebs cycle. Several types of lipids can be microbially degraded. Triglycerides are degraded by extracellular lipases, releasing fatty acids from the glycerol backbone. Phospholipids are degraded by phospholipases, releasing fatty acids and the phosphorylated head group from the glycerol backbone. Lipases and phospholipases act as virulence factors for certain pathogenic microbes.

A beer-making microbiologist noticed that no matter how long the brewing process went, 3% alcohol was the maximum produced. Hypothesize what is causing this low level of alcohol in reference to the brewer's recipe and recommend how a higher alcohol yield could be achieved. Ethanol is toxic at high concentrations, but ignore this factor to focus on microbial metabolism.

Answers will vary but one explanation is a low substrate concentration resulted in low fermentation to produce ethanol. *Providing more carbohydrates such as glucose to the yeast in the recipe for the same growth period would increase fermentation activity and ethanol production. Another explanation is that there may be too much oxygen introduced during the brewing process, which would *result in the complete oxidation of glucose instead of fermentation to ethanol.* The brewer would need to take more precautions to exclude oxygen during brewing.

In an aquatic microbial community where a photoautotroph, chemoorganoheterotroph, and nitrogen fixing bacterium are present, predict an environmental perturbation that would cause only one to be outcompeted by the other two groups and explain how each group would respond.

Answers will vary but should highlight a unique feature of one of the groups such as: photoautotrophs are sensitive to photon (light) availability, chemoorganoheterotrophs require organic molecules for carbon, and nitrogen fixing bacteria use N2 gas. So if there is any environmental disturbance, where these microbes don't get sunlight, then only Photoautotrophs would be outcompeted by other two groups. This is because other two are not dependant on sunlight for their metabolic processes. We are considering three different types of metabolic pathways in the microbes. All three of them have different processes to obtain energy and nutrients. But chemoorganoheterotrophs and nitrogen fixing bacteria might not need sunlight to get nutrients or energy, as they depend on organic molecules for nutrients and energy. Though there are a few examples of photosynthetic nitrogen fixers, but remaining would survive without sunlight. In case of photoautotrophs, sunlight is essential for their survival.

. Why must autotrophic organisms also respire or ferment in addition to fixing CO2?

Autotrophs must respire or ferment to consume the organic molecules they form. They don't fix carbon for heterotrophs but use it for their own metabolic needs.

Define catabolism and anabolism.

Catabolism = chemical reactions that break down complex molecules into simpler ones Anabolism = chemical reactions that convert simpler molecules into more complex ones

The bacterium E. coli is capable of performing aerobic respiration, anaerobic respiration, and fermentation. When would it perform each process and why? How is ATP made in each case?

E. coli has all the genes necessary to perform each of the processes and is an example of a facultative bacteria. Meaning, that if the environmental conditions change to provide an appropriate inorganic final electron acceptor for respiration, it will switch to cellular respiration. It would do this because respiration allows for more ATP production per glucose molecule. Aerobic: when O2 is the final electron except/ glycolysis,krebs cycle, electron transport and chemiosmosis=ATP **Oxidative phosphorylation Anaerobic: when inorganic molecules are the final electron acceptor/glycolysis,krebs cycle, electron transport and chemiosmosis=ATP **Oxidative phosphorylation Fermentation: when organic molecules (usually pyruvate) is final electron acceptor/ glycolysis, fermentation=ATP **Substrate level phosphorylation

Explain the differences in both the carbon source and energy source for chemoorganotrophic, chemolithotrophic and phototrophic metabolism.

Energy source vs Carbon Source Chemoorganotrophic - chemical vs. organic Chemolithotrophic - chemical vs. inorganic Phototrophic - light vs. organic

Explain how enzymes lower the activation energy of a reaction.

Enzymes lower the activation energy by binding to the reactant molecules (such as substrates) and holding them in such a way as to speed up the reaction.

. How can human activity lead to eutrophication?

Eutrophication is typically the result of human activities, as it is the excess amounts of nitrogen, iron, and phosphorus in water. One example is the overuse of fertilizers so it runoffs into rivers and streams.

Describe the differences between fermentation and respiration.

Fermentation and cellular respiration differ in that fermentation does not require oxygen while cellular respiration does. Fermentation and cellular respiration are also different because water molecules are not produced during fermentation but are produced during cellular respiration. All fermentation reactions occur in the cell's cytoplasm but during cellular respiration, only glycolysis occurs in the cytoplasm. Lastly, fermentation produces a net gain of 2 ATPs while cellular respiration produces a net gain of 32 ATPs.

Be able to write an example of an oxidation-reduction reaction and be able to identify the electron donor and the electron acceptor.

H2 + S → H2S (H2 is the donor, S is the acceptor)

Why would an organism perform cyclic phosphorylation instead of noncyclic phosphorylation?

If a cell's need for ATP is significantly greater than its need for NADPH, it may bypass the production of reducing power through cyclic-phosphorylation

. Why are some microbes, including Streptococcusspp., unable to perform aerobic respiration, even in the presence of oxygen?

In aerobic respiration, the final electron acceptor at the end of the ETS is an osygen molecule that becomes reduced to water by the final ETS carrier. This electron carrier cytochrome oxidase differs from bacteria to bacteria. Streptococcusspp is unable to perform aerobic respiration because of one of 3 reasons The cell lacks genes that encode an appropriate cytochrome oxidase for ETS The cell lacks genes that encode enzymes to minimizing the damaging effects of oxygen radicals produced during aerobic respiration The cell lacks a sufficient amount of oxygen to carry out aerobic respiration ** Note - probably #2 or #3 because it is the Streptococcus genus so it is genetically determined.

How does the location of ATP synthase differ between prokaryotes and eukaryotes? Where do protons accumulate as a result of the ETS in each cell type?

In prokaryotic cells, protons flow from the outside of the cytoplasmic membrane into the cytoplasm. In eukaryotic cells, protons flow from the inner mitochondrial membrane space to the mitochondrial matrix.

. What is the relationship between chemiosmosis and the proton motive force?

In the ETS, there is an electrochemical gradient that is formed by the accumulation of protons on one side of the membrane compared to the other; this is known as the proton motive force. In Chemiosmosis, it is the process of the flow of hydrogens ions across the membrane through a channel in the membrane via the membrane-bound enzyme, ATP synthase.

Explain the role of NAD+/NADH in electron transfer.

NAD+ is reduced to NADH and is used as an electron carrier for glycolysis to produce ATP.

In considering the symbiotic relationship between Rhizobiumspecies and their plant hosts, what metabolic activity does each organism perform that benefits the other member of the pair

Nitrogen fixation Prokaryotes like Rhizobium bacteria fix nitrogen and live symbiotically in the root nodules of legumes. This provides the plant with needed organic nitrogen while the bacteria receives fixed carbon as sugar in exchange.

Do you think that β-oxidation can occur in an organism incapable of cellular respiration? Why or why not?

No because they wouldn't be able to get the full amount of ATP out of the Krebs cycle.

In cells, can an oxidation reaction happen in the absence of a reduction reaction? Explain.

No. Oxidation and reduction reactions occur in tandem in a reaction called a redox reaction. They occur in tandem because electrons can move from one molecule to another: one is losing electrons (oxidation). and the other is gaining electrons (reduction).

. How can fermentation be used to differentiate various types of microbes?

Specific types of microbes may be distinguished by their fermentation pathways and products -Microbes also be differentiated according to the substrates they are able to ferment

What is substrate-level phosphorylation? When does it occur during the breakdown of glucose to CO2?

Substrate-level phosphorylation is a process of forming ATP by the physical addition of a phosphate group to ADP can take place in the cytoplasm during glycolysis, inside the mitochondrial matrix during the Krebs cycle. This process occurs during the energy-pay off phase.

. Why is the Krebs cycle important in both catabolism and anabolism?

The Krebs cycle is important to both because its intermediate compounds can be used in synthesizing a wide variety of cellular molecules like: amino acids, fatty acids, chlorophylls and nucleotides/ making it both anabolic and catabolic. (SUCH AS ATP and NADH) Catabolism and anabolism is important in the Krebs cycle because it is a closed loop: the last step of the pathway regenerates the compound in the first step. Catabolism is the breaking down of molecules. Anabolism is the forming of molecules.

Describe (in general) how the proton motive force is generated and how this leads to the formation of ATP.

The Proton Motive Force is electrochemical gradient that is formed by the accumulation of protons on one side of the membrane compared to the other. This gradient emphasizes the capacity to perform work. This foce drive hydrogen ions back across the membrane through hydrogen ion travels provided by ATP synthases.

. How are the products of lipid and protein degradation connected to glucose metabolism pathways?

The degradation of lipids and proteins are catabolic pathways for breaking down molecules that will find a way into glycolysis and the Krebs cycle The resulting products of lipid catabolism/degradation are glycerol and fatty acids. and they can be further degraded. Glycerol is used in glycolysis and the fatty acids are catabolized in B-oxidation.

. What is the function of photosynthetic pigments in the light-harvesting complex?

The function is to harvest photons and transfer light energy to the reaction-center chlorophyll.

. What would be the consequences to a cell of having a mutation that knocks out coenzyme A synthesis?

The two-carbon, Acetyl, wouldn't be able to be transferred to the Krebs cycle which means that it would not be able to perform the Krebs cycle. Therefore, not form enough ATP. If the coenzyme A is not synthesized, the substrate will not be binded to the enzyme's active site and will not be transferred to the Kreb's cycle. It will result in an inactive enzyme.

What is the function of molecules like NAD+/NADH and FAD/FADH2in cells?

These compounds function as mobile electron carriers: they bind to and transport high energy electrons between compounds in pathways.

***Be able to use the Redox tower to discern relative electron donor/acceptor potential.

Top = strong donors = oxidizers ( Bottom = strong acceptors = reducers

Consider a pizza dough made by vigorously mixing to form gluten and evenly disperse the ingredients such as baker's yeast (Saccharomyces cerevisiae). Predict the metabolic differences yeast would have in a thinly flattened dough and in a spherical dough ball.

While making a spherical dough, there will be mixing of oxygen and thus initially there will be aerobic metabolism of Saccharomyces cerevisiae inside the dough ball as well as on the surface of the dough. But as the oxygen inside the dough ball gets depleted, the yeast will begin anaerobic fermentation especially in the centre but the surface will continue aerobic metabolism. On the other hand flattened dough will have higher surface area exposed to the oxygen to support the aerobic metabolism of the yeast. Thus there will be higher aerobic metabolism of yeast as compared to that in spherical dough.

Is life dependent on the carbon fixation that occurs during the light-independent reactions of photosynthesis? Explain.

Yes, because light independent reactions drive the energetically unfavorable process of "fixing" inorganic CO2 in an organic form, sugar