Biology 101

What is a reaction center (in any photosystem) made of?

A reaction center in any photosystem is made up of a complex of proteins and pigments that includes a primary electron acceptor and a specialized chlorophyll molecule called the reaction center chlorophyll. The reaction center is the site where the initial step of photosynthesis occurs, which involves the transfer of energy from the excited pigment molecules to the reaction center chlorophyll, leading to the production of high-energy electrons that are used to drive the photosynthetic electron transport chain.

Under "normal" conditions the ratio of carboxylation:oxygenation reactions carried out by Rubisco in typical C3 plants is 3:1. How might a rise in the CO2 concentration in the atmosphere affect this ratio? Explain.

A rise in the CO2 concentration in the atmosphere is likely to increase the ratio of carboxylation:oxygenation reactions carried out by Rubisco in typical C3 plants. This is because higher atmospheric CO2 concentration would increase the CO2 concentration in the chloroplasts of plants, making it easier for Rubisco to bind to CO2 and perform carboxylation. As a result, the rate of carboxylation reactions would increase, while the rate of oxygenation reactions (which is a competing reaction with carboxylation) would decrease, leading to a higher ratio of carboxylation:oxygenation reactions. This phenomenon is known as CO2 fertilization effect, which can increase the efficiency of photosynthesis in C3 plants.

According to Sutherland, when a cell receives an external signal, it goes through three processes. List them.

According to Earl Sutherland's theory of signal transduction, when a cell receives an external signal, it goes through three processes: reception, transduction, and response. Reception is the detection of the signal by the cell's receptor molecules. Transduction involves the conversion of the signal into a form that can be recognized and acted upon by the cell. Response is the cellular reaction to the signal, which can include changes in gene expression, metabolism, or cell behavior.

What is activation energy? What is the usual source for this energy for a reaction?

Activation energy is the minimum amount of energy required to initiate or start a chemical reaction. It is the energy required to overcome the potential energy barrier between the reactants and the transition state of the reaction. Thermal energy or heat is the usual source of activation energy for a reaction, as it increases the kinetic energy and collisions between reactant molecules. Other sources of activation energy include light, electricity, and catalysts.

Glycoaldehyde inhibits the enzyme phosphoribulokinase. This enzyme catalyzes the ATPdependent conversion of Ribulose-5-P (Ru-5P) to Ribulose-1,5-bisphosphate (RuBP). What will be the consequence of adding this inhibitor to chloroplasts of a plant?

Adding glycoaldehyde, an inhibitor of phosphoribulokinase, to chloroplasts of a plant will result in a decrease in the production of RuBP from Ru-5P, ultimately leading to a decrease in the rate of carbon fixation via the PCR cycle. As a result, the plant may experience a reduction in growth and yield, as well as a decrease in the availability of energy-rich compounds like glucose and sucrose. Additionally, the plant may have to rely on alternative metabolic pathways to sustain its energy needs.

Describe how allosteric inhibitors and activators carry out their functions.

Allosteric regulation refers to the process by which a molecule binds to an enzyme at a site distinct from the active site, altering the enzyme's conformation and modulating its activity. Allosteric inhibitors bind to the enzyme and decrease its activity, while allosteric activators enhance enzyme activity. This mechanism is critical for regulating metabolic pathways and maintaining homeostasis in the body.

What has to happen to amino acids before they are fed into the catabolic pathways for carbohydrates (glycolysis, pyruvate oxidation, citric acid cycle)?

Amino acids must undergo deamination before they can be fed into the catabolic pathways for carbohydrates. This process involves the removal of the amino group (-NH2) from the amino acid, which generates ammonia (NH3) and a carbon skeleton. The carbon skeleton can then enter the catabolic pathways for carbohydrates, while the ammonia is converted into less toxic compounds and ultimately excreted from the body.

What is the difference between anabolic and catabolic pathways?

Anabolic pathways are metabolic pathways that build complex molecules from simpler ones, usually requiring energy in the form of ATP. Examples of anabolic pathways include the synthesis of proteins from amino acids, the synthesis of DNA from nucleotides, and the synthesis of carbohydrates from simple sugars. In contrast, catabolic pathways are metabolic pathways that break down complex molecules into simpler ones, releasing energy in the process. Examples of catabolic pathways include the breakdown of glucose during cellular respiration and the breakdown of fatty acids during beta-oxidation.

How is it possible for us to enjoy apples in NYC in the spring when apples are harvested in early fall?

Apples are harvested in early fall and can be stored for months in cold storage facilities, which are kept at low temperatures and controlled humidity levels. This helps to slow down the natural ripening process and extend the shelf life of the apples. During the spring, these stored apples can be distributed to markets and grocery stores for consumption. Additionally, apples can be imported from regions where they are in season, such as South America or New Zealand, to meet the demand during the off-season.

As the concentration of CO2 in the atmosphere rises, some have argued that the potential increase in carbon fixation might actually be hurting the nutritional values of our crops. Why? How could farmers rectify this problem? Design an experiment to determine whether your suggestion works for future changes in the atmosphere.

As CO2 concentration rises, the balance between macronutrients (such as nitrogen and phosphorus) and micronutrients (such as zinc and iron) in plants can be disrupted, resulting in decreased nutritional quality. This is because increased carbon fixation can lead to dilution of these micronutrients in plant tissues. To rectify this problem, farmers can apply micronutrient fertilizers to crops to ensure sufficient micronutrient uptake. An experiment to determine whether this suggestion works for future changes in the atmosphere could involve growing two sets of crops in controlled environments with different CO2 concentrations. One set would receive only macronutrient fertilizers while the other set would receive both macronutrient and micronutrient fertilizers. After harvest, the nutrient content of the crops could be analyzed and compared to determine if the addition of micronutrient fertilizers improved the nutritional quality of the crops grown at higher CO2 concentrations.

A cell wall degrading enzyme AoXyn11A (Wild Type) extracted from a microorganism has a temperature optimum of 55C. Genetically engineered version of the same enzyme have several extra amino acids and either extra hydrogen bonds (AoXyn11AC5) or an extra disulfide bridge (AoXyn11AC5-C32). See the figure from lecture slides (do not memorize). Which enzyme is more stable at higher temperatures? Based on the data shown, which modification to the enzyme made it more stable at higher temperatures?

Based on the data shown in the figure, the genetically engineered version of the enzyme with the extra disulfide bridge (AoXyn11AC5-C32) appears to be more stable at higher temperatures. This is because the activity of this variant remains relatively high even at 65°C, while the activity of the wild-type and the variant with extra hydrogen bonds (AoXyn11AC5) drops significantly at this temperature. The extra disulfide bridge in AoXyn11AC5-C32 may be responsible for the increased stability at higher temperatures. Disulfide bridges can provide additional structural stability to proteins by covalently linking different parts of the protein, thereby reducing the protein's flexibility and increasing its rigidity. The rigidity provided by the disulfide bridge may help to maintain the protein's three-dimensional structure and function at higher temperatures where wild-type or the variant with extra hydrogen bonds may have experienced partial denaturation or inactivation.

A fungal cell has a potential of -180 mV (negative inside). There is more Ca2+ outside the cell than inside the cell. What can we conclude about the movement of Ca2+ in this case? a. Ca2+ will enter the cell through open channels via passive transport. b. Ca2+ will exit the cell through open channels via passive transport. c. Ca2+ will enter the cell only through active transport. d. Ca2+ will exit the cell passively through a carrier protein. e. We need more information.

Ca2+ will enter the cell only through active transport.

Is chemical synaptic signaling an example of autocrine or paracrine signaling? Explain.

Chemical synaptic signaling is an example of paracrine signaling. In this type of signaling, neurotransmitters are released by one neuron and act locally on neighboring neurons or cells. The signaling molecules (neurotransmitters) are not released into the bloodstream, but rather act on nearby cells within a short range. Autocrine signaling occurs when a cell secretes a signaling molecule that binds to receptors on its own surface, whereas paracrine signaling occurs when the signaling molecules are released by one cell and act on nearby cells.

What is a cofactor as opposed to a coenzyme?

Cofactors are non-protein molecules that assist enzymes in catalyzing reactions, and are usually metal ions or inorganic molecules. Coenzymes are a type of cofactor that are organic molecules, derived from vitamins, and often act as carriers of chemical groups or electrons between substrates during the reaction.

Consider competitive and non-competitive inhibitors. How does each affect the enzyme?

Competitive inhibitors bind to the active site of an enzyme, preventing the substrate from binding and reducing the rate of the reaction. They do not affect the enzyme's conformation or catalytic activity but compete with the substrate for the active site. Non-competitive inhibitors, on the other hand, bind to an allosteric site on the enzyme, leading to a conformational change that alters the enzyme's catalytic activity. Non-competitive inhibitors can bind to the enzyme-substrate complex and decrease the rate of the reaction by blocking the enzyme's catalytic activity.

What are connexins and connexons?

Connexins are a family of proteins that are the building blocks of gap junctions, which are channels that allow the direct exchange of ions and small molecules between adjacent cells. Each connexin protein has four transmembrane domains, two extracellular loops, and one cytoplasmic loop. Connexons, on the other hand, are hexameric structures composed of connexin proteins. Each connexon is formed by the docking of six connexin proteins, which create a cylindrical pore through which small molecules and ions can pass. Two connexons from adjacent cells can come together to form a gap junction channel, allowing for direct communication between the two cells.

Cyanides attach to the iron within cytochrome c oxidase and inhibit its activity. Antimycin A inhibits electron transport within Complex III. What would each inhibitor do to electron transport in the mitochondria? To the proton gradient? To ATP synthesis? Explain.

Cyanide inhibits the activity of cytochrome c oxidase (Complex IV), which blocks the transfer of electrons to oxygen and leads to a decrease in electron transport, collapse of the proton gradient, and inhibition of ATP synthesis. Antimycin A inhibits electron transport within Complex III, resulting in a buildup of electrons in the upstream carriers, a decrease in electron transport, and inhibition of ATP synthesis.

Review the slides for electron transport in the mitochondria. Explain how donation of electrons by NADH and FADH2 to the ETC leads to the synthesis of ATP.

During electron transport in the mitochondria, NADH and FADH2 donate electrons to the electron transport chain. The electrons are passed down a series of protein complexes, ultimately reducing oxygen to water and generating a proton gradient across the inner mitochondrial membrane. This proton gradient drives the synthesis of ATP through oxidative phosphorylation, as protons flow back into the mitochondrial matrix through ATP synthase, leading to the production of ATP from ADP and inorganic phosphate. NADH generates more ATP than FADH2 because it contributes to a larger proton gradient.

Review the slides for electron transport in the mitochondria from lecture notes. Mark the specific steps that contribute to the formation of the proton gradient across the membrane, adding protons to the intermembrane space and removing protons from the matrix.

During electron transport in the mitochondria, several steps contribute to the formation of the proton gradient across the inner mitochondrial membrane, adding protons to the intermembrane space and removing them from the matrix. Specifically, the proton gradient is established by the pumping of protons across the inner mitochondrial membrane by Complexes I, III, and IV of the electron transport chain. As electrons pass through these complexes, protons are pumped from the matrix into the intermembrane space, creating a proton gradient. This gradient then drives the synthesis of ATP through oxidative phosphorylation.

Why is it important for complexes I, III, and IV in the mitochondria to be transmembrane proteins while complex II is not?

During electron transport in the mitochondria, several steps contribute to the formation of the proton gradient across the inner mitochondrial membrane, adding protons to the intermembrane space and removing them from the matrix. Specifically, the proton gradient is established by the pumping of protons across the inner mitochondrial membrane by Complexes I, III, and IV of the electron transport chain. As electrons pass through these complexes, protons are pumped from the matrix into the intermembrane space, creating a proton gradient. This gradient then drives the synthesis of ATP through oxidative phosphorylation.

List the steps in the photochemical reactions that directly help establish a proton gradient across the thylakoid membrane.

During the photochemical reactions of photosynthesis, light energy is absorbed by photosystems in the thylakoid membrane. This energy is used to pump protons from the stroma into the thylakoid lumen, creating a concentration gradient. This gradient is used to power ATP synthesis and drives the conversion of NADP+ to NADPH, which are both used in the later stages of photosynthesis.

What is the difference between endocrine and neuroendocrine signaling?

Endocrine signaling involves the secretion of hormones by endocrine cells into the bloodstream to reach target cells located in distant parts of the body. The hormones bind to specific receptors on the target cells, triggering a response. In contrast, neuroendocrine signaling involves the release of hormones from specialized nerve cells called neuroendocrine cells. These cells are located in the hypothalamus and pituitary gland in the brain and release hormones into the bloodstream in response to neural signals. Neuroendocrine signaling plays a crucial role in the regulation of physiological processes such as growth, metabolism, and reproduction.

Which of the following is a part of the first law of thermodynamics? a. Energy can be neither created nor destroyed. b. Energy cannot be transformed. c. The entropy of the universe is constant. d. The entropy of the universe is decreasing. e. Potential energy is the energy of motion.

Energy can be neither created nor destroyed.

Explain why increasing temperature can increase the rate of an enzymatic reaction up to a certain temperature, but above that increasing temperature reduces the rate of the reaction.

Enzymatic reactions depend on the energy of the reacting molecules and the protein structure of the enzyme that catalyzes the reaction. When temperature increases, the thermal energy of the system rises, which results in an increase in the kinetic energy of the molecules. This increases the frequency of molecular collisions, allowing more substrate molecules to enter the active site of the enzyme, resulting in an increase in the rate of reaction. However, enzymes are sensitive to changes in temperature, and if the temperature exceeds the enzyme's optimal temperature, the protein structure of the enzyme begins to change. The enzyme will lose its three-dimensional structure or denature, resulting in a loss of catalytic activity, and the rate of reaction will decrease. Therefore, the rate of enzymatic reactions increases with temperature up to a certain point, but above the optimal temperature, increasing the temperature decreases the rate of the reaction.

Both FADH2 and NADH donate electrons to the electron transport chain. Which does it at a lower energy level? Which leads to establishing a larger proton gradient across the inner mitochondrial membrane?

FADH2 donates electrons to the ETC at a lower energy level than NADH because it enters the chain at Complex II. NADH, on the other hand, enters at Complex I, which has a higher potential energy. NADH leads to the establishment of a larger proton gradient across the inner mitochondrial membrane compared to FADH2 because it pumps more protons out of the matrix and into the intermembrane space.

Review Figure 9.6 from the textbook. Explain what is happening. Why is it important for the alpha subunit of the G protein to function as a GTPase enzyme to hydrolyze its bound GTP to GDP?

Figure 9.6 in the textbook shows the process of G protein signaling, where an extracellular signaling molecule activates a G protein-coupled receptor (GPCR), leading to the activation of the alpha subunit of the G protein. The alpha subunit exchanges GDP for GTP and activates an effector protein, leading to downstream signaling. The GTPase activity of the alpha subunit is essential to turn off the signaling cascade by hydrolyzing GTP to GDP and reassociating with the beta and gamma subunits, providing critical negative feedback and regulation of G protein signaling.

In the absence of oxygen, our cells switch to fermentation. In anaerobic fermenters, there is no aerobic respiration, only glycolysis and fermentation. Why must glycolysis be paired with fermentation? What does fermentation accomplish?

Glycolysis must be paired with fermentation in anaerobic fermenters because it regenerates the oxidizing agent, NAD+, required for the continuation of glycolysis. Fermentation allows for the production of ATP in the absence of oxygen by transferring electrons from NADH to pyruvate or another organic molecule, producing either lactic acid or ethanol and CO2 as end products. This allows for a continuous supply of ATP for the cell's energy needs in the absence of oxygen.

Sea lettuce (Ulva) and Nori (Porphyra) have different combinations of pigments and absorb light maximally at different wavelengths. See the figure from lecture notes. Sea lettuce is typically found in shallow coastal waters while Nori is found in deeper waters. Some have suggested that the reason they are restricted to their respective depths has to do with the available light and their respective action spectra due to their pigments. However, you also must consider that this depth restriction might have to do with nutrient requirements, the intensity of light (not the wavelengths), and maybe even presence of grazers (animals that eat them). Design an experiment to test whether the available light wavelengths at different water depths (and not something else) can explain why Nori are found in deep waters. Make sure to include all elements of experimental design we have reviewed in class and lab in your answer.

Hypothesis: The action spectrum of Nori suggests that it absorbs more blue light, which penetrates deeper in water, so Nori should be able to grow in deep water where blue light is more abundant than other wavelengths. Experimental design: a. Choose a deep water site and a shallow water site with similar nutrient concentrations and absence of grazers. b. Deploy photosynthetically active radiation (PAR) sensors at both sites at various depths. c. Use a spectrophotometer to measure the absorption spectra of Nori at different depths of the deep water site. d. Collect samples of Nori and measure their photosynthetic rates at different depths. e. Repeat steps c and d at the shallow water site. Controls: a. Measure PAR at both sites and ensure that light intensity is not a confounding variable. b. Use a nutrient-free seawater control to ensure that nutrient availability is not a confounding variable. c. Use an herbivore-free control to ensure that grazing pressure is not a confounding variable. Data analysis: a. Plot the action spectrum of Nori against the PAR data collected at both sites. b. Determine whether the absorption spectrum of Nori corresponds to the wavelengths of light that penetrate to deep water. c. Compare the photosynthetic rates of Nori at different depths at both sites. Conclusion: a. If Nori absorbs more blue light and shows higher photosynthetic rates in deep water, then the available light wavelengths at different water depths may explain why Nori is found in deep water. b. If Nori shows no difference in photosynthetic rates at different depths between the two sites, then other factors such as nutrient availability or grazing pressure may explain the depth restriction of Nori.

Oral secretion products from chewing insects have been suggested as triggers that augment the release of plant volatiles. Caterpillars of Pieris brassicae species have a -glucosidase enzyme present in their oral secretions that might trigger volatile emissions in cabbage plants. Design an experiment to determine whether the protein -glucosidase is as effective as a chewing caterpillar of Pieris brassicae in eliciting a defense response from cabbage plants through release of plant volatiles. Include all elements of experimental design in your answer

Hypothesis: The protein β-glucosidase present in oral secretions of Pieris brassicae species triggers the release of plant volatiles in cabbage plants, similar to a chewing caterpillar of the same species. Variables: Independent variable: Presence of β-glucosidase enzyme Dependent variable: Release of plant volatiles Controlled variables: Species and age of cabbage plants, amount and duration of enzyme or caterpillar exposure, environmental conditions such as temperature and light. Experimental groups: Group 1: Cabbage plants exposed to β-glucosidase enzyme Group 2: Cabbage plants exposed to Pieris brassicae caterpillars Control group: Cabbage plants not exposed to enzyme or caterpillars Procedure: Select healthy cabbage plants of similar age and size Randomly assign plants to the experimental groups and control group For Group 1, apply a standardized amount of β-glucosidase enzyme to the leaves of each plant using a spray bottle or dropper. For Group 2, place a single Pieris brassicae caterpillar on each plant. Control group plants should be left undisturbed. After a predetermined amount of time, collect and analyze samples of air surrounding each plant to measure volatile organic compounds (VOCs) released by the plant. This can be done using gas chromatography or other appropriate methods. Repeat the experiment multiple times to ensure reliable results. Data analysis: Compare the levels of VOCs released by plants in each group to determine whether β-glucosidase enzyme has a similar effect on cabbage plants as chewing caterpillars of Pieris brassicae species. Use appropriate statistical tests to determine whether any observed differences between groups are significant. Conclusion: If the levels of plant volatiles released by Group 1 are similar to those released by Group 2, then the results suggest that the β-glucosidase enzyme in oral secretions of Pieris brassicae species is an effective trigger for the release of plant volatiles in cabbage plants.

Chewing by insects has been suggested as a trigger for the release of plant volatiles to warn neighboring plants that an herbivore attack is imminent. However, since plants can sense sound (yes, they can "hear"), some have argued that the sound of chewing on a nearby plant is the warning to the nearby plants. Design an experiment to determine whether the signal that warns the neighboring plants about the imminent herbivore attack is a) the plant volatiles released from the plants that are being chewed by the insects, or b) the sound of chewing. Include all elements of experimental design in your answer.

Hypothesis: The signal that warns neighboring plants about the imminent herbivore attack is the release of plant volatiles from the plants that are being chewed by insects. Materials: Three identical chambers (A, B, and C) with controlled temperature, humidity, and lighting conditions. 10 healthy and identical plants of the same species (e.g., Arabidopsis thaliana). 10 identical pots with soil for the plants. A speaker and a microphone for recording and playing sounds. A group of insects that feed on the chosen plant species (e.g., aphids). Methods: Plant preparation: All plants should be grown under identical conditions until they are mature enough to withstand insect feeding. The 10 plants should be divided into two groups of 5 plants each, with each group having a control (uninjured) and a treatment (injured) set. Label the plants and pots to ensure that each plant's condition is recorded accurately throughout the experiment. Insect feeding and sound recording: In chamber A, place 5 control plants and 5 treatment plants. In chamber B, place only the 5 control plants. In chamber C, place only the 5 treatment plants. In chamber A, introduce the group of insects that feed on the chosen plant species and allow them to feed on the treatment plants for a specified duration. During the feeding time in chamber A, record the sounds of insect feeding with the microphone and store the recording. After the specified duration of feeding, remove the insects from the chamber A and close it for an additional specified duration. After this duration, open the chamber A, and remove the treatment plants. In chambers B and C, do not introduce any insects but play the recorded sound of insect feeding for the same duration as in chamber A. Volatile collection and analysis: After removing the treatment plants from chamber A, collect volatiles from the control and treatment plants in all three chambers using headspace solid-phase microextraction (HS-SPME). Analyze the volatile samples using gas chromatography-mass spectrometry (GC-MS) to identify and quantify the volatile compounds. Compare the volatile profiles of the control and treatment plants in all three chambers to determine if the plant volatile emissions in the control plants differ from those in the treatment plants. Results: If the hypothesis is correct, the volatile profiles of the control and treatment plants in chamber A should differ significantly from those in chambers B and C, indicating that the plant volatile emissions in the control plants differ from those in the treatment plants. If the sounds of chewing are the warning signal, the volatile profiles of the control and treatment plants in chambers B and C should differ significantly from each other, indicating that the plants can hear and respond to the sound of chewing. Conclusion: Based on the results, the hypothesis can be either supported or rejected, and the warning signal for the neighboring plants can be identified. If the hypothesis is supported, it suggests that the release of plant volatiles from the plants that are being chewed by insects is the warning signal to the neighboring plants.

The PCO cycle costs a plant an NADH. Do you agree or disagree with this statement? Explain.

I disagree with the statement that the PCO cycle costs a plant an NADH. The PCO cycle actually generates an NADPH molecule, which is a reducing equivalent that can be used in other metabolic processes. The cycle uses ATP as an energy source, but it produces more ATP than it consumes. Therefore, the PCO cycle is a net energy-producing process that generates NADPH as a reducing equivalent, and does not cost a plant an NADH.

Suppose you have two variants of the same enzyme. For the same reaction, they have the same Vmax, but different Km values. What does that tell you about the two variants? Draw the curves.

If two variants of the same enzyme have the same Vmax but different Km values, it means that they have the same maximum velocity of the reaction but different affinities for the substrate. A lower Km value indicates a higher affinity of the enzyme for its substrate, meaning that the enzyme can bind to the substrate more easily and at lower substrate concentrations. The variant with the lower Km value has a higher initial rate of reaction and reaches Vmax at a lower substrate concentration compared to the variant with the higher Km value.

Signaling molecules can move directly between cells in both plant and animal cells. Compare and contrast the structure of Gap Junctions and Plasmodesmata, and how they both allow this to happen.

In both plant and animal cells, signaling molecules can move directly between cells through plasmodesmata in plants and gap junctions in animal cells. However, plasmodesmata are larger and more selective compared to gap junctions. In plants, they allow for the exchange of small molecules, ions, and proteins between cells, while in animal cells, gap junctions mainly facilitate the exchange of small molecules and ions. Additionally, animal cells also use other forms of cell-to-cell communication such as paracrine, endocrine, and synaptic signaling.

In enzymatic reactions, what is meant by "an induced fit"?

In enzymatic reactions, an induced fit refers to the conformational change that occurs in an enzyme when it interacts with its substrate. The enzyme's active site changes shape slightly upon substrate binding, allowing the enzyme to more closely bind the substrate and form the enzyme-substrate complex. This conformational change facilitates the chemical reaction between the enzyme and substrate and enables the reaction to occur more efficiently. The induced fit model suggests that the interaction between enzyme and substrate is dynamic and that the binding of substrate induces a change in the enzyme's structure, leading to optimal alignment of the active site residues and the substrate for efficient catalysis.

Review the figures for fermentation. In each, explain where the redox reaction is. Make sure to identify the functional groups in the substrate and the final product in each.

In lactate fermentation, the redox reaction occurs during the conversion of pyruvate to lactate, where NADH is oxidized to NAD+. Pyruvate, a 3-carbon molecule, is reduced by NADH to form lactate, also a 3-carbon molecule. In alcohol fermentation, the redox reaction occurs during the conversion of pyruvate to ethanol, where NADH is oxidized to NAD+. Pyruvate, a 3-carbon molecule, is first decarboxylated to form acetaldehyde, a 2-carbon molecule. Acetaldehyde is then reduced by NADH to form ethanol, also a 2-carbon molecule.

In the absence of oxygen, pyruvate will not enter the mitochondria. Explain the mechanism why.

In the absence of oxygen, the electron transport chain in the mitochondria cannot function, which prevents pyruvate from entering the mitochondria for oxidative metabolism. Instead, pyruvate is converted to lactate or ethanol through fermentation pathways, which regenerate NAD+ and allow glycolysis to continue. This results in a limited production of ATP due to the low efficiency of fermentation compared to oxidative phosphorylation.

Review the slide showing electron transport in the thylakoids. What oxidizes each of the following: • P680 • Pheo • OEC • QB • P700

In the electron transport chain of the thylakoid membrane: • P680 is oxidized by light energy to form P680+. • Pheo is oxidized by P680+ to form Pheo+. • OEC (oxygen-evolving complex) is oxidized by P680+ to form O2. • QB (plastoquinone) is reduced by accepting two electrons and two protons from the stroma to form QBH2. • P700 is oxidized by accepting an electron from plastocyanin (PC) to form P700+.

Consider a proton-sucrose symporter in the cell membrane of a plant cell. What do you expect to be the source of energy for the movement of protons? What do you expect to be the source of energy for the movement of sucrose?

In the proton-sucrose symporter of a plant cell, the energy for the movement of protons is derived from the proton electrochemical gradient across the membrane. This gradient is generated by the action of the proton pump. The energy for the movement of sucrose, on the other hand, comes from the electrochemical gradient of protons, which is used to power the transport of sucrose through the symporter. This is an example of secondary active transport, where the energy stored in the proton gradient is used to drive the transport of sucrose.

Graph the effects of substrate concentration on the rate of an enzymatic reaction given a fixed concentration of enzymes (without any inhibitor). On your graph mark Vmax and Km.

In this graph, the x-axis represents the substrate concentration, while the y-axis represents the reaction rate. The curve shows how the rate of the reaction changes as the substrate concentration increases. As the substrate concentration increases, the rate of the reaction initially increases and eventually levels off. The maximum rate that the reaction can achieve is represented by Vmax, which is the point where the enzyme becomes saturated with substrate molecules. At this point, all of the enzyme active sites are bound to substrate molecules, and the reaction rate cannot increase any further. The substrate concentration at which the reaction rate is half of Vmax is represented by Km, which is a measure of the enzyme's affinity for the substrate. A lower Km value indicates a higher affinity for the substrate, meaning that the enzyme can achieve half of its maximum rate at a lower substrate concentration.

As the concentration of CO2 in the atmosphere rises, some have argued that this might actually be good for plants. Focusing on your answer only to the question 8 above, do you agree or disagree with this argument? Explain.

It can be argued that an increase in atmospheric CO2 concentration could benefit plants by increasing the ratio of carboxylation to oxygenation reactions carried out by Rubisco. This is because higher CO2 concentrations would favor carboxylation over oxygenation and reduce photorespiration, leading to an increase in photosynthetic efficiency. However, it's important to note that other factors, such as temperature, water availability, and nutrient availability, can also affect plant growth and productivity.

Review the figures for lactate fermentation and alcohol fermentation. Compare and contrast the two.

Lactate fermentation and alcohol fermentation are two types of fermentation processes that occur in the absence of oxygen. Lactate fermentation is common in animal cells and some bacteria, where pyruvate is converted to lactate. Alcohol fermentation is common in yeast and some bacteria, where pyruvate is converted to ethanol and carbon dioxide. Both processes regenerate NAD+ so that glycolysis can continue. However, alcohol fermentation produces carbon dioxide as a byproduct while lactate fermentation does not.

Review the figure (do not memorize) about the biosynthesis and function of MoCo. Consider the pathway leading to the synthesis of the molybdenum cofactor for sulfite oxidase. Mutations in the gene MOCS1 mean the person does not have a functional enzyme for step 1. What does that mean for the synthesis of cPMP (cyclic pyranopterin monophosphate)? How about MPT (molybdopterin)? How about the cofactor for sulfite oxidase? Why would such mutations lead to developmental delays and seizures? Why would Nulibry work as a drug to ameliorate the problem caused by these mutations?

Mutations in the MOCS1 gene prevent the synthesis of the precursor for the molybdenum cofactor, leading to a non-functional sulfite oxidase and toxic buildup of sulfites, which can cause developmental delays and seizures. Nulibry works by restoring the levels of cPMP and MPT, allowing for the proper functioning of sulfite oxidase and preventing the buildup of sulfites.

What are the possible fates of an electron of a pigment once it has been excited?

Once a pigment molecule has been excited, its electron can have several possible fates: It can return to its ground state by releasing the excess energy as heat or fluorescence. It can transfer the energy to another pigment molecule, which in turn can excite an electron and continue the energy transfer. It can transfer the energy to a nearby electron acceptor, which can then become reduced and continue the electron transport chain. It can be transferred to a different electron acceptor outside of the pigment complex, such as the electron transport chain in the thylakoid membrane. The ultimate fate of the electron depends on the specific context and environment in which the pigment is located.

What is one hypothesis as to why Rubisco has evolved to carry out both oxygenation and carboxylation reactions?

One hypothesis is that Rubisco evolved to carry out both oxygenation and carboxylation reactions because of its ancient origin. Rubisco is believed to have evolved in a time when atmospheric CO2 levels were high and O2 levels were low. However, as O2 levels began to rise, Rubisco may have acquired the ability to carry out oxygenation reactions as a way to protect the plant from photorespiration, which can occur when O2 competes with CO2 for the active site of Rubisco. In this way, the ability to carry out both oxygenation and carboxylation reactions may have helped plants to adapt to changing atmospheric conditions over time.

Why is oxygen a bigger problem under hot and dry conditions?

Oxygen is a bigger problem under hot and dry conditions because when stomata are closed to conserve water, the concentration of carbon dioxide decreases while the concentration of oxygen increases in the leaf. With more oxygen available, Rubisco is more likely to carry out the oxygenation reaction, leading to photorespiration. In hot and dry conditions, the rate of photorespiration increases because the plant needs to close its stomata to prevent water loss, and this results in an increase in oxygen concentration and a decrease in carbon dioxide concentration in the leaf. As a result, more energy and resources are wasted in photorespiration, reducing the efficiency of photosynthesis and limiting plant growth.

Why is oxygen a problem in photosynthesis?

Oxygen is a problem in photosynthesis because it competes with carbon dioxide for the active site of the enzyme rubisco during the carbon fixation step of the Calvin cycle. When rubisco binds to oxygen instead of carbon dioxide, a byproduct called phosphoglycolate is produced instead of the desired 3-carbon molecule. This process is known as photorespiration and can result in a net loss of fixed carbon and energy for the plant. This is particularly problematic for plants in hot and dry environments where the stomata are closed to prevent water loss, leading to higher levels of oxygen relative to carbon dioxide in the chloroplast.

In linear electron transport in the thyalkoids: What oxidizes PC? What reduces PC? What oxidizes P680? What reduces Fd?

P680 is oxidized by the primary electron acceptor of PSII, while PC is reduced by electrons passing from PSII to PSI. Fd is reduced by electrons passed along the ETC between PSII and PSI and donates those electrons to NADP+ reductase, which reduces NADP+ to NADPH, while the proton gradient generated across the thylakoid membrane drives ATP synthesis via ATP synthase.

Review the figure showing the effect of pH on activity of Pepsin and Trypsin. What are the optimal pH and the pH ranges for these enzymes? Explain why an enzyme has an optimal pH and if the pH goes above or below that optimum the rate of the reaction goes down.

Pepsin is an enzyme that functions in the acidic environment of the stomach, and it has an optimal pH range of 1.5 to 2.5. Trypsin is an enzyme that functions in the alkaline environment of the small intestine, and it has an optimal pH range of 7.5 to 8.5. The optimal pH is the pH at which the enzyme exhibits the maximum catalytic activity. If the pH goes above or below the optimal pH range, the rate of the reaction goes down. This is because the enzyme molecule becomes denatured or loses its shape, making it less effective in catalyzing the reaction. At extreme pH values, the enzyme can be irreversibly denatured, which means it permanently loses its catalytic activity. Therefore, maintaining the pH within the optimal range is important for ensuring the efficiency of enzyme-catalyzed reactions.

Plants make and store cyanide in their cells. What is the purpose of cyanide in the plants?

Plants produce cyanide as a defense mechanism against herbivores and pathogens. Cyanogenic glycosides, the inactive form of cyanide, are stored in the plant until they are broken down by specific enzymes, releasing hydrogen cyanide (HCN). HCN acts as a deterrent or poison, protecting the plant from being eaten or damaged. In some plants, cyanogenic glycosides serve as a storage mechanism for nitrogen and carbon that can be mobilized in times of stress or nutrient deficiency.

Compare and contrast primary and secondary active transport.

Primary active transport involves the direct use of ATP to move molecules against their concentration gradient, while secondary active transport uses the energy stored in the electrochemical gradient of one molecule to drive the transport of another molecule against its concentration gradient. Both mechanisms require the presence of membrane transport proteins and play crucial roles in maintaining cellular homeostasis.

A series of enzymes catalyze the reaction: A → B → C → D. Product D binds to enzyme X, which converts A to B, at a position remote from its active site. This binding decreases the activity of enzyme X. What type of inhibitor is D for enzyme X? Inhibition of this pathway by product D is called _________________.

Product D is a non-competitive inhibitor for enzyme X because it binds to an allosteric site on enzyme X and decreases its activity, rather than competing with the substrate A for the active site. The inhibition of this pathway by product D is called feedback inhibition or feedback control.

In bacteria, to what does "quorum sensing" refer?

Quorum sensing in bacteria refers to the ability of bacteria to communicate and coordinate their behavior by producing and sensing chemical signals called autoinducers. These signals allow bacteria to detect the density of their population and regulate gene expression accordingly, which can lead to changes in behavior such as the formation of biofilms, virulence, and bioluminescence.

Refer to the figure showing activation of receptor tyrosine kinases. For a receptor tyrosine kinase to carry out its function in a cell, list the steps in order from reception of the external signal to activation of signaling proteins that lead to the cellular response.

Receptor tyrosine kinases (RTKs) are transmembrane receptors that are activated by extracellular signaling molecules. Upon ligand binding, RTKs undergo dimerization and autophosphorylation, which leads to the activation of downstream signaling pathways involving signaling proteins such as Grb2, SOS, Ras, and Raf. These signaling pathways ultimately lead to changes in gene expression and cellular behavior, such as cell proliferation, differentiation, or migration.

Some photosynthetic organisms contain chloroplasts that lack photosystem II, yet are able to survive. These organisms CANNOT do the following: a. Release O2 through photosynthesis. b. Fix CO2 through photosynthesis c. Absorb light at 680 nm d. Make ATP through electron transport

Release O2 through photosynthesis.

Compare and contrast simple diffusion, facilitated diffusion, and active transport by pumps.

Simple diffusion is the passive movement of molecules down their concentration gradient, facilitated diffusion is the passive movement of molecules with the help of a transport protein, and active transport is the active movement of molecules against their concentration gradient with the expenditure of energy in the form of ATP.

Consider a steroid hormone. Why is there no receptor in the plasma membrane for a steroid hormone? Explain what is happening in Figure 9.4 in the textbook.

Steroid hormones are lipid-soluble and can readily pass through the plasma membrane to enter the cell. Once inside the cell, they bind to intracellular receptors located in the cytoplasm or nucleus. These receptors are transcription factors that bind to specific DNA sequences in the promoter region of target genes, leading to changes in gene expression and ultimately changes in cellular processes. Figure 9.4 in the textbook shows the mechanism of action of a steroid hormone, specifically cortisol, which binds to its intracellular receptor and enters the nucleus. The cortisol-receptor complex then binds to specific DNA sequences in the promoter region of target genes, leading to changes in gene expression and protein production. In this case, the target gene encodes for an enzyme involved in gluconeogenesis, which is upregulated by cortisol to increase glucose production.

Compare and contrast active transport of Na+ through a Na+ /K+ pump and active transport of glucose through a Na+ /glucose symporter.

The Na+/K+ pump uses ATP hydrolysis to move three Na+ ions out of the cell and two K+ ions into the cell, which creates an electrochemical gradient that is important for many cellular processes. On the other hand, the Na+/glucose symporter uses the energy from the Na+ gradient created by the Na+/K+ pump to move glucose molecules into the cell, in a coupled transport mechanism. The Na+/K+ pump creates an electrochemical gradient, while the Na+/glucose symporter relies on the Na+ gradient created by the pump to move glucose into the cell.

Review the diagram of the PCR Cycle. What are the three major phases in the cycle? Be able to circle each phase from initial substrates to final products. Make sure you can identify the reactants and products in each phase. In which phase(s) is ATP used? In which phase(s) is NADPH used? What is reduced to what in the reduction phase?

The PCR (Calvin-Benson-Basham) cycle is a process that takes place in the stroma of the chloroplast in photosynthetic organisms, and it is responsible for the fixation of atmospheric carbon dioxide into organic compounds. The cycle has three phases: carbon fixation, reduction, and regeneration. In the carbon fixation phase, CO2 is fixed into a 3-carbon compound through the enzyme Rubisco. In the reduction phase, ATP and NADPH are used to convert the 3-carbon compound into G3P. In the regeneration phase, some of the G3P is used to regenerate the starting molecule and the remaining is used to synthesize other organic compounds.

Where does the PCR (Calvin-Benson-Basham) cycle take place?

The PCR (Calvin-Benson-Basham) cycle takes place in the stroma of the chloroplasts in photosynthetic cells. The stroma is a dense fluid-filled space surrounding the thylakoid membranes, where the light-independent reactions of photosynthesis occur. The enzymes and other components of the PCR cycle are located in the stroma, where they carry out the carbon fixation, reduction, and regeneration reactions that ultimately produce carbohydrates and other organic compounds.

The figure below shows the absorption spectrum for chlorophyll a (solid line) and the action spectrum for photosynthesis (dashed line). Why are they different (meaning the peaks and valleys are not a perfect match)?

The absorption spectrum of chlorophyll a represents the wavelengths of light that chlorophyll a can absorb, while the action spectrum for photosynthesis represents the efficiency of photosynthesis at different wavelengths of light. The peaks and valleys in each spectrum are not a perfect match because photosynthesis is not solely dependent on chlorophyll a; other pigments, such as chlorophyll b and carotenoids, also play a role in absorbing light and transferring energy to chlorophyll a. Additionally, different wavelengths of light can have different energy levels and be more or less efficient at driving photosynthesis, leading to differences between the two spectra.

Sucrase has a temperature range of 30-45C and an optimum of 37C. Draw a graph showing the activity curve for this enzyme to show how temperature affects its activity.

The activity of sucrase is expected to increase as the temperature increases within its range of 30-45C. The activity should increase rapidly from 30C, reach a maximum at 37C (its optimal temperature), and then decrease as the temperature continues to increase beyond 37C. At temperatures below the optimum, the rate of reaction will be slower due to less kinetic energy being available for the reaction to occur. As the temperature increases from the optimum, the enzyme will become increasingly unstable and will begin to denature, which will result in a decrease in the rate of reaction. Overall, the activity curve for sucrase should resemble a bell-shaped curve, with the peak activity occurring at 37C and the activity decreasing on either side of this temperature range.

If you subject plant mitochondria to cyanide, the plants survive because of the presence of the alternative oxidase that allows them to bypass complexes III and IV. As far as we know, is this a defensive mechanism that has evolved to protect the plants against cyanide poisoning? Explain

The alternative oxidase in plant mitochondria is not known to have specifically evolved as a defense against cyanide poisoning, but rather as a regulatory mechanism to control mitochondrial respiration and ROS levels during stress. While the alternative oxidase can help plants survive in the presence of cyanide by bypassing complexes III and IV, the evolutionary origins and functions of this pathway are still being studied.

What are the costs and benefits of the PCO cycle?

The benefits of the PCO (photorespiratory carbon oxidation) cycle include the salvage of carbon that would otherwise be lost through the oxygenation reaction of Rubisco, and the production of glycine, serine, and CO2 that can be used for other metabolic pathways. However, the cycle also has significant costs, including the consumption of ATP and NADPH, and the release of toxic byproducts such as ammonia and glycolate. Additionally, the energy expended during photorespiration may reduce the efficiency of photosynthesis, ultimately limiting plant growth and productivity.

During a laboratory experiment, you discover that an enzyme-catalyzed reaction has a ∆G of -20 kcal/mol. If you reduce the amount of enzyme in the reaction by 50%, what will be the ∆G for the new reaction? Explain.

The change in free energy (∆G) of a reaction is independent of the amount of enzyme present. Therefore, reducing the amount of enzyme in the reaction by 50% will not affect the ∆G of the reaction. The ∆G value remains at -20 kcal/mol, assuming that other factors, such as temperature and pH, remain constant. However, reducing the amount of enzyme can affect the rate at which the reaction occurs. With fewer enzymes present, the reaction rate may be slower, and the time required to reach equilibrium may be longer.

In electron transport, as electrons move from complex to complex, the energy level keeps dropping. What is happening to the energy being released by the electrons?

The energy released by the electrons as they move through the electron transport chain is used to pump protons across the inner mitochondrial membrane, creating a proton gradient. This gradient stores energy that can be used to generate ATP through chemiosmosis. Therefore, the energy released by the electrons is not lost but rather stored in the proton gradient, which is then used to produce ATP.

Review the experiment carried out by Jagendorf from class notes. What is the question being asked? What are the alternative and null hypotheses? What is the experimental prediction? What should be a control treatment (not shown in the figure)?

The experiment carried out by Jagendorf aimed to investigate the mechanism of ATP synthesis in chloroplasts, specifically to test the hypothesis that a proton gradient is required for ATP synthesis in these organelles. The null hypothesis for this experiment is that ATP synthesis in chloroplasts is not dependent on a proton gradient. The alternative hypothesis is that ATP synthesis in chloroplasts is dependent on a proton gradient. To test this hypothesis, Jagendorf and colleagues used chloroplasts that were isolated and illuminated with light to generate a proton gradient. They then added ADP and Pi to the chloroplast suspension and measured the rate of ATP synthesis. The experimental prediction was that ATP synthesis would only occur when a proton gradient was established, and that without a gradient, no ATP synthesis would occur. A control treatment in this experiment would be to repeat the same procedure with the exception of omitting the ADP and Pi, since this would allow the researchers to measure the background levels of ATP present in the chloroplasts before the addition of substrates.

Refer to the figure showing the ligand-gated ion channel receptor. Explain what is happening.

The figure shows a ligand-gated ion channel receptor, which is a type of membrane protein that is activated by the binding of a specific ligand or chemical messenger, such as a neurotransmitter. The binding of the ligand causes the receptor to change its conformation, which leads to the opening of an ion channel in the membrane. This allows ions such as sodium (Na+) or calcium (Ca2+) to flow into or out of the cell, depending on the type of channel. The movement of ions across the membrane generates an electrical signal that can trigger a variety of cellular responses, such as the release of neurotransmitters or the contraction of muscle cells.

In a given photosystem, when does the first chemical reaction occur?

The first chemical reaction occurs when a pigment molecule within the antenna complex absorbs light energy and transfers it to the reaction center. This excites an electron in the reaction center, which is then passed along a series of electron acceptors until it reaches an electron acceptor molecule that can transfer the electron to an electron transport chain. This is the start of the light-dependent reactions of photosynthesis, which ultimately lead to the generation of ATP and NADPH.

State the first and second laws of thermodynamics.

The first law of thermodynamics, or the law of conservation of energy, states that energy cannot be created or destroyed, only converted from one form to another. The second law of thermodynamics states that the total entropy of an isolated system always increases over time, and that the degree of disorder or randomness in the system always increases spontaneously. Together, these two laws provide fundamental principles for understanding energy and its transformations in physical and chemical systems.

Hydrolysis of sucrose to glucose and fructose is spontaneous. However, at room temperature, sucrose dissolved in water remains stable for a very long time and does not break down into the two monomers. Explain why this reaction does not happen quickly.

The hydrolysis of sucrose to glucose and fructose is a spontaneous reaction, but its reaction rate is very slow at room temperature in the absence of a catalyst. The stability of sucrose in water is due to the relatively stable glycosidic bond between the glucose and fructose units, the poor nucleophilic nature of water, and the low thermal energy of the system at room temperature. The reaction requires a catalyst to increase the reaction rate by lowering the activation energy required to break the glycosidic bond.

An inhibitor that prevents QB from oxidizing QA will not stop electron transport, while an inhibitor that prevents PQ from reducing the Cyt b6-f complex will. Explain why.

The inhibitors that affect electron transfer in the photosynthetic electron transport chain can have different effects on electron flow and ATP and NADPH production. Inhibitors that block specific steps in the electron transport chain can disrupt the normal electron flow and cause a reduction in the synthesis of ATP and NADPH, ultimately impacting photosynthesis.

Compare and contrast symport and antiport.

The key difference between symport and antiport is the direction of movement of the transported solutes. In symport, both solutes are transported in the same direction across the membrane, while in antiport, the solutes are transported in opposite directions. For example, in a Na+/glucose symporter, Na+ and glucose are transported together into the cell, while in a Na+/Ca2+ antiporter, Na+ is transported out of the cell while Ca2+ is transported into the cell.

In the carotenoid structure shown on the right, identify the light-absorbing region.

The light-absorbing region in the carotenoid structure shown on the right is the long polyene chain of conjugated double bonds, indicated by the alternating double bonds and single bonds. This region absorbs light in the blue-green range of the visible spectrum.

In the structure of chlorophyll shown on the right, identify the light-absorbing region.

The light-absorbing region of chlorophyll is the porphyrin ring, which is the large ring structure in the middle of the molecule that contains the magnesium ion at its center. The long hydrocarbon tail attached to the porphyrin ring is responsible for anchoring the molecule in the thylakoid membrane of the chloroplast, while the various functional groups attached to the ring participate in electron transfer during photosynthesis.

In the thylakoid membranes, what is the main role of the antenna (LHC) pigment molecules?

The main role of the antenna pigment molecules (Light-Harvesting Complexes or LHCs) in the thylakoid membranes is to absorb light energy and transfer it to the reaction center of the photosystem, where it drives the electron transfer that ultimately leads to the production of ATP and NADPH during the light-dependent reactions of photosynthesis. The LHCs act as light-gathering antennae that capture photons of different wavelengths and transfer the absorbed energy to the reaction center chlorophylls, thereby expanding the range of light that can be used for photosynthesis.

Review the structures of chlorophyll a versus chlorophyll b (a and b on the right), do not memorize the figure. What is the major difference? Does this have any consequences for the pigments?

The major difference between chlorophyll a and chlorophyll b is that the latter contains a carbonyl group in place of a methyl group in the porphyrin ring. This difference in chemical structure affects the absorption spectrum of the pigment, as chlorophyll b has an additional peak of absorption in the blue region of the spectrum, which allows it to absorb light that chlorophyll a cannot. This difference in absorption spectra between the two pigments allows plants to capture a wider range of wavelengths of light for photosynthesis, increasing their efficiency.

Which of the following is true for exergonic reactions? a. A net input of energy is necessary for the reaction to proceed. b. The products have less free energy than the reactants. c. The products have more free energy than the reactants. d. The reactants will always be completely converted to products. e. The entropy of the system is reduced.

The products have less free energy than the reactants.

Review the figure showing the detailed steps in regeneration. Follow the 15 carbons from start as G3P to finish as RuBP.

The regeneration phase of the PCR cycle involves the rearrangement of the remaining three-carbon molecules of G3P into five-carbon ribulose bisphosphate (RuBP) molecules, which are then used to continue the cycle. The detailed steps in the regeneration process include phosphorylation of one G3P molecule, followed by a series of enzymatic reactions that convert it to ribulose 5-phosphate (Ru5P) and then to ribulose 1,5-bisphosphate (RuBP) through a sequence of additional reactions. The 15 carbons are thus used to regenerate three molecules of the five-carbon RuBP that are required to start the next round of the PCR cycle.

Explain why the sodium-potassium pump and the proton pump are electrogenic

The sodium-potassium pump and the proton pump are electrogenic because they move charged ions across the cell membrane, creating a separation of charge and a potential difference across the membrane. The sodium-potassium pump moves positively charged Na+ ions out of the cell and K+ ions into the cell, while the proton pump moves positively charged H+ ions out of the cell. Both pumps are important for many cellular processes and their electrogenic nature is essential for maintaining the proper electrochemical gradient necessary for various functions.

Review the figure showing how the sodium-potassium pump works. Describe the steps involved.

The sodium-potassium pump is an active transport pump that uses energy in the form of ATP to move sodium ions out of the cell and potassium ions into the cell, against their concentration gradients. This creates an electrochemical gradient that is essential for many cellular processes. The pump works by binding to intracellular sodium ions, triggering ATP hydrolysis and causing a conformational change in the pump, which releases the sodium ions and allows extracellular potassium ions to bind.

Review the figure (do not memorize) regarding the synthesis of glutamine from glutamic acid. Why is energy coupling required for synthesis of glutamine?

The synthesis of glutamine from glutamic acid requires the use of energy to drive the reaction forward because the reaction involves the transfer of an amino group from an amine donor (usually ammonia or an amino acid) to glutamic acid. This transfer requires the formation of a new peptide bond, which is energetically unfavorable, and thus, energy must be input into the system to facilitate the reaction. The energy required is provided by ATP hydrolysis, which is coupled to the synthesis of glutamine through the action of the enzyme glutamine synthetase.

Review the figure showing the thermal denaturation half-times at 37C for myofibrillar ATPase extracted from fish species taken from 6 habitats. These are all the same enzyme. How come some of them are highly unstable at 37C while others are highly stable? What about the proteins could account for the differences observed?

The thermal denaturation half-time is a measure of the thermal stability of proteins and is determined by the temperature at which the protein loses its native conformation and becomes unfolded. The thermal stability of a protein is affected by various factors such as its amino acid sequence, protein folding, and interactions with other molecules. The thermal denaturation half-time for myofibrillar ATPase extracted from fish species taken from 6 different habitats reveals significant differences in the thermal stability of the enzyme across different species. These differences could be attributed to differences in the amino acid sequences, protein folding, and interactions with other molecules such as chaperones or co-factors. It is possible that these differences reflect adaptations to different environmental conditions, as species living in different habitats may have evolved to maintain the stability of their proteins under specific environmental conditions. Understanding the factors that affect the thermal stability of proteins can help us to develop strategies to improve their stability and prevent denaturation, which is critical in various biotechnological and industrial applications.

Both facilitated diffusion and active transport share the following characteristics: a. The use of transport proteins is required to move the solute. b. The rate of transport linearly increases with solute concentration. c. There is a concentration gradient across the membrane. d. The direction of transport is down the concentration gradient.

The use of transport proteins is required to move the solute. There is a concentration gradient across the membrane.

Consider the alternative oxidase in plants. Describe two examples of how specific plants we looked at in class use this system for specific purposes.

Thermogenic plants, such as the sacred lotus and skunk cabbage, use the alternative oxidase system to generate heat. This allows them to maintain a warm temperature in their flowers even when the surrounding air is cold. The heat serves several functions, such as attracting pollinators and facilitating the release of volatiles that repel herbivores. The alternative oxidase is crucial for this process as it allows for respiration to occur without producing ATP, which would otherwise dissipate the energy as heat.

You have isolated thylakoids from plant chloroplasts. You divide them into several test tubes with the appropriate solution to keep them healthy. All test tubes have a ready supply of NADP+ , ADP, and Pi (inorganic phosphate). You subject them to similar light levels to allow for electron transport to take place. Compound X can compete with NADP+ to accept electrons from Fd through the enzyme FNR in the Electron Transport Chain; in doing so it changes from X to X- (an unbalanced negative charge as it does not combine with a proton). You divide the test tubes into two groups. You add compound X to group 1. You add only the solvent in which compound X is dissolved to group 2. You measure the rates of ATP synthesis in each test tube, then calculate means and standard deviations for your measurements for each of the treatments. Draw a hypothetical column graph showing the effect of the treatments on the rate of ATP synthesis. Make sure to label the axes properly. Make sure the treatments are distinguishable on your graph. Make sure means and standard deviations are distinguishable on your graphs. Mark the dependent and independent variables on your graph.

Title: Effect of Compound X on ATP Synthesis in Isolated Thylakoids X-axis: Treatment Groups (Group 1 and Group 2) Y-axis: Rate of ATP Synthesis (measured in arbitrary units) The graph should have two bars, one for each treatment group (Group 1 and Group 2), each with its own mean rate of ATP synthesis and standard deviation. The mean rate of ATP synthesis should be labeled on the y-axis in arbitrary units. The independent variable is the presence or absence of Compound X, which is labeled on the x-axis as the two treatment groups. The dependent variable is the rate of ATP synthesis, which is shown on the y-axis. Group 1 should have a bar that is lower than Group 2, indicating a lower rate of ATP synthesis due to the presence of Compound X. The bars should be labeled with the means and standard deviations of the rate of ATP synthesis for each group, and the legend should clearly distinguish between the two treatment groups.

When you have a severe fever, what may be a grave consequence if this is not controlled?

When a person has a severe fever, it can have grave consequences if it is not controlled. One of the most significant risks is the potential for damage to the body's tissues and organs, particularly the brain. High temperatures can lead to the denaturation of proteins and enzymes in the body, which can result in irreversible damage to cells and tissues.

Plant mitochondria have an alternative oxidase that allows them to bypass complexes III and IV. This means electrons from ubiquinone go directly to this alternative oxidase, which then passes the electrons to oxygen reducing it to water. Note that this alternative oxidase does not pump protons across the membrane. Compare the proton gradient established across the inner mitochondrial membrane, the relative amount of ATP synthesized, and the energy released as heat when this alternative oxidase is used as opposed to when the normal electron transport pathway (including complexes III, IV, and cytochrome c) is used. Note: both systems are used in a plant mitochondrion, and the proportions can be adjusted depending on the needs of the plant!

When the alternative oxidase is used in plant mitochondria, the proton gradient across the inner mitochondrial membrane is weaker, resulting in a lower amount of ATP synthesized and more energy released as heat compared to the normal electron transport pathway. However, the alternative oxidase can be beneficial in certain situations, such as during periods of high energy demand or stress, when the plant may need to prioritize the generation of heat over the production of ATP.

As soils get dry, roots send a hormone to the leaves to cause the stomata to close to conserve water. What would that do to the PCR (Calvin) cycle? Explain.

When the stomata of leaves close, it limits the entry of CO2 into the leaf and the exit of O2 produced by the plant. The decreased availability of CO2 inside the leaf would slow down the rate of the PCR cycle as CO2 is a necessary substrate for the cycle. This would ultimately reduce the rate of photosynthesis and carbon fixation in the plant. In addition, as the stomata close, it would also limit the escape of O2, which could result in photorespiration, further reducing the efficiency of the PCR cycle.

An uncoupler is a molecule that allows protons to move down their gradient across a membrane. If an uncoupler is added to the intermembrane space of a mitochondrion, what will that do to a) ATP synthesis, and b) electron transport?

a) ATP synthesis: The addition of an uncoupler to the intermembrane space will disrupt the proton gradient across the inner mitochondrial membrane by allowing protons to move freely across the membrane. As a result, the energy stored in the proton gradient will be dissipated as heat rather than being used to generate ATP through oxidative phosphorylation. Thus, the addition of an uncoupler will decrease or even completely inhibit ATP synthesis. b) Electron transport: The addition of an uncoupler to the intermembrane space will not affect the electron transport chain directly. However, it will cause the rate of electron transport to increase in order to restore the proton gradient that has been disrupted by the uncoupler. This is because the proton gradient is normally maintained by the proton pumping activities of Complexes I, III, and IV, which slow down when the gradient collapses. By increasing the rate of electron transport, the proton pumping activities of the complexes will increase, which will help restore the proton gradient across the inner mitochondrial membrane.

Which of the following moves materials against a concentration gradient? a. active transport b. dialysis c. facilitated diffusion d. simple diffusion e. osmosis

active transport

A transport system in which transport of an ion in one direction provides the energy for active transport in the opposite direction is an example of a. antiport b. active diffusion c. symport d. cotransport e. osmosis

antiport

Select all that apply: In cyclic electron flow in the thylakoid membranes electrons from ferredoxin (Fd) move to plastoquinone (PQ). Therefore, cyclic electron flow includes: a. Reduction of NADP+ to make NADPH b. Splitting of water to release molecular oxygen c. Formation of a proton gradient across the thylakoid d. Reduction of pheophytin (Pheo) by P680 e. Oxidation of PQH2 by the Cytochrome complex

c. Formation of a proton gradient across the thylakoid e. Oxidation of PQH2 by the Cytochrome complex

As the concentration of CO2 in the atmosphere rises, plants might respond differently to these changes. A) Rising CO2 concentrations in the leaf air spaces can lead to closure of stomata (lower water loss than before). B) Alternatively, they may keep their stomata open for similar durations (same amount of water loss as before). How will each (A vs. B) affect water conservation versus CO2 uptake? How about rates of photosynthesis versus water loss? Consider one plant species, such as wheat (Triticum aestivum). How will you design an experiment to determine what the response of this species will be to higher levels of CO2 in the atmosphere as predicted for the immediate future?

f rising CO2 concentrations in leaf air spaces lead to closure of stomata, it will conserve water but decrease CO2 uptake, leading to lower rates of photosynthesis. Alternatively, if plants keep their stomata open for similar durations, they will lose the same amount of water as before but with increased CO2 uptake, leading to higher rates of photosynthesis. To determine the response of wheat to higher levels of CO2 in the atmosphere, an experiment can be designed by growing wheat plants under controlled conditions in a greenhouse with different CO2 concentrations, such as 400 ppm (current concentration) and 800 ppm (predicted concentration for the future). The experiment can measure the rates of photosynthesis, water use efficiency, and biomass accumulation of the wheat plants under different CO2 concentrations. The stomatal conductance and water potential can also be measured to determine the water conservation strategies adopted by the plants. The results of the experiment can help to understand how the predicted increase in atmospheric CO2 concentration will affect the growth and productivity of wheat and other crop species, and how farmers can adapt their agricultural practices to these changes.

The voltage across a membrane is called the a. electrochemical gradient b. turgor pressure c. membrane potential d. chemical gradient e. electron potential

membrane potential

Explain how the energy of the photons absorbed by the pigments in the light harvesting complexes associated with PSI and PSII leads to the synthesis of O2, ATP, and NADPH. In your answer follow the fate of the excited electrons and the protons.

photons generated in the process drive the establishment of a proton gradient across the thylakoid membrane, which powers ATP synthesis and the reduction of NADP+ to NADPH. The splitting of water molecules by PSII also releases oxygen gas, which is a waste product of photosynthesis.

Fill in the blank: In __________________ the protein that transports a substance also hydrolyzes ATP to power the transport directly.

primary active transport

In a system in which temperature is uniform, free energy is a. the energy available to do work. b. equivalent to entropy. c. the total energy absorbed by the system d. the kinetic energy of the system e. the total energy of the system.

the energy available to do work.

Fill in the blanks: Following the splitting of water, the resulting protons are released into the _____, contributing to the proton gradient across the _____ membrane.

thylakoid lumen thylakoid

In mitochondria, what oxidizes each of the following? • Complex I • Complex II • Complex III • Complex IV • Cytochrome c

• Complex I (NADH dehydrogenase) oxidizes NADH, which donates its electrons to Complex I via FMN (flavin mononucleotide). • Complex II (succinate dehydrogenase) oxidizes succinate to fumarate, which donates its electrons to the electron transport chain via FAD (flavin adenine dinucleotide). • Complex III (cytochrome bc1 complex) oxidizes ubiquinol (QH2), which donates its electrons to the electron transport chain via cytochrome c. • Complex IV (cytochrome c oxidase) oxidizes cytochrome c, which donates its electrons to Complex IV, ultimately reducing oxygen to water. • Cytochrome c acts as an electron carrier between Complexes III and IV, shuttling electrons from Complex III to Complex IV.