Cell Biology Final
Indicate true (T) and false (F) statements below regarding the genetic systems of mitochondria and chloroplasts. Your answer would be a four-letter string composed of letters T and F only, e.g. TFTT. Which is the most incorrect of the answers. Explain why. ( ) Most proteins in these organelles are encoded by the organelle's genome. ( ) Mammalian mtDNA can make up less than 1% of the total cellular DNA. ( ) In some highly specialized animal cells, mtDNA can comprise as much as 99% of the cellular DNA. ( ) The genetic systems of these organelles are most similar to extremophilic archaea.
ANSWER: FTTF The genetic systems of mitochondria and chloroplasts resemble those of prokaryotes. However, intracellular gene transfer to the nucleus over an evolutionary time scale has shrunk their genomes to a level such that most of their proteins are encoded by the nucleus in modern organisms. Depending on the number of mitochondria and their chromosome copy number, mitochondrial DNA (mtDNA) can account for less than 1% to about 99% of total DNA weight in a cell.
Indicate true (T) and false (F) statements below regarding the evolution of photosynthesis and oxidative phosphorylation. Your answer would be a five-letter string composed of letters T and F only, e.g. TTFTF. Which is the most incorrect of all the answers? Why? ( ) Chloroplasts are thought to descend from ancient purple sulfur bacteria. ( ) Mitochondria are thought to descend from ancient α-proteobacteria. ( ) The first photosynthetic cyanobacteria evolved before the first aerobic proteobacteria. ( ) All photosynthetic and aerobic bacteria are thought to have evolved from a common ancestor capable of fermentation and membrane electron transport.
ANSWER: FTTT Aerobic proteobacteria evolved from ancestral purple non-sulfur bacteria only after the atmosphere of the Earth became oxidizing. Chloroplasts are thought to have arisen from cyanobacteria.
Mitotic segregation of organelles can lead to so-called homoplasmy, when all organelles in each cell carry the same genome. In contrast, heteroplasmy describes the presence of organelles within the same cell that are different with respect to their genomic sequences. Would you expect a defect in the mitochondrial fusion machinery to favor homoplasmy (M) or heteroplasmy (T)? Write down M or T as your answer. Explain why.
ANSWER: M Mitochondrial fusion works to ensure an even distribution of mitochondrial DNA throughout the cell. Fusion can reduce the effect of mitotic segregation and favor heteroplasmy. Thus, a defect in fusion should favor homoplasmy.
Indicate whether each of the following descriptions better applies to the genome of mitochondria (M) or nuclei (N) in vertebrates. Your answer would be a four-letter string composed of letters M and N only, e.g. MNMN. ( ) It has a higher percentage of noncoding DNA. ( ) It has a stricter codon usage. ( ) Its genes are present at higher copy numbers per cell. ( ) Its evolutionary clock ticks much faster.
ANSWER: NNMM Mitochondria have a dense packing of genes in their genome, a relaxed codon usage, and occasional variant genetic codes. Mutation rate is much higher for mitochondrial DNA, making it useful for phylogenetic studies on relatively recent evolutionary changes.
Indicate whether each of the following descriptions better applies to cytochrome c oxidase complex (O), cytochrome c reductase complex (R), or NADH dehydrogenase complex (N). Your answer would be a four-letter string composed of letters O, R, and N only, e.g. RONN. ( ) It is the largest of the three respiratory complexes. ( ) It accounts for the majority of O2 uptake in most cells. ( ) It employs the Q cycle to increase proton pumping. ( ) It contains separate modules for electron transport and proton pumping.
ANSWER: NORN NADH dehydrogenase complex is the largest respiratory enzyme complex embedded in the inner mitochondrial membrane and contains separate modules for electron transport (from NADH to ubiquinone) and proton pumping (across the membrane out of the matrix). The cytochrome c reductase complex reduces cytochrome c using electrons delivered by ubiquinol by the Q cycle mechanism. Finally, the cytochrome c oxidase complex accepts electrons from cytochrome c and reduces O2.
Consider two organisms, one with a much larger mitochondrial genome than the other. Which one is expected to show more deviations from the universal genetic code: the one with the larger mitochondrial genome (L) or the one with a smaller genome (S)? Write down L or S as your answer. Explain your reasoning
ANSWER: S Apparently, the unusually small number of genes in mitochondrial genomes allows random drift to result in deviations of the genetic code.
The synthetic toxin 2,4-dinitrophenol can uncouple ATP synthesis from mitochondrial respiration by decreasing the permeability of the inner membrane to protons. What would be the effect of dinitrophenol treatment on the amount of ATP produced by mitochondria and on the rate of ATP transport across the inner membrane, respectively? What is the most incorrect of the answers below? Explain why. A. Positive; positive B. Positive; negative C. Negative; positive D. Negative; negative
ASNWER: D By diminishing the electrochemical gradient across the inner membrane, the toxin interferes with ATP synthesis and ATP/ADP exchange, both of which are driven by the gradient.
Indicate which letter (A to D) in the schematic drawings below of a mitochondrion and a chloroplast corresponds to each of the following features. Your answer would be a four-letter string composed of letters A to D only, e.g. BDCA. Each letter should be used once. [21] ( ) Crista ( ) Stroma ( ) Matrix ( ) Thylakoid
Answer: ACBD. The stroma and matrix are analogous, whereas the thylakoid space is an extra compartment not found in mitochondria.
In addition to their respiratory function, mitochondria have other important roles in cellular metabolism. Which of the following processes is NOT carried out mainly by mitochondria? [5] A. Biosynthesis of cardiolipin B. Biosynthesis of fatty acids C. Catabolism of amino acids D. Biosynthesis of heme E. Biosynthesis of iron-sulfur clusters
Answer: B. Fatty acid biosynthesis is confined to the cytosol, where the citrate exported from mitochondria is used to produce acetyl CoA in the initial step.
When the special pair in a photosystem is excited by a quantum of light, charge separation can occur. Where does this take place? What is the charge of the ionized chlorophyll? A. In the antenna complex; positive B. In the antenna complex; negative C. In the reaction center; positive D. In the reaction center; negative
Answer: C. Ionization of chlorophyll occurs primarily in the reaction center and results in the transfer of an electron from the pigment to an electron carrier. In the antenna complex, excitation normally leads to resonance energy transfer.
The electrons used in carbon fixation by chloroplasts ultimately come from: A. Atmospheric oxygen B. Atmospheric carbon dioxide C. Water D. Glyceraldehyde 3-phosphate
Answer: C. Two water molecules provide four electrons and four protons and produce one molecule of oxygen in the electron-transfer reactions.
The water-splitting step in photosynthesis: A. occurs on the stromal side of the thylakoid membrane. B. is catalyzed by an iron-sulfur cluster. C. consumes H+ and therefore contributes to the proton gradient across the thylakoid membrane. D. generates all the O2 in the Earth's atmosphere. E. All of the above.
Answer: D. This step is catalyzed by an enzyme that contains a manganese cluster and is located on the lumenal side of the membrane. It generates O2 as well as H+ in the lumen.
In the following schematic drawing of the inner and outer mitochondrial membranes, in what region (A to D) would you expect to find more ATP synthase dimers?
Answer: D. The ATP synthase dimers tend to localize at the tip of the cristae where the membrane curvature is greatest.
Indicate whether each of the following descriptions better applies to the light (L) or dark (D) reactions in plant chloroplasts. Your answer would be a five-letter string composed of letters L and D only, e.g. DDDLD. ( ) It produces the sugar glyceraldehyde 3-phosphate. ( ) It involves the electron-transfer chain embedded in the thylakoid membrane. ( ) It involves O2 production. ( ) It involves fixation of CO2. ( ) It generates ATP.
Answer: DLLDL. The light reactions (or photosynthetic electron-transfer reactions) occur in complexes embedded in the thylakoid membrane. The dark reactions (carbon-fixation reactions) begin in the stroma.
ATP synthase molecules in mitochondria form dimers that are localized mostly to sharp cristae ridges. What should happen if subunits of the synthase that are required for dimerization are mutated in yeast? A. Oxygen consumption would drop B. Cristae ridges would disappear C. Cell growth would slow down D. Monomeric ATP synthases would distribute randomly over the inner membrane E. All of the above
Answer: E. Dimerization of ATP synthase has a key role in controlling the curvature of the inner membrane
Which of the following is true regarding light-harvesting complexes in plant chloroplasts? A. They contain chlorophyll and other pigments. B. They are found in both photosystem I and photosystem II. C. They can protect the cell by preventing the generation of reactive oxygen species. D. They cannot carry out charge separation. E. All of the above.
Answer: E. Light-harvesting antenna complexes, found in both photosystems, contain chlorophyll molecules as well as orange carotenoid pigments. They help prevent the formation of harmful oxygen radicals. They collect the energy of a sufficient number of photons for photosynthesis, and pass the energy to the special pair in the reaction center, where the charge-separation step takes place.
In actively respiring mitochondria, where in the following schematic drawing of the inner and outer mitochondrial membranes would you expect to find the lowest local pH?
Answer: E. The ATP synthase dimers create proton "sinks" or "traps" at the cristae tips, which helps them make efficient use of the protons that are pumped out of the matrix.
Indicate true (T) and false (F) statements below regarding carbon fixation in plant cells. Your answer would be a five-letter string composed of letters T and F only, e.g. TTFTF. ( ) Carbon fixation in photosynthetic cells eventually generates glucose, the major form of sugar that is transported to other plant tissues. ( ) Plant cells can generate fat droplets in their chloroplasts using glyceraldehyde 3-phosphate. ( ) ATP generated in the light cycle is the major source of ATP used by the plant cell to power all of its biochemical reactions. ( ) Plant cells can generate starch granules in their chloroplasts using glyceraldehyde 3-phosphate. ( ) Pyruvate is generated in the chloroplast by the glycolytic pathway.
Answer: FTFTF. Fat droplets and starch granules can be generated in chloroplasts from accumulated glyceraldehyde 3-phosphate. Sucrose is made mostly in the cytosol and is transported as the main form of sugar to other plant tissues. Also in the cytosol, the glycolytic pathway produces metabolites that can be used to generate ATP in mitochondria, as similarly occurs in animal cells.
Indicate whether each of the following statements better describes ATP production in chloroplasts (C) or in mitochondria (M). Your answer would be a four-letter string composed of letters C and M only, e.g. MCMM. ( ) The electrochemical gradient that drives ATP production is dominated by the electrical component. ( ) It involves a significant pH difference across the membrane. ( ) The ATP synthase molecules form dimers. ( ) The ATP synthase molecules are distributed randomly in flat membrane regions.
Answer: MCMC. Whereas a pH difference predominates in chloroplasts, the contribution of membrane potential to the proton-motive force is greater in mitochondria. Chloroplast ATP synthases do not form dimers. The mitochondrial ATP synthase complexes, in contrast, form long rows of dimers along the cristae ridges and are not distributed randomly in the membrane
Indicate true (T) and false (F) statements below regarding mitochondria. Your answer would be a four-letter string composed of letters T and F only, e.g. TFTT. ( ) Mitochondria are small round organelles that are often associated with actin filaments of the cytoskeleton. ( ) In sperm cells, mitochondria are seen wrapping tightly around the nucleus. ( ) Mitochondria are large enough to be seen with modern light microscopy, and can occupy as much as 20% of cytoplasmic volume. ( ) The outer mitochondrial membrane is freely permeable to ions and small molecules.
FFTT
For mitochondria that are active in respiration, indicate whether the movement of each of the following molecules into (I) or out of (O) the matrix is thermodynamically favorable. Your answer would be a four-letter string composed of letters I and O only, e.g. IOOI. ( ) O2 ( ) H+ ( ) ADP ( ) CO2
IIIO In mitochondria that are active in respiration, O2 and ADP are constantly consumed to produce H2O and ATP, respectively. This creates concentration gradients that favor the movement of these molecules into the organelle. The opposite is true for CO2 which is generated inside the matrix in decarboxylation reactions of the citric acid cycle. Protons are actively pumped out of the matrix by the proteins of the electron-transport chain, and power ATP production when they move into the matrix down their electrochemical gradient
Two haploid budding yeast cells are allowed to mate. One of them carries a mutation in its mitochondrial DNA that makes the yeast cell resistant to an antifungal drug. If the resulting diploid zygote is allowed to propagate (in the absence of the drug), how do you predict that the fraction of drug-resistant cells will change over time in the population? Choose the best curve (A to F) from the following graph. Note that the "population" is only composed of one cell at the beginning of the experiment. The curves are smoothened to cancel stochastic fluctuations that happen at such low population sizes. Explain your answer.
ANSWER: B Negative curve to 0 The zygote is resistant to the drug. However, over generations, mitotic segregation of mitochondrial DNA will randomly give rise to cells that only contain the wild-type, non-resistant organelles, and this should occur in about half of the population.
Which of the following probably occurred first on Earth? Explain your reasoning. A. H2O photosynthesis B. H2S photosynthesis C. O2 respiration D. Eukaryotic photosynthesis
ANSWER: B The earliest forms of photosynthesis used molecules such as H2S.
What is the main reason why atmospheric oxygen levels did not rise immediately after the mass production of the gas by photosynthetic bacteria? What would have happened if oxygen levels drastically went up? A. Because oxygen was rapidly consumed by aerobic microorganisms. B. Because oxygen was dissolved in water. C. Because large amounts of ferrous ions reduced the oxygen molecules. D. Because oxygen was rapidly recycled by early photosynthetic bacteria.
ANSWER: C Only after the supply of ferrous iron (Fe2+) was exhausted did the level of O2 in the atmosphere begin to rise steeply.
Which of the following does NOT occur in the normal process of light-driven production of ATP and NADPH in plant chloroplasts? Explain your answer. A. The cytochrome b6-f complex pumps protons from the stroma into the thylakoid lumen. B. The oxygen-evolving enzyme generates protons in the thylakoid lumen. C. The ferredoxin-NADP+ reductase generates protons in the thylakoid lumen. D. The ATP synthase transports protons from the thylakoid lumen to the stroma.
ANSWER: C The production of NADPH occurs on the stromal side of the thylakoid membrane and consumes two protons per molecule of NADPH generated
Order the following metabolic innovations to reflect the most likely order in which they evolved during biological evolution. Your answer would be a four-letter string composed of letters A to D only, e.g. BDCA. Explain your answer. (A) Using light energy to generate reducing power (B) Splitting of water molecules (an electron source) (C) Fermentation of organic material (D) Reduction of molecular oxygen (a terminal electron acceptor)
ANSWER: CABD Aerobic metabolism evolved after molecular oxygen became abundant due to the activity of ancient cyanobacteria. Fermentation is thought to have arisen before the harnessing of light energy to produce reducing power.
Indicate whether each of the following descriptions better applies to chloroplasts (C) or mitochondria (M). Your answer would be a five-letter string composed of letters C and M only, e.g. MMMMC. ( ) Extensive editing occurs on their RNAs. ( ) They utilize dynamin-like GTPases to divide from the outside. ( ) The organization of gene clusters in their genome is strikingly similar to cyanobacteria. ( ) They typically have larger genomes. ( ) They have a more ancient endosymbiotic relationship with their host.
ANSWER: CMCCM The chloroplast was derived later than the mitochondrion in the evolutionary history of the eukaryotic cell. Chloroplasts are generally larger than mitochondria and contain larger genomes. They share many striking similarities with bacteria, including similar genome organization and similar division mechanisms. Despite this, RNA-editing and RNA processing are prevalent in chloroplasts and are catalyzed by proteins not found in bacteria.
You have isolated mitochondria from a liver tissue sample, suspended them in a hypotonic buffer that causes them to swell and burst their outer membrane, and then added sucrose to a final concentration of about 25%. You then layer the suspension on a density gradient, ultracentrifuge, collect the different fractions, and analyze their protein content. Which of the following proteins would you expect to be highly enriched in the lower density and higher density fractions, respectively? Explain why you chose your answer and not the other options. A. Cytochrome oxidase; porin B. Cytochrome oxidase; ATP synthase C. ATP synthase; cytochrome oxidase D. Porin; ATP synthase
ANSWER: D The low-density fractions would mostly contain outer-membrane components such as porins, while the high-density fractions correspond to the matrix and inner membrane.
The water-splitting step in photosynthesis: Find a figure in the book that visually summarizes your answer and attach it below. A. occurs on the stromal side of the thylakoid membrane. B. is catalyzed by an iron-sulfur cluster. C. consumes H+ and therefore contributes to the proton gradient across the thylakoid membrane. D. generates all the O2 in the Earth's atmosphere. E. All of the above
ANSWER: D This step is catalyzed by an enzyme that contains a manganese cluster and is located on the lumenal side of the membrane. It generates O2 as well as H+ in the lumen
In mammals, mitochondria are inherited: Explain why. A. in a non-Mendelian fashion. B. maternally. C. cytoplasmically. D. uniparentally. E. All of the above
ANSWER: E A mammalian zygote's mitochondria almost exclusively come from the egg.
Sort the following molecules to reflect the order in which they transfer electrons in noncyclic photophosphorylation in plants. Your answer would be an eight-letter string composed of letters A to H only, e.g. FCDEHGBA. Explain your answer. [30] (A) Ferredoxin-NADP+ reductase (B) Plastoquinone (C) Ferredoxin (D) Cytochrome b6-f complex (E) H2O (F) Plastocyanin (G) Photosystem I (H) Photosystem II
ANSWER: EHBDFGCA Please refer to Figure 14-52.
Sort the following molecules to reflect the order in which they carry electrons in the respiratory chain. Your answer would be a seven-letter string composed of letters A to G only, e.g. GFADCBE. Find a figure in the book that visually summarizes your answer and attach it below. (A) NADH dehydrogenase complex (B) Cytochrome c oxidase complex (C) Cytochrome c reductase complex (D) Cytochrome c (E) Ubiquinone (F) NADH (G) H2O
ANSWER: FAECDBG This chain transports electrons from NADH to oxygen.
Indicate whether each of the following descriptions better matches the outer mitochondrial membrane (O), the intermembrane space (S), the crista membrane portion of the inner mitochondrial membrane (I), or the matrix (M). Your answer would be a four-letter string composed of letters O, S, I, and M only, e.g. OMIM. ( ) It is where NADH is produced. ( ) It is composed of 75% protein by weight. ( ) It is where the respiratory chain is located. ( ) It has the same electrochemical potential for H+ as the cytoplasm.
MIIS The electrochemical gradient of protons is established across the inner membrane, with higher potential on the outer side. However, there is no such gradient across the outer membrane, which is freely permeable to protons. The crista membrane houses the respiratory-chain proteins and other proteins at a very high density. The citric acid cycle proteins that generate NADH, on the other hand, are located in the matrix, which is approximately 50% protein by weight.
Who has a different mitochondrial DNA in a family? Explain why. A. The son B. The father C. The mother D. The daughter E. The maternal grandmother
ANSWER: B Mitochondria are inherited maternally, and a genetic disease caused by mutations in the mitochondrial genome in a founder female would be inherited by all descendants.
Indicate whether each of the following descriptions better applies to photosystem I (1) or photosystem II (2). Your answer would be a four-digit number composed of digits 1 and 2 only, e.g. 2212. Find a figure in the book that visually summarizes your answer and attach it below. ( ) It reduces plastoquinone. ( ) It uses a manganese cluster to oxidize water. ( ) It is confined to unstacked thylakoids. ( ) It contains the special pair P680
ANSWER: 2212 Whereas photosystem I (with the special pair P700) is confined to unstacked stroma thylakoids, the stacked grana thylakoids contain photosystem II (with special pair P680). The excited P680 chlorophyll in photosystem II withdraws electrons from water held by a manganese cluster linked to the protein. The electrons are eventually passed on to plastoquinone.
A hypothetical electron-transport chain contains an electron donor (1), an electron carrier (2), and an electron acceptor (3). Which of these molecules has the highest redox potential? Write down 1, 2, or 3 as your answer. Explain why you chose your answer and not the other options.
ANSWER: 3 Higher redox potential corresponds to an increased affinity for electrons. Consecutive electron carriers along the electron-transport chain have increasingly higher redox potentials.
