In actively respiring liver mitochondria, the pH in the matrix is about half a pH unit

Human females have 23 different chromosomes, whereas human males have 24.

The four core histones are relatively small proteins with a very high proportion of positively charged amino acids; the positive charge helps the histones bind tightly to DNA, regardless of its nucleotide sequence.

Nucleosomes bind DNA so tightly that they cannot move from the positions where they are first assembled.

In a comparison between the DNAs of related organisms such as humans and mice, identifying the conserved DNA sequences facilitates the search for functionally important regions.

Gene duplication and divergence is thought to have played a critical role in the evolution of increased biological complexity.

DNA isolated from the bacterial virus M13 contains 25% A, 33% T, 22% C, and 20% G. Do these results strike you as peculiar? Why or why not? How might you explain these values?

A segment of DNA from the interior of a single strand is shown in Figure Q41. What is the polarity of this DNA from top to bottom?

Human DNA contains 20% C on a molar basis. What are the mole percents of A, G, and T?

Chromosome 3 in orangutans differs from chromosome 3 in humans by two inversion events that occurred in the human lineage (Figure Q42). Draw the intermediate chromosome that resulted from the first inversion and explicitly indicate the segments included in each inversion.

Assuming that the 30-nm chromatin fiber contains about 20 nucleosomes (200 bp/nucleosome) per 50 nm of length, calculate the degree of compaction of DNA associated with this level of chromatin structure. What fraction of the 10,000-fold condensation that occurs at mitosis does this level of DNA packing represent?

In contrast to histone acetylation, which always correlates with gene activation, histone methylation can lead to either transcriptional activation or repression. How do you suppose that the same modificationmethylationcan mediate different biological outcomes?

Why is a chromosome with two centromeres (a dicentric chromosome) unstable? Would a backup centromere not be a good thing for a chromosome, giving it two chances to form a kinetochore and attach to microtubules during mitosis? Would that not help to ensure that the chromosome did not get left behind at mitosis?

Look at the two yeast colonies in Figure Q43. Each of these colonies contains about 100,000 cells descended from a single yeast cell, originally somewhere in the middle of the clump. A white colony arises when the Ade2 gene is expressed from its normal chromosomal location. When the Ade2 gene is moved to a location near a telomere, it is packed into heterochromatin and inactivated in most cells, giving rise to colonies that are mostly red. In these largely red colonies, white sectors fan out from the middle of the colony. In both the red and white sectors, the Ade2 gene is still located near telomeres. Explain why white sectors have formed near the rim of the red colony. Based on the patterns observed, what can you conclude about the propagation of the transcriptional state of the Ade2 gene from mother to daughter cells in this experiment?

Mobile pieces of DNAtransposable elements that insert themselves into chromosomes and accumulate during evolution make up more than 40% of the human genome. Transposable elements of four typeslong interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), long terminal repeat (LTR) retrotransposons, and DNA transposonsare inserted more-or-less randomly throughout the human genome. These elements are conspicuously rare at the four homeobox gene clusters, HoxA, HoxB, HoxC, and HoxD, as illustrated for HoxD in Figure Q44, along with an equivalent region of chromosome 22, which lacks a Hox cluster. Each Hox cluster is about 100 kb in length and contains 9 to 11 genes, whose differential expression along the anteroposterior axis of the developing embryo establishes the basic body plan for humans (and for other animals). Why do you suppose that transposable elements are so rare in the Hox clusters?

The three respiratory enzyme complexes in the mitochondrial inner membrane tend to associate with each other in ways that facilitate the correct transfer of electrons between appropriate complexes.

The number of c subunits in the rotor ring of ATP synthase defines how many protons need to pass through the turbine to make each molecule of ATP.

Mutations that are inherited according to Mendelian rules affect nuclear genes; mutations whose inheritance violates Mendelian rules are likely to affect organelle genes.

In the 1860s, Louis Pasteur noticed that when he added O2 to a culture of yeast growing anaerobically on glucose, the rate of glucose consumption declined dramatically. Explain the basis for this result, which is known as the Pasteur effect.

Heart muscle gets most of the ATP needed to power its continual contractions through oxidative phosphorylation. When oxidizing glucose to CO2, heart muscle consumes O2 at a rate of 10 mol/min per g of tissue, in order to replace the ATP used in contraction and give a steadystate ATP concentration of 5 mol/g of tissue. At this rate, how many seconds would it take the heart to consume an amount of ATP equal to its steady-state levels? (Complete oxidation of one molecule of glucose to CO2 yields 30 ATP, 26 of which are derived by oxidative phosphorylation using the 12 pairs of electrons captured in the electron carriers NADH and FADH2.)

Both H+ and Ca2+ are ions that move through the cytosol. Why is the movement of H+ ions so much faster than that of Ca2+ ions? How do you suppose the speed of these two ions would be affected by freezing the solution? Would you expect them to move faster or slower? Explain your answer.

If isolated mitochondria are incubated with a source of electrons such as succinate, but without oxygen, electrons enter the respiratory chain, reducing each of the electron carriers almost completely. When oxygen is then introduced, the carriers become oxidized at different rates (Figure Q141). How does this result allow you to order Figure p14.10/14.04 Problem p14.60/14.35 0 50 100 reduced cytochrome (percent) time add succinate add O2 (a + a3) c c1 b Figure Q141 Rapid spectrophotometric analysis of the rates of oxidation of electron carriers in the respiratory chain (Problem 147). Cytochromes a and a3 cannot be distinguished and thus are listed as cytochrome (a + a3). What we dont know What structures are needed to form the barriers that separate and maintain the differentiated membrane domains in a single continuous membraneas for the cristae and inner boundary membrane in mitochondria? How does a eukaryotic cell regulate the many functions of mitochondria, including ATP production? What are the origins and evolutionary history of photosynthetic complexes? Are there undiscovered types of photosynthesis present on Earth to help answer this question? Why is the mutation rate so much higher in mitochondria than in the nucleus (and chloroplasts)? Could this high rate have been useful to the cell? What mechanisms and pathways have been used during evolution to transfer genes from the mitochondrion to the nucleus? the electron carriers in the respiratory chain? What is their order?

Normally, the flow of electrons to O2 is tightly linked to the production of ATP via the electrochemical gradient. If ATP synthase is inhibited, for example, electrons do not flow down the electron-transport chain and respiration ceases. Since the 1940s, several substances such as 2,4-dinitrophenolhave been known to uncouple electron flow from ATP synthesis. Dinitrophenol was once prescribed as a diet drug to aid in weight loss. How would an uncoupler of oxidative phosphorylation promote weight loss? Why do you suppose dinitrophenol is no longer prescribed?

In actively respiring liver mitochondria, the pH in the matrix is about half a pH unit higher than it is in the cytosol. Assuming that the cytosol is at pH 7 and the matrix is a sphere with a diameter of 1 m [V = (4/3)r3], calculate the total number of protons in the matrix of a respiring liver mitochondrion. If the matrix began at pH 7 (equal to that in the cytosol), how many protons would have to be pumped out to establish a matrix pH of 7.5 (a difference of 0.5 pH units)?

ATP synthase is the worlds smallest rotary motor. Passage of H+ ions through the membrane-embedded portion of ATP synthase (the Fo component) causes rotation of the single, central, axle-like subunit inside the head group. The tripartite head is composed of the three dimers, the subunit of which is responsible for synthesis of ATP. The rotation of the subunit induces conformational changes in the dimers that allow ADP and Pi to be converted into ATP. A variety of indirect evidence had suggested rotary catalysis by ATP synthase, but seeing is believing. To demonstrate rotary motion, a modified form of the 33 complex was used. The subunits were modified so they could be firmly anchored to a solid support and the subunit was modified (on the end that normally inserts into the Fo component in the inner membrane) so that a fluorescently tagged, readily visible filament of actin could be attached (Figure Q142A). This arrangement allows rotations of the subunit to be visualized as revolutions of the long actin filament. In these experiments, ATP synthase was studied in the reverse of its normal mechanism by allowing it to hydrolyze ATP. At low ATP concentrations, the actin filament was observed to revolve in steps of 120 and then pause for variable lengths of time, as shown in Figure Q142B. A. Why does the actin filament revolve in steps with pauses in between? What does this rotation correspond to in terms of the structure of the 33 complex? B. In its normal mode of operation inside the cell, how many ATP molecules do you suppose would be synthesized for each complete 360 rotation of the subunit? Explain your answer.

How much energy is available in visible light? How much energy does sunlight deliver to Earth? How efficient are plants at converting light energy into chemical energy? The answers to these questions provide an important backdrop to the subject of photosynthesis. Each quantum or photon of light has energy hv, where h is Plancks constant (6.6 1037 kJ sec/photon) and v is the frequency in sec1. The frequency of light is equal to c/, where c is the speed of light (3.0 1017 nm/ sec) and is the wavelength in nm. Thus, the energy (E) of a photon is E = hv = hc/ A. Calculate the energy of a mole of photons (6 1023 photons/mole) at 400 nm (violet light), at 680 nm (red light), and at 800 nm (near-infrared light). B. Bright sunlight strikes Earth at the rate of about 1.3 kJ/sec per square meter. Assuming for the sake of calculation that sunlight consists of monochromatic light of wavelength 680 nm, how many seconds would it take for a mole of photons to strike a square meter? C. Assuming that it takes eight photons to fix one molecule of CO2 as carbohydrate under optimal conditions (810 photons is the currently accepted value), calculate how long it would take a tomato plant with a leaf area of 1 square meter to make a mole of glucose from CO2. Assume that photons strike the leaf at the rate calculated above and, furthermore, that all the photons are absorbed and used to fix CO2. Figure p14.04/14.07 Problem p14-31/14-47 actin filament direction of rotation inner membrane matrix (A) (B) 0 1 2 3 4 5 0 20 40 60 80 100 revolutions time (seconds) Figure Q142 Experimental set-up for observing rotation of the subunit of ATP synthase (Problem 1410). (A) The immobilized 33 complex. The subunits are anchored to a solid support and a fluorescent actin filament is attached to the subunit. (B) Stepwise revolution of the actin filament. The indicated trace is a typical example from one experiment. The inset shows the positions in the revolution at which the actin filament pauses. (B, from R. Yasuda et al., Cell 93:11171124, 1998. With permission from Elsevier.) 811 Figure p14.23/14.15 Problem p14.109/14.80 REFERENCES D. If it takes 468 kJ/mole to fix a mole of CO2 into carbohydrate, what is the efficiency of conversion of light energy into chemical energy after photon capture? Assume again that eight photons of red light (680 nm) are required to fix one molecule of CO2.

In chloroplasts, protons are pumped out of the stroma across the thylakoid membrane, whereas in mitochondria, they are pumped out of the matrix across the crista membrane. Explain how this arrangement allows chloroplasts to generate a larger proton gradient across the thylakoid membrane than mitochondria can generate across the inner membrane.

Examine the variegated leaf shown in Figure Q143. Yellow patches surrounded by green are common, but there are no green patches surrounded by yellow. Propose an explanation for this phenomenon.