Molecular Biology Of The Cell 6th Edition Bruce Alberts, Alexander D. Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter - Solutions

Figure Q9–2 shows a diagram of the human eye. The refractive indices of the components in the light path are: cornea 1.38, aqueous humor 1.33, crystalline lens 1.41, and vitreous humor 1.38. Where does the main refraction—the main focusing—occur? What role do you suppose the lens plays?Figure
The diagrams in Figure Q9–1 show the paths of light rays passing through a specimen with a dry lens and with an oil-immersion lens. Offer an explanation for why oil immersion lenses should give better resolution. Air, glass, and oil have refractive indices of 1.00, 1.51, and 1.51,
A fluorescent molecule, having absorbed a single photon of light at one wavelength, always emits it at a longer wavelength.Is the statement true? Explain why or why not.
Because the DNA double helix is only 2 nm wide well below the limit of resolution of the light microscope— it is impossible to see chromosomes in living cells without special stains.Is the statement true? Explain why or why not.
Detailed analysis of the regulatory region of the Lac operon has revealed surprising complexity. Instead of a single binding site for the Lac repressor, as might be expected, there are three sites termed operators: O1, O2, and O3, arrayed along the DNA as shown in Figure Q8–7. To probe the
Imagine that a random perturbation positions a bistable system precisely at the boundary between two stable states (at the orange dot in Figure Q8–6). How would the system respond?Figure Q8-6 2 - concentration of X concentration of Y
Examine the network motifs in Figure Q8–5. Decide which ones are negative feedback loops and which are positive. Explain your reasoning.Figure Q8-5 (A) ACTIVATING (B) ACTIVATING INPUT INPUT GENE X GENE X GENE Y GENE Y GENE Z GENE Z (C) ACTIVATING (D) ACTIVATING INPUT INPUT GENE X GENE X GENE Y
You have just gotten back the results from an RNAseq analysis of mRNAs from liver. You had anticipated counting the number of reads of each mRNA to determine the relative abundance of different mRNAs. But you are puzzled because many of the mRNAs have given you results like those shown in Figure
Discuss the following statement: “We would have no idea today of the importance of insulin as a regulatory hormone if its absence were not associated with the human disease diabetes. It is the dramatic consequences of its absence that focused early efforts on the identification of insulin and the
Explain the difference between a gain-of-function mutation and a dominant-negative mutation. Why are both these types of mutation usually dominant?
In the very first round of PCR using genomic DNA, the DNA primers prime synthesis that terminates only when the cycle ends (or when a random end of DNA is encountered). Yet, by the end of 20 to 30 cycles—a typical amplification—the only visible product is defined precisely by the ends of the
You want to amplify the DNA between the two stretches of sequence shown in Figure Q8–3. Of the listed primers, choose the pair that will allow you to amplify the DNA by PCR.Figure Q8-3 DNA to be amplified 5'-GACCTGTGGAAGC- -САТАСGGGAТTGA-3' 3'-CTGGACACCTTCG- GTATGCCCTААСТ-5' primers (1)
You have isolated the proteins from two adjacent spots after two-dimensional polyacrylamide-gel electrophoresis and digested them with trypsin. When the masses of the peptides were measured by MALDI-TOF mass spectrometry, the peptides from the two proteins were found to be identical except for one
How many copies of a protein need to be present in a cell in order for it to be visible as a band on an SDS gel? Assume that you can load 100 μg of cell extract onto a gel and that you can detect 10 ng in a single band by silver staining the gel. The concentration of protein in cells is about 200
Hybridoma technology allows one to generate monoclonal antibodies to virtually any protein. Why is it, then, that genetically tagging proteins with epitopes is such a commonly used technique, especially since an epitope tag has the potential to interfere with the function of the protein?
Tropomyosin, at 93 kd, sediments at 2.6S, whereas the 65-kd protein, hemoglobin, sediments at 4.3S. (The sedimentation coefficient S is a linear measure of the rate of sedimentation.) These two proteins are drawn to scale in Figure Q8–1. How is it that the bigger protein sediments more slowly
A common step in the isolation of cells from a sample of animal tissue is to treat the tissue with trypsin, collagenase, and EDTA. Why is such a treatment necessary, and what does each component accomplish? And why does this treatment not kill the cells?
After a sudden increase in transcription, a protein with a slow rate of degradation will reach a new steady state level more quickly than a protein with a rapid rate of degradation.Is the statement true? Explain why or why not.
The rate of change in the concentration of any molecular species X is given by the balance between its rate of appearance and its rate of disappearance.Is the statement true? Explain why or why not.
To judge the biological importance of an interaction between protein A and protein B, we need to know quantitative details about their concentrations, affinities, and kinetic behaviors.Is the statement true? Explain why or why not.
If each cycle of PCR doubles the amount of DNA synthesized in the previous cycle, then 10 cycles will give a 103-fold amplification, 20 cycles will give a 106-fold amplification, and 30 cycles will give a 109-fold amplification.Is the statement true? Explain why or why not.
Given the inexorable march of technology, it seems inevitable that the sensitivity of detection of molecules will ultimately be pushed beyond the yoctomole level (10–24 mole). Is the statement true? Explain why or why not.
Because a monoclonal antibody recognizes a specific antigenic site (epitope), it binds only to the specific protein against which it was made.Is the statement true? Explain why or why not.
If you insert a β-galactosidase gene lacking its own transcription control region into a cluster of piRNA genes in Drosophila, you find that β-galactosidase expression from a normal copy elsewhere in the genome is strongly inhibited in the fly’s germ cells. If the inactive β-galactosidase gene
Examine the two pedigrees shown in Figure Q7–3. One results from deletion of a maternally imprinted autosomal gene. The other pedigree results from deletion of a paternally imprinted autosomal gene. In both pedigrees, affected individuals (red symbols) are heterozygous for the deletion. These
Imagine the two situations shown in Figure Q7–2. In cell 1, a transient signal induces the synthesis of protein A, which is a transcription activator that turns on many genes including its own. In cell 2, a transient signal induces the synthesis of protein R, which is a transcription repressor
How is it that protein–protein interactions that are too weak to cause proteins to assemble in solution can nevertheless allow the same proteins to assemble into complexes on DNA?
Some transcription regulators bind to DNA and cause the double helix to bend at a sharp angle. Such “bending proteins” can affect the initiation of transcription without directly contacting any other protein. Can you devise a plausible explanation for how such proteins might work to modulate
The nucleus of a eukaryotic cell is much larger than a bacterium, and it contains much more DNA. As a consequence, a transcription regulator in a eukaryotic cell must be able to select its specific binding site from among many more unrelated sequences than does a transcription regulator in a
What are the two fundamental components of a genetic switch?
Comparisons of the patterns of mRNA levels across different human cell types show that the level of expression of almost every active gene is different. The patterns of mRNA abundance are so characteristic of cell type that they can be used to determine the tissue of origin of cancer cells, even
A small portion of a two-dimensional display of proteins from human brain is shown in Figure Q7–1. These proteins were separated on the basis of size in one dimension and electrical charge (isoelectric point) in the other. Not all protein spots on such displays are products of different genes;
In most differentiated tissues, daughter cells retain a memory of gene expression patterns that were present in the parent cell through mechanisms that do not involve changes in the sequence of their genomic DNA.Is the statement true? Explain why or why not.
CG islands are thought to have arisen during evolution because they were associated with portions of the genome that remained unmethylated in the germ line.Is the statement true? Explain why or why not.
Once cells have differentiated to their final specialized forms, they never again alter expression of their genes.Is the statement true? Explain why or why not.
In terms of the way it interacts with DNA, the helix–loop–helix motif is more closely related to the leucine zipper motif than it is to the helix turn–helix motif.Is the statement true? Explain why or why not.
Imagine a warm pond on the primordial Earth. Chance processes have just assembled a single copy of an RNA molecule with a catalytic site that can carry out RNA replication. This RNA molecule folds into a structure that is capable of linking nucleotides according to instructions in an RNA template.
If an RNA molecule could form a hairpin with a symmetric internal loop, as shown in Figure Q6–5, could the complement of this RNA form a similar structure? If so, would there be any regions of the two structures that are identical? Which ones?Figure Q6-5 C-U 5'-G-C-A C-C-G. II I U G-G-C 3'-c-G-U
What is so special about RNA that it is hypothesized to be an evolutionary precursor to DNA and protein? What is it about DNA that makes it a better material than RNA for storage of genetic information?
Most proteins require molecular chaperones to assist in their correct folding. How do you suppose the chaperones themselves manage to fold correctly?
Both hsp60-like and hsp70 molecular chaperones share an affinity for exposed hydrophobic patches on proteins, using them as indicators of incomplete folding. Why do you suppose hydrophobic patches serve as critical signals for the folding status of a protein?
Prokaryotes and eukaryotes both protect against the dangers of translating broken mRNAs. What dangers do partial mRNAs pose for the cell?
Which of the following mutational changes would you predict to be the most deleterious to gene function? Explain your answers.1. Insertion of a single nucleotide near the end of the coding sequence.2. Removal of a single nucleotide near the beginning of the coding sequence.3. Deletion of three
After treating cells with a chemical mutagen, you isolate two mutants. One carries alanine and the other carries methionine at a site in the protein that normally contains valine (Figure Q6–4). After treating these two mutants again with the mutagen, you isolate mutants from each that now carry
The human α-tropomyosin gene is alternatively spliced to produce different forms of α-tropomyosin mRNA in different cell types (Figure Q6–3). For all forms of the mRNA, the protein sequences encoded by exon 1 are the same, as are the protein sequences encoded by exon 10. Exons 2 and 3 are
You have attached an RNA polymerase molecule to a glass slide and have allowed it to initiate transcription on a template DNA that is tethered to a magnetic bead as shown in Figure Q6–2. If the DNA with its attached magnetic bead moves relative to the RNA polymerase as indicated in the figure, in
In which direction along the template must the RNA polymerase in Figure Q6–1 be moving to have generated the supercoiled structures that are shown? Would you expect supercoils to be generated if the RNA polymerase were free to rotate about the axis of the DNA as it progressed along the
Protein enzymes are thought to greatly outnumber ribozymes in modern cells because they can catalyze a much greater variety of reactions and all of them have faster rates than any ribozyme.Is the statement true? Explain why or why not.
During protein synthesis, the thermodynamics of base-pairing between tRNAs and mRNAs sets the upper limit for the accuracy with which protein molecules are made.Is the statement true? Explain why or why not.
Wobble pairing occurs between the first position in the codon and the third position in the anticodon.Is the statement true? Explain why or why not.
Since introns are largely genetic “junk,” they do not have to be removed precisely from the primary transcript during RNA splicing.Is the statement true? Explain why or why not.
The consequences of errors in transcription are less severe than those of errors in DNA replication.Is the statement true? Explain why or why not.
Cre recombinase is a site-specific enzyme that catalyzes recombination between two LoxP DNA sites. Cre recombinase pairs two LoxP sites in the same orientation, breaks both duplexes at the same point in each LoxP site, and joins the ends with new partners so that each LoxP site is regenerated, as
In addition to correcting DNA mismatches, the mismatch repair system functions to prevent homologous recombination from taking place between similar but not identical sequences. Why would recombination between similar, but nonidentical sequences pose a problem for human cells?
Draw the structure of the double Holliday junction that would result from strand invasion by both ends of the broken duplex into the intact homologous duplex shown in Figure Q5–3. Label the left end of each strand in the Holliday junction 5ʹ or 3ʹ so that the relationship to the parental and
With age, somatic cells are thought to accumulate genomic “scars” as a result of the inaccurate repair of double- strand breaks by nonhomologous end joining (NHEJ).Estimates based on the frequency of breaks in primary human fibroblasts suggest that by age 70, each human somatic cell may carry
If you compare the frequency of the sixteen possible dinucleotide sequences in the E. coli and human genomes, there are no striking differences except for one dinucleotide, 5ʹ-CG-3ʹ. The frequency of CG dinucleotides in the human genome is significantly lower than in E. coli and significantly
You are investigating DNA synthesis in tissue-culture cells, using 3H-thymidine to radioactively label the replication forks. By breaking open the cells in a way that allows some of the DNA strands to be stretched out, very long DNA strands can be isolated intact and examined. You overlay the DNA
The laboratory you joined is studying the life cycle of an animal virus that uses circular, double-strand DNA as its genome. Your project is to define the location of the origin(s) of replication and to determine whether replication proceeds in one or both directions away from an origin
If DNA polymerase requires a perfectly paired primer in order to add the next nucleotide, how is it that any mismatched nucleotides “escape” this requirement and become substrates for mismatch repair enzymes?
Discuss the following statement: “Primase is a sloppy enzyme that makes many mistakes. Eventually, the RNA primers it makes are replaced with DNA made by a polymerase with higher fidelity. This is wasteful. It would be more energy-efficient if a DNA polymerase made an accurate copy in the first
DNA repair enzymes preferentially repair mismatched bases on the newly synthesized DNA strand, using the old DNA strand as a template. If mismatches were instead repaired without regard for which strand served as template, would mismatch repair reduce replication errors? Would such a mismatch
To determine the reproducibility of mutation frequency measurements, you do the following experiment. You inoculate each of 10 cultures with a single E. coli bacterium, allow the cultures to grow until each contains 106 cells, and then measure the number of cells in each culture that carry a
DNA repair mechanisms all depend on the existence of two copies of the genetic information, one in each of the two homologous chromosomes.Is the statement true? Explain why or why not.
When bidirectional replication forks from adjacent origins meet, a leading strand always runs into a lagging strand.Is the statement true? Explain why or why not.
In a replication bubble, the same parental DNA strand serves as the template strand for leading-strand synthesis in one replication fork and as the template for lagging-strand synthesis in the other fork.Is the statement true? Explain why or why not.
In E. coli, where the replication fork travels at 500 nucleotide pairs per second, the DNA ahead of the fork— in the absence of topoisomerase would have to rotate at nearly 3000 revolutions per minute.Is the statement true? Explain why or why not.
Mobile pieces of DNA—transposable elements— that insert themselves into chromosomes and accumulate during evolution make up more than 40% of the human genome. Transposable elements of four types—long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), long
Look at the two yeast colonies in Figure Q4–3. 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
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
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 modification methylation— can mediate different biological outcomes?
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
Chromosome 3 in orangutans differs from chromosome 3 in humans by two inversion events that occurred in the human lineage (Figure Q4–2). Draw the intermediate chromosome that resulted from the first inversion and explicitly indicate the segments included in each inversion. two inversions
Human DNA contains 20% C on a molar basis. What are the mole percents of A, G, and T?
A segment of DNA from the interior of a single strand is shown in Figure Q4–1. What is the polarity of this DNA from top to bottom?Figure Q4-1 A CH20. 0-p-O CH20 O-P=O CH20.
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?
Gene duplication and divergence is thought to have played a critical role in the evolution of increased biological complexity.Is the statement true? Explain why or why not.
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.Is the statement true? Explain why or why not.
Nucleosomes bind DNA so tightly that they cannot move from the positions where they are first assembled.Is the statement true? Explain why or why not.
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.Which statements are true? Explain why or why not.
Human females have 23 different chromosomes, whereas human males have 24.Is the statement true? Explain why or why not.
Synthesis of the purine nucleotides AMP and GMP proceeds by a branched pathway starting with ribose 5-phosphate (R5P), as shown schematically in Figure Q3–4. Using the principles of feedback inhibition, propose a regulatory strategy for this pathway that ensures an adequate supply of both AMP and
How do you suppose that a molecule of hemoglobin is able to bind oxygen efficiently in the lungs, and yet release it efficiently in the tissues?
The enzyme hexokinase adds a phosphate to D-glucose but ignores its mirror image, L-glucose. Suppose that you were able to synthesize hexokinase entirely from D amino acids, which are the mirror image of the normal L-amino acids.A. Assuming that the “D” enzyme would fold to a stable
Many enzymes obey simple Michaelis–Menten kinetics, which are summarized by the equationrate = Vmax [S]/([S] + Km)where Vmax = maximum velocity, [S] = concentration of substrate, and Km = the Michaelis constant.It is instructive to plug a few values of [S] into the equation to see how rate is
The protein SmpB binds to a special species of tRNA, tmRNA, to eliminate the incomplete proteins made from truncated mRNAs in bacteria. If the binding of SmpB to tmRNA is plotted as fraction tmRNA bound versus SmpB concentration, one obtains a symmetrical S-shaped curve as shown in Figure Q3–3. $1.0 0.75 0.5 0.25 10-11 10-9 concentration of SmpB (M) 10-7 10-5 fraction bound$
An antibody binds to another protein with an equilibrium constant, K, of 5 × 109 M–1. When it binds to a second, related protein, it forms three fewer hydrogen bonds, reducing its binding affinity by 11.9 kJ/mole. What is the K for its binding to the second protein? (Free-energy change is
Rous sarcoma virus (RSV) carries an oncogene called Src, which encodes a continuously active protein tyrosine kinase that leads to unchecked cell proliferation. Normally, Src carries an attached fatty acid (myristoylate) group that allows it to bind to the cytoplasmic side of the plasma membrane. A
Titin, which has a molecular weight of about 3 × 106, is the largest polypeptide yet described. Titin molecules extend from muscle thick filaments to the Z disc; they are thought to act as springs to keep the thick filaments centered in the sarcomere. Titin is composed of a large number of
A common strategy for identifying distantly related homologous proteins is to search the database using a short signature sequence indicative of the particular protein function. Why is it better to search with a short sequence than with a long sequence? Do you not have more chances for a “hit”
The so-called kelch motif consists of a fourstranded β sheet, which forms what is known as a β propeller. It is usually found to be repeated four to seven times, forming a kelch repeat domain in a multidomain protein.One such kelch repeat domain is shown in Figure Q3–1. Would you classify this
Consider the following statement. “To produce one molecule of each possible kind of polypeptide chain, 300 amino acids in length, would require more atoms than exist in the universe.” Given the size of the universe, do you suppose this statement could possibly be correct? Since counting atoms
Continual addition and removal of phosphates by protein kinases and protein phosphatases is wasteful of energy—since their combined action consumes ATP— but it is a necessary consequence of effective regulation by phosphorylation.Is the statement true? Explain why or why not.
Enzymes that undergo cooperative allosteric transitions invariably consist of symmetric assemblies of multiple subunits.Is the statement true? Explain why or why not.
Higher concentrations of enzyme give rise to a higher turnover number.Is the statement true? Explain why or why not.
An enzyme reaches a maximum rate at high substrate concentration because it has a fixed number of active sites where substrate binds.Is the statement true? Explain why or why not.
Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules.Is the statement true? Explain why or why not.
Intrinsically disordered regions of proteins can be identified using bioinformatic methods to search genes for encoded amino acid sequences that possess high hydrophobicity and low net charge.Is the statement true? Explain why or why not.
Each strand in a β sheet is a helix with two amino acids per turn.Is the statement true? Explain why or why not.
In the absence of oxygen, cells consume glucose at a high, steady rate. When oxygen is added, glucose consumption drops precipitously and is then maintained at the lower rate. Why is glucose consumed at a high rate in the absence of oxygen and at a low rate in its presence?

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Molecular Biology Of The Cell 6th Edition Bruce Alberts, Alexander D. Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter - Solutions

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