Questions and Answers of Molecular Cell Biology

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
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
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
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
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 -
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
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
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
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
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
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
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
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,
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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).
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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?
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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