Questions and Answers of Molecular Cell Biology

“Diffusion” sounds slow—and over everyday distances it is—but on the scale of a cell it is very fast. The average instantaneous velocity of a particle in solution—that is, the velocity
The three molecules in Figure Q2–2 contain the seven most common reactive groups in biology. Most molecules in the cell are built from these functional groups. Indicate and name the functional
A histidine side chain is known to play an important role in the catalytic mechanism of an enzyme; however, it is not clear whether histidine is required in its protonated (charged) or unprotonated
The molecular weight of ethanol (CH3CH2OH) is 46 and its density is 0.789 g/cm3.A. What is the molarity of ethanol in beer that is 5% ethanol by volume? [Alcohol content of beer varies from about 4%
The organic chemistry of living cells is said to be special for two reasons: it occurs in an aqueous environment and it accomplishes some very complex reactions. But do you suppose it is really all
The oxygen consumed during the oxidation of glucose in animal cells is returned as CO2 to the atmosphere.Is the statement true? Explain why or why not.
The criterion for whether a reaction proceeds spontaneously is ΔG not ΔG°, because ΔG takes into account the concentrations of the substrates and products.Is the statement true? Explain why or
Linking the energetically unfavorable reaction A → B to a second, favorable reaction B → C will shift the equilibrium constant for the first reaction.Is the statement true? Explain why or why not.
If an oxidation occurs in a reaction, it must be accompanied by a reduction.Is the statement true? Explain why or why not.
Animals and plants use oxidation to extract energy from food molecules.Is the statement true? Explain why or why not.
Most of the interactions between macromolecules could be mediated just as well by covalent bonds as by noncovalent bonds.Is the statement true? Explain why or why not.
A 10–8 M solution of HCl has a pH of 8.Is the statement true? Explain why or why not.
Rates of evolution appear to vary in different lineages. For example, the rate of evolution in the rat lineage is significantly higher than in the human lineage. These rate differences are apparent
When plant hemoglobin genes were first discovered in legumes, it was so surprising to find a gene typical of animal blood that it was hypothesized that the plant gene arose by horizontal transfer
Animal cells have neither cell walls nor chloroplasts, whereas plant cells have both. Fungal cells are somewhere in between; they have cell walls but lack chloroplasts. Are fungal cells more likely
Genes participating in informational processes such as replication, transcription, and translation are transferred between species much less often than are genes involved in metabolism. The basis for
The genes for ribosomal RNA are highly conserved (relatively few sequence changes) in all organisms on Earth; thus, they have evolved very slowly over time. Were ribosomal RNA genes “born”
How many possible different trees (branching patterns) can in theory be drawn to display the evolution of bacteria, archaea, and eukaryotes, assuming that they all arose from a common ancestor?
It is not so difficult to imagine what it means to feed on the organic molecules that living things produce. That is, after all, what we do. But what does it mean to “feed” on sunlight, as
You have begun to characterize a sample obtained from the depths of the oceans on Europa, one of Jupiter’s moons. Much to your surprise, the sample contains a life form that grows well in a rich
Since it was deciphered four decades ago, some have claimed that the genetic code must be a frozen accident, while others have argued that it was shaped by natural selection. A striking feature of
Most of the DNA sequences in a bacterial genome code for proteins, whereas most of the DNA sequences in the human genome do not.Which statements are true? Explain why or why not.
Horizontal gene transfer is more prevalent in single- celled organisms than in multicellular organisms.Which statements are true? Explain why or why not.
Each member of the human hemoglobin gene family, which consists of seven genes arranged in two clusters on different chromosomes, is an ortholog to all of the other members.Which statements are true?
Beautiful models of macromolecules such as protems and nucleic acids are generated from files of atomic coordinates obtained usually from x-ray diffraction of crystallized samples or NMR analysis of
Chemical modifications to amino acids contribute to the diversity and function of proteins. For instance, -y-carboxylation of specific amino acids is required to make some proteins biologically
The K+ channel is an example of a transmembrane protein (a protein that spans the phospholipid bilayer of the plasma membrane). What types of amino acids are likely to be found?(a) Lining the channel
This is the single-letter amino acid abbreviation for a peptide. What is the net charge of this peptide at pH 7.0? An enzyme called a protein tyrosine kinase can attach phosphates to the hydroxyl
Explain why the process of cell fusion is necessary to produce monoclonal antibodies used for research.
Much of what we know about cellular function depends on experiments utilizing specific cells and specific parts (e.g., organelles) of cells. What techniques do scientists commonly use to isolate
The gecko is a reptile with an amazing ability to climb smooth surfaces, including glass. Recent discoveries indicate that geckos stick to smooth surfaces via van der Waals interactions between
Each of the cytochromes in the mitochondrion contains prosthetic groups. What is a prosthetic group? Which type of prosthetic group is associated with the cytochromes? What property of the various
Mitochondrial oxidation of fatty acids is a major source of ATP, yet fatty acids can be oxidized elsewhere. What organelle, besides the mitochondrion, can oxidize fatty acids? What is the fundamental
Describe the step-by-step process by which electrons from glucose catabolism in the cytoplasm are transferred to the electron transport chain in the mitochondrial inner membrane. In your answer, note
Fermentation permits the continued extraction of energy from glucose in the absence of oxygen. If glucose catabolism is anaerobic, why is fermentation necessary for glycolysis to continue?
Maximal production of ATP from glucose involves the reactions of glycolysis, the citric acid cycle, and the electron transport chain. Which of these reactions requires O2, and why? Which, in certain
The mitochondrial inner membrane exhibits all of the fundamental characteristics of a typical cell membrane, but it also has several unique characteristics that are closely associated with its role
The proton-motive force (pmf) is essential for both mitochondrial and chloroplast functions. What produces the pmf, and what is its relationship to ATP? The compound 2, 4-dinitrophenol (DNP), which
Imagine that you are investigating the transepithelial transport of radioactive glucose. Intestinal epithelial cells are grown in culture to form a complete sheet so that the fluid bathing the apical
Movement of glucose from one side to the other side of the intestinal epithelium is a major example of transcellular transport. How does the Na+/K+ ATPase power the process? Why are tight junctions
Describe the symport process by which cells lining the small intestine import glucose. What ion is responsible for the transport, and what two particular, features facilitate the energetically
In the case of the bacterial sodium/leucine transporter, what is the key distinguishing feature about the bound sodium ions that ensures that other ions, particularly K+, do not bind?
Plants use the proton electrochemical gradient across the vacuole membrane to power the accumulation of salts and sugars in the organelle. This creates a hypertonic situation. Why does this not
Patch clamping can be used to measure the conductance properties of individual ion channels. Describe how patch clamping can be used to determine whether or not the gene coding for a putative
The membrane potential in animal cells, but not in plants, depends largely on resting K+ channels. How do these channels contribute to the resting potential? Why are these channels considered to be
Certain proton pump inhibitors inhibit secretion of stomach acid and are among the most widely sold drugs in the world today. What pump does this type of drug inhibit, and where is this pump located?
Describe a negative feedback mechanism for controlling rising cytoplasmic Ca2+ concentration in cells that require rapid changes in Ca2+ concentration for normal functioning. How would a drug that
Explain why the coupled reaction ATP → ADP + Pi in the P-class ion pump mechanism does not involve direct hydrolysis of the phosphoanhydride bond.
Name the four classes of ATP-powered pumps that produce active transport of ions and molecules. Indicate which of these classes transport ions only and which transport primarily small organic
GLUT1, found in the plasma membrane of erythrocytes, is a classic example of a uniporrer.a. Design a set of experiments to prove that GLUT1 is indeed a glucose-specific uniporter rather than a
An H+ ion is smaller than an H20 molecule, and a glycerol molecule, a three-carbon alcohol, is much larger. Both readily dissolve in H20. Why do aquaporins fail to transport H+ whereas some can
Name the three classes of transporters. Explain which one or more of these classes is able to move glucose and which move bicarbonate (HC03–) against an electrochemical gradient. In the case of
Uniporrers and ion channels support facilitated diffusion across biomembranes. Although both are examples of facilitated diffusion, the rates of ion movement via an ion channel are roughly 104- to
Acetic acid (a weak acid with a pK. of 4.75) and ethanol (an alcohol) are each composed of two carbons, hydrogen, and oxygen, and both enter cells by passive diffusion. At pH 7, one is much more
Nitric oxide (NO) is a gaseous molecule with lipid solubility similar to that of O2 and CO2. Endothelial cells lining arteries use NO to signal surrounding smooth muscle cells to relax, thereby
The behavior of receptor X (XR), a transmembrane protein present in the plasma membrane of mammalian cells, is being investigated. The protein has been engineered as a fusion protein containing the
Explain the mechanism by which statins lower "bad" cholesterol.
Phospholipids and cholesterol must be transported from their site of synthesis to various membrane systems within cells. One way of doing this is through vesicular transport, as is the case for many
The biosynthesis of cholesterol is a highly regulated process. What is the key regulated enzyme in cholesterol biosynthesis? This enzyme is subject to feedback inhibition. What is feedback
Fatty acids must associate with lipid chaperones in order to move within the cell. Why are these chaperones needed, and what is the name given to a group of proteins that arc responsible for this
What are the common fatty acid chains in phosphoglyccrides, and why do these fatty acid chains differ in their number of carbon atoms by multiples of 2?
Phospholipid biosynthesis at the interface between the endoplasmic reticulum (ER) and the cytosol presents a number of challenges that must be solved by the cell. Explain how each of the following is
What is the likely identity of these membrane-associated proteins: (a) Released from the membrane with a high-salt solution causing disruption of ionic linkages; (b) Not released from the
What are detergents? How do ionic and nonionic detergents differ in their ability to disrupt cell membrane structure?
Although both faces of a biomembranc are composed of the same general types of macromolecules, principally lipids and proteins, the two faces of the bilayer are not identical. What accounts for the
Proteins may be bound to the exoplasmic or cytosolic face of the plasma membrane by way of covalently attached lipids. What arc the three types of lipid anchors responsible for tethering proteins to
Identify the following membrane-associated proteins based on their structure: (a) Tetramers of identical subunits, each with six membrane-spanning α: helices; (b) Trimers of identical
Name the three groups into which membrane-associated proteins may be classified. Explain the mechanism by which each group associates with a biomembrane.
Why are water-soluble substances unable to freely cross the lipid bilayer of the cell membrane? How does the cell overcome this permeability barrier?
Lipid bilayers are considered to be two-dimensional flu ids. What does this mean? What drives the movement of lipid molecules and proteins within the bilayer? How can such movement be measured? What
Biomembranes contain many different types of lipid molecules. What arc the three main types of lipid molecules found in biomembranes? How are the three types similar, and how are they different?
Explain the following statement: The structure of all biomembranes depends on the chemical properties of phospholipids, whereas the function of each specific biomembrane depends on the specific
When viewed by electron microscopy, the lipid bilayer is often described as looking like a railroad track. Explain how the structure of the bilayer creates this image.
The nematode worm C. elegans is amenable as a model for siRNA studies. In this experiment, adult nematodes are fed bacteria expressing a double-stranded RNA to suppress the expression of the unc18
Mouse liver cells were homogenized and the homogenate subjected to equilibrium density-gradient centrifugation with sucrose gradients. Fractions obtained from these gradients were assayed for marker
shRNAs and siRNAs can be used to successfully knock down the expression of any specific protein in a given cell line or organism. The utility of one over the other is debarable, but there are merits
Hoechst 33258 is a chemical dye that binds specifically to DNA in live cells, and when excited by UV light, it fluoresces in the visible spectrum. Name and describe one specific method, employing
In certain electron microscopy methods, the specimen is not d1rectly imaged. How do these methods provide information about cellular structure, and what types of structures do they visualize? What
What general transcription factors associate with an RNA polymerase II promoter in addition to the polymerase? In what order do they bind in vitro? What structural change occurs in the DNA when an
Expression of recombinant proteins in yeast is an important tool for biotechnology companies that produce new drugs for human use. In an attempt to get a new gene X expressed in yeast, a researcher
Most humans are infected with herpes simplex virus-1 (HSV-1), the causative agent of cold sores. The HSV-1 genome comprises about I 00 genes, most of which are expressed in infected host cells at the
mRNA localization now appears to be a common phenomenon. What benefit docs mRNA localization have for a cell? What is the evidence that some mRNAs are directed to accumulate in specific subcellular
mRNA stability is a key regulator of protein levels in a cell. Briefly describe the three mRNA degradation pathways. A yeast cell has a mutation in the DCPl gene, resulting in decreased uncapping
Speculate about why plants deficient in Dicer activity show increased sensitivity to infection by RNA viruses.
RNA knockdown has become a powerful tool in the arsenal of methods ro deregulate gene expression. Briefly describe how gene expression can be knocked down. What effect would introducing siRNAs to TSC
A protein complex in the nucleus is responsible for transporting mRNA molecules into the cytoplasm. Describe the proteins that form this exporter. What two protein groups are likely behind the
As DNA is found in the nucleus, transcription is a nuclearlocalized process. Ribosomes responsible for protein synthesis are found in the cytoplasm. Why is hnRNP trafficking to the cytoplasm
RNA editing is a common process occurring in the mitochondria of trypanosomes and plants, in chloroplasts, and in rare cases in higher eukaryotes. What is RNA editing, and what benefit does it
You obtain the sequence of a gene containing 10 exons, 9 introns, Jnd a 3' UTR containing a polyadenylation consensus sequence. The fifth intron also contains a polyadenylation site. To test whether
What are the mechanistic similarities between group II intron self-splicing and spliceosomal splicing? What is the evidence that there may be an evolutionary relationship between the two?
What is the difference between hnRNAs, snRNAs, miRNAs, siRNAs, and snoRNAs?
There are a number of conserved sequences found in an mRNA which dictate where splicing occurs. Where are these sequences found relative to the exon/intron junctions? What is the significance of
True or False? The CTD is responsible for mR.t'\IA-processing steps that are specific for mRNA, and not other forms of RNA. Explain why you chose true or false.
Describe three types of post-transcriptional regulation of protein-coding genes.
In eukaryotes, the three RNA polymerases, Pol I, II, and III, each transcribes unique genes required for the synthesis of ribosomes: 25S and 18S rRNAs (Pol 1), 55 rRNA (Pol III), and mRNAs for
Name four major classes of DNA-binding proteins that are responsible for controlling transcription, and describe their structural features.
Upon identification of the DNA regulatory sequence responsible for translating a given gene, you note that it is enriched with CG sequences. Is the corresponding gene likely to be a highly expressed
Some organisms have mechanisms in place that will override transcription termination. One such mechanism using the Tat protein is employed by the HIV retrovirus. Explain why Tat is therefore a good
You are curious to identify the region of.gene X sequence that serves as an enhancer for gene expression. Design an experiment to investigate this issue.
Compare/contrast bacterial and eukaryotic gene expression mechanisms.

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