Questions and Answers of Molecular Cell Biology

Recall that the Trp repressor binds to a site in the operator region of tryptophan-producing genes when tryptophan is abundant, thereby preventing transcription. What would happen to the expression
Prokaryotcs and lower eukaryotes such as yeast have DNA-regulatory elements called upstream activating sequences. What arc the comparable sequences found in higher eukaryotic species?
The yeast two-hybrid method is a powerful molecular genetic method to identify a protcin(s) that interacts with a known protein or protein domain. You have isolated the glucocorticoid receptor (GR)
You have isolated a new protein called STICKY. You can predict from comparisons with other known proteins that STICKY contains a bHLH domain and a Sin3-interacting domain. Predict the function of
Using CREB and nuclear receptors as examples, compare and contrast the structural changes that take place when these transcription factors bind to their co-activators.
Give two examples of how gene expression may be repressed without altering the gene-coding sequence.
Describe the structural features of transcriptional activator and repressor proteins.
Describe the methods used to identify the location of DNA-binding proteins in the regulatory regions of genes.
What is the difference between a promoter-proximal element and a distal enhancer? What are the similarities?
Describe the methods used to identify the location of DNA control elements in promoter proximal regions of genes.
What do TATA boxes, initiators, and CpG islands have in common? Which was the first of these to be identified? Why?
The CTD of the largest subunit of RNA polymerase II can be phosphorylated at multiple serine residues. What are the conditions that lead to the phosphorylated versus unphosphorylated RNA polymerase
What types of genes are transcribed by RNA polymcrases I, II, and III? Design an experiment to determine whether a specific gene is transcribed by RNA polymerase II.
The concentration of free glutamine affects transcription of the enzyme glutamine synthetase in E. coli. Describe the mechanism for this.
Describe the molecular events that occur at the lac operon when E. coli cells are shifted from a glucose-containing medium to a lactose-containing medium.
Satellite DNA is a known component of our genome and can be found in both coding and noncoding DNA. When it is found in coding DNA, the number of repeats can result in altered proteins. Bur the
To determine whether gene transfer from an organelle genome to the nucleus can be observed in the laboratory, a chloroplast transformation vector was constructed that contained two selectable
Describe the problem that occurs during DNA replication at the ends of chromosomes. How are telomeres related to this problem?
Replication and segregation of eukaryotic chromosomes require three functional elements: replication origins, a centromere, and telomeres. How would a chromosome be affected if it lacked (a)
Certain organisms contain cells that possess polytene chromosomes. What are polytene chromosomes, where are they found, and what function do they serve?
What is chromosome painting, and how is this technique useful? How can chromosome paint probes be used to analyze the evolution of mammalian chromosomes?
What is FISH? Briefly describe how it works. How is FISH used to characterize chromosomal translocations associated with certain genetic disorders and specific types of cancers?
Describe the general organization of a eukaryotic chromosome. What structural role do scaffold-associated regions (SARs) or matrix attachment regions (MARs) play? Why does it make sense that
How do chromatin modifications regulate transcription? What modifications are observed in regions of the genome that are actively being transcribed? What about for regions that are not actively
The DNA in a cell associates with proteins to form chromatin. What is a nucleosome? What role do histones play in nucleosomes? How are nucleosomes arranged in condensed 30-nm fibers?
What are paralogous and orthologous genes? What are some of the explanations for the finding that humans are a much more complex organism than the roundworm C. elegans, yet have only fewer than one
Mitochondria and chloroplasts are thought to have evolved from symbiotic bacteria present in nucleated cells. What is the experimental evidence from this chapter that supports this hypothesis?
Discuss the role that transposons may have played in the evolution of modern organisms. What is exon shuffling? What role do transposons play in the process of exon shuffling?
Retrotransposons are a class of mobile elements that transpose via an RNA intermediate. Contrast the mechanism of transposition between rctrotransposons that contain long terminal repeats (LTRs) and
Mobile DNA elements that can move or transpose to a new site directly as DNA are called DNA transposons. Describe the mechanism by which a bacterial DNA transposon, called an insertion sequence, can
Much of the human genome consists of repetitious DNA. Describe the difference between microsatellite and minisatellite DNA. How is this repetitious DNA useful for identifying individuals by the
Sequencing of the human genome has revealed much about the organization of genes. Describe the differences between solitary genes, gene families, pseudogenes, and tandemly repeated genes.
Genes can be transcribed into mRNA for protein-coding genes or into RNA for genes such as ribosomal or transfer RNAs. Define a gene. For the following characteristics, state whether they apply
A culture of yeast that requires uracil for growth (urÎ±3ÍžË‰ was mutagenized, and two mutant colonies, X and Y, have been isolated. Mating type a cells of mutant X
Two methods for functionally inactivating a gene without altering the gene sequence are by dominant-negative mutations and RNA interference (RNAi). Describe how each method can inhibit expression of
The ability to selectively modify the genome in the mouse has revolutionized mouse genetics. Outline the procedure for generating a knockout mouse at a specific genetic locus. How can the loxP-Cre
Genetic linkage studies can usually only roughly locate the chromosomal position of a "disease" gene. How can expression analysis and DNA sequence analysis help locate a disease gene within the
How can linkage-disequilibrium mapping sometimes provide a much higher resolution of gene location than classical linkage mapping?
DNA polymorphisms can be used as DNA markers. Describe the d1fferences between SNP and SSR polymorphisms. How can these markers be used for DNA-mapping studies?
In determining the identity of the protein that corresponds to a newly discovered gene, it often helps to know the pattern of tissue expression for that gene. For example, researchers have found that
Northern blotting, RT-PCR, and microarrays can be used to analyze gene expression. A lab studies yeast cells, Comparing their growth in two different sugars, glucose and galactose. One student is
A number of foreign proteins have been expressed in bacterial and mammalian cells. Describe the essential features of a recombinant plasmid that are required for expression of a foreign gene. How can
Southern and Northern blotting are powerful tools in molecular biology based on hybridization of nucleic acids. How are these techniques the same? How do they differ? Give some specific applications
In 1993, Ka'ry Mullis won the Nobel Prize in Chemistry for his invention of the PCR process. Describe the three steps in each cycle of a PCR reaction. Why was the discovery of a thermostable DNA
A DNA library is a collection of clones, each containing a different fragment of DNA, inserted into a cloning vector. What is the difference between a eDNA and a genomic DNA library? You would like
Bacterial plasmids often serve as cloning vectors. Describe the essential features of a plasmid vector. What are the advantages and applications of plasmids as cloning vectors?
Restriction enzymes and DNA ligase play essential roles in DNA cloning. How is it that a bacterium that produces a restriction enzyme does not cut its own DNA? Describe some general features of
Jane has isolated a mutant strain of yeast that forms red colonies instead of the normal white when grown on a plate. To determine the mutant gene, she decides to use functional complementation with
Describe how complementation analysis can be used to reveal whether two mutations are in the same or in different genes. Explain why complementation analysis will not work with dominant mutations?
What is a temperature-sensitive mutation? Why are temperature-sensitive mutations useful for uncovering the function of a gene?
Genetic mutations can provide insights into the mechanisms of complex cellular or developmental processes. How might your analysis of a genetic mutation be different depending on whether a particular
Protein synthesis in eukaryotes normally begins at the first AUG codon in the mRNA. Sometimes, however, the ribo-somes do not begin protein synthesis at this first AUG but scan past it (leaky
a. Detail the key differences between lytic and nonlytic viral infection and provide an example of each.b. Which of the following processes occurs in both lytic and nonlytic viral infections?(i)
Identify the specific types of point mutations below (you are viewing the direct DNA version of the RNA sequence).Original sequence: 5' AUG TCA GGA CGT CAC TCA GCT 3'Mutation A: 5' AUG TCA GGA CGT
The DNA repair systems preferentially target the newly synthesized strand. Why is this important?
a. Look at the figure below. Explain why it is necessary for Okazaki fragments to be formed as the lagging strand is produced (instead of a continuous strand).b. If the DNA polymerase in the figure
Use the key provided below to determine the amino acid sequence of the polypeptide produced from the following DNA sequence. lntron sequences are highlighted. Note: Not all amino acids in the key
You have learned about the events surrounding DNA replication and the central dogma. Identify the steps associated with these processes that will be adversely affected in the following scenarios.a.
Contrast prokaryotic and eukaryotic gene characteristics.
a. Which of the following DNA strands, the top or bottom, would serve as a template for RNA transcription if the DNA molecule were to unwind in the indicated direction?5'
The genome of a retrovirus can integrate into the host-cell genome. What gene is unique to retroviruses, and why is the protein encoded by this gene absolutely necessary for maintaining the
What is the name given to the process that can repair DNA damage and generate genetic diversity? Briefly describe the similarities and differences of the two processes.
DNA-repair systems are responsible for maintaining genomic fidelity in normal cells despite the high frequency with which mutational events occur. What type of DNA mutation is generated by (a)
Eukaryotes have repair systems that prevent mutations due to copying errors and exposure to mutagens. What are the three excision-repair systems found in eukaryotes, and which one is responsible for
What characteristic of DNA results in the requirement that some DNA synthesis is discontinuous? How are Okazaki fragments and DNA ligase utilized by the cell?
How would a mutation in the poly (A)-binding protein gene affect translation? How would an electron micrograph of polyribosomes from such a mutant differ from the normal pattern?
The transcription of many bacterial genes relies on functional groups called operons, such as the tryptophan operon. What is an operon? What advantages are there to having genes arranged in an
While investigating the function of a specific growth factor receptor gene from humans, researchers found that two types of proteins are synthesized from this gene. A larger protein containing a
What are the major differences in the synthesis and structure of prokaryotic and eukaryotic mRNAs?
What difference between RNA and DNA helps to explain the greater stability of DNA? What implications does this have for the function of DNA?
Preparing plasmid (double-stranded, circular) DNA for sequencing involves annealing a complementary, short, single-stranded oligonucleotide DNA primer to one strand of the plasmid template. This is
What are Watson-Crick base pairs? Why are they important?
Proteomics involves the global analysis of protein expression. In one approach, all the proteins in control cells and treated cells are extracted and subsequently separated using two-dimensional gel
Mass spectrometry is a powerful tool in proteomics. What are the four key features of a mass spectrometer? Describe briefly how MALDI and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)
Physical methods are often used to determine protein conformation. Describe how x-ray crystallography, cryoelectron microscopy, and NMR spectroscopy can be used to determine the shape of proteins.
Various methods have been developed for detecting proteins. Describe how radioisotopes and autoradiography can be used for labeling and detecting proteins. How does Western blotting detect proteins?
Chromatography is an analytical method used to separate proteins. Describe the principles for separating proteins by gel filtration, ion-exchange, and affinity chromatography.
A number of techniques can separate proteins on the basis of their differences in mass. Describe the use of two of these techniques, centrifugation and gel electrophoresis. The blood proteins
The function of proteins can be regulated in a number of ways. What is cooperativity, and how does it influence protein function? Describe how protein phosphorylation and proteolytic cleavage can
Proteins are degraded in cells. What is ubiquitin, and what role does it play in tagging proteins for degradation? What is the role of proteasomes in protein degradation? How might proreasome
A healthy adaptive immune system can raise antibodies that recognize and bind with high affinity to almost any stable molecule. The molecule to which an antibody binds is known as "antigen."
The following reaction coordinate diagram charts the energy of a substrate molecule (S) as it passes through a transition state (Xt) on its way to becoming a stable product (P) alone or in the
Enzymes catalyze chemical reactions. What constitutes the active sire of an enzyme? What are the turnover number (kcat), the Michaelis constant (K111), and the maximal velocity ( Vmax,) of an enzyme?
Proper folding of proteins is essential for their biological activity. In genetal, the functional conformation of a protein is the conformation with lowest energy. This means that if an unfolded
The three-dimensional structure of a protein is determined by its primary, secondary, and tertiary structures. Define the primary, secondary, and tertiary structures. What are some of the common
The graph below illustrates the effect that the addition of a strong base such as sodium hydroxide has on the pH of an aqueous 0.1 M solution of an amino acid. Assume that prior to the addition of
During much of the "Age of Enlightenment" in eighteenth- century Europe, scientists toiled under the belief that living things and the inanimate world were fundamentally distinct forms of matter.
According to health experts, saturated fatty acids, which come from animal fats, are a major factor contributing to coronary heart disease. What distinguishes a saturated fatty acid from an
The ΔG0' for the reaction X + Y → XY is -1000 cal/mol. What is the ΔG at 25oC (298 Kelvin) starting with 0.01 M each X, Y, and XY? Suggest two ways one could make this reaction energetically
What is the ionization state of phosphoric acid in the cytoplasm? Why is phosphoric acid such a physiologically important compound?
Consider the binding reaction L + R → LR, where L is a ligand and R is its receptor. When 1 X 10-3 M L is added to a solution containing 5 X 10-2 M R, 90 percent of the L binds to form LR. What is
Ammonia (NH3) is a weak base that under acidic conditions becomes protonated to the ammonium ion in the following reaction:NH3 + H+ → NH4+NH3 freely permeates biological membranes, including
Calculate the pH of 1 L of pure water at equilibrium. How will the pH change after 0.008 moles of the strong base NaOH are dissolved in the water? Now, calculate the pH of a 50 mM aqueous solution of
The chemical basis of blood-group specificity resides in the carbohydrates displayed on the surface of red blood cells. Carbohydrates have the potential for great structural diversity. Indeed, the
Name the compound shown below.Is this nucleotide a component of DNA, RNA, or both? Name one other function of this compound. IN HN, E 8CH 9, N. 'N. Н,N 5" -0-P-0-0-P-0-0-P-0 — сн, Н Н Н Н 2"
In the 1960s, the drug thalidomide was prescribed to pregnant women to treat morning sickness. However, thalidomide caused severe limb defects in the children of some women who took the drug, and its
Disulfide bonds help to stabilize the three-dimensional structure of proteins. What amino acids are involved in the formation of disulfide bonds? Does the formation of a disulfide bond increase or
Olfaction occurs when volatile compounds bind to specific odorant receptors. In mammals, each olfactory receptor neuron in the olfactory nasal epithelium expresses a single type of odorant receptor.
Compare the structures and functions of the receptor molecules for salty and sour taste; the taste receptor molecules for sweetness, bitterness, and umami; and odor-receptor molecules.
Compare and contrast electrical and chemical synapses.

Showing 400 - 500 of 706