Question: This chapter describes different types of TEs,

> What evolutionary factors can cause allele frequencies to change and possibly lead to a genetic polymorphism? Discuss the relative importance of each type of process.

> What is the gene pool? How is a gene pool described in a quantitative way?

> Gradients of morphogens can be preestablished in the oocyte. Also, later in development, morphogens can be secreted from cells. How are these two processes similar and different?

> When an activator protein interacts with mediator, how does this affect the function of RNA polymerase?

> What is positional information? Discuss three different ways that cells obtain positional information. Which of these three ways do you think is the most important for the formation of a segmented body pattern in Drosophila?

> Explain what a morphogen is, and describe how it exerts its effects. What do you expect will happen when a morphogen is expressed in the wrong place in an embryo? List five examples of morphogens that function in Drosophila.

> Here are schematic diagrams of mutant Drosophila larvae. The left side of each pair shows a wild-type larva, with gray boxes showing the sections that are missing in the mutant larva. Which type of gene is defective in each larva: a gap gene, a pair-rul

> Discuss the morphological differences between the parasegments and segments of Drosophila. Discuss the evidence, providing specific examples, that suggests the parasegments of the embryo are the subdivisions for the organization of gene expression.

> Which of the following statement(s) is/are true with regard to positional information in Drosophila? A. Morphogens are a type of molecule that conveys positional information. B. Morphogenetic gradients are established only in the oocyte, prior to ferti

> If you observed fruit flies with the following developmental abnormalities, would you guess that a mutation has occurred in a segmentation gene or a homeotic gene? Explain your guess. A. Three abdominal segments were missing. B. One abdominal segment h

> Discuss the morphological differences between animal and plant development. How are the developmental processes different at the cellular level? How are they similar at the genetic level?

> What is a meristem? Explain the role of meristems in plant development.

> What is a totipotent cell? In each of the following types of organisms, which cells are totipotent? A. Humans B. Corn C. Yeast D. Bacteria

> The MyoD gene in mammals plays a role in skeletal muscle-cell differentiation, whereas the Hox genes are homeotic genes that play a role in the differentiation of particular regions of the body. Explain how the functions of these genes are similar and di

> If a repressor prevents TFIID from binding to the TATA box, why does this inhibit transcription?

> What is cell differentiation? Discuss the role of myogenic bHLH proteins in the differentiation of muscle cells. Explain how they work at the molecular level. In your answer, explain how protein dimerization is key to gene regulation.

> Discuss the similarities and differences between the bithorax and Antennapedia complexes in Drosophila and the Hox gene complexes in mice.

> What is a heterochronic mutation? How does it affect the phenotypic outcome of an organism? What phenotypic effects would you expect if a heterochronic mutation affected the cell lineage that determines the fates of intestinal cells?

> A hypothetical cell lineage is shown here. A gene, which we will call gene X, is activated in the B-1 cell, so the B-1 cell will progress through the proper developmental stages to produce three nerve cells (D-1, D-2, and D-3) and one muscle cell (D-4).

> Cloning of mammals (such as Dolly the sheep) is described in Chapter 22. Based on your understanding of animal development, explain why an enucleated egg is needed to clone mammals. In other words, what features of the oocyte are essential for animal dev

> The arrangement of body axes of the fruit fly are shown in Figure 26.5g. Are the following statements true or false with regard to body axes in the mouse? A. Along the anteroposterior axis, the head is posterior to the tail. B.

> What is the difference between a maternal-effect gene and a zygotic gene? Of the following genes that play a role in Drosophila development, which are maternal-effect genes and which are zygotic? Explain your answer. A. nanos B. Antp C. bicoid D. lab

> Explain how loss-of-function mutations in the following categories of genes would affect the morphologies of Drosophila larvae: A. Gap genes B. Pair-rule genes C. Segment-polarity genes

> If a mutation in a homeotic gene produced the following phenotypes, would you expect it to be a loss-of-function or a gain-of function mutation? Explain your answer. A. An abdominal segment has antennae attached to it. B. The most anterior abdominal se

> Based on the photographs in Figure 26.13, in which segments is the Antp gene normally expressed? From Figure 26.13: (a) Normal fly (b) Antennapedia mutant

> Explain how an α helix in a transcription factor protein is able to function as a recognition helix.

> What would you predict to be the phenotype of a Drosophila larva whose mother was homozygous for a loss-of-function allele in the nanos gene?

> Describe the molecular features of the homeobox and homeodomain. Explain how these features are important in the function of homeotic genes.

> Discuss the role of homeotic genes in development. Explain what happens to the phenotype of a fruit fly when a gain-of-function mutation in a homeotic gene causes the protein to be expressed in an abnormal region of the embryo. What are the consequences

> With regard to development, what are the roles of the maternal effect genes versus the zygotic genes? Which types of genes are needed earlier in the development process?

> Describe the function of the Bicoid protein. Explain how its ability to exert its effects in a concentration-dependent manner is a critical feature of its function.

> Discuss how the anterior portion of the anteroposterior axis is established in Drosophila. What aspects of oogenesis are critical in establishing this axis? What do you think would happen if the bicoid mRNA was not trapped at the anterior end but instead

> What four types of cellular processes must occur to enable a fertilized egg to develop into an adult multicellular animal? Briefly discuss the role of each process.

> Explain the difference between gene modification and gene addition. Are the following examples of gene modification or gene addition? A. A mouse model to study cystic fibrosis B. Introduction of a pesticide-resistance gene into corn using the T-DNA vec

> When comparing (i.e., aligning) two or more genetic sequences, it is sometimes necessary to put in gaps. Explain why. Discuss two changes (i.e., two types of mutations) that could happen during the evolution of homologous genes that would explain the occ

> What is the difference between similarity and homology?

> Which of these mechanisms is the most energy-efficient way to regulate gene expression? From figure 15.1: REGULATION OF GENE EXPRESSION Gene Regulatory transcription factors can activate or inhibit transoription. The arrangements and composition of

> A multiple-sequence alignment of five homologous proteins is shown here: Discuss some of the interesting features that this alignment reveals. 50 1 MLAFLNOVRK PTLDLPLEVR RKMWFKP FM. OSYLVVFIGY LTMYLIRKNF 2 MLAFLNOVRK PILDLALDVR RKMWFKP FM. OSYLVVFIG

> Discuss the distinction between sequence recognition and pattern recognition.

> Besides the examples listed in Table 24.3, list five types of short sequences that a geneticist might want to locate within a DNA sequence.

> Which of the following examples is likely to be caused by a somatic mutation? A. A purple flower has a small patch of white tissue. B. One child, in a family of seven, is an albino. C. One apple tree, in a very large orchard, produces its apples 2 wee

> What is a database? What types of information are stored within a database? Where does the information come from? Discuss the objectives of a genome database.

> An individual carries a somatic mutation that changes a lysine codon into a glutamic acid codon. Prior to acquiring this mutation, the individual had been exposed to UV light, proflavin, and 5-bromouracil. Which of these three agents would be the most li

> In the treatment of cancer, the basis for many types of chemotherapy and radiation therapy is that mutagens are more effective at killing dividing cells than nondividing cells. Explain why. What are possible harmful side effects of chemotherapy and radia

> A segment of DNA has the following sequence: TTGGATGCTG AACCTACGAC A. What would the sequence be immediately after reaction with nitrous acid? Let the letters H represent hypoxanthine and U represent uracil. B. Let’s suppose this DNA was reacted with n

> What is the difference between an autonomous and a nonautonomous transposable element? Is it possible for nonautonomous TEs to move? If yes, explain how. 

> The occurrence of multiple transposons within the genome of organisms has been suggested as a possible cause of chromosomal rearrangements such as deletions, translocations, and inversions. How could the occurrence of transposons promote these types of s

> How does micF antisense RNA affect the translation of ompF mRNA?

> What features distinguish a transposon from a retrotransposon? How are their sequences different, and how are their mechanisms of transposition different?

> Let’s suppose that a species of mosquito has two different types of simple transposons that we will call X elements and Z elements. The X elements appear quite stable. In a population of 100 mosquitoes, it is found that every mosquito has 6 X elements, a

> Do you consider TEs to be mutagens? Explain.

> Which types of TEs have the greatest potential for proliferation: insertion elements, simple transposons, or retrotransposons? Explain your choice

> Discuss the reasons why the proteome is larger than the genome of a given species.

> Why does transposition always produce direct repeats in the chromosomal DNA?

> For insertion elements and simple transposons, what is the function of the inverted repeat sequences during transposition?

> If you were examining a sequence of chromosomal DNA, what characteristics would cause you to believe that the sequence contained a transposable element?

> According to the scenario shown in Figure 20.7, how many segments of DNA (one, two, or three) are removed during site-specific recombination within the gene that encodes the κ (kappa) light chain for IgG proteins? How many segments are splice

> Explain how the presence of tryptophan favors the formation of the 3–4 stem-loop.

> Describe the functions of the RAG1 and RAG2 and NHEJ proteins.

> Briefly describe three ways that antibody diversity is increased

> What type of DNA structure is recognized by RecG and RuvABC? Do you think these proteins recognize DNA sequences? Be specific about what type(s) of molecular recognition these proteins can perform.

> Discuss the concerns that some people have with regard to the uses of genetically engineered organisms.

> Discuss some of the worthwhile traits that can be modified in transgenic plants.

> As described in Chapter 5, not all inherited traits are determined by nuclear genes (i.e., genes located in the cell nucleus) that are expressed during the life of an individual. In particular, maternal effect genes and mitochondrial DNA are notable exce

> Give the meanings of the following terms: genomics, functional genomics, and proteomics.

> Ehler-Danlos syndrome is a rare disorder caused by a mutation in a gene that encodes a protein called collagen (type 3 A1). Collagen is found in the extracellular matrix that plays an important role in the formation of skin, joints, and other connective

> Gaucher disease (type I) is due to a defect in a gene that encodes a protein called acid β-glucosidase. This enzyme plays a role in carbohydrate metabolism within lysosomes. The gene is located on the long arm of chromosome 1. People who inherit two defe

> Discuss why a genetic disease might have a particular age of onset. Would an infectious disease have an age of onset? Explain why or why not.

> What type of bonding interaction causes stem-loops to form?

> Figure 25.1 illustrates albinism in two different species. Describe two other genetic disorders found in both humans and animals. From Figure 25.1:

> We often speak of diseases such as phenylketonuria (PKU) and achondroplasia as having a genetic basis. Explain whether the following statements are accurate with regard to the genetic basis of any human disease (not just PKU and achondroplasia). A. An i

> In general, why do changes in chromosome structure or number tend to affect an individual’s phenotype? Explain why some changes in chromosome structure, such as reciprocal translocations, do not.

> Many genetic disorders exhibit locus heterogeneity. Define and give two examples of locus heterogeneity. How does locus heterogeneity confound a pedigree analysis?

> When the DNA of a human cell becomes damaged, the p53 gene is activated. What is the general function of the p53 protein? Is it an enzyme, transcription factor, cell-cycle protein, or something else? Describe three ways in which the synthesis of the p53

> With regard to cancer cells, which of the following statements are true? A. Cancer cells are clonal, which means they are derived from a single mutant cell. B. To become cancerous, cells usually accumulate multiple genetic changes that eventually resul

> A p53 knockout mouse in which both copies of p53 are defective has been produced by researchers. This type of mouse appears normal at birth. However, it is highly sensitive to UV light. Based on your knowledge of p53, explain the normal appearance at bir

> The rb gene encodes a protein that inhibits E2F, a transcription factor that activates several genes involved in cell division. Mutations in rb are associated with certain forms of cancer, such as retinoblastoma. Under each of the following conditions, w

> Relatively few inherited forms of cancer involve the inheritance of mutant oncogenes. Instead, most inherited forms of cancer are defects in tumor-suppressor genes. Give two or more reasons why inherited forms of cancer seldom involve activated oncogenes

> A genetic predisposition to developing cancer is usually inherited as a dominant trait. At the level of cellular function, are the alleles involved actually dominant? Explain why some individuals who have inherited these dominant alleles do not develop c

> How does tryptophan affect the function of trp repressor?

> A genetic predisposition to developing cancer is usually inherited as a dominant trait. At the level of cellular function, are the alleles involved actually dominant? Explain why some individuals who have inherited these dominant alleles do not develop c

> What is a retroviral oncogene? Is it necessary for viral infection and proliferation? How have retroviruses acquired oncogenes?

> What is a proto-oncogene? What are the typical functions of proteins encoded by proto-oncogenes? At the level of protein function, what are the general ways that proto-oncogenes can be converted to oncogenes?

> What is the difference between an oncogene and a tumor-suppressor gene? Give two examples of each type of gene.

> Explain, at the molecular level, why human genetic diseases often follow a simple Mendelian pattern of inheritance, whereas most normal traits, such as the shape of your nose or the size of your head, are governed by multiple gene interactions.

> Some people have a genetic predisposition for developing prion diseases. Examples are described in Table 25.6. In the case of Gerstmann-Straüssler-Scheinker disease, the age of onset is typically 30–50 years, and the dura

> What is a prion? Explain how a prion relies on normal cellular proteins to cause a disease such as mad cow disease.

> What is the purpose of the International HapMap Project? How will it help researchers who study disease-causing alleles?

> Describe the two assumptions that underlie the identification of disease-causing alleles via haplotypes.

> Sandhoff disease is due to a mutation in a gene that encodes a protein called hexosaminidase B. This disease has symptoms that are similar to those of Tay-Sachs disease. Weakness begins in the first 6 months of life. Individuals exhibit early blindness a

> Which data provide the strongest evidence that O1 is not the only operator site?

> Marfan syndrome is due to a mutation in a gene that encodes a protein called fibrillin-1. It is inherited as a dominant trait. The fibrillin-1 protein is the main constituent of extracellular microfibrils. These microfibrils can exist as individual fiber

> Lesch-Nyhan syndrome is due to a mutation in a gene that encodes a protein called hypoxanthine-guanine phosphoribosyltransferase (HPRT). HPRT is an enzyme that functions in purine metabolism. People afflicted with this syndrome have severe neurodegenerat

> Achondroplasia is a rare form of dwarfism caused by an autosomal dominant mutation that affects the gene that encodes a fibroblast growth factor receptor. Among 1,422,000 live births, the number of babies born with achondroplasia was 31. Among those 31 b

> Like Hurler syndrome, Fabry disease involves an abnormal accumulation of substances within lysosomes. However, the lysosomes of individuals with Fabry disease show an abnormal accumulation of lipids. The defective enzyme is α-galactosidase A, which is a

> Hurler syndrome is due to a mutation in a gene that encodes a protein called α-l-iduronidase. This protein functions within lysosomes as an enzyme that breaks down mucopolysaccharides (a type of polysaccharide that has many acidic groups at

> With regard to pedigree analysis, make a list of observations that distinguish recessive, dominant, and X-linked patterns of inheritance.

> What part of the A. tumefaciens DNA gets transferred to the genome of a plant cell during infection?

> What is a transgenic organism? Describe three examples.

> What is a mouse model for human disease?