Assigned Problems for Exam 3

A normal female is discovered with 45 chromosomes, one of which exhibits a Robertsonian translocation containing most of chromosomes 15 and 21. Discuss the possible outcomes in her offspring when her husband contains a normal karyotype.

1. normal 2. translocation carrier c. down syndrome: Trisomy 21

Discuss the concepts of homologous chromosomes, diploidy, and haploidy. What characteristics do two homologous chromosomes share?

Chromosomes that are homologous share many properties including overall length, position of the centromere, banding patterns, type and location of genes, and autoradiographic pattern. Diploidy is a term often used in conjunction with the symbol 2n. It means that both members of a homologous pair of chromosomes are present. Haploidy refers to the presence of a single copy of each homologous chromosome (n).

What functional information about a genome can be determined through applications of chromatin immnoprecipitation (ChIP)?

Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell.

Review the Chapter Concepts list on page 188. These all center around chromosome aberrations that create variations from the "normal" diploid genome. Write a short essay that discusses five altered phenotypes that result from specific chromosomal aberrations.

Deletions, duplications, inversions, translocations, and copy number variations

Given the end results of the two types of division, why is it necessary for homologs to pair during meiosis and not desirable for them to pair during mitosis?

During meiosis I chromosome number is reduced to haploid complements. This is achieved by synapses of homologous chromosomes and their subsequent separation. It would seem to be more mechanically difficult for genetically identical daughters to form from mitosis if homologous chromosomes paired. By having chromosomes unpaired at metaphase of mitosis, only centromere division is required for daughter cells to eventually receive identical chromosomal complements.

Explain why meiosis leads to significant genetic variation while mitosis does not.

First, through independent assortment of chromosomes at anaphase I of meiosis, daughter cells may contain different sets of maternally and paternally derived chromosomes. Second, crossing over, which happens at a much higher frequency in meiotic cells as compared with mitotic cells, allows maternally and paternally derived chromosomes to exchange segments, thereby increasing the likelihood that daughter cells are genetically unique.

What is functional genomics? How does it differ from comparative genomics?

Functional genomics seeks to understand functional components within the genome and similarities of genomes across phylogenetic and evolutionary distances. Comparative genomics analyzes the arrangement and organization of families of genes within and among genomes.

Review the Chapter Concepts list on page 522. All of these pertain to how genomics, bioinformatics, and proteomics approaches have changed how scientists study genes and proteins. Write a short essay that explains how recombinant DNA teachniques were used to identify and study genes compared to how modern genomic techniques have revolutionized the cloning and analysis of genes.

Include a description of traditional recombinant DNA technology involving cutting and splicing genes, as well as modern methods of synthesizing genes of interest, PCR amplification, microarray analysis, and etc.

Review the Chapter Concepts list on pg. 40. The first five concepts provide a modern interpretation of Mendelian postulates. Based on these concepts, write a short essay that correlates Mendel's four postulates with what is now known about genes, alleles, and homologous chromosomes.

Include: 1. Factors occur in pairs. 2. Some genes have dominant and recessive alleles. 3. Alleles segregate from each other during gamete formation. When homologous chromosomes separate from each other at Anaphase I, alleles will go to opposite poles of the meiotic apparatus. 4. One gene pair separates independently from other gene pairs. Different gene pairs on the same homologous chromosomes or on non-homologous chromosomes will separate independently from each other during meiosis.

Which of Mendel's postulates can only be demonstrated in crosses involving at least two pairs of traits? State the postulates.

Independent assortment

Describe the phases of the cell cycle and the events that characterize each phase.

Mitotic (M) phase includes mitosis and cytokinesis, and interphase, during which the cell grows and duplicates its chromosomes. Interphase, usually lasting 90% of the cell cycle, includes the G1 phase the first growing phase, the S phase is the DNA synthesis, and the G2 phase the 2nd gap that makes proteins to divide and gear up from mitosis.

Examine Figure 2-12, which shows oogenesis in animal cells. Will the genotype of the second polar body always be identical to that of the ootid? Why or why not?

Not necessarily; if crossing over occurs in meiosis I, then the chromatids in the secondary oocyte are not identical. Once they separate during meiosis II, unlike chromatids, they reside in the ootid and the second polar body.

Observe the following pedigree for myopia in humans on page 61. Predict whether the disorder is inherited as the result of a dominant or recessive trait. Determine the most probable genotype for each individual based on your prediction.

The gene is inherited as an autosomal recessive. I-1 (aa), I-2 (Aa or AA), I-3 (Aa), I-4 (Aa) II-1 (Aa), II-2 (Aa), II-3 (Aa), II-4 (Aa), II-5 (aa), II-6 (AA or Aa), II-7 (AA or Aa) III-1 (AA or Aa), III-2 (aa), III-3 (AA or Aa)

What evidence suggests that Down syndrome is more often the result of nondisjunction during oogenesis rather than during spermatogenesis?

The incidence of Down syndrome births increases with increasing age of the mother.

List and describe three major goals of the Human Genome Project.

The main goals of the Human Genome Project are to establish, categorize, and analyze functions for human genes. As stated in the text: - To analyze genetic variations between humans, including the identification of single-nucleotide polymorphisms - To map and sequence the genomes of several model organisms used in experimental genetics, including E. coli, S. cerevisiae, C. elegans, D. melanogaster, and M. musculus - To develop new sequencing technologies, such as high-throughput computer-automated sequencers, to facilitate genome analysis - To disseminate genome information, both among scientists and the general public

What is the effect of a rare double crossover (a) within a chromosome segments that is heterozygous for a pericentric inversion; and (b) within a segment that is heterozygous for a paracentric inversion?

The rare double crossovers within the boundaries of a paracentric or pericentric inversion produce only minor departures from the standard chromosomal arrangement as long as the crossovers involve the same two chromatids. With two-strand double crossovers, the second crossover negates the first. However, three-strand and four-strand double crossovers have consequences that lead to anaphase bridges as well as a high degree of genetically unbalanced gametes.

When two plants belonging to the same genus but different species are crossed, the F1 hybrid is more viable and has more ornate flowers. Unfortunately, this hybrid is sterile and can only by propagated by vegetative cuttings. Explain the sterility of the hybrid and what would have to occur for the sterility of this hybrid to be reversed.

The sterility of interspecific hybrids is often caused by a high proportion of univalent in meiosis I. As such, viable gametes are rare and the likelihood of two such gametes "meeting" is remote. Even if partial homology of chromosomes allows some pairing, sterility is usually the rule. The horticulturist may attempt to reverse the sterility by treating the sterile hybrid with colchicine. Such a treatment, if successful, may double the chromosome number, and each chromosome would then have a homolog with which to pair during meiosis.

Based on the preceding cross, what is the probability that an organism in the F2 generation will have round seeds and green cotyledons and be true breeding?

WWgg = 1/16

For a species with a diploid number of 18, indicate how many chromosomes will be present in the somatic nuclei of individuals that are haploid, tetraploid, trisomic, and monosomic.

haploid = 9 tetraploid = 36 trisomic = 19 monosomic = 17

In this chapter, we focused on the Mendelian postulates, probability, and pedigree analysis. We also considered some of the methods and reasoning by which these ideas, concepts, and techniques were developed. On the basis of these discussions, what answers would you propose to the following questions: (a) How was Mendel able to derive postulates concerning the behavior of "unit factors" during gamete formation, when he could not directly observe them? (b) How do we know whether an organism expressing a dominant trait is homozygous or heterozygous? (c) In analyzing genetic data, how do we know whether deviation from the expected ratio is due to chance rather than to another, independent factor? (d) Since experimental crosses are not performed in humans, how do we know how traits are inherited?

(a) 1. results of various crosses provided the basis for knowing that factors can remain hidden in some circumstances, thereby implying to participating elements, one dominating the other. 2. predictable ratios in crosses support of the hypothesis of two hereditary elements involved in the expression of a given Gene. 3. by noting that traits passed unaltered from parental to subsequent Generations, Mendel not only postulated the unit or particulate nature of hereditary elements, but also describe their behavior. (b) by conducting a test cross, one readily tests whether an organism is homozygous or heterozygous for a given trait. (c) chi-square analysis (d) by pedigree analysis

(a) If an organism has a diploid number 16, how many chromatids are visible at the end of mitotic prophase? (b) How many chromosomes are moving to each pole during anaphase of mitosis?

(a) 32 (b) 16

In a cross between a black and a white guinea pig, all members of the F1 generation are black. The F2 generation is made up of approximately 3/4 black and 1/4 white guinea pigs. (a) Diagram this cross, showing the genotypes and phenotypes. (b) What will the offspring be like if two F2 white guinea pigs are mated? (c) Two different mating were made between black members of the F2 generation, with following results. Cross 1 - All black Cross 2 - 3/4 black, 1/4 white Diagram each of the crosses.

(a) WW (black) x ww (white) -F1 Ww (black) Ww (black) x Ww (black) -F2 WW (black), Ww (black), ww (white) (b) all white offspring (ww x ww) (c) most likely genotypes for cross 1: (WW x WW or WW x Ww); most likely genotype for cross 2: (Ww x Ww)

Albinism, caused by a mutational disruption in melanin production, has been observed in many species, including humans. In 1991, the only documented observation of an albino humpback whale was observed near New South Wales. Recently, Polanowski and coworkers studied the genetics of humpback whales from the east coast of Australia, including Migaloo. (a) Do you think that Migaloo's albinism is more likely caused by a dominant or recessive mutation? Explain your reasoning. (b) What data would be helpful in determining the answer to part a?

(a) recessive because it is not very observable (b) punnett square, pedigree, observations of other species like it or not like it

In this chapter, we focused on how chromosomes are distributed during cell division, both in dividing somatic cells (mitosis) and in gamete- and spore-forming cells (meiosis). We found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, answer the following questions. (a) How do we know that chromosomes exist in homologous pairs? (b) How do we know that DNA replication occurs during interphase, not early in mitosis? (c) How do we know that mitotic chromosomes are derived from chromatin?

(a) when somatic cells from the same species are examined, they contain the same number of chromosomes, and the length and centromere placements of nearly all chromosomes can be matched into pairs (b) the initiation and completion of DNA synthesis can be detected by the incorporation of labeled precursors into DNA. DNA content in a G2 nucleus is twice that of a G1 nucleus. (c) if the fibers compromising the mitotic chromosomes are loosened, they reveal fibers like those of interphase chromatin. electron microscope observations indicate that mitotic chromosomes are in varying states of extensively folded structures derived from chromatin.

(a) Assuming that Migaloo's albinism is caused by a rare recessive gene, what would be the likelihood of the establishment of a natural robust subpopulation of albino white humpback whales in this population? (b) Assuming that Migaloo's albinism is caused by a rare dominant gene, what would be the likelihood of the establishment of natural robust subpopulation of albino white humpback whales in this population?

(a, b) Consider that is a gene is recessive, it takes two copies of the gene to produce the recessive phenotype. If, however, a gene is dominant, it only takes one copy.

Contrast spermatogenesis and oogenesis. What is the significance of the formation of polar bodies?

-oogenisis: nuclear activity is "off-center" producing first and second polar bodies by unequal cytoplasmic division; each ooganium and primary oocyte produce one ootid -spermatogenesis: each spermatogonium and primary spermatocyte produces four spermatids

Describe the significance of the Genome 10K plan.

-to establish functional categories for all human genes -to develop new sequencing technologies, such as high-throughput computer-automated sequencers, in order to facilitate genome analysis -to analyze genetic variations between humans, including the identification of single-nucleotide polymorphisms (SNPs) -to map and sequence the genomes of several model organisms used in experimental genetics, including E. coli, S. cerevisiae, C. elegans, D. melanogaster, and M. musculus -to disseminate genome information among both scientists and the general public

A human female with Turner syndrome (47, X) also expresses the X-linked trait hemophilia, as did her father. Which of her parents underwent nondisjunction during meiosis, giving rise to the gamete responsible for the syndrome?

If the father had hemophilia, it is likely that the Turner syndrome individual inherited the X chromosome from the father and no sex chromosome from the mother. If nondisjunction occurred in the mother, during either meiosis I or meiosis II, an egg with no X chromosome can be the result.

What is the probability that, in an organism with a haploid number of 10, a sperm will be formed that contains all 10 chromosomes whose centromeres were derived from maternal homologs?

One half of each tetrad will have a maternal homolog: (1/2)^10.

What advantages were provided by Mendel's choice of the garden pea in his experiments?

Pisum sativum is easy to cultivate. It is naturally self-fertilizing, but it can be crossbred. It has several visible features that are consistent under a variety of environmental conditions, yet contrast due to genetic circumstances. Seeds could be obtained from local merchants.

Which of Mendel's postulates are illustrated by the pedigree that you constructed in Problem 3? List and define these postulates.

Unit factors in pairs, dominance and recessiveness segregation.

In a family of five children, what is the probability that (a) all are males? (b) three are males and two are females? (c) two are males and three are females? (d) all are the same sex? Assumes that the probability of a male child is equal to the probability of a female child (p = 1/2).

(a) 1/2 (b) 10/32 (c) 10/32 (d) 1/16

Assumes that Migaloo's albinism is caused by a rare recessive gene. (a) In a mating of two heterozygous, normally pigmented whales, what is the probability that the first three offspring will all have normal pigmentation? (b) What is the probability that the first female offspring is normally pigmented? (c) What is the probability that the first offspring is a normally pigmented female?

(a) 27/64 (b) 3/4 (c) 3/8

An organism has a diploid number of 16 in a primary oocyte. (a) How many tetrads are present in the first meiotic prophase? (b) How many dyads are present in the second meiotic prophase? (c) How many monads migrate to each pole during the second meiotic anaphase?

(a) 8 (b) 8 (c) 8

Using the forked-line, or branch diagram, method, determine the genotypic and phenotypic ratios of these crosses: (a) AaBbCc x AaBBCC (b) AaBBCc x aaBBCc (c) AaBbCc x AaBbCc

(a) A_B_C_ = 12/16 & aaB_C_ = 4/16 (b) A_BBC_ = 3/8 & A_BBcc = 1/8 & aaBBC_ = 3/8 (c) see page A-15

In this chapter, we have focused on chromosomal mutations resulting from a change in number or arrangement of chromosomes. In our discussions, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions? (a) How do we know that the extra chromosomes causing Down syndrome is usually maternal in origin? (b) How do we know that human aneuploidy for each of the 22 autosomes occurs at conception, even though most often human aneuploids do not survive embryonic or fetal development and thus are never observed at birth? (c) How do we know that specific mutant phenotypes are due to changes in chromosome number or structure? (d) How do we know that the mutant Bar-eye phenotype in Drosophilia is due to a duplicated gene region rather than to a change in the nucleotide sequence of a gene?

(a) Chromosome analysis, as well as the striking correlation between incidence of Down syndrome births and maternal age. (b) Aborted fetuses of trisomies for every human chromosome have been recovered. (c) Representative karotypes of these phenotypes have clear chromosomal aberrations of number and structure compared to those of normal individuals. (d) The studies of Calvin Bridges and Herman J. Muller comparing polytene X chromosome banding patterns revealed that a copy of the region designated as 16A present on both X chromosomes of wild-type flies is duplicated in Bar flies and triplicated in double Bar flies.

In this chapter, we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in this chapter, what answers would you propose to the following fundamental questions: (a) How do we know which contigs are part of the same chromosome? (b) How do we know if a genomic DNA sequence contains a protein-coding gene? (c) What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms? (d) How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome? (e) What evidence indicates that gene families result from gene duplication events? (f) How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show cell- and tissue-specific expression?

(a) Generally, contigs are suspected to be part of the same chromosome in that their end sequences overlap. (b) Identification of a protein-coding region is suspected if similar sequences are conserved in other species and various upstream, downstream, splicing, and punctuation sequences are present and in the proper reading frames. (c) Comparisons of base sequence data with other organisms indicate conservation of a considerable number of sequences. Because of such conservation, functional relationships are supported. Adding additional support are comparative mutation analyses indicating similar function. (d) Proteomics is the identification and analyis of proteins in cells, tissues, and organisms. Genome annotation provides an estimate of the number of protein coding genes, whereas a number of sophisticated techniques including electrophoresis, chromatography, spectrophotometry, and microarrays indicate the number of proteins actually produced. The finding that there are many more types of proteins than genes in the genome has generated a number of explanations. (e) By comparing the amino acid sequences of proteins, the base sequences of genes, and intron/exon architecture, researchers have determined that many genes originated by duplication. Sequence divergence often alters duplicated genes, thus providing the raw material for the evolution of new genes. (f) Microarrays provide a method for identifying active genes by the hybridization of complementary gene products to stretches of DNA. Different hybridization patterns indicate that although some genes are expressed in almost all cells, others show cell- and tissue-specific expression.

A species of cereal rye has a chromosome number of 14, while a species of Canadian wild rye has a chromosome number of 28. Sterile hybrids can be produced by crossing cereal with wild. (a) What would be the expected chromosome number in the somatic cells of the hybrids? (b) Given that none of the chromosomes pair at meiosis I in the sterile hybrid, speculate on the anaphase I separation patterns of these chromosomes.

(a) The chromosome number in the somatic tissue of the hybrid would be the summation of the haploid numbers of each paternal species: 7 +14 = 21. (b) Given that no homologous chromosome pairing occurs at metaphase I, one would expect 21 univalent's and random "1 x 0" separation of chromosomes at anaphase I.

An interesting procedure has been applied for assessing the chromosomal balance of potential secondary oocytes for use in human in vitro fertilization. Using fluorescence in situ hybridization, Kuliev and Verlinsky were able to identify individual chromosomes in first polar bodies and thereby infer the chromosomal makeup of "sister" oocytes. Assume that when examining a first polar body you saw that it had one copy of each chromosome but two copies of chromosome 21. What would you expect to be the chromosomal 21 complement in the secondary oocyte? What consequences are likely in the resulting zygote, if the secondary oocyte was fertilized?

(a) The correct answer is that it would have a monad and a dyad for chromosome 21. (b) It could have no copies of chromosome 21. It could have one copy of chromosome 21. It could have two copies of chromosome 21. It could have three copies of chromosome 21.

Draw all possible conclusions concerning the mode of inheritance of the trait portrayed in each of the following limited pedigrees. (a-d).

(a) There are two possibilities. Either the trait is dominant, in which case I-1 is heterozygous aas are II-2 and II-3, of the trait is recessive and I-1 is homozygous and I-2 is heterozygous. Under the condition of recessiveness, both II-1 and II-4 would be heterozgyous; II-2 and II-3 are homozygous. (b) recessive: parents Aa, Aa (c) recessive: parents Aa, Aa (d) recessive or dominant, not sex-linked; if recessive, parents Aa, aa

In a sequence encompassing 99.4 percent of the euchromatic regions of human chromosome 1, Gregory et. all identified 3141 genes. (a) How does one identify a gene within a raw sequence of bases in DNA? (b) What features of a genome are used to verify likely gene assignments? (c) Given that chromosome 1 contains approximately 8 percent of the human genome, and assuming that there are approximately 20,000 genes, would you consider chromosome 1 to be "gene rich"?

(a) To annotate a gene, one identifies gene-regulatory sequences found upstream of genes, downstream elements, and in-frame triplet nucleotides that are part of the coding region of the gene. In addition, 5' and 3' splice sites that are used to distinguish exons from introns as well as polyadenylation sites are also used in annotation. (b) Similarity to other annotated sequences often provides insight as to a sequence's function and may serve to substantiate a particular genetic assignment. Direct sequencing of cDNAs from various tissues and developmental stages aids in verification. (c) Taking an average of 20,000 for the estimated number of genes in the human genome and computing the percentage represented by 3141 gives 15.7 percent. It appears as if chromosome 1 is gene rich.

In one of Mendel's dihybrid crosses, he observed 315 round, yellow, 108 round, green, 101 wrinkled, yellow, and 32 wrinkled, green F2 plants. Analyze these data using the X^2 test to see if (a) they fit a 9:3:3:1 ratio. (b) the round: wrinkled data fit a 3:1 ratio. (c) the yellow: green data fir a 3:1 ratio.

(a) X^2 = 0.47, they do fit (b) X^2 = 0.35, they do fit (c) X^2 = 0.01, they do fit

Define these pairs of terms, and distinguish from them. (a) aneuploidy/euploidy (b) monosomy/trisomy (c) Patau syndrome/Edwards syndrome (d) autopolyploidy/allopolyploidy (e) autotetraploid/amphidiploid (f) paracentric inversion/pericentric inversion

(a) condition in which the chromosome number is not an exact multiple of the haploid set (2n-1 monosomy, 2n+1 trisomy)/condition in which the chromosome number is not exact multiple of the haploid set (polyploidy >2n, 3n triploid, 4n tetraploid, etc.) (b) the condition of having a diploid chromosome complement in which one (usually the X) chromosome lacks its homologous partner/A genetic disorder in which a person has three copies of a chromosome instead of two (c) A condition in which a person has an extra chromosome 13/A condition that causes severe developmental delays due to an extra chromosome 18 (d) polyploid condition resulting from the addition of one or more extra sets of chromosomes identical to the normal haploid component of the same species/polyploid condition resulting from the union of two or more chromosome sets from different species due to hybridization (f) inversion does not include the centromere/inversion does include the centromere (e) has three sets of chromosomes, all with the same karyotype/an interspecific hybrid having a complete diploid chromosome set from each parent form.

What role do the following cellular components play in the storage, expression, or transmission of genetic information: (a) chromatin (b) nucleolus (c) ribosome (d) mitochondria (e) centriole (f) centromere

(a) during the interphase of a cell cycle, chomosomes are not condensed. these are called chromatin. chromatin contain the genetic material responsible for maintaining the hereditary information and production of the phenotype. (b) the nucleolus is a structure that is produced by activity of the nucleolar organizer region in eukaryotes. composed of ribosomal DNA and protein, it is the structure of the production of ribosomes. some nuclei have more than one nucleolus. they are not present during meiosis or mitosis because in the condensed state of chromosomes there is little to no RNA synthesis. (c) the structure where various RNAs, enzymes, and other molecular species assemble in the primary sequence of a protein. any ribosome can be used in the translation of any mRNA. (d) membrane-bound structure located in the cytoplasm. site of oxidative phosphorylation and production of relatively large amounts of ATP. (e) involved in the migration of chromosomes during mitosis and meiosis (f) serves as an attachment point for sister chromatids and a region where the spindle fibers attach to chromosomes. divides during mitosis and meiosis II; aids in the partitioning of chromosomal material into daughter cells

Albinism in humans is inherited as a simple recessive trait. For the following families, determine the genotypes of the parents and offspring. (When two alternative genotypes are possible, list both.) (a) Two normal parents have five children, four normal and one albino. (b) A normal male and an albino female have six children, all normal. (c) A normal male and an albino female have six children, three normal and three albino. (d) Construct a pedigree of the families in (b) and (c). Assume that one of the normal children in (b) and one of the albino children in (c) become the parents of eight children. Add these children to the pedigree, predicting their phenotypes (normal or albino).

(a) parents: Aa x Aa, offspring: AA, Aa, aa (b) parents: male: AA; female: aa, offspring: Aa (c) parents: male: Aa; female: aa, offspring: Aa & aa (d) 4 normal; 4 albino

Discuss how Mendel's monohybrid results served as the basis for all but one of his postulates. Which postulate was not based on these results? Why?

1. when two independent events occur simultaneously, the probability of the two outcomes occurring and combination is equal to the product of their individual probabilities of occurrence. 2. independent assortment cannot be demonstrated by a monohybrid cross because two Gene pairs must be involved to do so.

It can be said that modern biology is experiencing an "omics" revolution. What does this mean? Explain you answer.

A number of new subdisciplines of molecular biology will provide the infrastructure for major advances in our understanding of living systems. The following terms identify specific areas within that infrastructure: - Proteomics: proteins in a cell or tissue - Metabolomics: enzymatic pathways - Glycomics: carbohydrates of a cell or tissue - Toxicogenomics: toxic chemicals - Metagenomics: environmental issues - Pharmacogenomics: customized medicine - Transcriptomics: expressed genes

Because of its accessibility and biological significance, the proteome of human plasma has been intensively studied and used to provide biomarkers for such conditions as myocardial infarction and congestive heart failure. Polanski and Anderson have compiled a list of 1261 proteins, some occurring in plasma, that appear to be differential expressed in human cancers. Of these 1261 proteins, only 9 have been recognized by the FDA as tumor-associated proteins. First, what advantage should there be in using plasma as a diagnostic screen for cancer? Second, what criteria should be used to validate that a cancerous state can be assessed through the plasma proteome?

Because blood is relatively easy to obtain in a pure state, its components can be analyzed without fear of tissue-site contamination. Second, blood is intimately exposed to virtually all cells of the body and may therefore carry chemical markers to certain abnormal cells its represents. Theoretically, it is an ideal probe into the human body. However, when blood is removed from the body, its proteome changes, and those changes are dependent on a number of environmental factors. Thus, what might be a valid diagnostic for one condition might not be so for other conditions. In addition, the serum proteome is subject to change depending on the genetic, physiologic, and environmental state of the patient. Age and sex are additional variables that must be considered. Validation of a plasma proteome for a particular cancer would be strengthened by demonstrating that the stage of development of the cancer correlates with a commensurate change in the proteome in a relatively large, statistically significant pool of patients. Second, the types of changes in the proteome should be reproducible and, at least until complexities are clarified, involve tumorigenic proteins. It would be helpful to have comparisons with archived samples of each individual at a disease-free time.

Review the Chapter Concepts list on page 16. All of these pertain to conceptual issues involving mitosis or meiosis. Based on these concepts, write a short essay that contrast mitosis and meiosis, including their respective roles in organisms, the mechanisms by which they achieve their respective outcomes, and the consequences should either process fail to by executed with absolute fidelity.

Compared with mitosis, which maintains chromosomal constancy, meiosis provides for a reduction in chromosome number and an opportunity for the exchange of genetic material between homologous chromosomes. In mitosis that is no change in chromosome number or kind in the two daughter cells, whereas in meiosis numerous potentially different haploid (n) cells are produced. During oogenesis, only one of the four meiotic products is functional; however, four of the four meiotic products of spermatogenesis are potentially functional.

What are gene microarrays? How are microarrays used?

Most microarrays, known also as gene chips, consist of a glass slide that is coated, using a robotic system, with single-stranded DNA molecules. Some microarrays are coated with single-stranded sequences of expressed sequenced tags or DNA sequences that are complementary to gene transcripts. A single microarray can have as many as 20,000 different spots of DNA, each containing a unique sequence. Researchers use microarrays to compare patterns of gene expression in tissues under different conditions or to compare gene-expression patterns in normal and diseased tissues. In addition, microarrays can be used to identify pathogens. Microarray databases allow investigators to compare any given pattern to others worldwide.

BLAST searches and related applications are essential for analyzing gene and protein sequences. Define BLAST, describe basic features of this bioinformatics tool, and provide an example of information provided by a BLAST search.

One initial approach to annotating a sequence is to compare newly sequenced genomic DNA to the known sequences already stored in various databases. The NCBI provides access to BLAST software, which directs searches through databanks of DNA and protein sequences. A segment of DNA can be compared to sequences in major databases such as GenBank to identify matches that align in whole or in part. One might seek similarities to a sequence on chromosome 11 in a mouse and find that or similar sequences in a number taxa. BLAST will compute a similarity score or identity value to indicate the degree to which two sequences are similar. BLAST is one of many sequence alignment algorithms that may sacrifice sensitivity for speed.

Pigeons may exhibit a checkered or plain color pattern. In a series of controlled mating's, the following data were obtained. P1 Cross: -36 checkered (checkered x checkered) -38 checkered (checkered x plain) -35 plain (plain x plain) Then F1 offspring were selectively mated with the following results. F1 x F1 Crosses: -34 checkered (checkered a x plain c) -17 checkered & 14 plain (checkered b x plain c) -28 checkered & 9 plain (checkered b x checkered b) -39 checkered (checkered a x checkered b) How are the checkered and plain patterns inherited? Select and assign symbols for the genes involved, and determine the genotypes of the parents and offspring in each cross.

P = checkered; p = plain Cross (a): PP x PP or PP x Pp -Notice in cross (d) that the checkered offspring, when crossed to plain, produce only checkered F2 progeny and in cross (g) when crossed to checkered still produce only checkered progeny. From this additional information, one can conclude that in the progeny of cross (a) these are no heterzygotes and the original cross must have been PP x PP. Cross (b): PP x pp Cross (c): because all the offspring from this cross are plain, there is no doubt that the genotype of both parents is pp. Genotypes of all individuals: (a) PP x PP = PP (b) PP x pp = Pp (c) pp x pp = pp (d) PP x pp = Pp (e) Pp x pp = Pp & pp (f) Pp x Pp = PP & Pp & pp (g) PP x Pp = PP & Pp

Describe the events that characterize each stage of mitosis.

Prophase is the first phase is when the two sister chromatids pair up and the nucleoli disappears. Prometaphase is the second phase where the microtubules begin to separate from each other, each pair of microtubules attach to the kinetochores and some nonkinetohore microtubules interact with those from the opposite pole of the spindle. Metaphase is the third phase where the chromosomes are lined up on the invisible line of the metaphase plate. Anaphase is the fourth phase where the two daughter chromosomes begin to separate from each other to opposite poles. Telophase is the last phase where the two daughter nuclei form creating two identical nuclei.

Annotation of a proteome attempts to relate each protein to a function in time and space. Traditionally, protein annotation depended on an amino acid sequence comparison between a query protein and a protein with known function. If the two proteins shared a considerable portion of their sequence, the query would be assumed to share function of the annotated protein. Following is a representation of this method of protein annotation involving a query sequence and three different human proteins. Note that the query sequence aligns to common domains within the three other proteins. What arguments might you present to suggest that the function of the query is not related to the function of the other three proteins?

Since structural and chemical factors determine the function of a protein, it is likely to have several proteins share a considerable amino acid sequence identity, but not be functionally identical. Since the in vitro function of such a protein is determined by secondary and tertiary structures, as well as local surface chemistries in active or functional sites, the nonidentical sequences may have considerable influence on function. Note that the query matches to different site positions within the target proteins. A number of other factors suggesting different functions include associations with other molecules, chemical nature and position of binding domains, posttranslational modification, signal sequences, and so on.

Considering the Mendelian traits round versus wrinkled and yellow versus green, consider the crosses below and determine the genotypes of the parental plants by analyzing the phenotypes of their offspring. (pg. 50)

Suggested symbolism: w = wrinkled seeds W = round seeds g = green cotyledon G = yellow cotyledon (a) notice a 3:1 ratio for seed shape, therefore Ww x Ww; and no green cotyledons, therefore GG x GG or GG x Gg. Putting the two characteristics together give WwGG x WwGG or WwGG x WwGg. (b) wwGg x WwGg (c) WwGg x WwGg (d) WwGg x wwgg

Describe the human genome in terms of genome size, the percentage of the genome that codes for proteins, how much is composed of repetitive sequences, and how many genes it contains. Describe two other features of the human genome.

The human genome is composed of over 3 billion nucleotides in which about 2 percent code for genes. Genes are unevenly distributed over chromosomes, with clusters of gene-rich regions separated by gene-pool one. Human genes tend to be larger and contain more and larger introns than in invertebrates such as Drosophilia. It is estimated that at least half of the genes generate products by alternatively splicing. Hundreds of genes have been transferred from bacteria into vertebrates. Duplicated regions are common, which may facilitate chromosomal rearrangement. The human genome appears to contain approximately 20,000 protein-coding genes. However, there is still uncertainty as to the total number.

What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.

analyze biological data sets (DNA and/or protein sequences) with mathematics and computer programs. Examples: o Functional genomics o Comparative genomics o Metagenomics

Metagenomics studies generate very large amounts of sequence data. Provide examples of genetic insight that can be learned from metagenomics.

has appropriated the tools used for standard genomics and applied them to the study of the entire communities of microbes—without the need to isolate and culture the individual microbial species

What are pseudogenes, and how are they produced?

nonfunctional versions of genes that resemble gene sequences but contain significant nucleotide changes which prevent their expression. they are formed via gene duplication and subsequent mutation

Mendel crossed peas having round seed and yellow cotyledons (seed leaves) with peas having wrinkled seeds and green cotyledons. All the F1 plants had round seed with yellow cotyledons. Diagram this cross through the F2 generation, using both the Punnett square and forked-line, or branch diagram, methods.

not this one exactly but the idea behind it