CHAPTER 8

Learning Objectives

  1. Describe the parts of a chromosome by their function, location, and general biochemical properties.
  2. Describe how polytene chromosomes are produced, and illustrate their value in studying detailed genetic organization along interphase chromosomes.
  3. Describe band staining in mitotic chromosomes, and illustrate its significance in mapping chromosomes.
  4. Explain the structure and function of the nucleolar organizer region of metaphase and polytene chromosomes.
  5. Explain the relationships and differences between cytological chromosome maps and recombination (genetic) chromosome maps.
  6. Describe (generally) how DNA fragments are used to locate certain loci in the cytological map.
  7. Describe how deletions of chromosomes can be mapped in heterozygotes using polytene chromosomes.
  8. Describe how pseudodominance and a series of overlapping deletions can identify the physical location of a locus in a polytene chromosome.
  9. Describe the effects of duplications in forming alleles at the Bar eye locus in Drosophila melanogaster, how they are mapped cytologically, and how they are mapped by recombination.
  10. Define and describe the origin of a "gene family" using Human hemoglobin genes.
  11. Describe the nature of chromosome duplications, deficiencies, inversions and translocations, and how each affects pairing in Meiosis I, and consequently they affect the genetic (recombination) map.
  12. Explain and diagram the experiment that demonstrated that the Variegated Position Effect of heterochromatin was due to the proximity of heterochromatin rather than a high frequency of somatic mutation.
  13. Illustrate how the detailed banding patterns of metaphase chromosomes are useful to identify homologus regions and arms of a chromosome even when they occur in different species.

Many terms are used to describe chromosome shapes (morphology) when condensed at metaphase. For illustration purposes, only one chromatid may be drawn since sister chromatids are identical in shape. These may be arranged from a photograph of the "spread" chromosomes in metaphase, or late prophase, in an orderly way to form a karyotype.

DEFINE, and use the words to draw your attention to the process or dynamic aspects or consequences of the situation giving rise to the term:

  1. Primary Constriction: region of the centromere; appears to be "pinched" and sister chromatids are "held" together in a karyotype by the kinetochore
  2. Telocentric: centromere (and kinetochore location) very near the end, appears as if on the end of the chromosome;
  3. Acrocentric: centromere neither near the end nor at the midpoint of the chromosome.
  4. Metacentric: centromere at the midpoint of the chromosome
  5. Acentric: a chromosome without a centromere, and thus cannot move on the spindle
  6. Nucleolar organizers: secondary constrictions of the chromosomes where the nucleoli are found in interphase; they have highly specific positions on the DNA and contain genes for ribosomal RNA; there positions are used as landmarks for cytogenetic studies. Since no kinetochore forms, the chromatids are not connected at secondary constrictions. Since these loci actively transcribe rRNA late into Prophase, they are less coiled and folded, causing them to appear thinner, "constricted," when viewed cytologically with a microscope at metaphase.
  7. Chromosomal satellite: short region of "thicker" chromosome distal to the nucleolar organizing region
  8. Heterochromatin (facultative and constitutive): densely staining highly compact regions of the chromosome during interphase and prophase; c- permanent feature of a specific chromosome location, coded in the DNA and thereby it is hereditary; f- may be present or absent in any particular chromosomal region, and formation is an indication of gene activity regulation -- inactive or slightly active when staining darkly.
  9. Euchromatin: lightly staining regions in prophase, but darkly stained in polytene chromosomes unless "puffed"
  10. Endomitosis: a process in which many chromosome replicas are produced but do not separate into different nuclei
  11. Polytene Chromosomes: the bundles of multiple replicas of DNA sets produced by repeated passes through the S-phase without mitosis; remain co-aligned along the length of the chromatid strands, forming giant chromosomes; often the homologus chromosomes are paired in somatic cells; cells with polytene chromosomes cannot undergo mitosis. When loci are active, they often cause a loosening of the chromosome fibers, and form a "puff".
  12. Deletion: loss of a segment of a chromosome
  13. Duplication: additional copy of part of a chromosome, often located adjacent to original part prior to duplication
  14. Translocation: part of a chromosome moved to another location, usually on a non-homologous chromosome
  15. Inversions: part of a chromosome removed and reinserted in the opposite direction of the same chromosome
  16. Deletion Loop: cytogenetic configuration seen when chromosomes are paired, caused by the failure of the corresponding segment on the normal chromosome to have a homologus region with which to pair because of the deleted region
  17. Pseudodominance: phenotypic expression of the recessive allele on a normal chromosome when the region in which it is located has been deleted from the other homolog; expression of a recessive allele when present in a single dose. Although not usually included in the definition, all X-linked alleles (except for any loci that share homology in the Y-chromosome) in the heterogametic sex are functionally equivalent to pseudodominant alleles. Instead, for the hemizygous sex chromosome, we say that dominance is not defined. (Note: some loci may be shared by both X- and Y-chromosomes in homologous regions of the chromosomes, and interactions are like autosomal loci, including expression of dominance).
  18. Tandem sequence: a duplication with both copies oriented the same in the chromosome; ABCBCD
  19. Reverse order: a duplication with copies oriented in opposite directions; ABCCBD
  20. Inversion Loop: meiotically paired homologs that are heterozygous for an inversion, which demonstrates that homologous pairing is region by region within the chromosome pair; homologus pairing of polytene chromosomes also shows an inversion loop in interphase
  21. Paracentric Inversion: centromere not included in the inverted segment
  22. Pericentric Inversion: centromere is included in the inverted segment
  23. Dicentric bridge: a chromosome with two kinetochores that move in opposite directions at anaphase, stretching the intervening segment between them; bridge eventually is broken, causing deletions
  24. Acentric fragment: a part of a chromosome without a centromere, and therefore does not form a kinetochore
  25. Reciprocal Translocation: a segment from one chromosome is exchanged with a segment from another nonhomologous chromosome. Two simultaneous translocations.
  26. Position-effect variegation: a translocation involving the movement of a gene close to heterochromatin, resulting in an erratic expression of the allele from cell to cell. Heterochromatin often is involved in delaying the unfolding of a chromosome in interphase, after mitosis, so that loci that "should" be active in G1 remain folded in a protein "matrix." (note "spreading effect") The variegation has considerable variable expressivity. An actual photo of the phenotype may show the color differences is more "mottled" than spotted.
  27. Slipped pairing and crossover: a way that can produce mutations, including duplications of segments of chromosomes, sometimes forming gene families and also formation of a homozygous cell when crossovers are somatic from a heterozygous cell in the absence of changes in the alleles themselves.
  28. "Centric fusion": a form of reciprocal translocation whereby two telocentric chromosomes may be combined to form an acrocentric or metacentric chromosome, reducing the number of chromosomes in the haploid set. Sometimes allows the establishment of phylogenetic relatedness of species. Terminology is a misnomer since the centromeres do not actually "fuse", but one centromere is lost after the translocation has removed all essential loci attached to it.

QUESTIONS: (with guides to answers; answer the questions in parentheses)

  1. What is the best known of all kinds of "clastogens" (mutagens that break chromosomes)? Is the instability of chromosomes only due to mutagens? Why or why not? Answer: ionizing radiation. Note: It is known that certain genetic factors, or special regions in the DNA, produce chromosome breaks and major rearrangements. (Explain why, or how, this genetic breaking of chromosomes can be achieved.)
  2. What are the genetic properties of deletions? Answer: failure of the damaged chromosome to survive as a homozygote (recessive lethal), suppression of crossing over in the region of the deletion, lack of revertability, pseudodominance, and cytogenetically by deletion loops. Deletions change the genetic map. When homozygous the map is missing loci in the deletion and the map is shorter. When heterozygous, the loci on either side map are closer due to no crossing over where pairing is impossible. (Explain "why" for each of these answers.)
  3. Why are duplications important evolutionarily and give an example? Answer: They supply additional genetic material that is capable of evolving new function since one functional copy is present. ex: Hb genes (Note: What are "gene families" and how do they originate?)
  4. Once an adjacent tandem duplication arises in a population, how can homozygosity of such a duplication result in higher orders of duplication? Give an example. Answer: by crossing-over when the chromosomes are asymmetrically paired. ex: Bar locus in Drosophila. (Diagram and explain this process.)
  5. Why are heterozygotes for inversions usually viable? Answer: There is no net loss or gain of genetic material. (Explain why this is true both for males and females in Drosophila. Why is this important in Drosophila? How does this feature allow the development of "supergenes" on the chromosome, and "fix" epistatic genotypes?)
  6. How are dicentric bridges and acentric fragments produced? Draw the way. What happens to these two structures during Anaphase I? Answer: In a paracentric inversion where the crossover has occurred within the inversion loop, the acentric fragment is lost and the bridge piece usually breaks as the homologs separate. (Diagram how the loop forms a bridge and an acentric fragment remains.)
  7. What are the two mechanisms that reduce the number of recombinants recovered from an organism heterozygous for an inversion? Answer: 1. inhibiting crossing over in the area of the inversion by problems with mechanical pairing, 2. selectively eliminating the products of the crossovers in the inversion loops through zygotic mortality. The reduced number of crossover products recovered reduces the genetic map, and loci on either side of the inversion map appear very close together. If the inversion is homozygous, the total map is not changed in length, but the gene order is changed. (Construct an hypothetical data set for a testcross that illustrates no. 2.)
  8. Draw the pairing configuration of a reciprocal translocation. Identify the homologous centromeres. Differentiate between adjacent-1 segregation, alternate segregation and adjacent-2 segregation. Which is the rarest type of segregation? Which type of segregation results in two complete and viable cells? Which common type of segregation occurs in the carrier of familial Downs? refer to the tables and figures in translocations, and recall that Familial Downs is due to translocation of part of chromosome-21 to another chromosome.
  9. Give an example of position-effect variegation and explain how it works. White eye locus in Drosophila located on the tip of the X chromosome. The translocation changed the state of the gene, w+, which made it more variable in its expression in somatic cells. The w+ gene in the translocation is not expressed in some cells, thereby allowing the expression of w. The unstable expression of a gene is a reflection of its position in the genome. However, the information in the w+ is not changed, only its expression. (Diagram this explanation, and explain how we know that the translocation was NOT the cause of the position-effect variegation.)

Homework: Study the Chapter Integration Problem thoroughly. Problems 4, 8, 11, 17.

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