CHAPTERS 16
Supplemented with 17, 18 & 23

Define:

1. Nucleosome: Histone-DNA octamer complex of H2a, H2b, H3 and H4 in the core, around which 140 bp and DNA are wound.
2. Solenoid structure: coils of nucleosomes, about six per turn formed when H1 is complexed with the nucleosome and DNA. The H1 histones complex then with about six nucleosome/DNA/H1 units to form the solenoid.
3. Chromomere: the densely staining bands in Drosophila; may represent one cistron.
4. Scaffold: Core of protein for organizing loops of DNA in eukaryote, consisting mostly of topoisomerase II enzyme (eg. gyrase, requires ATP, cuts both strands) and "manages" the organization of the "skeins" of DNA coiled in solenoid fashion around nucleosomes.
5. Scaffold Attachment Regions (SAR): Regions of the chromosomes with sequences known to be specific for topoisomerase binding, found only in untranscribed regions of the eukaryotic chromosomes. The attachment regions are spaced along the chromosomes, with the interveining regions containing several loci.
6. Centromeric DNA: Regions of DNA which cannot act as origins of replication, and presumably are sites for formation of kinetochores. Often highly repetitive DNA of short sequence length are found around the centromeric DNA, and form constitutive heterochromatin.
7. Telomeres: Sequences of DNA at ends of chromosomes, which may be associated with both cell lifespan and stabilize the ends of linear chromosomes. They have simple repeats added by telomerase, forming a longer "tail" of single stranded DNA that folds back on itself in a "hairpin" configuration, binding G-G in an unusual mode.
8. Pseudogenes: nonfunctional copies of genes that are remnants of the evolutionary process; may lack promoter region; may be produced by incorporation of DNA from mRNA synthesized by reverse transcriptase.
9. Constitutive heterochromatin: consistently dense staining chromosomal elements or specific segments in all cells of a species. Tight compact region of the chromosome, assumed to be inactive, although they probably have important structural functions in chromosome function.
10. Facultative heterochromatin: chromosomal regions within the same species that sometimes appear densely staining in the cells and other times appear as euchromatin. They generally are inactive when densely staining.

    When a chromosomal region is inactivated in development, the pattern is often passed to cells derived from it mitotically by "imprinting". Discussed on pages 698-700 in Chapter 23, imprinting is the mode by which the Barr bodies are determined in mammals with 2 or more X chromosomes. For your interest, the "random" inactivation and imprinting of the additional X chromosomes is contrasted with the marsupial pattern whereby the paternal X chromosome is the one inactivated. A similar nonrandom event in mammals occurs in postembryonic tissues.

11. Satellite, B- or accessory chromosomes: Chromosomes composed entirely of heterochromatin
12. Spreading effect: inactivation of genes in the euchromatin by sequentially inactivating genes outward from the heterochromatin, like a domino effect. (A distal gene can not be inactivated without the proximal gene being inactivated first.)
13. Position effect enhancers and suppressors: Mutants that enhance or suppress spreading effect of heterochromatin. (see pp. 500-501 of text). These mutants demonstrate genetic control of the formation of constitutive heterochromatin. They express a dosage effect and suggest that the material that forms heterochromatin (chromosomal proteins, probably) are in limited supply and can be a limiting factor in the degree of forming heterochromatin at a particular chromosomal site.
14. Polytene chromosome bands, transcription units, and translation units: The bands are "dynamic" structures that can unfold or fold, affecting transcription. However, until detailed biochemical "tracking" of the products of a single band or group of bands was possible, the relationships remained largely speculative. Using deletion mapping combined with molecular isolation, it has been found that a cistron is approximately one band. However, when mRNA's have been isolated, more than one polypeptide per locus is implicated. The explanation is found in Chapter 18, where hnRNA processing may omit certain exons. Many examples have now been found in eukaryotes.

Questions:

1. Describe the super-coiling process in eukaryotic cells. (see text)
2. Name five sources of untranslated DNA in eukaryotes. highly repetitive sequences (constitutive heterochromatin), intervening sequences (introns), spacer sequences, rRNA and tRNA genes (Which of these are transcribed altho not translated?)
3. If the basic metabolic processes exist in both prokaryotes and multicellular eukaryotes, then what might be the reason for the larger genome found in eukaryotes? introns, coding involved in the more elaborate regulation of gene activity (not new gene functions necessarily, although this probably is a factor as well eg. hormone loci, histone loci).
4. What is the function(s) of genes that are found in multiple copies in the genome? increased gene products, related sequences that have diverged during evolution, more specialized protein products from the same original locus (eg. Hb loci, & the immune system to be covered soon)
5. What is a gene family and give an example? genes that are derived from a common ancestral gene, ex: Hb loci How can pseudogenes in a gene family arise?
6. Are all heterochromatic chromosomes functionally inert? Give an example. Y-chromosome in Drosophila composed of heterochromatin, but it contains 6 active loci for male fertility.
7. Describe the nature and characteristics of constitutive heterochromatin with respect to: structure, function, constitution, affects on crossing-over, euchromatin inactivation, and the spreading effect.
   1. highly coiled, densely staining, basically inert,
   2. may contain sequences of highly repetitive DNA,
   3. often located near the centromeres, telomeres in Drosophila,
   4. crossing over is reduced between loci that closely flank large blocks of heterochromatin,
   5. can cause inactivation of a wild-type allele moved within close proximity to the heterochromatin in position effect variegation.
   6. Has a spreading effect that inactivates genes in a linear fashion in the adjacent euchromatin.
   7. Inactivating event occurs early in development, so that all daughter cells that are derived from an affected cell are deactivated. All daughter cells inherit loci with fixed functional states, even if expression of that loci does not occur until later in ontogeny (development).
8. Discuss dosage compensation and X-chromosome inactivation in mammals. Is it a random process? When in development does it occur? What activates the dosage compensation in females? Is the whole X inactive?
   1. The X chromosome from the father or mother can be the one inactivated, it is a "random" process, realizing that "random" implies that both X chromosomes may be inactivated in an unpredicable way. There are examples of non-randomness in certain tissues.
   2. Inactivation occurs early in development due to the presence of mosaics. (several potential precursor cells) Mosaics are the result of imprinting, whereby the cellular "descendents" created by subsequent mitotic events carry the same "setting of the control switches" and maintain the same chromosome in the inactivated state.
   3. Once inactivation occurs, the state is inherited somatically since clone cells all express the same allele.
   4. dosage compensation is determined by number of X chromosomes, NOT the phenotypic sex of the organism
   5. the short end of the X-chromosome remains active in Barr bodies

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