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Molecular Structure of Chromosomes and Transposable Elements
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The prevalence of highly repetitive sequences seems rather strange to many geneticists. Do they seem strange to you Why or why not Discuss whether or not you think they have an important function.
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Highly repetitive sequence:
The segments of DNA (deoxyribonucleic acid), which are repeated many times in genome, are known as highly repetitive DNA. Highly repetitive sequences are relatively short for each copy, they are ranging from few nucleotides to hundred in length. For example, in humans Alu family sequences found nearly 300bp (base pair) long.
They are very similar to satellite DNA. They are found in a group in a tandem array or mix together in genome. Highly repetitive sequences are do not code for proteins. While studying the DNA renaturation process the highly repetitive DNA renatures earlier due to high the presence of highly complementarity.
Prevalence of highly repetitive sequences seems rather strange to many geneticists:
It seems to be a strange the DNA has no clear function. It is a waste of energy. Maybe the function, we do not know about yet. The evolution also allows the bad things to build up within genomes like genes which cause the diseases.
May be it is another example of the negative consequences of evolution. By this way Prevalence of highly repetitive sequences seems rather strange to many geneticists.
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Bacterial and eukaryotic chromosomes are very compact. Discuss the advantages and disadvantages of having a compact structure.
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Bacterial chromosomes:
Bacterial chromosome is short DNA (deoxyribonucleic acid) molecule but it lacks protein coat. The DNA is double helix and closed circular in nature. In bacteria chromosome size is
bp (base pairs). In bacterial chromosomal replication three major steps are involved they are initiation, elongation and termination.
Eukaryotic chromosomes:
Eukaryotes contain multiple pairs of linear chromosomes. In eukaryotes chromosomes are composed of DNA coiled and condensed around nuclear proteins known as histones. They consist of repeated units of chromatin known as nucleosomes. In eukaryotes chromatin not only allows large amount of DNA fit in to a small place, but also helps in regulate gene expression.
Advantages and disadvantages of bacterial and eukaryotic compact structure:
• Bacterial chromosomal DNA is folded in to compact structure, so it occupying relatively small part of the cell.
• Bacterial chromosome is organized into independently supercoiled loops known as domains. Domain allows the chromosomal DNA to undergoing structural changes in cellular process.
• In eukaryotic chromosomes consists complex made up of protein and DNA and organized in condensed manner, it permits the large amount of DNA storage in the nucleus of the cell.
Functions of chromosomes:
Chromosomes store the genetic code and they determine the sex. They control cell division. They are also formation of protiens and storagE.
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Describe the two main mechanisms by which the bacterial DNA becomes compacted.
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Bacterial DNA:
Bacteria contain one long stranded DNA (chromosome), which is present in the cytoplasm. DNA is ranges from 139 kilo base pairs to 13,000 kilo base pairs. Like eukaryotes bacterial DNA is not packed with histones to form chromatins. It exists as highly compact and super coiled structurE.Two main mechanisms by bacterial DNA become compacted:
Bacterial DNA first mechanism is arranged loop domains and loops of DNA are anchored to DNA-binding proteins. Another mechanism of bacterial DNA is to forming DNA double helix; super coiled to make it more compact like twisting rubber banD.
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Take two pieces of string that are approximately 10 inches each, and create a double helix by wrapping them around each other to make 10 complete turns. Tape one end of the strings to a table, and now twist the strings three times (360° each time) in a right-handed direction. Note: As you are looking down at the strings from above, a right-handed twist is in the clockwise direction.
A. Did the three turns create more or fewer turns in your double helix How many turns are now in your double helix
B. Is your double helix right-handed or left-handed Explain your answer.
C. Did the three turns create any supercoils
D. If you had coated your double helix with rubber cement and allowed the cement to dry before making the three additional right-handed turns, would the rubber cement make it more or less likely for the three turns to create supercoiling Would a pair of cemented strings be more or less like a real DNA double helix than an uncemented pair of strings Explain your answer.
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In Part II of this textbook, we considered inheritance patterns for diploid eukaryotic species. Bacteria frequently contain two or more nucleoids. With regard to genes and alleles, how is a bacterium that contains two nucleoids similar to a diploid eukaryotic cell, and how is it different
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Let's suppose you have isolated chromatin from some bizarre eukaryote with a linker region that is usually 300-350 bp in length. The nucleosome structure is the same as in other eukaryotes. If you digested this eukaryotic organism's chromatin with a high concentration of DNase I, what would be your expected results
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We seem to know more about the structure of eukaryotic chromosomal DNA than bacterial DNA. Discuss why you think this is so, and list several experimental procedures that have yielded important information concerning the compaction of eukaryotic chromatin.
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Two circular DNA molecules, which we will call molecule A and molecule B, are topoisomers of each other. When viewed under the electron microscope, molecule A appears more compact than molecule B. The level of gene transcription is much lower for molecule A. Which of the following three possibilities could account for these observations
First possibility: Molecule A has three positive supercoils, and molecule B has three negative supercoils.
Second possibility: Molecule A has four positive supercoils, and molecule B has one negative supercoil.
Third possibility: Molecule A has zero supercoils, and molecule B has three negative supercoils.
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Coumarins and quinolones are two classes of drugs that inhibit bacterial growth by directly inhibiting DNA gyrase. Discuss two reasons why inhibiting DNA gyrase also inhibits bacterial growth.
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As described in Chapter 9, one bp of DNA is approximately 0.34 nm in length. A bacterial chromosome is about 4 million bp in length and is organized into about 100 loops that are about 40,000 bp in length.
A. If it was stretched out linearly, how long (in micrometers) would one loop be
B. If a bacterial chromosomal loop is circular, what would be its diameter (Note: Circumference = D , where D is the diameter of the circle.)
C. Is the diameter of the circular loop calculated in part B small enough to fit inside a bacterium The dimensions of the bacterial cytoplasm, such as E. coli , are roughly 0.5 m wide and 1.0 m long.
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Explain how a renaturation experiment can provide quantitative information about genome sequence complexity.
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What is a bacterial nucleoid With regard to cellular membranes, what is the difference between a bacterial nucleoid and a eukaryotic nucleus
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Discuss and make a list of the similarities and differences between bacterial and eukaryotic chromosomes.
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Why is DNA supercoiling called supercoiling rather than just coiling Why is positive supercoiling called overwinding and negative supercoiling called underwinding How would you define the terms positive and negative supercoiling for Z DNA (described in Chapter 9)
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An organism contains 20% highly repetitive DNA, 10% moderately repetitive DNA, and 70% unique sequences. Draw the expected C 0 t curve that would be obtained from this organism.
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In viral replication, what is the difference between self-assembly and directed assembly
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In a renaturation experiment, does the copy number affect only the rate of renaturation, or does it also affect the rate of denaturation Explain your answer.
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Let's suppose you have isolated DNA from a cell and viewed it under a microscope. It looks supercoiled. What experiment would you perform to determine if it is positively or negatively supercoiled In your answer, describe your expected results. You may assume that you have purified topoisomerases at your disposal.
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When chromatin is treated with a moderate salt concentration, the linker histone H1 is removed (see Figure 10.13a). Higher salt concentration removes the rest of the histone proteins (see Figure 10.19b). If the experiment of Figure 10.12 were carried out after the DNA was treated with moderate or high salt, what would be the expected results
FIGURE 10.13 The nucleosome structure of eukaryotic chromatin as viewed by electron microscopy. The chromatin in (a) has been treated with moderate salt concentrations to remove the linker histone, H1. It exhibits the classic beads-on-a-string morphology. The chromatin in (b) has been incubated without added NaCl and shows a more compact morphology.
FIGURE 10.12 DNase I cuts chromatin into repeating units containing 200 bp of DNA. Starting material: Nuclei from rat liver cells.
FIGURE 10.19 The importance of histone proteins and scaffolding proteins in the compaction of eukaryotic chromosomes. (a) A metaphase chromosome. (b) A metaphase chromosome following treatment with high salt concentration to remove the histone proteins. The black arrow on the right points to an elongated strand of DNA. The white arrow on the left points to the scaffold (composed of nonhistone proteins), which anchors the bases of the radial loops. As shown earlier in Figure 10.18d, this scaffold contains protein filaments.
FIGURE 10.18 The steps in eukaryotic chromosomal compaction leading to the metaphase chromosome.
FIGURE 10.12 DNase I cuts chromatin into repeating units containing 200 bp of DNA. Starting material: Nuclei from rat liver cells.
FIGURE 10.19 The importance of histone proteins and scaffolding proteins in the compaction of eukaryotic chromosomes. (a) A metaphase chromosome. (b) A metaphase chromosome following treatment with high salt concentration to remove the histone proteins. The black arrow on the right points to an elongated strand of DNA. The white arrow on the left points to the scaffold (composed of nonhistone proteins), which anchors the bases of the radial loops. As shown earlier in Figure 10.18d, this scaffold contains protein filaments.
FIGURE 10.18 The steps in eukaryotic chromosomal compaction leading to the metaphase chromosome.
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Bacterial chromosomes have one origin of replication, whereas eukaryotic chromosomes have several. Would you expect viral chromosomes to have an origin of replication Why or why not
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