Chap 12 DNA Organization and Chromosomes

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If chromosome preparations were heat denatured and then treated with Giemsa stain, heterochromatin regions (condensed and inactive) near the centromere pick up the stain.

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Bacteria such as Escherichia coli has a circular chromosome.

The DNA is associated with histone-like proteins, such as HU and H, that promote replication and transcription.

The chromosome can be visualized under the electron microscope if the cell is lysed in a hypotonic medium.

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If mitotic chromosomes are treated with the proteolytic enzyme trypsin followed by Giemsa staining, a G-banding pattern emerges that can be used to identify chromosomes and chromosomal mutations.

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The G-banding patterns can be systematically used to identify chromosomes and regions on each chromosome.

This X chromosome shows the banding nomenclature along its p ("petite") and q ("queue") arms.

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Viral chromosomes can be either DNA or RNA, and either single or double stranded. They can be circular or linear molecules, and are tightly packed in a protein coat.

Bacterial chromosomes are always circular, double-stranded DNA molecules, compacted into a structure called the nucleoid.

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In situ hybridization between a radioactive probe containing mouse satellite DNA and mitotic chromosomes. The grains in the autoradiograph localize the heterochromatic regions near the centromeres containing satellite DNA, which are composed of short repetitive sequences.

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DNA near the centromere (CEN) of yeast is about 125 bp and can be divided into 3 regions. CEN sequences are highly conserved and are very similar among the chromosomes (3, 4, 6, 11). This is not surprising since CEN play scritical roles in centromere functions of chromosome attachment to spindle fibers and segregation in cell division.

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  1. In the first level of DNA packing, A 2-nm diameter DNA molecule is coiled around 2 tetramers of histone proteins into a nucleosome that is about 11 nm in diameter. Histone H1 acts as a spacer between nucleosomes. continue

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  1. The 11-nm fiber is packed into a 30-nm solenoid consisting of several nucleosomes coiled together.
  2. During condensation to the mitotic chromosome, the 30-nm fiber forms a series of looped domains that further condense into a 300-nm chromatin fiber.
  3. The 300-nm fibers then coil into the chromatid arms seen in metaphase chromosomes.   video

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In eukaryotic chromatin, DNA is associated various proteins, including histones and nonhistones.
Histones are large proteins rich in positively charged amino acids (lysine and arginine) bound to the negatively charged phosphate groups of nucleotides and function to pack 2-m long lengths of DNA into a 10-µm diameter nucleus.

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Lampbrush chromosomes are found in most vertebrate oocytes, where they can be isolated during diplonema stage of prophase I, where they uncoil during transcription.

The central axis is made up of two DNA helices representing sister chromatids, while loops are composed of one DNA double helix, active in transcribing RNA,

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Each nucleosome consists of a core of 147 base pairs of DNA coiled around 2 tetramers of histone proteins in a left-handed superhelix.

Nucleosomes are linked together via short segments of spacer DNA and H1 histone into repeating units of about 200 base pairs.

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The repeating units of nucleosome resemble "beads on a string".
Digestion with a nuclease produces 200 base-long particles of nucleosomes where the DNA is protected by its associated histone proteins.

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The bacteriophage T2 has a double stranded, linear DNA genome.

The nucleotide sequences of individual viruses are circular permutations of a common sequence.

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The bacteriophage λ (lambda) possesses a linear double-stranded DNA molecule prior to infection, which closes to form a ring upon infection of the host cell, as seen in the electron micrograph at right.

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Giant polytene chromosomes, found in the somatic cells of some fly larvae, represent paired homologs.

The DNA of each chromosome undergoes many rounds of replication, but without strand separation or cell division.

Each chromosome may have over 1000 strands that remain attached to one large centromere and aligned with one another, exhibiting banding patterns under a light microscope.

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DNA strands in bands (B) can uncoil, or puff, (P) during transcription. Thus bands may indicate the presence of genes, while interband (IB) regions are devoid of genes.

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Repetitive DNA can be grouped into many categories.

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Most eukaryotic DNA exhibit a uniform density (indicating similar G-C/A-T rations), and are detected in a main band when analyzed with sedimentation equilibrium centrifugation.

Often, as seen in this profile of mouse DNA, a satellite DNA band with a different density is also observed.

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A normal Watson–Crick right-handed double helix with 20 complete turns (linking number L = 20) forms an energetically relaxed circle if its ends are sealed.

  • Q: How many nucleotides are in this molecule of 20 turns?

  • A: 208, since each turn of the helix contains 10.4 nucleotides.

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    If such a molecule were underwound by 2 full turns (L = 18) and sealed, the resulting circle is energetically strained, and will spontaneously form two negative (left-handed) supercoils, reestablishing the total number of original turns in the helix.

    The supercoiled structure is more compact and stable, and most circular DNA molecules in bacteria and phages are supercoiled.

    For example, the virus SV40 contains 5200 base pairs, and has a relaxed L of 500 (L = 5200 / 10.4 = 500). When circular SV40 DNA is analyzed, it is found to have an L of 475, with 25 negative supercoils.

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    Telomeric DNA sequences are found at the ends of linear eukaryote chromosomes and consist of short tandem repeats: in humans, the sequence GGGATT is repeated many times.

    The RNA-containing enzyme telomerase catalizes the replication of the telomere, and is active in immortalized cells such as germ-line and cancer cells.

    This enzyme is inactive in normal somatic cells. Therefore, DNA at the ends of linear chromosomes become shorter after each replication, resulting in cell aging.