Topic 19, Chromosome structure
    and DNA sequence organization

How is the DNA organized in the cell?

  1. Viruses:
    A. DNA or RNA in different viruses
    B. Single-stranded or double-stranded in different viruses
    C. Circular or linear in different viruses
    D. Usually one DNA molecule/viral particle
    E. The DNA is packaged into the heads in a very compact manner
    F. The DNA is not associated with histones or in nucleosomes

  2. Bacteria
    A. The DNA is in the center of the cell in a "nucleoid" or bacterial nucleus
        (not a true nucleus),
        it is referred to as a bacterial chromosome (not a true chromosome)
    B. DNA
    C. Circular
    D. Double-stranded
    E. Usually one DNA molecule per cell, but plasmids may also be present
    F. The DNA is not associated with histones or in nucleosomes
    G. Will not discuss supercoiling

  3. Mitochondria
    A. The DNA is present as a circular molecule
    B. Double-stranded
    C. No histone or nucleosomes
    D. Maternally inherited
    E. Sizes
        1. Animals, 16-18 kb (one kb = 1000 bases)
        2. Plants, much larger
            a. Saccharomyces = 75 kb
            b. Pea = 110 kb
            c. Aribdopsis = 367 kb
    F. Several identical copies of the mitochondrial DNA molecule are in each mitochondrion
        1. 5-10 identical DNA molecules are present in each mitochondrion in vertebrates
        2. 20-50 identical DNA molecules are present in each mitochondrion in plants
    G. The complete nucleotide sequence of mitochondrial DNA has been determined
        in humans and several other mammals
        1. Codes for mRNA, rRNA, tRNA, and contains the genetic information for 17 proteins
        2. Mitochondria have several hundred proteins, and the vast majority of these are coded
            for by genes in the nuclear genome, they are made on cytoplasmic ribosomes and then
            transported into the mitochondria
    H. Mitochondrial ribosomes are different in size from cytoplasmic ribosomes
    I. Mitochondria have all components of transcriptional and translational systems and produce
        a small number of their own polypeptides

  4. Chloroplast
    A. The DNA in chloroplasts is present as a circular molecule
    B. Double-stranded
    C. No histone or nucleosomes
    D. Maternally inherited
    E. Sizes
        1. Chlamydomonas, 195 kb, ~75 copies/chloroplast
        2. Higher plants (sweet pea), 134 kb
    F. Several identical copies of the chloroplast DNA are present per chloroplast
        1. 20-40 copies/chloroplast in corn and 20-40 chloroplasts per cell;
            therefore, about 15% of the cell's DNA is chloroplast DNA
    G. Ribosomes are present that are the size of bacterial ribosomes
    H. Have complete transcriptional and translation machinery and make proteins
    I. Both mitochondria and chloroplasts are believed to have arisen as endosymbionts

  5. Centriolar DNA???
    A. There is some evidence that centrioles may contain DNA, but there is also evidence
        that they do not, so they may contain DNA

  6. DNA organization in eukaryotes
    A. Eukaryotes have much more DNA per chromosome and per cell than bacteria
        1. E. coli has 1200 micrometers of DNA /cell
        2. Humans have 14,000 to 73,000 micrometers of DNA per chromosome
        3. All 46 chromosomes together in a human cell have 2 meters of DNA which
            is contained in a nucleus that is 5 micrometers in diameter
        4. The DNA in a chromosome is about 10,000 times as long as a metaphase chromosome
        5. We have an imperfect understand of how the DNA is arranged in eukaryotic chromosomes
    B. Eukaryotic chromosomes have DNA, RNA, histone protein, and non-histone protein
        1. Histones are of 5 types which are all rich in basic amino acids (lysine and arginine)
            a. The 5 types of histones are: H1, H2a, H2b, H3, and H4
            b. The H1, H2a, H2b, H3, and H4 histones are present in a 1:2:2:2:2 ratio respectively
    C. Nucleosomes
        1. Discovery of nucleosomes
            a. If chromatin is treated with detergents and examined with an electron microscope,
                you see 100 angstrom beads on a string (Olins and Olins 1973)
            b. If you treat chromatin with certain endonucleases (micrococcal nuclease),
                you get DNA pieces that are 200 base pairs long or multiples of 200 bases
                Thus, the digestion is not random, but the DNA is protected from enzymatic
                digestion in regions 200 bases long
        2. Description of nucleosomes
            a. They have 2 copies each of H2a, H2b, H3, and H4 in the form of an octamer with
                about 200 bases pairs of DNA wrapped around the core two times
            b. H1 particles are on the DNA between each nucleosome
            c. The DNA associated with nucleosomes forms fibers which are 100 angstroms
                (10 nm) in diameter
            d. These are further coiled into solenoids which are 300 angstroms (30 nm) in diameter
            e. The solenoids are coiled into 200 nm chromatin fibers

  7. Repetitive DNA
    A. Certain DNA sequences in eukaryotes are present in multiple copies
    B. In fact, certain sequences are present thousands of times

  8. C-value paradox
    A. C-value is the amount of DNA contained in a haploid genome of an organism
    B. Bacteria have 104 to 106 base pairs while eukaryotes have 107 to 1011 base pairs per genome
        therefore, eukaryotes have ~1,000,000 as much DNA as bacteria and viruses
    C. Clearly, there are not a million times as many genes in eukaryotes as there are in bacteria.
        What is this additional DNA doing?
    D. Also, closely-related forms can have as much as a 10-fold difference in the amount of DNA
    E. We now know that most of the DNA in eukaryotes is not transcribed, only about 5% of the
        DNA in a human is transcribed.  This accounts for part of the difference.

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Updated 12/8/00