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Samford University -- Department of Biological and Environmental Sciences
Cell and Molecular Biology -- Biol 405

  DNA: The Genetic Material 

100+ Years of Genetics: In a little over a century, our understanding of the genetic material has progressed from a Austrian monk's hypotheses about the transmission of hereditary units to a detailed knowledge of how DNA directs cellular activity.
  • Genes as Units of Heredity: In the 1860s, Mendel postulated that there were units of heredity that we now call genes. He said they exist in pairs (alleles), the members of each pair segregate into separate gametes, and that the segregation of one pair is independent of the segregation of another pair.


  • Genes are on Chromosomes: In the early 1900s, it was proposed by Sutton and Boveri that genes are on chromosomes (the Chromosome Theory). Morgan and Bridges later proved this to be true by demonstrating that one gene in the fruit fly is on the X chromosome. Two pairs of alleles that are on the same pair of chromosomes will not segregate independently (contrary to Mendel's hypothesis), but will instead tend to move to the same gamete during meiosis (linkage).
  • The Genetic Material is DNA: In 1944, Avery, MacLeod, and McCarty showed that DNA was the genetic material of a bacterium that causes a type of pneumonia in mice. This experiment was based on the 1928 experiment of Griffith where he showed that some substance from dead IIIS bacteria (S cells have a capsule) could transform live IIR bacteria (R cells lack a capsule) into live IIIS cells. Avery et al. showed that Griffith's "transforming principle" was IIIS DNA.
The Structure of the Genetic Material: DNA is a polynucleotide (polymer of nucleotides).

  • Nucleotide: Each DNA nucleotide is composed of three subunits. (Nucleotide nomenclature.)
    • Phosphate: A phosphate group (PO4--) is attached to the 5' carbon of deoxyribose. DNA is negatively charged because of the phosphates (just one - charge after the phosphate links two nucleotides together).
    • Deoxyribose: Deoxyribose is a pentose sugar. Its carbons are numbered and given the prime (') designation to distinguish them from the carbons of the nitrogen bases. Deoxyribose is actually 2'-deoxyribose (ribose that has lost an oxygen atom from the 2' carbon). (Deoxyribose atom numbering)
    • Nitrogen Base: A nitrogen base is attached to the 1' carbon of deoxyribose. DNA's nitrogen is all in the bases. There are four possible bases divided into two classes.
      • Purines: Purine bases have a double ring structure and are larger than pyrimidines. There are two purines in DNA. (Purine atom numbering) Purines are attached by their position 9 nitrogen to the 1' carbon of deoxyribose.

        • Adenine (A): This purine base has an amino group (-NH2) at position 6.
        • Guanine (G): This purine base has an amino group at position 2 and a keto group (=O) at position 6.
      • Pyrimidines: Pyrimidines have a single ring structure and are smaller than purines. There are two pyrimidines in DNA. (Pyrimidine atom numbering) Pyrimidines are attached by their position 1 nitrogen to the 1' carbon of deoxyribose.
        • Cytosine (C): This pyrimidine base has a keto at position 2 and an amino group at position 4.
        • Thymine (T): This pyrimidine base has a keto at positions 2 and 4. (In RNA, uracil substitutes for thymine.)
  • The DNA Polynucleotide: The DNA polynucleotide is made by joining many nucleotides together into a polymer. The bond is a phosphodiester bond between the 3' carbon of one deoxyribose and the 5' carbon of the next deoxyribose. Therefore, a single strand of DNA has a sugar-phosphate backbone with the bases protruding off to one side. Any order of the bases is possible along one strand.
  • The Double Helix: In 1953, Watson and Crick proposed a 3-dimensional model for the structure of DNA: the double helix. Their work was based on the X-ray crystallography (X-ray diffraction) work of Franklin and Wilkins, on the work of Chargaff (Chargaff's Rules: A=T, G=C), and on a general understanding of the structure of the DNA polynucleotide (the information above). Their research was primarily model building and won them, along with Wilkins, the 1962 Nobel Prize. Here are the highlights of their model. (Watson and Crick's 1953 article in Nature.)
    • DNA has two, antiparallel strands: DNA has two polynucleotides running in opposite polarity.
    • Alpha-helix: The two strands are coiled in an alpha-helix (right-handed helix).
    • Specific Base Pairing: Base pairing holds an A of one strand to a T of the other strand and a G of one strand to a C of the other strand. This base pairing is by hydrogen bonding involving N, O, and H. There are three bonds that hold guanine to cytosine and two that hold adenine to thymine. (The answer is, "Yes you do.") Take a look at the PBS video from: "The Secret of Life" (click on "Watch the Video on the right of the page).
    • The Dimensions of the Double Helix: The bases are 3.4 (angstra) thick and stacked internally (i.e., the "distance between the bases" is 3.4 (angstra)). The width of the molecule is 20 (angstra) and it makes one complete turn (360) every 34 (angstra) of length. There are 10 base pairs per turn of the helix. (3-D DNA Viewer)(more)(more)(more)

The Structure of the Chromosome: Chromosomes are composed of DNA and protein. The DNA of a single chromosome is one long, continuous molecule (the unineme theory). The most abundant protein bound to chromosomes is the class of proteins called histones.
  • Histones: Histones are basic proteins (rich in the basic amino acids arginine and lysine) and therefore positively charged (binds to negatively charged DNA). There are 5 histones found in chromosomes: H1, H2a, H2b, H3, and H4.
  • The Nucleosome (called a chromatosome in your text): Two each of four of the histones (H2a, H2b, H3, and H4) form an octamer. A segment of DNA about 147 base pairs long wraps around this octamer almost twice. This structure (H2a2, H2b2, H32, H42 + 147 bp of DNA) is a nucleosome. (Research news)
  • The 30 nm Fiber: H1 binds to the DNA between nucleosomes, causing the nucleosomes to form a thicker fiber. This creates a fiber that is about 30 nm in diameter. This is the basic structure of the chromosome (chromatin). The packing ratio of the 30 nm fiber is about 40:1 (length of DNA : length of 30 nm fiber).
  • Further coiling: Further coiling and folding of the 30 nm fiber into an interphase chromosome (chromatin) resulting in about a 1000:1 packing ratio. During cell division, even further condensation results in a final packing ratio of at least 7000:1. (Chromosome packing figure links: 1; 2)(video -- don't listen too close because chromosomes ARE always present!!!)
 
  • Centromeres: The region where two daughter chromatids remain temporarily attached after chromosome replication is the centromere. It appears as a constriction in a metaphase chromosome and is the site of spindle fiber attachment. Certain proteins bind to the specific DNA sequences of the centromere and form the kinetochore (spindle microtubules attach here). Some proteins of the kinetochore are molecular motor that actively move the daughter chromosomes down the spindle during anaphase. Certain specific repeated sequence are important in centromere function, including AT-rich sequences. (New research news: A long noncoding RNA helps cells divide)
  • Telomeres: The ends of chromosomes have unique structure and are called telomeres. Human telomeres have the sequence AGGGTT repeated over and over. These regions are important in DNA replication, as we will see later.
Genomes: A single set (haploid set) of chromosomes constitutes an organism's genome. The size of the genome of organisms increases as we go "up" the phylogenetic ladder. Higher organisms have a lot of noncoding DNA, much of which may be "junk DNA." (Noncoding DNA Science magazine podcast)