DNA Types and Structure

The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival.

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Structure of DNA

The hereditary material DNA is a double-stranded nucleotide polymer: 

  • Organization of DNA:
    • In eukaryotic cells, DNA can be found in the cell nucleus and the mitochondria:
      • The chromosome is the organizing unit of DNA.
      • In humans: 46 homologous chromosomes (23 pairs)
      • Coding information contained within segments of chromosomes called genes
    • In prokaryotes, DNA is in cytoplasm as a plasmid or chromosome.
  • Structure of DNA:
    • 2 antiparallel strands (opposite polarity) forming a double-helix: 10.5 base pairs per turn of helix
    • Negatively charged sugar-phosphate backbone
    • Complementary strands held together by:
      • Hydrogen bonds
      • Van der Waals forces
      • Hydrophobic interactions between base pairs
    • Free 5’–3’ carbon ends on each strand
    • Described by James Watson and Francis Crick (awarded Nobel Prize in Physiology or Medicine in 1962)
    • Rosalind Franklin’s work with X-ray crystallography was essential to the discovery of DNA’s structure.
  • Nucleotides are the monomers that make up DNA:
    • Nucleotides in DNA (deoxyribonucleotides):
      • Deoxyadenosine triphosphate (dATP)
      • Deoxyguanosine triphosphate (dGTP)
      • Deoxycytidine triphosphate (dCTP)
      • Deoxythymidine triphosphate (dTTP)
    • Nucleotides are linked through 3’–5’ phosphodiester bonds:
      • Energy for synthesis comes from releasing 2 phosphates (dATP → deoxyadenosine monophosphate (dAMP)).
      • Synthesis occurs in 5’–3” direction.
      • Purines pair with pyrimidines:
        • Adenine (purine) ↔ thymine (pyrimidine)
        • Guanine (purine) ↔ cytosine (pyrimidine)

Organization and Packing of DNA in the Cell Nucleus

  • In the nucleus, DNA is condensed into chromosomes by nucleic proteins.
  • Order of DNA condensation: double-stranded DNA (dsDNA) → nucleosomes → solenoid strand → chromatin loops → chromosomes
    • Negatively charged dsDNA is wrapped around positively charged histone octamers to form nucleosomes.
    • Histones undergo modifications, which affect access to DNA and thus transcription (TX):
      • Acetylation (increases TX)
      • Methylation (increases or decreases TX, epigenetics → heritable)
      • Phosphorylation (increases or decreases TX)
      • Ubiquitylation
      • ADP-ribosylation
  • Forms of chromatin:
    • Euchromatin (decondensed form): transcriptionally active
    • Heterochromatin (condensed form): transcriptionally inactive
DNA packaging and the two states of chromatin

Packaging of DNA and the 2 states of chromatin:
Euchromatin (active) where DNA is being replicated or transcribed; and heterochromatin (silent), where DNA is not being replicated or transcribed.

Image: “The basic unit of chromatin organization is the nucleosome, which comprises 147 bp of DNA wrapped ar” by Sha, K. and Boyer, L. A. License: CC BY 3.0

Mitochondrial DNA

  • Mitochondrial DNA (mtDNA) represents 1% of cellular DNA.
  • Only inherited from the mother (non-Mendelian inheritance)
  • Characteristics of human mtDNA:
    • Circular, double-stranded, composed of heavy (H) and light (L) strands
    • Contains 16,569 base pairs
    • Encodes ribosomal RNAs, tRNAs, and protein subunits necessary for oxidative phosphorylation (ATP production)
    • High mutation rate (5–10 times that of nuclear DNA)
  • Presence of mtDNA led to theory of endosymbiosis:
    • Mitochondria 
    • Once free-living prokaryotic microbes
    • Engulfed by host cell and became organelles
    • Circular DNA
    • Replication by binary fission

Clinical Relevance

  • Mitochondrial myopathies: caused by mitochondrial diseases where “ragged red” muscle fibers are observed by biopsy. The myopathy resembles the accumulation of glycogen and neutral lipids, which may be correlated with an increased reactivity for succinate dehydrogenase and a decreased reactivity for cytochrome c oxidase. Both mitochondrial and nuclear DNA mutations underlie mitochondrial myopathy.
  • Genetic mutations: errors in the DNA that sometimes cause abnormal protein function. There are various types of mutations categories and subcategories including chromosomal, point, frameshift, and expansion mutations. Point mutations include missense, nonsense, single, and silent mutations.

References

  1. Weil, P. A. (2018). Nucleic acid structure & function. In Rodwell, V. W., et al. (Eds.), Harper’s illustrated biochemistry, 31e (). New York, NY: McGraw-Hill Education. https://accessmedicine.mhmedical.com/content.aspx?aid=1160190679
  2. Weil, P. A. (2018). DNA organization, replication, & repair. In Rodwell, V. W., et al. (Eds.), Harper’s illustrated biochemistry, 31e (). New York, NY: McGraw-Hill Education. https://accessmedicine.mhmedical.com/content.aspx?aid=1160190821
  3. Yu-Wai-Man, P., & Chinnery, P. F. (1993). Leber hereditary optic neuropathy. In Adam, M. P., et al. (Eds.), GeneReviews® (). Seattle (WA): University of Washington, Seattle. http://www.ncbi.nlm.nih.gov/books/NBK1174/

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