Molecular Biology: Eukaryotes

Eukaryotic chromosome organization

  • Chromosomal proteins
    1. Histones: responsible for the compact packing and winding of chromosomal DNA. DNA winds itself around histone octamers.
    2. nonhistone chromosomal proteins: all the other proteins are lumped together in this group. Responsible for various roles, such as regulatory and enzymatic.
  • Telomeres, centromeres
    • Telomere: the 2 ends of the chromosome.
    • Centromere: a region on the chromosome, can be at the center or close to one of the ends. After replication, sister chromatids are attached at the centromere. During mitosis, spindle fibers are attached at the centromere and pulls the sister chromatids apart.
  • A common question is what is the difference between chromatin and chromosome. The answer is chromatin is the "stuff" that chromosomes are made of. If the chromosome is a cotton shirt, then chromatin is cotton.

Control of gene expression in eukaryotes

  • Transcription regulation
    • Transcription factors (protein) bind to enhancers or silencers (DNA) to affect transcription. Enhancers increase transcription when bound, while silencers decrease it. The main difference in eukaryotes that sets them apart from prokaryotes is that enhancers/silencers can be very far away from the actual promoter, and can be upstream or downstream. The DNA must loop back on itself so that the transcription factor bound to enhancer/silencer can actually make contact with the promoter. Intermediate proteins are involved in the process.
    • Eukaryotes lack the bacterial transcription regulation mechanisms such as the operon (exists but very rare) and attenuation.
  • DNA binding proteins, transcription factors
    • DNA-binding proteins bind to DNA.
    • transcription factors bind to DNA, so they have a DNA-binding domain.
    • DNA-binding domains interact with the grooves in the double helix (major grooves and minor grooves).
    • Advanced: common DNA-binding domains include helix-turn-helix (HTH), zinc finger, basic-region leucine zipper (bZIP).
  • Cancer as a failure of normal cellular controls, oncogenes
    • Failure of normal cellular controls:
      • Cancer cells continue to grow and divide in situations normal cells would not.
      • Cancer cells fail to respond to cellular controls and signals that would halt this growth in normal cells.
      • Cancer cells avoid apoptosis (self-destruction) that normal cells undergo when extensive DNA damage is present.
      • Cancer cells stimulate angiogenesis (cause new blood vessels to grow to nourish the cancer cell).
      • Cancer cells are immortal while normal cells die after a number of divisions.
      • Cancer cells can metastasize - break off and then grow in another location.
    • Oncogenes: genes that cause cancer when activated. The product of many oncogenes are involved in speeding up cell division. Before an oncogene is activated, it is a harmless proto-oncogene. Something occurs that changes the proto-oncogene to an oncogene. The classic example of oncogene is the src.
    • Tumor suppressors: if the oncogene is the "bad" gene, tumor suppressors are the "good" genes. The product of many tumor suppressors are involved in slowing down or controlling cell division. If something happens that cause the tumor suppressor to no longer function, then the cell becomes cancerous. The classic example of tumor suppressor is the p53.
  • Post-transcriptional control
    • tRNAs and rRNAs modifications: some normal nucleotides are modified to control the structure of these RNAs.
    • mRNAs modifications
      • RNA splicing: sequences called introns are cut out, sequences called exons are kept and spliced (joined) together.
      • Alternate splicing: different ways of cutting up the RNA and rejoining the exons pieces make different final RNA products.
      • 5' capping and 3' poly-A tail: these help to protect the RNA from degradation so they can last longer.
    • After the correct modifications, RNA is transported out of the nucleus where they can function in translation.
    • After some time, RNA is degraded. The rate and timing of RNA degradation can be controlled by the cell.