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Chapter 16 Mind Map, DNA technology is now commonly used in the creation…

- - - - The fragments now made by restriction endonucleases can be separated and identified through gel electrophoresis to make a restriction map
      - When comparing species, one may look at the differences in their gel electrophoresis results. Closely related species will have similar markings and the opposite will be true for distant species
      - If two species are not closely related, their fragment profiles will differ. In this case, there is a restriction fragment length polymorphism (RFLP)
      - RFLP analysis is easy, quick, and inexpensive while also having a great many uses
    - - In many cases, the objective of the experiment is to locate and isolate one particular fragment (such as one with a specific gene)
      - Once mRNA is obtained, it can be mixed with reverse transcriptase (a virus enzyme that synthesizes DNA using RNA as a template)
      - This new complementary DNA (cDNA) is synthesized using a fluorescence, and allowed to form bonds with another fragment
      - Expression profiling uses cDNAs to examine gene expression during development or compare development in one species to that of another
      - Each type of cDNA is attached to many glass microscope slides in an orderly matrix, in other words, a microarray
- - - - DNA does not participate directly in protein synthesis, instead sending messenger RNA (mRNA) with the genetic information
      - Most of the DNA is stored in the nucleus, protected from the cytoplasm by the nuclear envelope
      - Histone proteins (special class of proteins) hold most nuclear DNA in an inert, resistant form
      - Histones form aggregates and DNA wraps around them, forming nucleosomes
      - The histones then bind the DNA into a tightly coiled structure called chromatin (so dense that enzymes cannot penetrate)
        
        Even when chromatin is exposed to DNA digesting enzymes (DNAases/ DNases), DNA is not extensively damaged
  - - - An example of degeneracy is when a mutation changes UCU to UCG but the amino acid Serine is still coded for
  - - - Exons are sequences of nucleotides with codons that will be expressed, and introns are sequences that break up exons but will not be expressed (introns are eventually removed)
  - - - A short series of DNA nucleotides that are self-complementary (RNA transcribed from them can double back on itself). Results in a hairpin loop
      - Downstream of the previous region of DNA is a long series of adenines. RNA polymerase may continue to read this region as if it were a part of the gene
- - - - Each type of protein has its own gene
- - - - Protein synthesis begins with the start codon (AUG) coding for methionine. There are two types of this amino acid however
      - The first type binds to the small ribosomal subunit with several initiation factors (eukaryotic initiation factors - eIFs) which can then bind to mRNA
      - If the ribosome binds incorrectly and is shifted downstream or upstream by one nucleotide, then a frameshift error could occur
    - - At the time of the binding, the small subunit already contains initiator tRNA in the P (protein) channel while the A (amino acid) channel is empty
      - Once an appropriate tRNA is placed in the A channel, enzymes will break the methionine from the tRNA in the P channel while simultaneously attaching it to the amino group in the A channel
      - With the empty tRNA now free, it is released from the P channel and the ribosome pulls itself along the mRNA for a distance of three nucleotides (ribosomal reading)
      - The process of the protein chain elongation will continue until the ribosome reaches a stop codon
    - - Once the stop codon is read by the ribosome, the protein chain is completed and the ribosome subunits detach from the mRNA