Topic 12, Genetic Code and Transcription

  1. Introduction
    Once it was established that DNA was the genetic material and that DNA directs the metabolic activities of cells by producing specific proteins (enzymes), geneticists wanted to know how DNA was involved in the production of proteins. They wanted to know:
    A. How does DNA make proteins (topic 12, transcription and topic 13, translation)
    B. How are genes regulated (turned on and off (topics 14 and 15)
         (this has to do with differentiation)
  2. Does DNA directly specify the amino acid sequence in proteins?
    A. Studies by Hammerling with Acetabularia
         1. Acetabularia is a very large (2 inches tall) unicellular green algae
         2. It can be cut into two parts, a part with a nucleus (nucleate part) and a part without a nucleus
             (anucleate part)
         3. Hammerling found that the anucleate part synthesized proteins ~2 weeks after the nucleus
             was removed
         4. He concluded that proteins are not made directly by the nucleus
    B. Studies by Brachet and Casperson (independent studies)
         1. They studied cells by using stains and determined the relative amounts of DNA and RNA
              in different parts of the cell
         2. They found that RNA was present in the nucleus and the cytoplasm
         3. They found that the amount of RNA in the cytoplasm was proportional to the amount of protein
             synthesis
              a.  Cells with high amounts of protein synthesis have high amounts of RNA in their cytoplasm and
              b.  Cells with low amounts of protein synthesis have low amounts of RNA in their cytoplasm
         4. They also found that protein synthesis stops in cells that were treated with RNase
         5. They concluded that RNA is made in the nucleus and transported into the cytoplasm where it is
              involved in protein synthesis

  3. Sidney Brenner's speculation about the number of nucleotides it would take to specify the 20 different types of amino acids
    A. Remember, there are 4 types of nucleotides and 20 types of amino acids and proteins come in different sizes and have different amino acid sequences
    B. Sidney Brenner realized that each base could only specify 4 types of amino acids, so a minimum of 3 bases (4x4x4) would be needed to specify 20 different types of amino acids

  4. Characteristics of the genetic code
    A. Triplet: three bases specify each amino acid (the genetic code is a triplet code)
         1. Code word = 3 consecutive nucleotides in the DNA
         2. Codon = 3 consecutive nucleotides in mRNA
         3. Anticodon = 3 consecutive nucleotides in tRNA that are complementary to a codon
    B. Unambiguous: each codon codes for the same amino acid in an organism
    C. Degenerate: more than one amino acid can code for the same amino acid (there are synonyms)
    D. Commaless: there are no spaces or punctuation between codons
    E. Non-overlapping: adjacent bases belong to one and only 1 codon
    F. Universal (nearly): The same coding dictionary is used by all organisms (with minor exceptions)
    G. The genetic code has punctuation: contains start and stop signals
         1. There is a codon (AUG) which is the start codon (equivalent to a capital letter in a sentence)
              a. Codes for formyl-methionine in prokaryotes and methionine in eukaryotes
              b. Codes for the first amino acid in all proteins
         2. There are 3 codons (UAA, UAG, and UGA) that are stop codons
             (equivalent to a period in a sentence)
              a. When any one of these codons is reached during transcription, transcription stops
              b. These codons do not code for any amino acid.
    H. In summary, we can think of a
        1. Nucleotide as a letter
        2. A codon or a amino acid as a 3-letter word
        3. A polypeptide as a sentence

  5. Deciphering the code
    A. Nirenberg and Matthaei, cell-free synthesis system and mRNA homopolymers
         (repeating sequence of a single nucleotide)
    B. Nirenberg, Matthaei, and Ochoa, cell-free synthesis and mRNA heteropolymers
         (containing more than one nucleotide)
    C. Nirenberg and Leder's triplet binding technique
    D. Using repeating copolymers (Khoranna)
    E. By 1966, the genetic code had been completely deciphered
    F. The coding dictionary
    G. Wobble hypothesis (Crick 1966)
        1. Crick proposed that pairing between the third nucleotide in a codon and the first position in an
            anticodon was less precise than at the other 2 bases (had wobble

  6. Transcription (write a copy of), see handout
    A. mRNA is transcribed from one strand (the template or sense strand) of the DNA double helix and the
         other strand (partner or antisense strand) is not copied
    B.Transcribed by the enzyme, RNA polymerase
    C. RNA polymerase binds to a specific sequence in the DNA (a promoter sequence)
    D. Steps in transcription, (initiation, elongation, and termination), see handout
    E. Thus, mRNA is transcribed using DNA as a template to make a complementary copy
    F. In eukaryotes, the initial transcript is much larger than the final mRNA
        1. The initial transcript is referred to as pre-messenger RNA (pre-mRNA) or
            heterogeneous nuclear RNA (hnRNA)
        2. Sequences are cleaved out of the pre-mRNA (intervening sequences = introns) and other sequences remain (exons)
        3. Additional sequences are added to the 5' end of the mRNA (the cap = 7 methyl guanosine)
            and the 3' end of the mRNA, the poly-A tail (a sequence of A's)

  7. Coupled transcription in prokaryotes and uncoupled transcription in eukaryotes
    A. In prokaryotes, there is no nuclear membrane, and translation occurs on a mRNA molecule
         while it is being transcribed
    B. In eukaryotes, the mRNA is transcribed in the nucleus and then passes through the nuclear membrane
         into the cytoplasm where it is translated

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           Updated 11/13/00