The Genetic Code

The Central Dogma: DNA makes RNA makes protein
Central Dogma


In principle: The DNA genotype does not produce the phenotype directly
A DNA gene contains the information necessary for the production of proteins,
        which is expressed biochemically through an intermediate molecule, RNA,
        which functions as a Genetic Code

Genetic Code ...
    is an RNA code
    specifies amino acids that make up proteins
         Protein expression leads directly (or indirectly) to the phenotype

    Allows logical inference of the protein product directly from DNA:
        see next section, and lab exercise
    was "cracked" before the details of translation were understood:
         we can talk about the Code before describing RNA translation

Alternative alleles of genes arise by mutation
     which alters the DNA sequence of genes  
         which may cause amino acid substitutions in proteins
             which may affect the function of those proteins
     Most genes are highly polymorphic

The Genetic Code is ... 

        a messenger RNA (mRNA) code
            i.e.., the code is written in RNA
            DNA is a coding molecule,
                    but not  the 'genetic code' in the biochemical sense

        in 64 triplets (codons) : 61 for amino acids + 3 'stops [iG1 7.19]
               mRNA codons are read 5'3'
               20 amino acids:  note 1- & 3-letter abbreviations
                                              [more on amino acids & proteins in next section]
                For example,

      5' - A U G U U C C C C A AG G U U G A - 3'
            met   phe   pro   lys   gly    *       
               M     F     P     K     G     *                     

       Degenerate: most amino acids are encoded by more than one codon
            first two positions are critical: third position can "wobble" [iG1 7.25, 26]
                  if third can be either puRine (R), or either pYrimidine (Y)
                      two-fold degeneracy
                  if third can be any base 
                      four-fold degeneracy
                  Leucine (leu) has six-fold degeneracy with six codons in unusual arrangement


# codons / amino acid

trp, met

1 @

ser, arg, leu

6 @


3 @

14 others

2 or 4 @

     Unambiguous: any one triplet codes for only one amino acid
                but not vice versa, because of wobble

        'Always' begins with an 'start' or 'initiator' codon:  AUG

        'Always' ends with a 'stop' or 'terminator' codon:  UAG, UAA, or UGA

     Universal (with some important exceptions)
            Five Kingdoms (animals, plants, algae, fungi, & monera)
                        use the same codes for nuclear DNA (nucDNA)

                Organelles (chloroplasts & mitochondria) have separate genomes:
                cpDNA & mitochondrial DNA codes are evolutionarily modified
                   e.g., UGA codes for trp in vertebrate mtDNA code  [iG1 7.Table 2]
                             termination codons may be formed by addition of "A"s to transcript
                             Lab exercises use mtDNA, so this code is important

Alterations of the Genetic Code: Mutations

    Mutations - interchanges of one base type for another
        transitions   - alternative pyrimidines [ CT ]  or purines [ AG ] [iGen3 07-03a,b]
        transversions -  purine  pyrimidine [C / T A / G]

        Recognized in individuals & populations as SNPs (single nucleotide polymorphisms)
                [SNPs, Mutations, & Mutants: a note on terminology & some lessons from history]

        Alternative nucleotide sequences of a gene correspond to alternative alleles
             or: a single gene occurs in variant forms (alleles)

  Single-base mutations
        Consequences of exon SNPs depend on position in triplet
[iGen3 07-03cd,fg]
            3rd position
                 typically a silent mutation - if position "wobbles", no change to amino acid
                 sometimes a missense mutation - results in different amino acids

           2nd position - always a missense mutation
           1st position - almost always a missense replacement
                                      [Leu codons are major exception]
            stop codon mutations may occur at any position: coding  non-coding triplet
                nonsense (termination) mutation terminates polypeptide prematurely [iGen3 07-04]
                    HOMEWORK: Identify all codons one step away from a termination codon
                                               [Hint: there are 18]

        mutations in non-coding DNA have variable effects
               Ex.: mutations in promoter regions
                       mutations at intron / exon splice junctions

Missense mutations in DNA cause substitutions in protein
   Proteins do not mutate! Watch your language!
      Consequences depend on position of substitution in polypeptide
        none:  substitution not in active site or binding site
        minor: substitution of same type (synonymous substitution)
             Allozymes are enzymes arising from minor allelic variants of enzyme genes
                    [see laboratory exercise]
        major: substitution affects structure / function (nonsynonymous substitution)
             Ex.: Glu Val   in beta-globin produces Sickle-cell hemoglobin (HbS)
                         HOMEWORK: What is the DNA mutation involved?

Insertion / Deletion (indel) mutations
        gain or loss of one or more nucleotides
        frameshift mutations  (examples)
              single & double nucleotide indel downstream amino acids change
                    nonsense mutation eventually (quickly) produced
              triplet indel - insertion / deletion of single amino acid
                   typically milder consequences
                   multiple triplet insertions produce major effects
                       Ex.: CGG repeats in
"Fragile X"
             length mutations - larger indels (102~6 bps)

Genes are highly polymorphic (w/ multiple alleles) wrt their mutational variation

        Phenylalanine Hydroxylase (PAH) (OMIM citation 261600)
             has 14 exons, encodes 2.4kb mRNA for 452 amino acid protein

        Of 68 alleles known to affect enzymatic activity of PAH  [Current GenBank List]
                68% miss-sense mutations (many produce Phenylketonuria (PKU))
                13% non-sense mutations (premature termination)
                  9% indel mutations
(single base 1~5 triplets whole exon)
                10% splice-site mutations (including most common variant allele)
        Most alleleic variants of the PAH locus are 3rd position silent
                no affect on PAH expression
                & therefore undetected

     (1) "What is a Gene?" Write an essay that that distinguishes Gene, Allele, and Locus
(2) Critique the following statements:
"PAH is the gene for Phenylketonuria (PKU)."
            "PKU is a genetic disease caused by absence of the PAH

Text material 2013 by Steven M. Carr