11.2: Overview of the Genetic Code
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)The genetic code is the information for linking amino acids in polypeptides in the order determined by the base sequence of three-base code words (codons) in a gene and its messenger RNA (mRNA). With a few exceptions (e.g., some prokaryotes, mitochondria, and chloroplasts), the genetic code is universal—it’s the same in all organisms, from viruses and bacteria to humans. Here we’ll look at the genetic code itself and at how the information in the RNA nucleotide sequences of transcribed genes is translated into polypeptides.
11.2.1. The Universal, Degenerate Genetic Code
The three-base code words (codons) of the (nearly) universal genetic code are shown in the “language” of RNA in Figure. 11.1 (below). A look at this table reveals that there is a single codon for each of two amino acids, methionine and tryptophan, but two or more for each of the other eighteen amino acids (and in one case six!). For this reason, we say that the genetic code is degenerate. The three stop codons in the standard genetic code “tell” ribosomes the location of the last amino acid to add to a polypeptide. While the last amino acid in a polypeptide can be any amino acid that is consistent with the function of the protein being made, evolution dictated that methionine will be the first amino acid of all polypeptides. Thus, AUG is the start codon for all polypeptides (regardless of their function) as well as for the insertion of methionine in the polypeptide where it is needed for its function. As we will see, all polypeptides begin life with a methionine at their amino-terminal end, but most lose the methionine after translation.
We will see in detail that ribosomes are mRNA translation machines and that the biological equivalent of the Enigma Machine is the tRNA decoding device. Each amino acid attaches to a specific tRNA whose short sequence contains a three-base anticodon that is complementary to an mRNA codon. Enzymatic reactions catalyze the dehydration synthesis reactions that link amino acids by peptide bonds in the order specified by mRNA codons.
11.2.2. Comments on the Nature and Evolution of Genetic Information
The near-universality of the genetic code from bacteria to humans implies that it was “fixed’” early in evolution. It is probable that portions of the code were in place even before life began. Once in place however, the genetic code was highly constrained against evolutionary change.
The degeneracy of the genetic code enabled (and contributed to) this constraint by permitting base changes in most codons without an effect on the amino acids that they encoded. We can compare our gene and other DNA sequences to those of different organisms precisely because the genetic code is universal and resistant to change. This is what allows us to compare different genomes and establish evolutionary relationships between larger groups of organisms (genus, family, order), between species, and even between individuals of a species.
In addition to constraints imposed by a universal genetic code, the genomes of some organisms show codon bias, a preference to use some but not other codons in their genes. Codon bias is seen in organisms that favor codons rich in A and T or in organisms that prefer codons richer in G and C. Interestingly, codon bias in genes often accompanies a corresponding genomic nucleotide bias. An organism with an A-T codon bias may also have an A-T biased genome; likewise, a bias toward G-C codons in genomes high in G and C. If you check back, you can recognize genomic nucleotide bias in Chargaff’s base ratios!
Here are two questions: What might lead to evolutionary selection of codon bias? Could an organism have survived with less than sixty-four triplet codons? We may never know the answer to the second question, but we can see an engineered E. coli living on sixty one codons at Survival on Less than 64 Codons.
Finally, we often think of genetic information in a genome as genes that specify protein sequences, in other words, coding DNA. On the other hand, obvious examples of noncoding but critically informational DNA include the genes for ribosomal and transfer RNAs The relative amounts of informational DNA (genes for polypeptides, rRNAs and tRNAs) and noninformational DNA range across species, although they are higher in prokaryotes than eukaryotes. In fact, ~88% of the E. coli genome encodes polypeptides, compared to the humans, in which that figure is less than ~1.5%!
Some of less obvious informative DNA in higher organisms is transcribed (e.g., introns). But other informative DNA is never transcribed. They may not be called genes, the latter include regulatory DNA sequences, sequences that support chromosome structure and other DNA that contribute to development and phenotype.
As for truly noninformative (useless) DNA in a eukaryotic genome, that amount is steadily shrinking as genome sequencing reveals novel DNA sequences, new potential genes, and thus, new RNAs with new functions (topics covered elsewhere in this text).