11.1: Introduction

While evidence was accumulating that DNA was “the stuff of genes,” many still believed that proteins were genes—at least until the experiments of Hershey and Chase. It was in this somewhat ambivalent context that investigators wondered about how genes (whether proteins or nucleic acids) might encode metabolically functional proteins such as enzymes—which, of course, are also proteins. In 1944, the physicist-philosopher Erwin Schrödinger published What Is Life? The Physical Aspect of the Living Cell. Targeting the lay reader, Schrödinger took a stab at explaining life, heredity, and development in terms of physical laws. Here in his own words is what he had to say about the chemistry of heredity, which—when deciphered— would dictate “patterns,” of development (abridging and highlighting courtesy of your author!):

THE HEREDITARY CODE-SCRIPT

Now, this pattern is known to be determined by the structure of that one cell, the fertilized egg. Moreover, we know that it is essentially determined by the structure of only a small part of that cell, its large nucleus. This nucleus…usually appears as a network of chromatine, distributed over the cell. But in the processes of cell division (mitosis and meiosis) it is seen to consist of a set of particles, usually fibre-shaped o rod-like, called the chromosomes, which number in man, 48 (2 × 24)…. I ought to have spoken of two sets, in order to use the expression in the customary strict meaning of the biologist. For the two sets are almost entirely alike. As we shall see in a moment, one set comes from the mother (egg cell), one from the father (fertilizing spermatozoon). It is these chromosomes, or probably only an axial skeleton fibre of what we actually see under the microscope as the chromosome, that contain in some kind of code-script the entire pattern of the individual’s future development and of its functioning in the mature state. Every complete set of chromosomes contains the full code; so there are, as a rule, two copies of the latter in the fertilized egg cell, which forms the earliest stage of the future individual. In calling the structure of the chromosome fibres a code-script we mean that the all-penetrating mind, once conceived by Laplace, to which every causal connection lay immediately open, could tell from their structure whether the egg would develop, under suitable conditions, into a black cock or into a speckled hen, into a fly or a maize plant, a rhododendron, a beetle, a mouse or a woman. To which we may add, that the appearances of the egg cells are very often remarkably similar; and even when they are not, as in the case of the comparatively gigantic eggs of birds and reptiles, the difference has not been so much the relevant structures as in the nutritive material which in these cases is added for obvious reasons. But the term code-script is, of course, too narrow. The chromosome structures…are at the same time instrumental in bringing about the development they foreshadow. They are law-code and executive power—or, to use another simile, they are architect’s plan and builder’s craft—in one. (From Schrödinger E: What is Life. Cambridge, Cambridge University Press; 1944.)

Once again, keep in mind that these speculations presage the identification of DNA as the genetic chemical. The terms code, broken, and deciphered themselves came from the recent World War II history. Winning the war relied on breaking enemy codes (see the Enigma Machine at the top of this chapter), as well as on hiding strategic battle information from the enemy (recall or look up the history of the Navajo Code Talkers).

In this chapter we look at just how the genetic code in DNA (and in fact, in messenger RNA) was broken. We describe the elegant experiments that deciphered first only one of the amino-acid codewords, then a few more of these three-base codons, and finally, all sixty-four possible codons that could be made using 4 different nucleotides. Of these, sixty-one encode amino acids and three are stop codons. Experiments like those that broke the genetic code also led to our understanding of the mechanism of protein synthesis. Early studies indicated that genes and proteins are colinear—that is, that the length of a gene was directly proportional to the polypeptide it encoded. If so, it follows that the lengths of mRNAs are also colinear with their translation products. Colinearity suggested the obvious hypothesis that translation proceeded in three steps (initiation, elongation, and termination), just like transcription itself.

We now know that initiation is a multi-step process involving the assembly of the initiation complex of a “translation machine” at a start codon near the 5’ end of the mRNA. This machine is made up of ribosomes, mRNA, several initiation factors, and requires a source of chemical energy for assembly. Since mature mRNAs are longer than needed to specify a polypeptide (even after splicing!), one function of initiation factors is to correctly position the ribosome and associated proteins near a start codon. The start codon specifies the first amino acid in a new polypeptide.

Once the initiation complex forms, elongation begins. Cycles of condensation reactions on the ribosome connect amino acids by peptide linkages, growing the chain from its amino end to its carboxyl end. Translation finishes when the ribosome moving along the mRNA encounters a stop codon. We will look at how we came to understand these discrete steps of translation.

Learning Objectives

When you have mastered the information in this chapter, you should be able to:

1. Compare and contrast the mechanisms and energetics of initiation, elongation and termination of translation and transcription.

2. Speculate on why the genetic code is universal (or nearly so).

3. Justify early thinking about a 4-base genetic code.

4. Justify early thinking about an overlapping genetic code (for example, one in which the last base of a codon could be the first base of the next codon in an mRNA.

5. Explain why all tRNA structures share some, but not other features.

6. Compare and Contrast the roles of ribosomal A, E and P sites in translation.

7. Trace the formation of an aminoacyl-tRNA and the bacterial Initiation Complex.

8. Describe the steps of translation that require chemical energy.

9. Formulate an hypothesis to explain why stop codons all begin with U.

10. Create a set of rules for inferring an amino acid sequence from a stretch of DNA sequence.

11. Speculate about why large eukaryotic genomes encode so few proteins.