Section H - Protein synthesis

The genetic code is the rules that specify how the nucleotide sequence of an mRNA is translated into the amino acid sequence of a polypeptide. The nucleotide sequence is read as triplets called codons. The codons UAG, UGA and UAA do not specify amino acids and are called termination codons or Stop codons. AUG codes for methionine and also acts as an initiation (Start) codon. 

Most amino acids in proteins are specified by more than one codon (i.e. the genetic code is degenerate). Codons that specify the same amino acid (synonyms) often differ only in the third base, the wobble position, where base-pairing with the anticodon may be less stringent than for the first two positions of the codon. 

The genetic code is not universal but is the same in most organisms. Exceptions are found in mitochondrial genomes where some codons specify different amino acids to that normally encoded by nuclear genes. In mitochondria, the UGA codon does not specify termination of translation but instead encodes for tryptophan. Similarly, in certain protozoa UAA and UAG encode glutamic acid instead of acting as termination codons. 

The mRNA sequence can be read by the ribosome in three possible reading frames. Usually only one reading frame codes for a functional protein since the other two reading frames contain multiple termination codons. In some bacteriophage, overlapping genes occur which use different reading frames. 

The genetic code During translation, the sequence of an mRNA molecule is read from its 5 end is a triplet code by ribosomes which then synthesize an appropriate polypeptide. Both in prokaryotes and eukaryotes, the DNA sequence of a single gene is colinear with the amino acid sequence of the polypeptide it encodes. In other words, the nucleotide sequence of the coding DNA strand, 5 to 3, specifies in exactly the same order the amino acid sequence of the encoded polypeptide, N-terminal 

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A substantial literature bears witness to the importance of investigating the effects of h amic substances on enzyme changes in plant tissues. In such studies it is usual to distinguish between an effect on enzyme development (synthesis), and an effect on enzyme activity yev se which is measured by adding the humic substances to the enzyme assay media. In this section, only protein synthesis generally and enzyme synthesis in particular, are considered because they relate directly to translation and/or transcription involving m-RNA. 

In maize roots only low levels of activity could be detected at the root tip (Stulen and Oaks, 1977), but relatively high levels were determined in mature sections 20-35 mm from the tip. When root tips were excised there was a threefold increase in AS activity in 5 h. The increase in activity in the root tip was sensitive to cordycepin, 6-methylpurine and cycloheximide suggesting that both RNA and protein synthesis were involved. 

Now we will return briefly to Sections 3.8-3.11 and 4.6-4.8 where we considered the general problem of multiple flows, here of H, C, N, O, S and P. We observe immediately that all the products are from the same small molecule environmental sources and are required to be formed in relatively fixed amounts using the same source of energy and a series of intermediates. Controlling all the processes to bring about optimum cellular production are feedbacks between them and linked with the code which generates proteins, and here we note particularly enzymes, i.e. catalysts. The catalysts are made from the amino acids, the synthesis of which they themselves manage, while the amino acids control the catalysts so as to maintain a restricted balanced set of reaction pathways in an autocatalytic assembly. It is also the feedback controls on both the DNA (RNA) from the same units used in the... 

Before proceeding it is worth noting that the prokaryotes established the fundamental features of life in the coordinated production of DNA, RNA, proteins, saccharides and lipids, mainly from H, C, N, O, S and P and in the functional use of many inorganic elements including Na, K, Mg, Ca, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cl and Se. In this book we deliberately stress this role of the available elements in the environment especially as they change with time in evolution in advance of that in cells. In evolution many of the functions of these molecules and ions remain only modified not fundamentally changed. While the uses of metal ions were restricted by equilibria (Sections 4.18 1.20), the synthesis of porphyrins allowed effectively novel elements,... 

The new solvent systems (Section 5.1.7.1) were an important advance and opened the way for the solution segment synthesis of even larger and more complex proteins. For example, human midkine (121 residues) containing 5 disulfide bonds was assembled from Boc-(l -59)-OH and H-(60-121)-OBzl, which were not soluble in DMSO, but were readily soluble in CHCl/TFE (3 1) (Scheme 12).[441 The coupling was undertaken with a water-soluble car-bodiimide containing HOOBt and was complete in one hour. 

X, N, Ep and H are needed for synthesis of FeMo-co and for its incorporation into the MoFe-protein.55/55a Nif A is an activator gene for the whole duster including the nifL gene product, which is altered by the presence of 02 or of glutamine. Accumulation of the latter in cells (see Section B,2) strongly represses transcription of the nitrogenase genes. 

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