Genetic Code

The genetic code includes the information for amino acid ordering, as well as information contained in other sequences of DNA molecules which serve ends other than translation into polypeptide chains. Examples of these latter types of regions in DNA are sequences which act as binding sites for endonucleases and RNA polymerase. The informational capability of the four-base system is enormous. 

The amino acid codons represent a prescription for pairing between molecules of tRNA—with their attached amino acids—and molecules of mRNA. Functionally, the code works via antiparallel pairing of codon and anticodon in an RNA species. Translation into polypeptides is directed only by those triplet nucleotides which lie between the start and stop signals in an mRNA molecule. The corresponding complementary regions in DNA are the structural genes which are transcribed into mRNA by RNA polymerase. 

However, the majority of base sequences in DNA serve functions other than coding for structural genes. As mentioned above, one important function is the binding of certain enzymes—for example, of endonucleases that cut the double strand of DNA. Other specific sequences are recognized by enzymes that bind and either initiate or terminate transcription. Still other sequences bind proteins that inhibit transcription. Translation into a polypeptide begins when an initiator codon in a strand of mRNA becomes bound to a ribosome, and continues consecutively, at the behest of the amino acid code, until a termination codon is reached. Translation from nucleotide to amino acid occurs at the level of the tRNA molecule, since on the one hand it pairs with mRNA by codon-anticodon pairing, while on the other it binds a specific amino acid. 

What accoimts for the great increase of nucleotide sequences in eukaryotic DNA as opposed to bacterial DNA Addressing this subject. Watts and Watts (1975) suggested one possible distribution of information in the genome. We have modified their table in light of the most recent information on the eukaryotic genome (Table 4). Apparently, 

More than 250 amino acids have been isolated from living systems, but only 20 appear to be encoded by the triplet nucleotide sequence in mRNA. Posttranslation modification accounts for the panoply of amino acids found in contemporary proteins. Hence, the limited number of amino acids encoded by the genome must be a consequence of evolutionary selection. Rohlfing and Saunders (1978) have proposed that it is the specific tripartite interaction among activating enzymes, tRNAs, and amino acid which explains why the amino acid code is limited to the 20 commonly found amino acids. 

Details of the genetic code were first worked out by Khorana and Nirenberg around 1961. There are four DNA bases and 20 different amino acids in proteins, which means that at least 20 different codes are required to carry alternative messages. 

With three adjacent bases in the codon unit, there are 4 = 64 ways of arrangement  

Were there are only two adjacent bases in the codon, the number of arrangements would be 4 = 16, which is insufficient. The amino acids specified by the 3-base code are listed in Table 11.23. Many of these amino acids are coded by more than one triplet and the code is therefore degenerate. More than one kind of t-RNA may code for the same amino acid. The code words appear to be the same for all life species. 

Thus the information necessary to specify the structures of thousands of different proteins (and enzymes) in the average living cell is stored in the base sequence of the DNA. This information is transcribed from DNA to m-RNA which carries it to the ribosomes where protein synthesis occurs. At the ribosomes, translation of the codons of the nucleic acid structure into the 20-letter alphabet of amino acids required for protein sequences, is accomplished by t-RNA. 

These desaiptions of replication and transmission of the genetic code represent a very simplified picture. Many details of these complex processes remain to be resolved. Only about 1% of the total DNA in humans is believed to be necessary for the synthesis of their different proteins. This is probably due to the repetitive nature of the exons and the useless introns. 

Reassignment of the platyhelminth mitochondrial genetic code from the standard inverte- 

eras = Taenia crassiceps E. multi = Echinococcus multilocularis E. gran G1/G4 = Echinococcus granulosus genotypes G1/G4 F. hep = Fasciola hepatica P. west 2N/3N = Paragonimus westermani diploid/triploid S. jap = Schistosoma japonicum S. malay = Schistosoma malayensis S. mek = Schistosoma mekongi S. man = Schistosoma mansoni. 

Gen Bank Code 1 standard code Basel = tTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG AAS = FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRWWAAAADDEEGGGG starts = i i i  

Gen Bank Code 5 invertebrate mitochondrial AAS = FFLijSSSSYY CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSWWAAAADDEEGGGG Starts = i iiii i  

Gen Bank Code 9 Rhabditophora mitochondrial code AAS = FFLLSSSSYY CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSWWAAAADDEEGGGG Starts = i i  

Diagram of the conalbumin primary transcript and the processed mRNA. The 16 introns, which are excised from the primary transcript, are shown in color. 

Before RNA splicing was discovered, the nucleus was observed to contain a significant amount of seemingly untranslated RNA. The collection of RNA molecules of widely varied sizes was given the name heterogeneous nuclear RNA (hnRNA), a term that is still sometimes used for nuclear RNA. 

Different snRNPs are found in eukaryotic cells which function in removing introns from primary RNA transcripts. The association of small RNAs, nuclear proteins, and the introns that they attach to is referred to as aspliceo-some. Small nuclear RNAs (designated U1 through U6) provide specificity to different spliceosomes so that they recognize different classes of introns. Introns are distinguished according to their three-dimensional structures and each class of introns is spliced out by a different mechanism. 

Class I introns were originally discovered in ciliated protozoa and subsequently were found in fungi, bacteriophages, and other organisms. The RNA itself in a class I in-tron has catalytic activity and class I introns remove themselves from primary RNA transcripts by a self-splicing reaction. Class I introns are not true enzymes in that they function only once. The nucleotides in the intron that is spliced out are recycled in the cell. 

Class II introns are removed from RNA by a selfsplicing reaction that proceeds through an intermediate structure called a lariat. The removal of class II introns from RNAs also results in the splicing together of exons on either side of the intron. The ability of class II introns to specifically bind to a 5 exon has led to their use as reagents to construct novel RNA molecules. Chemical derivatives of class II introns have been constructed that can carry out the reverse of the splicing reaction. When these introns insert themselves into RNA, they can be used to shuffle sequences or to link one RNA molecule to another. 

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The genetic code (Table 28 3) is the message earned by mRNA It is made up of triplets of adjacent nucleotide bases called codons Because mRNA has only four dif ferent bases and 20 ammo acids must be coded for codes using either one or two nucleotides per ammo acid are inadequate If nucleotides are read m sets of three how ever the four mRNA bases generate 64 possible words more than sufficent to code for 20 ammo acids... 

Section 28 11 Three RNAs are involved m gene expression In the transcription phase a strand of messenger RNA (mRNA) is synthesized from a DNA tern plate The four bases A G C and U taken three at a time generate 64 possible combinations called codons These 64 codons comprise the genetic code and code for the 20 ammo acids found m proteins plus start and stop signals The mRNA sequence is translated into a prescribed protein sequence at the ribosomes There small polynucleotides called... 

GENESEQ GENESIS Gene therapy Genetic code Genetic colonization Genetic engineering... 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

Translation of the Foreign Gene. The translation of a mRNA into a protein is governed by the presence of appropriate initiation sequences that specify binding of the mRNA to the ribosome. In addition, not all the codons of the genetic code are used equally frequently by all organisms. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

All of the 20 amino acids have in common a central carbon atom (Co) to which are attached a hydrogen atom, an amino group (NH2), and a carboxyl group (COOH) (Figure 1.2a). What distinguishes one amino acid from another is the side chain attached to the Ca through its fourth valence. There are 20 different side chains specified by the genetic code others occur, in rare cases, as" the products of enzymatic modifications after translation. 

The genetic code specifies 20 different amino acid side chains... 

If enzymes responsible for DNA repair are unable to remove the DNA adduct, or if an error takes place in the repair, then the error in the genetic code remains when the cell divides. Thus, cellular proliferation is also required, in addition to a mutation, for there to be a permanent effect of a chemical compound. Accumulation of genetic errors, i.e., mutations, has been suspected to be an important factor in chemical carcinogenesis. ... 

In one of the early experiments designed to elucidate the genetic code, Marshall Nirenberg of the U.S. National Institutes of Health (Nobel Prize in physiology or medicine, 1968) prepared a synthetic mRNA in which all the bases were uracil. He added this poly(U) to a cell-free system containing all the necessary materials for protein biosynthesis. A polymer of a single amino acid was obtained. What amino acid was polymerized ... 

What is the amino acid sequence of the fusion protein Where is the junction between /3-galactosidase and the sequence encoded by the insert (Consult the genetic code table on the inside front cover to decipher the amino acid sequence.)... 

The two strands which make up DNA are held together by hydrogen bonds between complementary pairs of bases adenine paired with thymine and guanine paired with cytosine. The integrity of the genetic code (and of life as we know it) depends on error-free transmission of base-pairing information. 

Atomic determinants for aminoacy lation of RNA minihelices and their relationship to genetic code 99ACR368. 

H. Gobind Khorana (medicine) interpretations of the genetic code and its function in protein synthesis... 

The following molecules are bases that are part of the nucleic acids involved in the genetic code. Identify (a) the hybridization of each C and N atom, (b) the number of a- and ir-bonds, and (c) the number of lone pairs of electrons in the molecule. 

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