Person Realise Review and Reinforce the Genetic Code Answer Key
J Bacteriol. 2019 Aug one; 201(15): e00091-19.
Published online 2019 Jul 10. Prepublished online 2019 Apr 22. doi:x.1128/JB.00091-19
Understanding the Genetic Code
Milton H. Saier, Jr.
aDepartment of Molecular Biological science, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
William Margolin, Editor
William Margolin, McGovern Medical School;
Abstract
The universal triple-nucleotide genetic code is often viewed as a given, randomly selected through evolution. However, as summarized in this article, many observations and deductions within structural and thermodynamic frameworks assist to explain the forces that must have shaped the code during the early evolution of life on World.
KEYWORD: Genetic code
INTRODUCTION
The universal triple-nucleotide genetic code, allowing DNA-encoded mRNA to be translated into the amino acid sequences of proteins using transfer RNAs (tRNAs) and many accompaniment and modification factors, is essentially common to all living organisms on Globe (one,–3). Thousands of studies have focused on various aspects of the genetic lawmaking, revealing aspects of the ground for its structure and development (iv,–6). And no wonder, since the lawmaking provides a molecular explanation for the transmission of information from Deoxyribonucleic acid to mRNA to protein (the fundamental dogma of biology). All of genetics and molecular biology depend on the forces and factors that decide how the nucleotide triplet code translates into amino acid sequences.
The codon cycle, used in nearly all textbooks and websites, has the nucleotide at position i determining the quadrant, with thymine (T, Deoxyribonucleic acid) or uracil (U, RNA) in the 1st quadrant and cytosine (C), adenine (A), and guanine (Yard) in the 2d, 3rd, and 4th quadrants, respectively (Fig. ane), where T, U, and C are modest bases (pyrimidines) while Yard and A are big bases (purines). This convention is technically correct but may not be optimally helpful for conceptualization of the forces that dictate the code. Instead, the second nucleotide position should be emphasized equally information technology is the one determining the nature of the amino acids encoded. How was this offset deduced?
The codon wheel as it appears in textbooks and websites. It allows whatsoever user to identify the amino acid encoded by any Deoxyribonucleic acid/RNA codon. Codon position ane is in the heart of the wheel, codon position 2 is in the center of the wheel, and codon position 3 is most the periphery of the wheel, side by side to the three-alphabetic character amino acrid designation at the outermost part of the bicycle. While technically right, this wheel does not facilitate learning the essential features determining the rules that brand sense of the code. TER, a polypeptide chain termination codon.
RELATIVE IMPORTANCE OF THE THREE CODON POSITIONS
Living organisms have DNA guanine/cytosine (GC) contents that range from about 20% GC to 80% GC or 80% AT to twenty% AT, respectively. When variations in the GC contents of the three codon positions, P1, P2, and P3, are plotted versus the GC contents of many genomes (Fig. 2), position one varies from 41% GC to 72% GC, a change of 31%. In contrast, position ii varies from 33% to 45%, a change of but 12%. Position three varies from 10% to 90%, a whopping fourscore% change (seven, 8). How did these differences arise during evolutionary history? Since point mutations normally arise randomly, with the advantageous ones being selected for while the deleterious ones are selected against, it can be assumed that these differences reflect the constraints imposed on mutations arising in these three codon positions. These constraints are apparently greatest for codon position 2 (P2) and least for codon position 3 (P3) (9). Equally nosotros shall see, this is because P2 specifies the blazon of amino acid, codon position i (P1) usually specifies the specific amino acid, and P3 is highly redundant as several bases specify a item amino acid. The different evolutionary rates of divergence can best be explained by the "negative selection principle," i.eastward., functionally less important parts evolve (change) more than rapidly than more of import parts (ten, eleven). Thus, it would appear that P2 in codons is near important, P1 is of intermediate importance, and P3 is least important for specifying the amino acids in proteins (7).
Correlation of Yard+C (GC) contents of the total genomic Dna of diverse organisms with the GC contents of the three codon positions. The first, 2d, and tertiary positions of the iii nucleotides in the mRNA codons, specifying amino acids in proteins, are labeled as such. (Modified from reference 7.)
AN Alternative CODON Cycle
The relative importance of the three codon positions can be meliorate understood if the helical cycle is plotted as shown in Fig. 3 (12, 13). With T/U in position 2 (quadrant 1, upper correct), all amino acids are strongly hydrophobic without exception, but with A in position ii (quadrant three; lower left), all amino acids are strongly hydrophilic, also without exception. With C or Yard in position 2, most codons code for semipolar amino acids. Thus, when C is in position 2 (quadrant 2 in Fig. 3), in that location is no exception, but with G in position 2 (quadrant 4 in Fig. three), there are ii exceptions. Arginine, a strongly hydrophilic residue, and opal (UGA), a concatenation termination codon, are found within this quadrant (13). Interestingly, nevertheless, UGA can also code for amino acids: l-selenocysteine (14, 15), l-tryptophan (16), and glycine (17), all semipolar residues (eighteen). 1 can imagine that the primordial code specified iii types of amino acids, ane hydrophobic, ane hydrophilic, and two semipolar.
Wheel representation of codon usage emphasizing the primary importance of the fundamental codon position (position 2) in determining the type of amino acrid, the secondary role of position 1 in determining the specific amino acid, and the relatively small function of the third (wobble) position for amino acrid specification. Equally in Fig. 1, the three-letter abbreviations of the amino acids are used. The three chain termination codons are indicated by name (UAA, ochre; UAG, bister; and UGA, opal). Quadrants 1 to 4 (Q1 to Q4, respectively) are indicated.
RELATED CODONS OFTEN SPECIFY RELATED AMINO ACIDS
Amino acids that exhibit like properties are oft encoded past codons that differ only in ane position, P1, P2, or P3. For example, Asp and Glu are the two strongly acidic amino acids in proteins, and they are encoded by GAPy and GAPu (Py, pyrimidine; Pu, purine), respectively, differing simply in P3. Moreover, Asn and Gln are derived from Asp and Glu by amidation, and their codons are AAPy (Asn) and CAPu (Gln), differing from those of their parental acidic amino acids only in P1. The two aliphatic hydroxy amino acids, Ser and Thr, are encoded by UCN and ACN (North, any nucleotide), respectively, differing only in P1. The ii strongly bones amino acids, Lys and Arg, are encoded past AAPu and AGPu, respectively, differing merely in P2, although Arg is as well encoded by CGN. The two closely related aromatic residues, Phe and Tyr, are encoded by UUPy and UAPy, respectively, also differing only in P2. Finally, the aliphatic hydrophobic amino acids are all encoded by codons with U in position 2 as noted above, and many such codons differ from each other only in a unmarried position.
THE WOBBLE POSITION: WHAT IS Of import FOR AMINO ACID SPECIFICATION IN P3?
What quality of the position iii nucleotide influences amino acid selection? Examination of the codon bicycle shown in Fig. three reveals that when P3 is important, it is only important whether the base in P3 is a purine (A or G) or a pyrimidine (U or C). Thus, merely the type of the base at position 3 is important (12) (see adjacent department). However, there are two exceptions: Ile/Met and Trp/opal (Fig. three). Three codons specify isoleucine (AUU, AUC, and AUA) with just one codon (AUG) specifying methionine, while one each specifies tryptophan (Trp; UGG) and concatenation termination (opal; UGA). Interestingly, though, as noted above, some organisms and organelles, including mitochondria, use both codons (UGG and UGA) to specify Trp, and so UGA is not a terminate codon (12). Similarly, when UGA specifies selenocysteine or glycine, it does not terminate extension of the growing polypeptide chain. In all other cases where P3 is important, only the blazon of base is important as noted higher up.
THE WOBBLE POSITION: WHEN IS P3 Of import?
Referring to Fig. iii once again, information technology can exist seen that when P2 is C, P3 is never important. When P2 is an A, P3 is always important, determined only by whether information technology is a purine or pyrimidine only not past which of the ii purines or pyrimidines it is. However, when P2 is a G or U, P3 is sometimes important. Thus, P2 primarily determines when P3 plays a role in specifying an amino acrid.
IF P2 IS A G OR U, WHEN IS P3 Of import?
When P2 is a G or U, the wobble position is of import if and but if P1 is an A or U, not when P1 is a G or C. Since an A-U base pair has two H bonds while a K-C base pair has three, this suggests that H-bond strength plays a dominant part although base of operations shape complementarity may also play a role (19). In other words, with P2 every bit a G or U, the type of base pair at P1 (A-U versus K-C) determines the importance of P3. The H-bond strength of P2 plus P1 likely is a formative gene, but, clearly, this does non provide a full explanation. We need to further refine our understanding of the specifications that determine the importance of P3.
THE H-BOND Force OF A-U (mRNA-tRNA) MAY NOT Be THE Aforementioned Equally U-A (mRNA-tRNA)
Careful consideration of Fig. 3 suggests that A-U (mRNA-tRNA) is not equivalent to U-A and that M-C is not equivalent to C-G. In fact, U-A probably forms stronger bonds than A-U, and C-G probably forms stronger bonds than One thousand-C. In other words, the H bonds may exist stronger when the pyrimidine is in the mRNA and the purine is in the tRNA. This explains why the wobble position is never important when C is in P2 of the mRNA although it is sometimes important when G is in P2 of the mRNA (that is, when an A or U is in P1). Similarly, the wobble position is sometimes of import when U is in P2 (that is, when A or U is in P1) merely always important when A is in P2. These differences in H-bond forcefulness between U-A and A-U or between C-G and Grand-C may have to do with the established fact that direct H bonds are the strongest (20), suggesting that both the numbers and configurations of the H bonds dictate their thermodynamic consequences. In this case, the curvature of the anticodon on the tRNA may be responsible. It has been argued that discrimination between tRNAs is dependent on steric (shape) complementarity of the bases (9, 21) and that base modification of the tRNAs could play a role (22).
DEPENDENCY OF TRANSLATION ON tRNA MODIFICATIONS
A new borderland in understanding the details of the central dogma of biology involves the effects of posttranscriptional tRNA modifications, some of which may be near universal across phyla while others are phylum specific (23). More than than 100 such tRNA modifications have been identified, a major fraction in their RNA anticodon loops (24). Modifications include deamination of adenosine to inosine, introduction of the modified nucleoside, queuosine, thiolation, methylation, isopentenylation, 5-methoxycarbonyl methylation, threonyl carbamoylation, and others (25,–28). These modifications are necessary for the speed and fidelity of translation. Hypomodification can inhibit translation and thereby inhibit growth (29, thirty). Changes in tRNA modifications have been shown to be involved in diseases in humans as well as bacterial pathogenesis.
Particularly relevant to this minireview, these modifications favor specific codon-anticodon affinities by stabilizing specific base pairs, thus fine-tuning poly peptide synthesis (31). Codon bias promotes preferential utilization of certain synonymous codons that differ simply in P3 of the codon (32). Moreover, modification-dependent tRNA cleavage tin can facilitate downregulation of poly peptide synthesis in response to stress signals (31). To make matters even more complicated, one tRNA modification may influence the action of an enzyme catalyzing some other modification reaction (33). From these observations, it is clear that numerous posttranscriptional modifications of tRNAs play important roles in the efficiency and accurateness of translation.
Chain INITIATION CODONS
Initiation codons, acting with an initiation tRNA, normally encode formyl methionine (fMet) in bacteria, chloroplasts, and mitochondria or methionine (Met) in archaea and the cytosol of eukaryotes (34,–36). The codon wobble position is P1, where the order of usage for prokaryotes is usually AUG > GUG > UUG > CUG. However, in loftier-GC-content organisms, the frequencies of GUG relative to those of AUG increase, and in many eukaryotes, the lodge of initiation codon usage is AUG > CUG > GUG > UUG (37, 38). While many codons can be used to initiate translation at depression frequencies (39), the initiation factors and mechanisms of concatenation initiation are complex merely similar in dissimilar organisms (twoscore), and either fMet or Met is used as the initiating amino acid, depending on conditions, regardless of the codon used (41). It should be reemphasized that Met codon discrimination depends on anticodon modifications and is often species specific (42, 43).
Chain TERMINATION (Cease OR NONSENSE) CODONS
UAA (ochre) is the all-time and most oftentimes used chain termination (cease or nonsense) codon, especially in low- or moderate-GC-content organisms (44). It well-nigh never codes for anything other than stop. UAG (amber), used in smaller amounts just almost invariant with respect to GC content, can besides code for pyrrolysine, which is an active-site residue in some methyltransferases (45). This amino acrid is found most frequently in archaea just occasionally in bacteria (46). Of the three terminate codons, UGA (opal) is used for concatenation termination primarily in high-GC-content organisms, but the bodily frequency depends also on the organismal blazon (44). These 3 codons are recognized by release factors (RFs): RF1 (which recognizes UAA and UAG), RF2 (which recognizes UAA and UGA), and RF3 (which functions to recycle RF1 and RF2 in Escherichia coli). These release factors may take coevolved with the terminate codons (47,–49). Thus, in most organismal phyla, UAA is used more than frequently than UAG or UGA (44). The importance of the UAA finish codon is illustrated by the observation that highly expressed genes predominantly stop with UAA (44).
It is interesting that all of the mutual nonsense codons use U in position one which is invariant, with two purines in positions 2 and 3. Since AU base pairs have two hydrogen (H) bonds while GC has three, the best stop codon (UAA) potentially would have only vi H bonds (2 per codon position) if it were to pair with its complementary sequence in a tRNA, while the other two would have seven (20). Codons, in general, have between six and nine H bonds, depending on their AU versus GC contents, suggesting that weaker hydrogen bonding potentially may have played a function in the choice of the chain termination codon(southward) early in the conception of the code.
AMINO ACIDS IN THE PREBIOTIC PRIMORDIAL SOUP
It seems probable that the earliest evolving microorganisms had to survive on compounds that were nowadays in the prebiotic primordial soup (l, 51). Stanley Miller'southward atmospheric spark belch experiments and subsequent studies showed that ten of the twenty common, naturally occurring amino acids in proteins could be generated abiotically by using false primordial Earth weather (52). Moreover, these compounds corresponded roughly in relative abundance to those in meteorites (53). These 10 abiotic amino acids, in order of their relative abundances, were Gly > Ala > Asp > Glu > Val > Ser > Ile > Leu > Pro > Thr (54). This club proved to correlate with the gratuitous energies of their syntheses, suggesting that thermodynamics determined their relative amounts. In more recent experiments, not but amino acids only also nucleic acid bases and fatty acids could be made from inorganic sources of hydrogen, carbon, nitrogen, and sulfur in the presence of UV radiation under plausible prebiotic conditions (55). These observations further strengthen the argument that prebiotic weather led to the synthesis of molecules that facilitated the development of elementary life forms from preexisting compounds. This argument is applicable regardless of whether life arose here on Earth or came here from some other source in outer space.
The eight height amino acids, listed in Table one, fall into three groups: the semipolar amino acids (Gly, Ala, and Ser), the acidic hydrophilic amino acids (Asp and Glu), and the aliphatic hydrophobic amino acids (Val, Ile, and Leu). And as discussed in a higher place, when the second base in a codon (P2) is G or C, semipolar residues are usually encoded. In the primordial code, if this were true, what semipolar amino acid would have been preferred? Examining the codon wheels in Fig. 1 and 3, we find that when C is in P2, Ala, Ser, Thr, and Pro are encoded, but when G is in P2, Gly and Ser are encoded. Thus, if we were to select a single primordial amino acrid, the virtually abundant one, Gly, is the preferred choice with Thou in P2, only Ala is the preferred choice with C in P2. Examining the codon wheels further, we note that if G is in P1, regardless of which base is at P2, Gly, Glu/Asp, Ala, and Val are encoded, which evidence to be the v most abundant amino acids predicted for the primordial soup (Tabular array 1). Thus, if we are to advise a primitive code involving specific amino acids, we might suggest just four or v amino acids encoded by four codons: GGN encoding Gly, GAN encoding Glu/Asp, GCN encoding Ala, and GUN encoding Val (where N is whatsoever base). Thus, it is possible that Yard (with three H bonds) in P1 yielded the four original codons, coding for the four or 5 most prevalent amino acids in the prebiotic soup.
TABLE 1
Properties of the 8 amino acids believed to be present in greatest amounts in the prebiotic primordial soup
| Amino acid | Rank in the soup a | Rank in proteins b | Polarity c | Hydrophobicity d | Vol (Å) e | Area (Å2) f |
|---|---|---|---|---|---|---|
| Glycine | i | 5 | 0 | −0.4 | 48 | 85 |
| Alanine | 2 | two | 0 | +0.8 | 67 | 113 |
| Serine | 6 | vii | 0.1 | +0.eight | 73 | 122 |
| Aspartate | 3 | 10 | l | −3.5 | 91 | 151 |
| Glutamate | four | half dozen | l | −three.5 | 109 | 183 |
| Valine | v | 3 | 0.1 | +4.ii | 105 | 160 |
| Isoleucine | 7 | iv | 0.1 | +iii.8 | 124 | 182 |
| Leucine | eight | one | 0.ane | +4.5 | 124 | 180 |
Data in Table i tabulate backdrop of the common amino acids: polarity, hydrophobicity (a positive [+] value) versus hydrophilicity (a negative [−] value), molecular book, and surface area (see besides the footnotes to Table 1) (56). The three groups of amino acids (semipolar, polar, and nonpolar) are clearly delineated on the basis of these backdrop, suggesting ways by which the types of amino acids could have been distinguished past an evolving coding organization. Of course, later on stepwise evolutionary events presumably involved expansion of the code to include somewhen all 20 common protein amino acids. Thus, expansion would result from the subdivision of codon blocks in which some of the similar codons assigned to an early on amino acid were reassigned to a late amino acid. These subdivisions would usually involve the introduction of related amino acids so equally to minimize the consequences of mutations and translational errors. The current code would thus be a relic of the early code (56).
WHY IS THE GENETIC CODE Then WELL CONSERVED?
The standard extant genetic code includes a number of pocket-sized organismal differences, particularly in eukaryotic organelles as well as in parasitic and symbiotic prokaryotes with small genomes. Still, the standard code is essentially universal (54). Several scientists have suggested why the lawmaking should be so well conserved, and the consensus is that there is probably more ane reason. One is referred to the "frozen accident." Past this, it is suggested that a codon reassignment gives rise to harmful effects on translation, decreasing the robustness of the standard, nonrandom code, which appears to be designed, in part, to minimize the deleterious consequences of mutations and errors in translation (56). This argument assumes that the code was optimized long ago, and so it is now almost perfect.
Whether this is true or not is controversial, but at least we tin can claim that the code is skilful enough and difficult to alter. Another argument suggests that codon variation among organisms would inhibit the occurrence of lateral (horizontal) transfer of genetic materials betwixt organisms. This would exist detrimental as adaptation to environmental changes often depends on interorganismal genetic exchange mechanisms, of which we currently recognize several (13). Lateral transfer is almost common in microbes that live in changing environments and that need to suit quickly to survive. Conditions that existed early during the development of the genetic code and early on life were, of class, very dissimilar from those we feel today, including anaerobiosis and high dissolved Fe2+ concentrations. Yet, regardless of weather condition, horizontal gene transfer was probably more important then than it is now (57).
BENEFITS OF A REDUNDANT GENETIC Lawmaking
As noted to a higher place, the genetic code is redundant, with as many as six synonymous codons specifying a unmarried amino acid. Synonymous rare codons are at present known to accept diverse functions, including regulation of cotranslational poly peptide folding, facilitation of covalent protein modifications during or afterwards synthesis, and co- or posttranslational secretion (58). It has likewise been argued that the redundant code decreases the deleterious consequences of random bespeak mutations (9, 59,–61). This is currently an agile field of research, and new advances are continuously being made.
Exchanging synonymous codons can crusade diseases in humans and other organisms (62, 63), an ascertainment that is not surprising when information technology is considered that translational pausing is programmed, allowing, for example, coordinated folding of the nascent proteins (64). Synonymous codon choice may also play a role in epigenetic modifications (65). Electric current studies indicate that there are boosted benefits equally noted above.
CODON FREQUENCIES VERSUS Cistron EXPRESSION LEVELS
For any organism, some codons specifying an amino acrid are used frequently while others are infrequently used (rare codons) although the set of preferred codons differs for phylogenetically distant organisms. This is a hot topic of investigation as ∼100 papers are published over a single yr on this subject alone. Figure 4 shows a schematic view of the utilise of the most common codons versus rare codons for genes expressed at different levels in a range of organisms. If expressed at loftier levels (e.grand., ribosomal proteins), the common codons are used with high frequency while rare codons are seldom used (Fig. iv, ruddy line) (58, 66). If a factor is expressed at very low levels (e.1000., the gene for the E. coli lactose repressor lacI (Fig. 4, light-green line), at that place is fiddling preference for common codons. Equally expected, moderately expressed genes, or highly expressed genes (e.yard., the lactose operon) induced under rare conditions (Fig. four, blueish line), use mutual codons with intermediate frequencies (67, 68). The presumption is that the use of mutual codons, respective to the most prevalent tRNAs, favors rapid and authentic translation and therefore increases the level of the gene product (67, 69). This is expected since a higher rate of translation should event if the cytoplasmic concentrations of the tRNAs used are high. Furthermore, it has been shown that the use of suboptimal codons leads to misincorporation of amino acids by the ribosome (70,–72). This is particularly detrimental for proteins needed in large amounts but of fiddling importance for proteins for which only a few copies are required (72).
Schematized correlation between the level of gene expression and the frequency of common versus rare codons used in the coding region of the corresponding gene. The red line represents the codon usage pattern for highly expressed genes, the blueish line shows the same for genes expressed at a moderate level or those that are induced to high levels only under certain conditions, and the greenish line represents the codon usage pattern for genes that are expressed at very low levels. Finally, the black line reveals the pattern for a cistron with little or no correlation of its codon usage with the frequency of codons used in the organism. Such a gene was presumably obtained by horizontal (lateral) gene transfer from an organism with a very dissimilar set of codon usage frequencies. Note that codon frequencies roughly correlate with the levels of the corresponding tRNAs in the cytoplasm of the organism in which that cistron evolved (68, 70, 92), and the levels of the tRNAs in the prison cell determine the do good for highly expressed genes using the commonly used codons. Genes expressed at depression levels do not adopt common codons because low rates of translation of these genes are not deleterious.
Horizontally transferred genes, obtained from another organism (which ofttimes has different codon preferences [73]), volition not prove a correlation with the codon preferences of the recipient organism (Fig. 4, black line). Studies have shown that information technology takes hundreds of millions of years for such a factor to come to equilibrium with the codon usage design of the recipient (74). For this reason, computer programs could be designed to estimate not only what type of organism the gene came from but also when in evolutionary history the transfer event occurred (75,–81). Merely additional benefits that result from the coding options chosen include maximizing recombinant gene expression, decision-making protein folding, and attenuating viruses.
FREQUENCIES OF AMINO ACIDS IN PROTEINS As A FUNCTION OF THE NUMBERS OF ENCODING CODONS
Test of Fig. 3 reveals that some amino acids (Trp and Met) take only one codon, while others (Leu, Ser, and Arg) have 6 codons each. All others have two, three, or four codons. In Fig. five, the pct of a detail amino acid in an array of randomly selected proteins is plotted versus the number of codons that specify that amino acid. Trp and Met are the rarest amino acids in proteins, and, as noted above, each is encoded past merely one codon. A quick perusal of Fig. v shows that while there is a rough correlation betwixt percentage occurrence in proteins and numbers of encoding codons, at that place is considerable besprinkle from a straight line. A similar plot with less scatter was obtained by King and Jukes when a set of proteins exclusively of mammalian origin was examined (82). Thus, codon numbers correlate roughly with relative amino acid frequencies in proteins. The availability of certain thermodynamically stable amino acids in the primordial soup may have played a office in the selection of the amino acids starting time to be incorporated into proteins (83, 84). This is because these are the amino acids that predominated before amino acid biosynthetic pathways evolved (run into "Amino Acids in the Prebiotic Primordial Soup" in a higher place) (85).
Plot of amino acid frequency in proteins versus the numbers of codons specifying these amino acids. The one-letter abbreviations of the amino acids are adjacent to the points representing the positions corresponding to their relative abundances, expressed as a pct of the total in proteins on the y axis. The numbers of codons that specify the amino acids are plotted on the x axis. The amino acrid frequencies in randomly selected representative proteins from all domains of living organisms were taken from Saier (13). (Republished from reference 13 with permission of the publisher.)
Which came start, the need for a greater amount of a detail amino acid or an increased number of codons? Possibly the former was the driving strength that was responsible for the differing numbers of codons used to specify the unlike amino acids. Nevertheless, the correlation observed in Fig. 5 leads to additional unanswered questions. Why does this correlation exist, and what does information technology tell us? While nosotros can guess at the answers, further inquiry will be needed to provide definitive answers.
TWELVE RULES SUMMARIZING THE FORCES THAT DETERMINE THE GENETIC CODE
Simple observations noted in this article correlate with and may provide an explanation for some of the factors influencing the specification of amino acids by codons within the genetic code. These are summarized hither. (i) Position 2 (P2) is most important of the three nucleotide codon positions because it specifies the type of amino acid, while position one (P1) determines the specific amino acid, sometimes with the aid of P3, the wobble position. (ii) The frequency of an amino acid in proteins roughly correlates with the number of codons that specify it. (three) Initiation codons, acting with an initiation tRNA, encode formyl methionine or methionine, simply the codon wobble position is P1 where the order of usage is AUG > GUG > UUG > CUG in many organisms and organelles. (four) Chain termination codons (UAA > UAG or UGA) have an invariant U in position 1 with two purines in P2 and P3; weak hydrogen (H) bonding may accept influenced their evolution. (5) Highly expressed genes use the well-nigh mutual codons in an organism while genes expressed at low levels utilize rare codons with higher frequencies, simply horizontally (laterally) transferred genes may show no correlation. (vi) When P3 is important for amino acid specification, it is important but whether P3 is a purine (A or G) or a pyrimidine (U or C) with just a couple of exceptions. (vii) Whether or not P3 is important is adamant by the nucleotide at P2: when P2 is a C, P3 is never important; when P2 is an A, P3 is always important; when P2 is a U or G, P3 is sometimes important. (viii) When P2 is a U or K, P3 is important only when P1 is an A or U just not when P1 is a G or C, so the numbers of H bonds in P2 plus P1 make up one's mind the importance of P3. (ix) It makes a difference if an A or U is in the mRNA or the tRNA to the H-bond strength. U-A (mRNA-tRNA) is stronger than A-U, and C-G is stronger than G-C. Thus, a pyrimidine in the mRNA forms stronger H bonds with the tRNA than when the corresponding H-bonded purine is in the mRNA. (10) Related amino acids are often encoded past similar codons, differing in a unmarried position, suggesting that one derived from the other. (xi) Rare synonymous codons tin be programmed for translational pausing, promoting cotranslational protein folding, covalent modification, and secretion. (xii) The most common amino acids in proteins are ofttimes, simply not always, the thermodynamically most stable ones.
These observations allow thermodynamic rationalization of many aspects of the genetic lawmaking and lead to postulates well-nigh how the code may accept evolved, first from four types of amino acids, so with the specification of certain specific amino acids, then past expansion with the specification of additional related amino acids.
CONCLUSIONS
Science strives to reveal the laws of nature, and critical to an agreement of all of biology is the central dogma, the basic framework whereby genetic information flows from DNA to RNA to protein. Conceptually, the RNA polymerase-mediated transcription of DNA to RNA is relatively straightforward, but the translation of RNA into proteins is much more complicated. Information technology is this terminal subject field, involving the triplet genetic code, that is the focus of this minireview. Based on our knowledge that C and U are pyrimidines, very different in structure from purines (G and A), and that A-U pairs class two hydrogen bonds while G-C pairs grade three, we have been able to come to of import suggestions regarding the thermodynamic basis for amino acid specification in proteins by the nucleotide codons in mRNAs. We are likewise able to formulate hypotheses, based on sound principles and compelling experimental evidence, equally to how this code arose. The appearance of the code, dictated by thermodynamic principles, probably followed a logical sequence of events in which a limited number of readily available amino acids, nowadays in the primordial soup, and a simple nucleotide code to specify as few as 4 amino acids but equally many as 8 or 10 amino acids gradually expanded as additional amino acids became bachelor due to evolving anabolic pathways. This would have involved the use of an increasing number of smaller blocks of codons specifying a correspondingly increased number of amino acids (54, 57, 85,–87). The next pace would be to experimentally examine these observations to test the hypotheses put forth and to generate a improve understanding of the fine details by which the virtually universal genetic lawmaking specifies the 22 encoded amino acids in proteins.
ACKNOWLEDGMENTS
I thank professors Steven Baird, Russ Doolittle, Adam Hockenberry, Jack Kyte, William Margolin, Arturo Medrano-Soto, Mauricio Montal, Sheila Podell, Ralf Rabus, Jack Trevors, and Chris Wills for helpful comments on the contents of this article.
The work reported has been used for teaching purposes at UCSD and was supported by grant GM077402 from the U.S. National Institutes of Health.
Biography
•
Milton H. Saier, Jr., is a professor of molecular biology at the University of California at San Diego. His current research focuses on molecular evolution involving several aspects of the central dogma of molecular biology. These include (i) membrane protein evolution, (ii) transport and metabolic regulation, and (3) transposon-mediated directed mutation. He has taught many graduate and undergraduate courses over the years, most recently including microbial biochemistry, microbial genetics, and microbial physiology besides as human touch on on the environment. He is a long-standing member of the ASM and the AAAS also every bit an honorary member of La Société Française de Microbiologie (SFM) and the Alexander von Humboldt Stiftung of Germany. His wife, Jeanne, and he have performed chamber music throughout most of their lives. They have 3 adult children, Hans, Anila, and Amanda, and six grandchildren.
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