Protein three-base-pair codons

The answer is b. (Murray, pp 452-467. Scriver, pp 3-45. Sack, pp 1-40. Wilson, pp 101-120.) The genetic code uses three-nucleotide words, or codons, to specify the 20 different amino acids (see the chart below). There are 64 different three-base pair codons (three positions with four possible nucleotides at each). It follows that the genetic code must be degenerate, i.e., different codons can specify the same amino acid. Three codons are reserved as stop signals that result in peptide chain termination. The linear correspondence of codons in DNA and of amino acids in protein domains is interrupted by the presence of introns in DNA. Codons differ from the dinucleotide tandem repeats that provide useful DNA polymorphisms, or the trinucleotide repeats that can be responsible for disease. The genetic code is universal in the sense that codon-amino acid relationships are the same in all organisms. 

As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

There are 20 naturally occurring amino acids that are assembled into proteins. If codons consisted of only two base pairs, each of which could be one of four nitrogenous bases, directions could be given for only 4x4= 16 amino acids. Using three bases per codon gives a total of 4 x 4 x 4 = 64 possibilities, which is more than sufficient. This provides for some redundancies for example, six different codons specify arginine. Codons also signal initiation and termination of a protein chain. 

The wobble (or third) base of the codon contributes to specificity, but, because it pairs only loosely with its corresponding base in the anticodon, it permits rapid dissociation of the tRNA from its codon during protein synthesis. If all three bases of a codon engaged in strong Watson-Crick pairing with the three... 

Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain.

Initiation of the polypeptide chain. mRNA bearing the code for the polypeptide is bound to the small sub-unit of RNA, followed by the initiating amino-acid, and is attached to its tRNA to form an initiation complex. The tRNA of the initiating amino-acid-base pairs with a specific nucleotide triplet or codon on the mRNA that signals the beginning of the polypeptide chain. This process requires GTP (ATP equivalent), plus three proteins called initiation factors. 

The sequence of bases (A, G, T, and C) in a strand of DNA specifies the order in which amino acids are assembled to form proteins. The genetic code is the collection of base sequences that correspond to each amino acid, codon. Since there are only four bases in DNA and twenty amino acids in protein, each codon must contain at least three bases.5 Two bases cannot serve as codons because there are only 42 possible pairs of four bases, but three bases can serve because there are 43 = 64 possible triplets. Since the number of possible triplets are more than enough, several codons designate the same ammo acid. In other words, the genetic code is highly redundant as shown in Table 7.1. For example, UCU, UCC, UCA, UCG, AGU, and AGC are all codes for serine. 

During translation the mRNA is read in a 5 to 3 direction and protein is made in an N-terminal to C-terminal direction. Translation relies upon aminoacyl-tRNAs that carry specific amino acids and recognize the corresponding codons in mRNA by anticodon-codon base-pairing. Translation takes place in three phases initiation, elongation and termination. 

The replacement of thymine by uracil has no significant effect on the hydrogen bonding, as RNA does not use base pairing to form complementary dimers it is of less importance than it would be for DNA, but the removal of the methyl group may have an influence on the tertiary structures that RNA can adopt. From this it is clear that DNA is a better method of storing information whereas RNA is more suited to turn that information into a protein sequence. This is done by the ribosome, composed of ribosomal RNA (rRNA), which translates the codons of the mRNA sequence into a protein by matching three base sequences to those of tRNA that have the appropriate amino acids attached. 

Gene mutations include base pair substitutions and frameshift mutations, where base pair substitutions arise from the substitution of one or several base pairs in the DNA, and frameshift mutations arise from an insertion or deletion involving a number of base pairs that is not a multiple of three and consequently disrupts the triplet reading frame, usually leading to the creation of a premature termination (stop) codon and resulting in a truncated protein product. 

The fidelity of protein synthesis requires the accurate recognition of three-base codons on messenger RNA. Recall that the genetic code relates each amino acid to a three-letter codon (Section 5.5.1). An amino acid cannot itself recognize a codon. Consequently, an amino acid is attached to a specific tRNA molecule that can recognize the codon by Watson-Crick base pairing. Transfer RNA serves as the adapter molecule that binds to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain. 

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