How To Read A Codon Chart Answer Key?
The genetic code links groups of nucleotides in an mRNA to the amino acids that make up a protein. Start codons mark the beginning of a translation, and stop codons indicate that the protein has finished synthesis. Follow that cell to the row corresponding to the codon’s second letter. Finally, follow that cell to the column corresponding to the codon’s third letter.
These relationships are summarized in a codon chart (or codon table). This article will help you learn how to read this answer key.
Start Codon
The start codon is the first amino acid in a polypeptide sequence and initiates mRNA translation into the protein. It is located at the +1 position of the 5′ untranslated region (UTR).
AUG is the standard start codon but is not the only one available in the genome. For example, a small fraction of genes may use another start codon called GUG, which codes for leucine. In rare cases, eukaryotes may even have AUA and AUM start codons that code for isoleucine.
During translation, the start codon interacts with nearby sequences or initiation factors to determine the best way to start a new mRNA strand. In addition, it also gives the small ribosomal subunit a reading frame or set of three nucleotides that identify the coding region and signal to other parts of the protein machinery to begin translating.
The mechanism of mRNA scanning for a suitable start codon is an important feature of many eukaryotic cells. A 40S ribosomal subunit loaded with initiation factors in these organisms recognizes the 5′ UTR region. It scans it in the direction of the coding sequence in order to find a suitable start codon for mRNA translation. The ribosome then reads the resulting nucleotides into a single mRNA strand that contains the amino acid coding sequence of the protein to be produced.
In this study, we used a database of 36 groups of closely related bacterial and archaeal genomes to reconstruct the evolution of start codons. We found that purifying selection affected AUG start codons, in the same way it does other codons. However, this selective pressure was significantly weaker than that on the same codon switches in coding regions, which led to conservative amino acid substitutions.
These substitutions are mainly between bulky hydrophobic amino acids and are mildly deleterious in the worst case. Our results, therefore, imply weak purifying selection on start codons, which may explain their non-optimal distribution.
To reconstruct the evolution of these codon switches, we compared their frequencies with those of the same codon switches in coding regions. Switching from AUG to GUG was significantly more frequent in start codons than in non-coding regions. Similarly, the switch from CUG to UUG was more frequent in start codons than in coding regions.
Interestingly, this difference was not significant between different prokaryotic phyla. Rather, the frequency of these switches was significantly higher in some phyla, such as Clostridia, than in others, such as Actinobacteria. Several factors, such as the lower GC content of these organisms, could explain this.
To assess whether these codon switches were selected against at the protein level, we analyzed their frequencies in a large set of ATGCs with over 12 genomes and over 1000 genes each. The dN/dS values (ratio of the estimated rates of non-synonymous and synonymous substitutions) were then used as a proxy for the strength of purifying selection on these codon switches. We found that these values were, on average, significantly stronger in coding regions than in start codons, which is expected given that all start codon switches involved bulky hydrophobic amino acids and resulted in conservative substitutions.
Stop Codon
A codon is the sequence of nucleotide bases that code for an amino acid in a protein. The human genetic code has three types of stop codons: TAG, TAA, and TGA (DNA) and UAA, UGA, and UGA (RNA).
DNA is a double-helix structure constructed of sugar and phosphate joined together by a set of bases that attach to specific partners. These are thymine (T), adenine (A), guanine (G), and cytosine (C). When these nucleotide bases come together in a gene’s DNA, they create a protein-coding region for an amino acid called a polypeptide. The polypeptide is then translated (copied) from RNA into protein.
Each molecule of RNA copies the nucleotide bases from DNA using a process called transcription. The protein-building machinery then reads the RNA molecules. Next, the machinery looks for a sequence of bases in the RNA called a codon.
The RNA codons tell the protein-building machinery which amino acids to bind to the ribosome and bring them into the growing polypeptide. The ribosome then translates these RNA codons into proteins.
In a normal cell, translation is highly accurate. This is because multiple quality control steps protect the ribosome. For example, the ribosome detects and prevents errors in aminoacyl-tRNA synthesis by basal translational readthrough. This is accomplished by a near-cognate tRNA synthetase that matches the anticodon of an mRNA codon to a complementary tRNA, which is then taken up and incorporated into the ribosome.
However, sometimes the ribosome misreads an mRNA containing a stop codon, causing it to continue synthesis. This is called nonsense suppression.
This happens because the mRNA has two different nucleotide bases in it, so the ribosome can’t recognize the start codon, or it doesn’t recognize it correctly. For this reason, mRNAs containing stop codons are usually pseudo uridylate by a guide RNA.
These pseudo uridylate mRNAs are made by guide RNAs that bind a special type of pyrimidine called PsAA, PsAG, or PsGA. These pyrimidines are similar to the five-carbon adenosine pyrimidine but have additional properties that make them harder to dissolve.
They also have a major groove imine that makes them less likely to be unstacked from the previous codon. This property could result from the pyrimidines’ chemistry, or it could be a physical difference between the pyrimidines and the nucleotide bases they bind.
Finally, it may be that mRNAs containing pseudo uridylate stop codons are resistant to a particular type of mutation called a point mutation. This type of mutation can occur anywhere along the DNA sequence, and it can change the amino acid sequence of a codon.
This type of mutation is not new; it can cause cell problems. For example, a point mutation in the codon can cause it to be transcribed incorrectly and/or its nucleic acids to change, resulting in a malfunctioning or even a dead cell.
Sense Codon
A codon chart (or codon table) is an important part of learning about genetic code. It shows the relationship between each amino acid’s tRNA, mRNA, and codons. It also tells you the number of times each amino acid is represented in the code. You can even play codon bingo, a fun way to learn the code.
61 sense codons map onto 20 canonical amino acids. This set of codons is essential for mapping protein sequences to ribosomes, and it governs how proteins are expressed in a cell. However, codons can be reassigned to non-canonical amino acids. For example, in model organisms such as Escherichia coli, sense codon reassignment has been accomplished by manipulating the host’s cellular aminoacyl-tRNA synthetase activity and regulating amino acid pools.
The efficiency of stop codon reassignment depends on the sequence of tRNAs, the mRNA’s release factors, and the mRNA’s structure. Sense codon reassignment can be improved by decreasing competition from endogenous tRNAs through genomic engineering. In other reports, we observed improvements in reassigning the arginine AGG codon via this strategy (Krishnakumar et al., 2013; Zeng et al., 2014; Mukai et al. al., 2015; Wang & Tsao, 2016).
In contrast, the efficiencies of sense codon reassignment by orthogonal tRNA/aaRS pairs were not significantly increased by decreasing competition from endogenous tRNAs. This was in contrast to the much greater reassignment efficiency of sense codons by natural, tyrosyl-incorporating orthogonal tRNA/aaRS combinations that were evaluated prior to our directed evolution workflow.
To reduce competition from endogenous tRNAs, we redesigned the arginine AGG tRNA/aaRS pair to compete favorably with ncAA-containing tRNAs. We then performed a screen for variants that reassigned AGG with better than 60% efficiency based on the ability of these variants to recognize ncAA-containing tRNAs in media containing ncAAs.
Compared with natural, tyrosyl-incorporating tRNA/aaRS pairs, the improved ncAA-incorporating tRNA/aaRS pair was significantly more efficient at reassigning AGG to tyrosine. This improvement was achieved by altering the interactions of the ncAA-incorporating tRNA/aaRS with both the ncAA-containing tRNA and the host’s ribosome.
Interestingly, the improved ncAA-incorporating version of this orthogonal pair was also more efficient than the native tRNA/aaRS at reassigning AGG with the amber stop codon. This suggests that the improvements achieved by modifying the interactions of the orthogonal tRNA/aaRS pair may be independent of and potentially combinable with the improvements selected through directed evolution.
Reading a codon chart answer key can be useful biology and genetics.
Here Are Some Steps To Follow:
Understand the basics: A codon is a sequence of three nucleotides in DNA or RNA that codes for a specific amino acid. A codon chart or table matches the three-letter codon sequence with the corresponding amino acid.
Find the chart: Look for a codon chart or table online, in a biology textbook, or provided by your instructor. The chart will typically be organized in rows and columns, with each row representing a codon and each column representing an amino acid.
Locate the codon: Find the codon you want to translate on the chart. The codon will comprise three letters, such as AUG or UGA.
Identify the amino acid: Follow the row containing the codon to the column corresponding to the codon’s first letter. Then, follow that cell to the row corresponding to the codon’s second letter. Finally, follow that cell to the column corresponding to the codon’s third letter The amino acid listed in that cell is the one that the codon codes for.
