What is Codon?
Molecular biologists define a codon as three nucleotides of DNA or RNA. Such is said to code for some particular amino acid, but it may also work as a signal in the course of regulation during the synthesis of protein. In brief, life proceeds generation after generation due to complex steps that involve the replication, transcription, and translation of the DNA and RNA code.
DNA is actually the fundamental molecule of life; it contains four nucleotide bases: adenine (A), guanine (G), cytosine (C), and thymine (T). This genetic code transcribes itself into RNA, which then becomes the blueprint for protein synthesis. In contrast to DNA, RNA contains adenine, guanine, cytosine, and uracil (U). Such sequences of nucleotides give instructions that would be needed to assemble amino acids in an exact order so that proteins could be formed.
Reading the genetic code occurs in triplets of nucleotides called codons. Every different codon designates either an amino acid or is a start or end signal for the protein synthesis process. Historically, Marshall Nirenberg and J. Heinrich Matthaei were the first scientists to discover a codon. The incredible poly-U experiment revealed that three uracil units in a sequence in RNA were coded for the amino acid phenylalanine. This important discovery opened up the scope for further investigation by Nirenberg and his colleagues, which later found all 64 codons and their respective amino acids. They, along with their colleagues, shared the Nobel Prize in Physiology or Medicine in 1968, awarded for the interpretation of the genetic code, for their distinguished contributions concerning this problem.
Essentially, it is the detailed list or plan that living cells use in translating information encoded within DNA or RNA sequences into proteins. Translation refers to the intricate process of subunit assembly that ribosomes perform from proteinogenic amino acids based on messenger RNA. This process is assisted by transfer RNA (tRNA) molecules, which are both carriers of amino acids and translators of the mRNA in triplets of nucleotides. What is remarkable is that this genetic code shows a surprisingly high degree of similarity between different organisms and can be elegantly summarized in a table of 64 entries.
To further understand the topic, codons have a very essential role in the process of how the amino acid will be added through the complex procedure of protein biosynthesis. Ordinarily, a sequence of three nucleotides in the nucleic acid corresponds to a particular amino acid. However, most genes employ the standard genetic code, while there are certain exceptions and alternative codes, such as those used by mitochondria.
What is a Codon Chart?
Another term for a codon chart is a codon table. The chart is considered an important scientific tool that can explain the association between groups of three nucleotides called codons and their corresponding amino acids. By checking this chart, it becomes possible to decipher information in DNA or RNA. The translation process would be much more straightforward, simply converting nucleotide sequences into the chain of amino acids that comprise the proteins.
There are 64 different codons in the chart. Out of these, there are 61 used to encode the 20 standard amino acids and three other stop codons, which eventually lead to a stop signal or the end of protein synthesis. One feature very characteristic of the genetic code-that it is both redundant and degenerate-is indicated by this chart of the codon. This implies that each codon represents one particular amino acid, but one amino acid can be represented by more than one codon. For instance, there is an amino acid called proline that has four different codons: CCU, CCC, CCA, and CCG.
Using the codon chart, one looks for the sequence of nucleotides within a given codon and crosses it with the chart to determine what amino acid the sequence corresponds to. The sequence of codons UAC shown in the chart corresponds to the amino acid tyrosine.
In particular, the codon chart is presented in the form of a table, which consists of 20 standard amino acids and their abbreviations in three-letter and one-letter forms. It looks like this:
- Alanine (Ala, A)
- Arginine (Arg, R)
- Asparagine (Asn, N)
- Aspartic acid (Asp, D)
- Cysteine (Cys, C)
- Glutamic acid (Glu, E)
- Glutamine (Gln, Q)
- Glycine (Gly, G)
- Histidine (His, H)
- Isoleucine (Ile, I)
- Leucine (Leu, L)
- Lysine (Lys, K)
- Methionine (Met, M)
- Phenylalanine (Phe, F)
- Proline (Pro, P)
- Serine (Ser, S)
- Threonine (Thr, T)
- Tryptophan (Trp, W)
- Tyrosine (Tyr, Y)
- Valine (Val, V)
| Amino Acid | Abbreviation | One-Letter Abbreviation |
| Alanine | Ala | A |
| Arginine | Arg | R |
| Asparagine | Asn | N |
| Aspartic acid | Asp | D |
| Cysteine | Cys | C |
| Glutamic acid | Glu | E |
| Glutamine | Gln | Q |
| Glycine | Gly | G |
| Histidine | His | H |
| Isoleucine | Ile | I |
| Leucine | Leu | L |
| Lysine | Lys | K |
| Methionine | Met | M |
| Phenylalanine | Phe | F |
| Proline | Pro | P |
| Serine | Ser | S |
| Threonine | Thr | T |
| Tryptophan | Trp | W |
| Tyrosine | Tyr | Y |
| Valine | Val | V |
Codon Chart
| First Base | Second Base | U | C | A | G |
|---|---|---|---|---|---|
| U | U | UUU Phe | UCU Ser | UAU Tyr | UGU Cys |
| UUC | UCC | UAC | UGC | ||
| C | UUA Leu | UCA Ser | UAA STOP | UGA STOP | |
| UUG | UCG | UAG STOP | UGG Trp | ||
| C | U | CUU Leu | CCU Pro | CAU His | CGU Arg |
| CUC | CCC | CAC | CGC | ||
| C | CUA Leu | CCA Pro | CAA Gln | CGA Arg | |
| CUG | CCG | CAG | CGG | ||
| A | U | AUU Ile | ACU Thr | AAU Asn | AGU Ser |
| AUC | ACC | AAC | AGC | ||
| C | AUA Ile | ACA Thr | AAA Lys | AGA Arg | |
| AUG Met | ACG | AAG | AGG | ||
| G | U | GUU Val | GCU Ala | GAU Asp | GGU Gly |
| GUC | GCC | GAC | GGC | ||
| C | GUA Val | GCA Ala | GAA Glu | GGA Gly | |
| GUG | GCG | GAG | GGG |
How do you read a codon table?
Reading a codon table is important to determine which amino acid is associated with a given three-nucleotide sequence-that is, a codon-from mRNA. Here is a simplified instruction on how to read a codon table:
- Know the Codon Table Format: A regular codon table is a 4×4 matrix, aligned around the four nucleotide bases: U (Uracil), C (Cytosine), A (Adenine), and G (Guanine). The mRNA sequence is read 5′ to 3′.
- First Base: The first letter of the codon (read from left to right) tells you which row to look at in the codon table. This is usually the leftmost column of the chart.
- Second Base: The second letter of the codon tells you the column. This is usually the top row of the chart.
- Third Base: You’ve looked up the row and column in the Codon table using the first two letters of your codon and you have found a list of codons for that cell. The third letter in your codon will indicate which amino acid (or Start/Stop signal) is in that cell.
- Find the Amino Acid: Once you exhaust all three letters of your codon when scanning the chart, you will see an abbreviation for one particular amino acid (such as Phe for Phenylalanine, Met for Methionine, etc) or a “Start” or “Stop” sign.
- Special Codons:
- Start Codon: AUG is the start codon and means Methionine or Met. It indicates translation starts.
- Stop Codons: There are three stop codons (UAA, UAG, UGA) that do not make an amino acid. Instead, they tell the process to stop.
- Practice: Try reading some sample codons using the table. For example, if you have the codon GCU, you start with G (row), go to C (column), and then find U in that cell. The result will be the amino acid Alanine (Ala).
Remember that the codon table is taken from mRNA sequences. If you are using DNA, replace all the Thymine (T) bases with Uracil (U) in order to apply the codon table.
Here is an example – How do you read a codon table?
To read the codon chart, find the amino acid that forms a three-nucleotide sequence, or codon, in mRNA. The chart translates mRNA to its equivalent amino acid. Here’s how it works:
- Axes Interpretation
- First Base – The left column represents the first base of the codon.
- Second Base – The top row represents the second base of the codon.
- Last Base in Codon- Each chart cell is divided by the codon’s third base.
- Find the Cell:
- First Base: Check the first nucleotide and go to the row on the left.
- Second Base: Check the second nucleotide and move to the top column.
- Determine the Amino Acid – The third base of your codon determines the amino acid. Cells contain codons, which are joined to their specific amino acids. Align your codon’s third base to find it.
- Special Codons:
- Start Codon: AUG is the start codon and corresponds to Methionine (Met), marking the beginning of translation in protein synthesis.
- Stop Codons: UAA, UAG, and UGA are stop codons that denote the end of translation without corresponding to an amino acid.
- Example – For codon UGC, begin with U (row), move to G (column), and locate C in that cell. The amino acid is Cys (Cysteine).
Remember, this codon chart is specific to mRNA sequences. If you’re working with DNA, you’d replace all the Thymine (T) bases with Uracil (U) to use this codon chart.
What are Start Codons?
- In molecular biology, the term “Start Codon” refers to any codons in an mRNA sequence that represent the beginning of the translation of a protein. Major categories of start codons are AUG, meaning the beginning of the translation process.
- A U G codes for methionine in eukaryotes but encodes formyl methionine (fMet) in prokaryotes. Such a divergence points to complex evolution of translation.
- Translation initiation, therefore, includes the start codon and initiation factors along with tRNA molecules to carry out their functions for the recognition of the AUG start codon that initiates the translation.
- Most of the time, AUG is the major start codon for translation, but not all the time; there are some exceptions, though. Alternative codons, which can start translation in eukaryotes, indicate the importance of AUG in translation.
- Prokaryotic organisms such as E. coli have more start codons. Besides the standard AUG, GUG and UUG also denote the initiation of translation.
What are Stop Codons?
- Stop codons are essential in the genetic code in the field of molecular biology. Out of the 64 codons, three are not used to specify amino acids and are referred to as “stop codons.”
- Stop codons, also referred to as termination codons or nonsense codons, are used to signify the end of the synthesis of proteins. The stop codons do not code for any amino acids but instead mark the termination point of ribosomes so that the protein is completed accurately.
- The three stop codons are UAA, UAG, and UGA, which were found in 1965 by experiments on the T4 bacteriophage by Sydney Brenner. Of these, the very first is UAG and for historical reasons, it has been called the “amber” codon, and UGA and UAA respectively called the “opal” and “ochre” codons.
- Stop codons, therefore, act as checkpoints in the process, ensuring that proteins are synthesized correctly and on time for proper functioning of cells and expression of genes.
What is Codon Translation?
Codon translation plays a very important role in the synthesis of proteins, an essential biological process that constitutes the assembly of proteins required to enable cell function and structure. It clarifies the genetic code with utmost detail regarding the proper construction of proteins.
The first step in protein synthesis is transcription. Here, RNA polymerase transcribes the genetic information of DNA into RNA. The product is a single-stranded molecule called messenger RNA (mRNA), carrying the genetic code.
Translation occurs in the cytoplasm following transcription. The mRNA with ribosomes and tRNA reads the genetic code to make polypeptide chains of amino acids. Translation is the decoding of the codons of mRNA, each encoding a specific amino acid. The tRNA molecules add an amino acid to the growing polypeptide chain. A stop codon in the mRNA terminates translation.
The shape of tRNA accounts for precision in the translation of codons. The cloverleaf-shaped form of tRNA is due to four double helical stems with three single stranded loops. The anticodon loop is a three-nucleotide sequence known as the anticodon, located in the central loop. It pairs with the codon on mRNA to ensure accurate placement of amino acids in the synthesis of proteins.
The chain of amino acids is shaped into a functional protein that will be used for cellular activities after transcription and translation. This gives a clue about the link of genetic information to proteins through codon translation and the complex nature of cellular biology.
References
- https://www.genscript.com/tools/codon-table
- https://www.shsu.edu/academics/agricultural-sciences-and-engineering-technology/documents/mRNAcodonchart.pdf
- https://bio.libretexts.org/Bookshelves/Genetics/Genetics_Agriculture_and_Biotechnology_(Suza_and_Lee)/zz_Back_Matter/21_Appendix_1_Codon_Table
- https://study.com/academy/lesson/making-sense-of-the-genetic-code-codon-recognition.html
- https://microbenotes.com/codon-chart-table-amino-acids/
- https://www.hgmd.cf.ac.uk/docs/cd_amino.html
- https://www.slideshare.net/erindenn/howtoreadacodontable
- https://www.britannica.com/science/genetic-code
- https://www.genomenon.com/codon-chart/
