Blog of Andrés Aravena
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# Homework 2, Bioinformatics 2022

03 October 2022. Deadline: Thursday, 6 October, 9:00. by Andrés Aravena, Ph.D.

# TL;DR

Read the document “Genetic Codes” at
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=tgencodes

# Genetic code

In the welcome survey we asked “What is a genetic code? how many exist?”

The sequence of nucleotides in DNA and RNA that determines the amino acid sequence of proteins.

• The genetic code is a set of triple nucleotide sequences, with each sequence corresponding to a codon in the mRNA, thus mediating transcription. There are 64 codes exist. But, as far as I know, the genetic code is not a fixed set. It depends on how it is read, and some mutations are even associated with these reading errors (frameshift mutations).

• Genetic code is a part of our DNA that includes genetic information. 64 different types of genetic code can exist.

• Codes to make proteins. In humans there is 64(4x4x4)-3(stop codons)=61 genetic code. I think that theoretically there can be more in a different genetic system. Like different types of nucleotides in different numbers can code different type of proteins.

• Since the triple base reading is equivalent to one genetic code and the known base is four bases (for DNA), 64 kinds of genetic codes can exist from 4x4x4.

• Genetic identity is basically our identity which is stored in our DNA and RNA. It stores 3 letters called codons. There are 64 different type of codons.

• The genetic code is used by cells to translate information encoded within codons (mRNA sequences of nucleotide triplets). There are sixty four codons, sixty one represent amino acid and three are stop signals.

All these answers are basically wrong. The genetic code is the rule that determines which amino acid is encoded by each codon, and which are the stop codons.

In other words, the genetic code is a table with two columns. In the first column there are 64 nucleotide triplets, in the second column we have the amino acid (or stop codon) encoded by the triplet. You can read more in the following resources:

• Genetic Code at Biology Dictionary <https://biologydictionary.net/genetic-code/>
• Genetic Code at National Human Genome Research Institute USA
<https://www.genome.gov/genetics-glossary/Genetic-Code>
• Genetic Code at Wikipedia <https://en.wikipedia.org/wiki/Genetic_code>

The genetic code was deciphered about ten years after the DNA helix structure was described by Watson & Crick. The same Crick was one of the authors of an interesting experiment in 1961 to determine if the codons were composed of three or four nucleotidesTwo nucleotides can form 16 combinations, which are not enough to encode the 20 naturally-occurring amino acids.

. He showed that codons are made of exactly three nucleotides.

In theory, each codon could codify for any amino acid. In 1954 the famous physicist George Gamow proposed a genetic code based only in mathematical considerations. There were no frame-shifts in that model. Later experiments proved him wrong. More details in the paper The Era of RNA Awakening: Structural biology of RNA in the early years by Alexander Rich.

## How many genetic codes?

If there are 64 possible codons, and each one can code for 21 amino acids/stop codon, then one can choose the first amino acid in 21 ways, the second one in 21 again, and so on. Thus, we have $21×21×21×\cdots×21 = 21^{64} = 4188271851027274266670020743752976432915773724299403513508038881183728210190544679681$ possible genetic codesIn fact, this is too much. Most of these genetic codes do not encode for all amino acids. The exact formula is complicated, and beyond our course.

.

Surprisingly, the first experiments showed that there was only one genetic code used by all cellular organisms. It was called universal genetic code. Later it was found that, in some cases, there are variations on the genetic code. For instance, mitochondrial genetic code is different.

NCBI shows 25 different (but similar) Genetic Codes Please read this document before next class.

The question we want to answer is “How can we compare the different genetic codes?”

More details about the Origin and evolution of the genetic code can be found in the literature.