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 best answer to the first question, in my opinion, was this

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

But there were no answers to the second questions. These are some of your answers

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:

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.

Deadline: Thursday, 6 October, 9:00.

Originally published at https://anaraven.bitbucket.io/blog/2022/bioinfo/homework02.html