This article covers
genetic code
Our genes are encoded books that contain the mysteries of life. In order to understand these secret messages, we would need to know the code and apply the same rules in reverse to decipher it. In this article, we take a closer look at the genetic code that makes it possible to “uncode” DNA and RNA sequences into the amino acids of proteins.
How our cells make proteins: transcription and translation
Our genes are written as base pairs of nucleotides (A, T, G, C) in DNA. In order for a gene to be able to fulfill its task, the genetic information must be read out in order to construct a protein. This process is calledgenetic expression.
There are two steps to making proteins from genes:
First, within the cell nucleus, a process that creates copies of a specific gene in the form ofRNA massager(mRNA), calledtranscription.
Second, these mRNAs are exported from the nucleus to the cytoplasmRibosomesto make polypeptides/proteins. This step is calledtranslation.
[On this picture] The central dogma of biology.
Genes contain the information to build proteins that maintain cell viability. This construction process is carried out in 2 phases: transcription and translation.
Copying DNA to RNA is easy: follow the rule of complementary base pairing. There are four choices of nitrogenous bases in DNA: adenine (A), thymine (T), cytosine (C), andGuanina (G). Each base can only be joined together, A to T and C to G. This is called the complementary base pairing rule of DNA.
To transcribe DNA into mRNA, the rule is the same. The only difference is thatUracillo (U)replaces thymine (T). So, G ↔ C, A → U and T → A. In our cell, transcription is done by an enzyme calledRNA-Polymerasein the cell nucleus, which can synthesize mRNA from a DNA template.
DNA to mRNA: using complementary base pairing rules
Knowing this rule, you can figure out the complementary strand of a single strand of DNA based on the base pair sequence alone. Suppose you know the following sequence of a DNA strand:
DNA (coding strand): 5'-TTG ACG ACA AGC TGT TTC-3'
Using the complementary base pairing rules, you can conclude that the complementary strand:
DNA (Matrizenstrang): 3'-AAC TGC TGT TCG ACA AAG-5'
The RNA strands are also complementary, except that RNA uses U instead of T. Therefore, you can also deduce the mRNA strand that would be made from the first strand of DNA. I would like:
RNAm: 5'-UUG ACG ACA AGC UGU UUC-3'
RNA to protein: genetic codon usage
While DNA (genes) and RNA (messengers) use similar codes made up of 4 units, proteins are constructed very differently. Proteins are made up of 20 so-called unitsamino acids. The translation of mRNA into protein becomes much more complicated. To control this translation, cells follow the genetic code. According to the genetic code, genetic information is organized into triplets of nucleotides, with each triplet being translated into an amino acid.
For example, the above mRNA is translated
Protein: Leu – Thr – Thr – Ser – Cys – Phe
[In this image] The process of gene expression. From a gene to a protein there are two stages, transcription and translation. DNA must be transcribed into mRNA by complementary base pairing (i.e. A pairs with U; T pairs with A; C pairs with G; G pairs with C). The mRNAs are then exported to the cytoplasm through nuclear pores and translated into proteins by ribosomes.
Note: A short chain of amino acids is often referred to as a "polypeptide". When the number of amino acids is added up (usually > 30 units) and the polypeptide chain folds into a 3D structure, we call it a "protein".
There are three characteristics of codons:
- Each codon specifies an amino acid. The full set of relationships between codons and amino acids is summarized in a condom map or table.
- like"BeginThe codon (AUG) marks the beginning of a protein. AUG encodes the amino acid called methionine.
- Three "arrest jailCodons mark the end of a protein and complete translation.
Who can read these codes? The ribosome as a decoding machine
Codons in an mRNA are read by aRibosomesduring translation. A ribosome is a particle-like cell organelle composed of ribosomal RNA (rRNA) and ribosomal proteins. A ribosome consists of two main components: the small and the large ribosomal subunit. Three tRNA binding sites (A, P, and E sites) between the two subunits. Read more aboutRibosomes.
[In this image] Ribosome.
Ribosomes act as coding machines to translate the mRNA code sequence into a protein. Scientists like to refer to ribosomes as molecular micromachines to marvel at how exquisitely engineered ribosomes are!
Transfer-RNA (tRNA)
IsTransfer-RNA (tRNA)it's a kind of RNA molecule. Its function is to transport the amino acid corresponding to the mRNA codon to the ribosome.
The tRNA contains a three-letter code on one side and a specific amino acid on the other side. The tRNA code (called the anticodon) must match the three-letter code (the codon) of the mRNA that is already on the ribosome. The specific amino acid that the tRNA carries is determined by the three-letter anticodon that it carries. For example, if the three-letter code on the mRNA is AUG, the tRNA bearing methionine (Met) will be selected and recruited to the ribosome. This is an essential part of the translation process and it's amazing how many "translation errors" occur.
[In this figure]A UAG anticodon on the tRNA matches the AUG on the (free) mRNA and carries the correct amino acid (methionine) to the ribosomes.
Protein translation begins with a start codon (always AUG → methionine) and continues until a stop codon is reached (any of three: UAA, UAG, or UGA). mRNA codons are read from the 5' end to the 3' end, and their order indicates the order of amino acids in a protein from the N-terminus to the C-terminus.
[In this figure]Directionality: Reading DNA and RNA from the 5' end to the 3' end. Instead, proteins or polypeptides are read from the N-terminus (amino group) to the C-terminus (carboxyl group). The start and end of a translation are marked by the start and stop codons, respectively.
Photo author:Akademie Khan
The amino acid codon diagram
The complete set of relationships between codons and amino acids (or termination signals) is givengenetic code. The genetic code is usually summarized in a codon diagram (or codon table), in which codons are translated into amino acids.
Click here to download the Amino Acid Codon Table PDF
[On this picture]The condom set can also be presented as a codon wheel.
Photo author:wiki
How to read the codon table?
The codon table may seem intimidating at first. Actually, it's not difficult at all once you understand his rule.
Take the ACU codon as an example. If you want to know which amino acid ACU encodes, first look at the left side of the table. Locate the "A" on the left axis, which refers to the first letter of the codon trio. All those codons beginning with "A" are on this line.
Then we look at the top of the table. This upper axis indicates the second letter of the codon trio. Once we find "C" along the top axis, it tells us which column our codon will be in. Find the square of the intersection of row "A" and column "C" in the table. You will see this box containing four codons and you will easily find what you are looking for.
In our example, ACU encodes Thr (or threonine). You may also notice that ACU, ACC, ACA, and ACG all code for the same amino acid. Note that many amino acids in the table are represented by more than one codon. For example, there are six different ways to "write" leucine in the language of mRNA (see if you can find all six).
[On this picture] How to read the amino acid codon table?
Follow steps 1 to 3 to find the codon triplet in the table.
In this table you can also see that UAA, UAG and UGA do not encode amino acids, which means they are stop codons.
[On this picture]For a codon wheel, the rule is the same: start in the center to find the first letter of the triplet, then go 2 to the peripheryDakota do Nortee 3thirdletters.
Ribosomes definition, structure if ...
Definition, structure, size, location and function of ribosomes
You and your family or classroom can play "Codon Bingo" to learn about the genetic code. Here is onedownloadable version.
Reference table: a summary of all amino acid codons
| amino acids | A code |
| Phenylalanin (Phe) | UUU, UUC |
| Leucine (Leu) | UUA, UUG, CUU, CUC, CUA, CUG |
| Methionin (Met)/Startcodon | RETURN |
| Selected (Selected) | GUU, GUC, GUA, GUG |
| Cool (Wesen) | UCU, UCC, UCA, UCG, AGU, AGC |
| Proline (Pro) | UCC, CCC, CCA, CCG |
| Treonina (Thr) | UCA, ACC, ACA, ACG |
| Orange (Unter) | UGC, CCG, CCG, CCG |
| Tyrosin (Tyr) | UAC, UAC |
| Histidine (to be) | CAU, CAC |
| Glutamine (Gln) | CAA, CAG |
| Asparagus (Asn) | UAA, AAC |
| Lys | AAA, AAG |
| Aspartic Acid (Asp) | GAU, GAK |
| Glutamic Acid (Glu) | GAA, GAG |
| Cystein (Cys) | UGU, UGC |
| Triptofano (Trp) | UGG |
| Arginine (Arg) | WEEK, CGC, CGA, CGG, AGA, AGG |
| Glicina (Gly) | GGU, GGC, GGA, GGG |
| Isoleucin (Ile) | My god, my god, my god |
| Stop codon | UAA, UAG, UGA |
Molecular structures of amino acids.
photo source:wiki
standard genetic code
The genetic code we mention here is universal; With only a few exceptions, virtually all species (from bacteria to humans) use the same set of standard codes. Some ciliates, such asParamecium bursaria, uses an unusual genetic code.
Another exception is mitochondrial DNA. Mitochondria have their own copies of DNA and an independent system of ribosomes and tRNA. If you are unfamiliar with mitochondria,Click here for more information on mitochondria..
The mitochondrial code differs slightly from the standard genetic code. In addition, different species have their own versions of mitochondrial codes. For example, our mitochondrial (vertebrate) code is different than that used by yeast. AGA and AGG encode arginine (Arg) in the standard genetic code. However, AGA and AGG act as stop codons in the vertebrate mitochondrial code. In addition, in the mitochondria, UGA and AUA change the stop and isoleucine (Ile) codons to methionine (Met) and tryptophan (Trp), respectively.
The same situation also occurs in the chloroplast and plastid codes of the plant.
Bias in codon usage
Although most organisms use the standard code, they may have their own biases as to which codons to use. For example, baker's yeast prefers to use UGU for cysteine. On the other hand, in human cells, we prefer UGC.
Bias in codon usage can be a result of natural selection (tRNA abundance). To enable labs to produce specific proteins in large numbers, researchers can use "codon optimization" to re-synthesize genes so that their codons are more appropriate for the desired expression host (i.e., human proteins inE coli.Bacteria).
What is the reading frame?
How is the DNA sequence read in triplets, which letter (respFrameshift) becomes a critical problem.
Let's look at an example. The mRNA can then be translated into three completely different orders of amino acids, depending on the frame in which it's read. How do our cells know which of these proteins to make?
[On this picture]Three possible reading frames can lead to completely different results.
Photo author:Akademie Khan
Our cells solve this problem with a very clever strategy: the "start codon". Since translation only starts at the start codon (AUG) and proceeds in consecutive groups of three, the position of the start codon ensures that the mRNA is read in the correct frame (in frame 3 in the example above).
What happens when the DNA sequences are wrong? mutation
mutations(Changes in DNA sequences) can derail genetic information and cause cells to make the wrong proteins. Mutations are the main cause of cancer and many genetic diseases.
Even a single base pair change (called a point mutation) can have significant consequences. Point mutations can have one of three effects.
quiet Mutation
First, the base substitution can be aquiet Mutationwhere the changed codon corresponds to the same amino acid. For example, changing from UCU to UCC has no effect since both codons encode serine (Ser) equally.
senseless mutation
Second, the base substitution can be asenseless mutationwhere the changed codon corresponds to a different amino acid. For example, when you switch from UCU to UGU, serine (Ser) is converted to cysteine (Cys). If this mutation occurs in the critical region (that is, the enzyme site) of the protein, a point mutation can disrupt the protein's overall function.
senseless mutation
Third, the base substitution can be asenseless mutationwhere the changed codon becomes a stop sign. This is the worst cause as translation ends too early resulting in a truncated protein.
[On this picture]The examples show the sequence of nonsense mutation and nonsense mutation.
Photo author:NIH
Mutations can also occur when nucleotides are added to or removed from the original DNA sequence. The insertion or deletion of "one or two" nucleotides can change the reading frame (Frameshift-Mutation). A frameshift can completely mess up the amino acid order "downstream" from the mutation site.
[On this picture]The example shows the consequence of the frameshift mutation.
Photo author:open taxes
How was the genetic code discovered?
Understanding the genetic code is the basis of modern biotechnology. Without the ability to read information from DNA, many exciting technologies and therapies will not exist, including personalized medicine, gene therapy, CRISPR gene editing, and recombinant protein drugs.
To crack the genetic code, researchers had to figure out how the nucleotide sequences in a DNA or RNA molecule might encode the amino acid sequence. In the mid-1950s, physicist George Gamow predicted that the genetic code will likely be composed of triplets of nucleotides because the possible combination of doubles is insufficient (4 × 4 = 16) and quadruples is too many (4x4x4x4 = 256). ) to cover 20 types of amino acids.
Actual experiments to identify the genetic code began in 1961 by American biochemist Marshall Nirenberg. Nirenberg was able to link the relationships between nucleotide triplets and specific amino acids through two experimental innovations:
- You can synthesize artificial mRNA molecules with specific and known sequences.
- He had a system for translating mRNA into polypeptides outside of a cell (a "cell-free" system). Nirenberg did this in a test tube with ruptured cytoplasmE coliBacterium containing all the necessary ingredients for translation.
Nirenberg started with an mRNA molecule consisting only of the uracil nucleotide (called poly-U). When he added poly-U mRNA to the cell-free system, he found that the polypeptides produced consisted solely of the amino acid phenylalanine (Phe). Nirenberg concluded that UUU might encode phenylalanine. Using the same approach, he discovered the triplet CCC codes for Proline (Pro).
Photo author:Akademie Khan
Following this concept, biochemist Har Gobind Khorana extended Nirenberg's experiment by synthesizing artificial mRNAs with more complex sequences. By 1965, Nirenberg, Khorana, and their colleagues had cracked the entire genetic code.
For their contributions, Nirenberg and Khorana (along with Robert Holley, another genetic code researcher) received the 1968 Nobel Prize in Physiology or Medicine.
[On this picture]The 1968 Nobel Prize in Physiology or Medicine was awarded jointly to Robert W. Holley, Har Gobind Khorana and Marshall W. Nirenberg "for their interpretation of the genetic code and its role in protein synthesis".
Photo author:or Nobel Prize
In my research where I need to clone a specific DNA for protein expression, I usually useEMBOSS Transeq von EMBL-EBI.
Step 1 - Paste part of DNA sequence, you can use your example sequence.
Step 2: Select the reading frame you want
Step 3: Choose the codon. I usually use the default code.
Step 4: Press Submit
Step 5: Wait for the protein sequence result!
