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The observation of a gene with a pattern of codon usage that differs substantially from that of the rest of the genome indicates that this gene may have entered the genome by horizontal transfer from a different species. The preferred codon usage is a useful consideration in "reverse genetics". If you know even a partial amino acid sequence for a protein and want to isolate the gene for it, the family of mRNA sequences that can encode this amino acid sequence can be determined easily.

Because of the degeneracy in the code, this family of sequences can be very large. Since one will likely use these sequences as hybridization probes or as PCR primers, the larger the family of possible sequences is, the more likely that one can get hybridization to a target sequence that differs from the desired one. Thus one wants to limit the number of possible sequences, and by referring to a table of codon preferences assuming they are known for the organism of interest , then one can use the preferred codons rather than all possible codons.

This limits the number of sequences that one needs to make as hybridization probes or primers. Wobble in the anticodon.

In contrast, the first two positions of the codon form regular Watson-Crick base pairs with the last two positions of the anticodon. This flexibility at the "wobble" position allows some tRNAs to pair with two or three codons, thereby reducing the number of tRNAs required for translation.

Wobble rules. Types of mutations. Base substitutions. Just as a reminder, there are two types of base substitutions. The same class of nucleotide remains.

Examples are A substituting for G or C substituting for T. Over evolutionary time, the rate of accumulation of transitions exceeds the rate of accumulation of transversions. Effect of mutations on the mRNA. Depending on the particular replacement, it may or may not have a detectable phenotypic consequence. Some replacements, e. Other replacements, such as valine for a glutamate at a site that causes hemoglobin to polymerize in the deoxygenated state, cause significant pathology sickle cell anemia in this example.

They almost always have serious phenotypic consequences. Not all base subsitutions alter the encoded amino acids. However, there are several exceptions to this rule. This is one of the strongest supporting arguments in favor of model of neutral evolution, or evolutionary drift, as a principle cause of the substitutions seen in natural populations.

The template strand of a sample of double-helical DNA contains the sequence:. Will the resulting amino acid sequence be the same as in b? Explain the biological significance of your answer. In sickle-cell hemoglobin there is a Val residue at position 6 of the b -globin chain, instead of the Glu residue found in this position in normal hemoglobin A.

Can you predict what change took place in the DNA codon for glutamate to account for its replacement by valine?

What is the sequence of the original codon for Lys? Deduce the sequence of the wild-type codon in each instance. What is the codon for Gln? What is the codon for Leu? Design a DNA probe that would allow you to identify the gene for a protein with the following amino-terminal amino acid sequence. The probe should be 18 to 20 nucleotides long, a size that provides adequate specificity if there is sufficient homology between the probe and the gene. While the rest of the crew tries to figure out if the fungus is friend or foe and gets all the camera time , you are assigned to determine its genetic code.

With the technologies of two centuries from now, you immediately discover that its proteins are composed of only eight amino acids, which we will call simply amino acids 1, 2, 3, 4, 5, 6, 7, and 8. Its genetic material is a nucleic acid containing only three nucleotides, called K, N and D, which are not found in earthly nucleic acids.

The results of frameshift mutations confirm your suspicion that the smallest possible coding unit is in fact used in this fungus. Insertions of a single nucleotide or three nucleotides into a gene cause a complete loss of function, but insertions or deletions of two nucleotides have little effect on the encoded protein. You make synthetic polymers of the nucleotides K, N and D and use them to program protein synthesis. The amino acids incorporated into protein directed by each of the polynucleotide templates is shown below.

Assume that the templates are read from left to right. Each codon corresponds to a single amino acid or stop signal , and the full set of codons is called the genetic code. The genetic code includes 64 possible permutations, or combinations, of three-letter nucleotide sequences that can be made from the four nucleotides. Of the 64 codons, 61 represent amino acids, and three are stop signals.

The genetic code is described as degenerate, or redundant, because a single amino acid may be coded for by more than one codon. The answer to this question lies in a series of complex mechanisms, most of which are associated with the cellular structure known as the ribosome.

In order to understand these mechanisms, however, it's first necessary to take a closer look at the concept known as the genetic code. At its heart, the genetic code is the set of "rules" that a cell uses to interpret the nucleotide sequence within a molecule of mRNA. This sequence is broken into a series of three-nucleotide units known as codons Figure 1. The three-letter nature of codons means that the four nucleotides found in mRNA — A, U, G, and C — can produce a total of 64 different combinations.

Of these 64 codons, 61 represent amino acids, and the remaining three represent stop signals, which trigger the end of protein synthesis. Because there are only 20 different amino acids but 64 possible codons, most amino acids are indicated by more than one codon. Note, however, that each codon represents only one amino acid or stop codon. This phenomenon is known as redundancy or degeneracy , and it is important to the genetic code because it minimizes the harmful effects that incorrectly placed nucleotides can have on protein synthesis.

Yet another factor that helps mitigate these potentially damaging effects is the fact that there is no overlap in the genetic code. This means that the three nucleotides within a particular codon are a part of that codon only — thus, they are not included in either of the adjacent codons. Figure 4: During initiation, the ribosome grey globe docks onto the mRNA at a position near the start codon red. The sugar-phosphate backbone of the mRNA strand is depicted as a segmented grey cylinder.

Attached to each segment is a nitrogenous base. The bases are represented by blue, orange, yellow, or green vertical rectangles that protrude from the backbone in an upward direction; they look like teeth on a comb. The ribosome is depicted as a translucent complex bound to nine nucleotides at the leftmost terminus of the mRNA strand. The complex is composed of a large cylindrical subunit on top of a smaller oviform subunit approximately one-fourth the size of the large subunit.

Inside the large subunit, the first three nucleotides in the mRNA sequence are bright red. Anticodons on five free-floating tRNA molecules are visible in the background. A portion of a large, circular, orange nucleus is visible in the left-hand side of the frame; the process illustrated here is shown occurring outside the nucleus.

At the start of the initiation phase of translation, the ribosome attaches to the mRNA strand and finds the beginning of the genetic message, called the start codon Figure 4. This codon is almost always AUG, which corresponds to the amino acid methionine. Next, the specific tRNA molecule that carries methionine recognizes this codon and binds to it Figure 5. At this point, the initiation phase of translation is complete.

For many proteins, translation is only the first step in their life cycle. Moderate to extensive post-translational modification is sometimes required before a protein is complete. For example, some polypeptide chains require the addition of other molecules before they are considered "finished" proteins. Still other polypeptides must have specific sections removed through a process called proteolysis.

Often, this involves the excision of the first amino acid in the chain usually methionine, as this is the particular amino acid indicated by the start codon. Once a protein is complete, it has a job to perform. Some proteins are enzymes that catalyze biochemical reactions. Other proteins play roles in DNA replication and transcription.

Yet other proteins provide structural support for the cell, create channels through the cell membrane, or carry out one of many other important cellular support functions. This page appears in the following eBook. Aa Aa Aa. The ribosome assembles the polypeptide chain. In the codon chart, the innermost circle represents the first nucleotide. The second inner circle represents the second nucleotide while the outermost circle represents the third nucleotide in a codon.

Now, to decipher the amino acid from the codon, one has to move from the innermost circle to the outermost circle, thus decoding the amino acid from the codon. The reading or the amino acid elucidation pattern for the DNA codon table remains the same. Even though uracil is replaced by thiamine in the DNA base sequence, the coded amino acid remains the same. This is an important point which one should remember to avoid any confusion between a DNA codon table and an RNA codon table. In the past, genetic codes were considered to be universal; however, studies have found a slight alteration in genetic code for mitochondria and certain ciliates.

In human mitochondria, the UGA codon is not decoded as a stop signal. Contrarily, UGA in human mitochondria codes for tryptophan amino acid. Similarly, the AUA codon in mitochondria codes for methionine instead of isoleucine. Thus, ample examples exist that prove that mitochondrial genetic code differs from the rest of the cell.

The difference in genetic code for mitochondria are represented in the table below. Similar to mitochondria, in certain ciliates, both UAA and UAG codons encode for amino acids and do not code for the stop signals. In such ciliates, the termination signal or the stop codon is encoded by the UGA codon. Thus, genetic codes are now not considered to be universal.

Earlier, it was considered that genetic codes are universal; however, these findings have negated this property of the genetic code. It is very clear from the above coon examples as well as from the codon charts that multiple codons encode one amino acid. The simple reason behind this is to enable resistance to mutations that might occur during various life processes as well as exposure to varied mutagens in our day-to-day lives.

Mutations occur frequently in the life of a living being; however, all mutations are not apparent or harmful, have you thought about it? Well, mutations alter the codon sequences and this alteration may change the resultant amino acid formation. However, change or mutation of the third nucleotide does not affect or alter the amino acid in the majority of the cases.

For example, CGU codes for arginine. The repetitiveness of the codons results in the translation of the same sequence of amino acids. This provides robustness to the genes to function normally even when they might have undergone some sort of mutation. The codon redundancy is also often known as degeneracy. Despite that, there are still certain mutations that prove lethal. A mutation in which the amino acid sequence came to an early halt can be lethal.

This happens when a sense codon mutated into becoming a stop codon. This codon will eventually terminate the translation process thus resulting in the non-expression of the required or essential amino acid to a protein. This tutorial looks at the mutation at the gene level and the harm it may bring. Learn about single nucleotide polymorphisms, temperature-sensitive mutations, indels, trinucleotide repeat expansions, and gene duplication Read More.

Genes are expressed through the process of protein synthesis. This elaborate tutorial provides an in-depth review of the different steps of the biological production of protein starting from the gene up to the process of secretion.

Also included are topics on DNA replication during interphase of the cell cycle, DNA mutation and repair mechanisms, gene pool, modification, and diseases The endoplasmic reticulum and Golgi apparatus are the organelles involved in the translation step of protein synthesis and the ensuing post-translational steps. Read this tutorial for more info



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