Cells perform many different functions. They produce energy, communicate with other cells, and compose the physical bulk of the body. One major function of cells is constructing proteins. Proteins are biological macromolecules that perform a diverse array of function in the body. Cells construct proteins based on information encoded in DNA. The process of extracting information from DNA to make proteins is called gene expression.
Fundamentally, gene expression has two steps:
- Transcription – During transcription, information in DNA is “copied” into the form of messenger RNA (mRNA)
- Translation – In this stage, mRNA is “read” by cellular machinery and the encoded proteins are made
In this article, we will take an in-depth view of translation and look at the molecular mechanisms behind this process. It is recommended you read this article on transcription first.
How Does mRNA Store Information?
To understand translation we must first understand how information for proteins is stored in mRNA. Strictly speaking, mRNA does not encode for a protein. Rather, mRNA encodes—gives instructions for—a sequence of amino acids called a polypeptide chain. Proteins are made out of numerous polypeptide chains.
Information in mRNA is stored in the form of sequences of nucleotide bases (A, C, G, and U) that are read in threes. A triplet of bases is called a codon. Each codon refers to a specific amino acid. For example, the codon ACG specifies the amino acid threonine. The order of codons in mRNA specifies the order of the amino acids in the polypeptide chain. So, and mRNA strand that contains the sequence AUUCAGUGU encodes for the amino acids isoleucine (AUU), glutamine (CAG), and cysteine (UGU) in that order.
The standard RNA codon table. Credit: WikiCommons CC0 1.0
In human RNA, there are 61 codons that encode for about 20 amino acids. There is also the special codon AUG called a “start codon” that tells where the gene begins. Lastly, there are three special codons that do not code for amino acids (UAA, UAG, UGA) that are called “stop codons”. Stop codons tell translation mechanisms when the polypeptide chain is complete.
Overview Of Translation
Translation is a complex process that requires some specialized machinery. Two types of molecules are involved in the translation process: tRNA and ribosomes.
tRNA
tRNAs (“transfer” RNAs) are molecules that bridge the gap between codons in mRNA and the amino acids they specify. One end of tRNA contains a sequence of bases called an anticodon that can bind to a specific codon via complementary base pairing. The other end of tRNA contains the amino acid specified by the codon. There are tRNA molecules that read each codon and bing the specified amino acid. tRNAs bind to mRNA and arrange the amino acids in the appropriate order.
Ribosomes
Ribosomes are the structures that physically assemble the protein. Ribosomes are composed of a complex web of special ribosomal RNA (rRNA) and proteins. Each ribosome has 2 parts: a small subunit and a large subunit. The small subunit is called the 40S subunit and the large the 60S subunit. The two parts of the ribosomes enclose the mRNA strand, almost like the two pieces of bread on a sandwich. Strictly speaking, ribosomes are NOT organelles because they lack a membrane. Prokaryotes also possess ribosome and prokaryotes do not have organelles.
mRNA strands are fed into ribosomes which read the codons. Ribosomes contain compartments for tRNA anticodons to bind to their corresponding mRNA codons. The three binding sites for tRNA on ribosome are called the A, P, and E sites. Ribosomes also contain enzymes that catalyze the reaction that binds amino acids together into a polypeptide chain.
Process of Translation
Translation itself can be broke down into three steps: initiation, elongation, and termination. The majority of these processes take place in the cell cytoplasm or in the endoplasmic reticulum. In eukaryotes, translation occurs entirely separately from transcription, because pre-mRNA script created in transcription must be modified before its translated. In prokaryotes, translation occurs directly after transcription. In some cases, translation of one end of an mRNA strand can begin while the other end is still being transcribed.
Initiation
In the first step of translation, initiation factor proteins are released. These are the proteins that trigger the first steps of the translation process. Translation initiators bind to the 5′ end of mRNA and bring it over to the ribosomes. The mRNA binds to the small subunit of the ribosome and is held in place. In eukaryotes, a tRNA molecule containing methionine binds to the small subunit and together they move down the mRNA strand until they reach the start codon, which is almost always the AUG codon. Once reached, the large ribosomal subunit encloses the rest of the strand, forming the completed initiation complex.
Eukaryotic initiation. tRNA containing methionine walks down the mRNA strand until it reaches the start codon. Credit: User07 via WikiCommons CC BY-SA 3.0
In prokaryotes, the story is a little bit different. In prokaryotes, the small ribosomal subunit does not travel down the mRNA strand looking for the AUG codon. Instead, it binds directly to certain sequences in the mRNA strand. Prokaryote translation mechanisms can recognize the area to start by the presence of Shine-Dalgarno sequences that occur before the start codon. Bacteria use Shine-Dalgarno sequences because one sequence of DNA can encode for multiple proteins
Elongation
One the methionine carrying tRNA finds the start codon, the next phase of translation begins. During elongation, the actual polypeptide chain is constructed. One can remember what happens during elongation by the name: In elongation, the polypeptide chain gets longer.
When elongation begins, the methionine carrying tRNA is located in the P site in the middle of the ribosome. Next to the P site is the A site, which is over an exposed codon on the mRNA strand. The A site is the “slot” for the next tRNA molecule that will bond with the exposed codon via complementary codon-anticodon pairing.
Once the next tRNA lands in the A site, the ribosome catalyzes a reaction that binds the two amino acids together. The reaction binding two amino acids is a hydrolysis (water removing) reaction that joins the amine group of one amino acid to the carboxyl group of another. This reaction transfers the methionine from the first tRNA to the tRNA in the A site. Now we have a primitive polypeptide chain consisting of two amino acids. The methionine is called the N-terminus end and the other is called the opposite end is called the C-terminus.
Most polypeptide chains are longer than two amino acids. Once the first peptide bond has been made, mRNA gets pulled through the ribosome by exactly one codon. This shift moves the tRNA with the chain from the A site to the P site and moves the empty tRNA in the P slot to the E (“exit’) slot where it is removed. The shift also exposes a new mRNA codon in the A site.
The process repeats down the mRNA strand until the polypeptide chain is complete. Some proteins only consist of a few dozen amino acids while others can have thousands. The longest known protein is called titin and consists of a chain of 33,000 amino acids.
Termination
How do the ribosomes know when the polypeptide chain is complete? That is the role of the last step of translation, called termination. Termination of translation mechanisms happens once a stop codon (UAA, UAG, UGA) enters the A site. When a stop codon enters the A site, it is recognized not by tRNA, but special proteins called release factors. These proteins cause ribosomal enzymes to add a water molecule to the last amino acid in the chain, causing the ribosomal subunits to dissociate and freeing the polypeptide chain. Afterward, the ribosomal subunits can be used again to translate another polypeptide chain.
Post-Translation Modification
Now that we have a complete polypeptide chain, it can go out and start doing work in the body, right? Well, not quite.
In prokaryotes, proteins are generally ready to go as soon as they are translated. In eukaryotes, however, polypeptide chains must often go through a handful of modifications before they are a full-blown functioning mature protein. These post-translation edits involve the alteration or removal of some amino acids. Some proteins require to be folded into complex 3-D shape and there exist enzymes that assist with the folding. Sometimes two folded polypeptide chains conglomerate to form a larger protein complex. Other times the addition or removal of amino acid group functions as a “tag” that tells the body where to protein is supposed to go.
In eukaryotes, mot post-translation modification happens in the endoplasmic reticulum and the Golgi apparatus. In the endoplasmic reticulum, proteins are folded or have sections snipped out or added. The mechanisms that handle these processes are very diverse. after being handled in the endoplasmic reticulum, proteins are encased in a membrane-bound vesicle and transported to the Golgi apparatus. Once there, they undergo a few last minute-edits before they are shipped out to their final destination.
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