where does tRNA form ( where does it come from) ?

It is coded by DNA, then it's transcribed by special polymerase, spliced and there we have it.

Hi, where does the Amino Acid comes from? The one the tRNA transports. Does it come from the Lysosome?

Amino Acids either come from exogenous origins (from the catabolism of ingested food), or anabolic from other precursors. These free amino acids are found in the *cytoplasm* and are brought to the ribosome.

What happens to tRNA molecules when they leave a ribosome?

They attach to amino acids (that have been obtained from our diet) in the cytosol and return to the ribosome if the same codons appear in the mRNA sequence, for them to be translated.

Does the Wobble Position apply to START and STOP codons as well?

From my understanding, it won't apply to the start codon, AUG, because there is only one possible codon available. If you look at the codons for an amino acid such as Leucine; CUU,CUC,CUA,CUG, there are multiple options available and the third letter varies, but all four codons code for Leucine. I think the wobble position will apply to the stop codons; UAA, UAG and UGA, because there is variation in the third letter. Note - I got the codons from the genetic code table, on the article 'The genetic code'. I'm not 100% sure that I am correct though

ATP is used to bind the amino acid to a tRNA. How is the actual peptide bond formed during translation? Wouldn't that also need energy?

Another good question. The bond in the aminoacyl-tRNA is higher energy than the peptide bond, so there is no new energy input required to form the peptide bond — the energy came from hydrolyzing ATP to AMP plus PPᵢ (pyrophosphate). However, a GTP is hydrolyzed to ensure that the correct aminoacyl-tRNA binds to mRNA-ribosome complex and another is used to move the ribosome along the mRNA by one codon. This discussion does a reasonable job of explaining the energetics of this process: https://biology.stackexchange.com/questions/40964/how-much-nucleoside-triphosphate-is-required-to-form-one-peptide-bond-during-pro

What is the difference between DNA replication and the process of DNA translation/transcription

Replication is making more DNA, transcription is DNA to mRNA, and translation is mRNA to proteins!

So, a tRNA is is L shaped in 3D and clover leaf shaped in 2D? That's a bit confusing..

You might find this exercise helpful to get a feel for how that works: https://www.youtube.com/watch?v=lw41sO1myKw&feature=youtu.be Basically two of the loops (D and T) are wrapped around each other, which converts the 2D clover leaf into an L-shape.

If there is a different tRNA needed to carry one of each of the different amino acids, then how many different (natural) amino acids are there?

There are 20 'standard' amino acids encoded by the triplets of the genetic code. However there are two more, selenocysteine and pyrrolysine that are incorporated in response to a given triplet in combination with another signal. But they are then also incorporated via tRNA. There are other amino acids found in proteins, but they are modified after incorporation, for example hydroxylysine so there aren't tRNAs for these. Also, in bacteria the first amino acid is often N-formylmethionine, but that is more considered a variation of methionine. So, often people will talk about 20, or maybe 22 amino acids. Just as an aside, some amino acids have several tRNAs to insert them at different codons (although some tRNAs can also recognise several codons).

You have mentioned that the two subunits (both) come together for initiation. Isn't that only true for prokaryotic cells?

You are correct, this article deals with prokaryotic translation. In eukaryotic translation, there are also ribosomal subunits which must come together around an mRNA, but the process is a whole lot more complex with lots of protein-RNA interactions and protein-protein interactions. The wiki article on eukaryotic translation has a nice overview diagram. I think people are still figuring out exactly how the process works in eukaryotes. https://en.wikipedia.org/wiki/Eukaryotic_translation

What is meant by the third position in reference to the 'wobble binding' of tRNA?

The third position refers to the third letter of the codon, reading from left to right (5' - 3' direction). If the codon was UUC, the third position would be C. There are some tRNA molecules that can bind with more than one codon, as in the example above. This is called wobble pairing, because the first position of the tRNA anticodon does not bind as tightly to the third postion of the codon, meaning the pairing between codon and anticodon is more flexible.

Main content

Course: Biology library > Unit 18

Lesson 3: Translation

tRNAs and ribosomes

Google Classroom

Structure and roles of transfer RNAs and ribosomes. Codons, anticodons, and wobble. Aminoacyl-tRNA synthetases.

Introduction

Translation requires some specialized equipment. Just as you wouldn't go to play tennis without your racket and ball, so a cell couldn't translate an mRNA into a protein without two pieces of molecular gear: ribosomes and tRNAs.

Ribosomes provide a structure in which translation can take place. They also catalyze the reaction that links amino acids to make a new protein.
tRNAs (transfer RNAs) carry amino acids to the ribosome. They act as "bridges," matching a codon in an mRNA with the amino acid it codes for.

Here, we’ll take a closer look at ribosomes and tRNAs. If you're not yet familiar with RNA (which stands for ribonucleic acid), I highly recommend checking out the nucleic acids section first so you can get the most out of this article!

Ribosomes: Where the translation happens

Translation takes place inside structures called ribosomes, which are made of RNA and protein. Ribosomes organize translation and catalyze the reaction that joins amino acids to make a protein chain.

Structure of the ribosome

A ribosome is made up of two basic pieces: a large and a small subunit. During translation, the two subunits come together around a mRNA molecule, forming a complete ribosome. The ribosome moves forward on the mRNA, codon by codon, as it is read and translated into a polypeptide (protein chain). Then, once translation is finished, the two pieces come apart again and can be reused.

Overall, the ribosome is about one-third protein and two-thirds ribosomal RNA (rRNA). The rRNAs seem to be responsible for most of the structure and function of the ribosome, while the proteins help the rRNAs change shape as they catalyze chemical reactions

^{1}

Below, you can see a 3D model of the ribosome. Proteins are colored in blue, while strands of rRNA are colored in tan and orange. The green spot marks the active site, which catalyzes the reaction that links amino acids to make a protein. It surprised me to see that the ribosome is wrinkly, kind of like the surface of a brain!

The animation below shows a model of the large ribosomal subunit from a prokaryote called Haloarcula marismortui. In the model, proteins are colored in blue, while strands of rRNA are colored in tan and orange. The green spot marks the active site, which catalyzes addition of a new amino acid to the polypeptide chain

^{2}

The ribosome has slots for tRNAs

As we saw briefly in the introduction, molecules called transfer RNAs (tRNAs) bring amino acids to the ribosome. We'll learn a lot more about tRNAs and how they work in the next section.

For now, just keep in mind that the ribosome has three slots for tRNAs: the A site, P site, and E site. tRNAs move through these sites (from A to P to E) as they deliver amino acids during translation.

Image modified from "Translation: Figure 3," by OpenStax College, Biology (CC BY 4.0).

To learn more about each site's unique "job," check out the article on stages of translation.

What exactly is a tRNA?

A transfer RNA (tRNA) is a special kind of RNA molecule. Its job is to match an mRNA codon with the amino acid it codes for. You can think of it as a kind of molecular "bridge" between the two.

Each tRNA contains a set of three nucleotides called an anticodon. The anticodon of a given tRNA can bind to one or a few specific mRNA codons. The tRNA molecule also carries an amino acid: specifically, the one encoded by the codons that the tRNA binds.

The two ends of a strand of DNA or RNA are different from each other. That is, a DNA or RNA molecule has directionality.

At the 5’ end of the chain, the phosphate group of the first nucleotide in the chain sticks out. The phosphate group is attached to the 5' carbon of the sugar ring, which is why this is called the 5' end.
At the other end, called the 3’ end, the hydroxyl of the last nucleotide added to the chain is exposed. The hydroxyl group is attached to the 3' carbon of the sugar ring, which is why this is called the 3' end.

Many processes, such as DNA replication and transcription, can only take place in one particular direction relative the the directionality of a DNA or RNA strand.

You can learn more in the article on nucleic acids.

There are many different types of tRNAs floating around in a cell, each with its own anticodon and matching amino acid. In fact, there are usually

40

60

different types, depending on the species

^{3}

. tRNAs bind to codons inside of the ribosome, where they deliver amino acids for addition to the protein chain.

Some tRNAs bind to multiple codons ("wobble")

Some tRNAs can form base pairs with more than one codon. At first, this seems pretty weird: doesn't A base-pair with U, and G with C?

Well...not always. (Biology is full of surprises, isn't it?) Atypical base pairs—between nucleotides other than A-U and G-C—can form at the third position of the codon, a phenomenon known as wobble.

Wobble pairing doesn't follow normal rules, but it does have its own rules. For instance, a G in the anticodon can pair with a C or U (but not an A or G) in the third position of the codon, as shown below

^{4}

. Rules like this ensure codons are read correctly despite wobble.

Image modified from "Translation: Figure 3," by OpenStax College, Biology (CC BY 4.0).

You may be wondering: why on Earth would a cell "want" a complicating factor like wobble? The answer may be that wobble pairing allows fewer tRNAs to cover all the codons of the genetic code, while still making sure that the code is read accurately.

The 3D structure of a tRNA

I like to draw tRNAs as little rectangles, to make it clear what's going on (and to have plenty of room to fit the letters of the anticodon on there). But a real tRNA actually has a much more interesting shape, one that helps it do its job.

A tRNA, like the one modeled below, is made from a single strand of RNA (just like an mRNA is). However, the strand takes on a complex 3D structure because base pairs form between nucleotides in different parts of the molecule. This makes double-stranded regions and loops, folding the tRNA into an L shape.

Great question! To answer it, let's take a quick look at the structure of DNA and RNA.

DNA and RNA strands are polymers of repeating units called nucleotides. Each nucleotide consists of a five-carbon sugar, one or more phosphate groups, and a nitrogenous base.

DNA has four types of nucleotides, each with a different nitrogenous base. The bases of DNA are adenine (A), thymine (T), guanine (G), and cytosine (C).
RNA also has four types of nucleotides. These nucleotides are similar to those of DNA, but contain a different sugar. Also, RNA has the base uracil (U) in place of thymine (T).

Certain types of nucleotides can form hydrogen bonds with one another. Specifically, A will typically form bonds with T (in DNA) or U (in RNA), while G will typically form bonds with C. These nucleotides can hydrogen bond with one another because their structures are complementary – that is, they fit together like chemical puzzle pieces. The formation of hydrogen bonds between nucleotide bases is called base pairing, and it plays an important role in many biological processes, including DNA replication and gene transcription.

For more information on base pairing and the structure of DNA and RNA, check out the article on nucleic acids.

One end of the L shape has the anticodon, while the other has the attachment site for the amino acid. Different tRNAs have slightly different structures, and this is important for making sure they get loaded up with the right amino acid.

Loading a tRNA with an amino acid

How does the right amino acid get linked to the right tRNA (making sure that codons are read correctly)? Enzymes called aminoacyl-tRNA synthetases have this very important job.

There's a different synthetase enzyme for each amino acid, one that recognizes only that amino acid and its tRNAs (and no others). Once both the amino acid and its tRNA have attached to the enzyme, the enzyme links them together, in a reaction fueled by the "energy currency" molecule adenosine triphosphate (ATP).

Occasionally, an aminoacyl-tRNA synthetase makes a mistake: it binds to the wrong amino acid (one that "looks similar" to its correct target). For example, the threonine synthetase sometimes grabs serine by accident and attaches it to the threonine tRNA. Luckily, the threonine synthetase has a proofreading site, which pops the amino acid back off the tRNA if it's incorrect

^{5}

Putting it all together

Once they're loaded up with the right amino acid, how do tRNAs interact with mRNAs and the ribosome to build a brand-new protein? Learn more about how this process works in the next article, on the stages of translation.

Attribution:

This article is a modified derivative of "Ribosomes and protein synthesis," by OpenStax College, Biology (CC BY 4.0). Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.61.

The modified article is licensed under a CC BY-NC-SA 4.0 license

Works cited:

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Ribosomes. In Campbell biology (10th ed., pp. 347-48). San Francisco, CA: Pearson.
Goodsell, D. S. (2000). Ribosomal subunits. In RCSB molecule of the month. Retrieved from http://pdb101.rcsb.org/motm/10.
OpenStax College, Biology. (2015, September 30). Ribosomes and protein synthesis. In OpenStax CNX. Retrieved from https://cnx.org/contents/s8Hh0oOc@8.57:FUH9XUkW@6/Translation.
Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Some transfer RNA molecules recognize more than one codon because of wobble in base-pairing. In Biochemistry. (5th ed., section 29.3.9). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22335/#_A4185_.
Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Proofreading by aminoacyl-tRNA synthetases increases the fidelity of protein synthesis. In Biochemistry. (5th ed., section 29.2.3). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22356/#_A4151_.

References

Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Aminoacyl-transfer RNA synthetases read the genetic code. In Biochemistry. (5th ed., section 29.2). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22356/.

Goodenbour, J. M. and Pan, T. (2006). Diversity of tRNA genes in eukaryotes. Nucl. Acids Res., 34(21), 6137-6146. http://dx.doi.org/10.1093/nar/gkl725.

Goodsell, D. (April 2001). Aminoacyl-tRNA synthetases. In RCSB molecule of the month. Retrieved from http://pdb101.rcsb.org/motm/16.

Nelson, D. L., Lehninger, A. L., and Cox, M. M. (2008). Protein synthesis. InPrinciples of biochemistry(5th ed., pp. 1075 -1099). New York, NY: W.H. Freeman & Company.

OpenStax College, Biology. (2015, September 30). Ribosomes and protein synthesis. In OpenStax CNX. Retrieved from https://cnx.org/contents/s8Hh0oOc@8.57:FUH9XUkW@6/Translation.

OpenStax College, Biology. (n.d). Translation. In OpenStax CNX. Retrieved from http://philschatz.com/biology-concepts-book/contents/m45479.html.

Purves, W. K., Sadava, D., Orians, G. H., and Heller, H. C. (2004). From DNA to protein: Genotype to phenotype. In Life: the science of biology (7th ed., pp. 233-256). Sunderland, MA: Sinauer Associates, Inc.

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Gene expression: From gene to protein. In Campbell biology (10th ed., pp. 333-359). San Francisco, CA: Pearson.

Transfer RNA / tRNA. (2014). In Scitable. Retrieved from http://www.nature.com/scitable/definition/trna-transfer-rna-256.

Wobble base pair. (2015, December 2). Retrieved December 21, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Wobble_base_pair.

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bob bobby
Posted 8 years ago. Direct link to bob bobby's post “where does tRNA form ( wh...”
where does tRNA form ( where does it come from) ?
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- Daltara Darana
  Posted 8 years ago. Direct link to Daltara Darana's post “It is coded by DNA, then ...”
  It is coded by DNA, then it's transcribed by special polymerase, spliced and there we have it.
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  (20 votes)
Katie9Adams
Posted 7 years ago. Direct link to Katie9Adams's post “What is the difference be...”
What is the difference between DNA replication and the process of DNA translation/transcription
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(3 votes)
Answer
- Emily
  Posted 7 years ago. Direct link to Emily's post “Replication is making mor...”
  Replication is making more DNA, transcription is DNA to mRNA, and translation is mRNA to proteins!
  Button navigates to signup page
  (31 votes)
fernandamn4
Posted 5 years ago. Direct link to fernandamn4's post “Hi, where does the Amino ...”
Hi, where does the Amino Acid comes from? The one the tRNA transports. Does it come from the Lysosome?
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(6 votes)
Answer
- Ivana - Science trainee
  Posted 5 years ago. Direct link to Ivana - Science trainee's post “Amino Acids either come f...”
  Amino Acids either come from exogenous origins (from the catabolism of ingested food), or anabolic from other precursors.
  
  These free amino acids are found in the cytoplasm and are brought to the ribosome.
  Comment on Ivana - Science trainee's post “Amino Acids either come f...”
  (9 votes)
mkussee
Posted 7 years ago. Direct link to mkussee's post “What happens to tRNA mole...”
What happens to tRNA molecules when they leave a ribosome?
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(5 votes)
Answer
- PlaceboGirl
  Posted 7 years ago. Direct link to PlaceboGirl's post “They attach to amino acid...”
  They attach to amino acids (that have been obtained from our diet) in the cytosol and return to the ribosome if the same codons appear in the mRNA sequence, for them to be translated.
  Button navigates to signup page
  (6 votes)
Priyanka
Posted 6 years ago. Direct link to Priyanka's post “ATP is used to bind the a...”
ATP is used to bind the amino acid to a tRNA.
How is the actual peptide bond formed during translation? Wouldn't that also need energy?
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(4 votes)
Answer
- tyersome
  Posted 6 years ago. Direct link to tyersome's post “Another good question. T...”
  Another good question.
  
  The bond in the aminoacyl-tRNA is higher energy than the peptide bond, so there is no new energy input required to form the peptide bond — the energy came from hydrolyzing ATP to AMP plus PPᵢ (pyrophosphate). However, a GTP is hydrolyzed to ensure that the correct aminoacyl-tRNA binds to mRNA-ribosome complex and another is used to move the ribosome along the mRNA by one codon.
  
  This discussion does a reasonable job of explaining the energetics of this process:
  https://biology.stackexchange.com/questions/40964/how-much-nucleoside-triphosphate-is-required-to-form-one-peptide-bond-during-pro
  Comment on tyersome's post “Another good question. T...”
  (7 votes)
Rose
Posted 6 years ago. Direct link to Rose's post “Does the Wobble Position ...”
Does the Wobble Position apply to START and STOP codons as well?
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(5 votes)
Answer
- S
  Posted 5 years ago. Direct link to S's post “From my understanding, it...”
  From my understanding, it won't apply to the start codon, AUG, because there is only one possible codon available. If you look at the codons for an amino acid such as Leucine; CUU,CUC,CUA,CUG, there are multiple options available and the third letter varies, but all four codons code for Leucine.
  
  I think the wobble position will apply to the stop codons; UAA, UAG and UGA, because there is variation in the third letter.
  
  Note - I got the codons from the genetic code table, on the article 'The genetic code'.
  
  I'm not 100% sure that I am correct though
  Button navigates to signup page
  (2 votes)
Priyanka
Posted 6 years ago. Direct link to Priyanka's post “So, a tRNA is is L shaped...”
So, a tRNA is is L shaped in 3D and clover leaf shaped in 2D?
That's a bit confusing..
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(3 votes)
Answer
- tyersome
  Posted 6 years ago. Direct link to tyersome's post “You might find this exerc...”
  You might find this exercise helpful to get a feel for how that works:
  https://www.youtube.com/watch?v=lw41sO1myKw&feature=youtu.be
  
  Basically two of the loops (D and T) are wrapped around each other, which converts the 2D clover leaf into an L-shape.
  Comment on tyersome's post “You might find this exerc...”
  (4 votes)
jessicabraun59
Posted 4 years ago. Direct link to jessicabraun59's post “If there is a different t...”
If there is a different tRNA needed to carry one of each of the different amino acids, then how many different (natural) amino acids are there?
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(2 votes)
Answer
- RowanH
  Posted 4 years ago. Direct link to RowanH's post “There are 20 'standard' a...”
  There are 20 'standard' amino acids encoded by the triplets of the genetic code. However there are two more, selenocysteine and pyrrolysine that are incorporated in response to a given triplet in combination with another signal. But they are then also incorporated via tRNA. There are other amino acids found in proteins, but they are modified after incorporation, for example hydroxylysine so there aren't tRNAs for these.
  Also, in bacteria the first amino acid is often N-formylmethionine, but that is more considered a variation of methionine. So, often people will talk about 20, or maybe 22 amino acids.
  Just as an aside, some amino acids have several tRNAs to insert them at different codons (although some tRNAs can also recognise several codons).
  Button navigates to signup page
  (3 votes)
Areeb
Posted 7 years ago. Direct link to Areeb's post “What is meant by the thir...”
What is meant by the third position in reference to the 'wobble binding' of tRNA?
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(1 vote)
Answer
- Rich B
  Posted 7 years ago. Direct link to Rich B's post “The third position refers...”
  The third position refers to the third letter of the codon, reading from left to right (5' - 3' direction). If the codon was UUC, the third position would be C. There are some tRNA molecules that can bind with more than one codon, as in the example above. This is called wobble pairing, because the first position of the tRNA anticodon does not bind as tightly to the third postion of the codon, meaning the pairing between codon and anticodon is more flexible.
  Comment on Rich B's post “The third position refers...”
  (5 votes)
arvintvk
Posted 7 years ago. Direct link to arvintvk's post “You have mentioned that t...”
You have mentioned that the two subunits (both) come together for initiation. Isn't that only true for prokaryotic cells?
Button navigates to signup pageButton navigates to signup page
(2 votes)
Answer
- Ryan Hoyle
  Posted 7 years ago. Direct link to Ryan Hoyle's post “You are correct, this art...”
  You are correct, this article deals with prokaryotic translation. In eukaryotic translation, there are also ribosomal subunits which must come together around an mRNA, but the process is a whole lot more complex with lots of protein-RNA interactions and protein-protein interactions. The wiki article on eukaryotic translation has a nice overview diagram. I think people are still figuring out exactly how the process works in eukaryotes.
  https://en.wikipedia.org/wiki/Eukaryotic_translation
  Button navigates to signup page
  (3 votes)