-14. -Abdulrahman Al-Hanbali. -Shahd Alqudah. -Dr Ma mon Ahram. 1 P a g e
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1 -14 -Abdulrahman Al-Hanbali -Shahd Alqudah -Dr Ma mon Ahram 1 P a g e
2 In this lecture we will talk about the last stage in the synthesis of proteins from DNA which is translation. Translation is the process where mrna gets translated to amino acid sequence. It involves interactions between three types of RNA molecules: - trna - rrnas (which exist in ribosomes) - mrna ( as a template for translation ) - trna: They are short RNA molecules (80 bases long) which can bind to an amino acid at a free end on the 3 terminal. This end contains a CCA sequence, where the amino acid can bind covalently to the ribose of the terminal adenosine (not to the base). When trna are bound to an amino acid we say that they are activated. This activation is catalyzed by an enzyme called Aminoacyl-tRNA synthetase. There is a special enzyme for every amino acid, so we have twenty Aminoacyl-tRNA synthetases. There is also another important region of the trna called the anticodon. It s a three-nucleotide sequence region which is complementary to the codon on the mrna and it binds antiparallel to it. - notice the anti-parallel alignment of mrnatrna complex. 2 P a g e
3 - Every three nucleotides in mrna code for certain amino acid. (codon) - Multiple codons code for one amino acid except for Methionine(only one codon). In mrna we have 64 codons (4^3), the important ones are (what you need to know): AUG which is the start codon as well as methionine. (that means the peptide chain always begins with methionine). UAA, UAG and UGA are the stop codons, those don t code for any amino acids. That means we have 61 different trna molecules each one with a special anticodon (there is no anticodons for the stop codons). Note that the codons are not universal -except for the start/stop codons- that means they differ between prokaryotes and eukaryotes. - Example (not to be memorized) :AUA in mitochondria(methionine) in cytosol (isoleucine). Wobble base pairing: Usually, the third base of the mrna codon (that binds to the first base on the trna anticodon - we read from 5' to 3' ) is degenerate, that means even if it varies, the amino acid usually stays the same. So if there was a mutation in the third base it won't change -usually- the amino acid. While if this mutation was in the first or second base the amino acid will change. -Wobble (the discoverer of this phenomenon ) noticed that the interaction between the 3 rd base of the codon and the 1 st of anticodon is flexible. * However, even if the amino acid changed due to a mutation in one base, it s usually changed to an amino acid of the same family and chemical characteristics (polar, non-polar...) so the overall structural change of the protein will be minimal. Note: The amino acid attached to trna is specified not only by the anticodon, but also identifier sequences. (from slides) 3 P a g e
4 - rrna: ribosomes: the sites of protein synthesis in both prokaryotic and eukaryotic cells. They consist from proteins and RNA, this RNA is called ribosomal RNA (rrna). The function of proteins is to maintain the structure, while the rrna makes the main enzymatic activity. Each ribosome is formed from two subunits: a small subunit and a large one. The large subunit (60s in Eukaryotes, 30s in Prokaryotes) has the peptidyl transferase activity (peptide formation). The small subunit (40s in Eukaryotes, 30s in Prokaryotes) is responsible for binding the mrna. The structure of the large subunit has three chambers: A. A-site: where the amino acyl trna binds. B. P-site: where the peptidyl transferase activity takes place. C. E-site: where the trna exits the ribosome. In the ribosome, the mrna is read from the 5 end to the 3 end. While the addition of amino acids is at the C-terminus (which means that the free terminus of the first amino acid is the N- terminus). This directionality is important because it gives an advantage for the prokaryotes, this advantage is they can couple the translation with the transcription (coupling in space & time). However this advantage is not found in the eukaryotes because of the nuclear membrane and because of the post-transcriptional modifications that are needed in eukaryotes (capping, splicing and polyadenylation). mrna is not transported outside the nucleus unless it is modified. 4 P a g e
5 - The process of translation: Translation is divided into three stages: initiation, elongation and termination. 1. Initiation: Usually, the start codon (AUG) is not the first codon in the mrna sequence. Instead, there is a sequence upstream of the start codon (toward the 5 end). This sequence is called the 5 untranslated region (UTR). It s called untranslated because even though it s part from the mature mrna, it doesn t make it to the final amino acid sequence. On the other end, the stop codon is also not the last codon and there is also a non-coding sequence downstream of it called the 3 -untranslated region We said that the first amino acid to be added in the translation process is methionine. However this methionine differ from prokaryotes to eukaryotes. In eukaryotes it is a normal methionine while in prokaryotes it s N-formylmethionine. A. In prokaryotes: if you recall, we said that the prokaryotic mrna is polycistronic, so how does the cell know where to start translation for each protein? It uses a sequence called the shine-dalgarno sequence. It is a sequence located upstream from the start codon that we want to start translation from. This sequence has a complementary sequence on the small ribosomal subunit. So the small subunit(30s) will scan the mrna until it finds the Shine-Dalgarno sequence, then it will bind to the mrna. This binding will stabilize the complex giving a signal for 5 P a g e
6 the ribosome to start translation from the first start codon after the Shine-Dalgarno sequence.(if there was an AUG codon before this sequence, it wouldn't be the start codon) After the binding of small subunit to mrna, a trna molecule carrying a N-formylmethionine binds to the start codon on the mrna. This trna-mrna-small subunit(30s) is called 30S initiation complex. GTP is needed for the formation of this complex in addition to a set of proteins (initiation factors) which are IF1, IF2 and IF3. After that the large subunit (50s) binds to the complex making the trna in the P-site. The complex is now called the 70S initiation complex. Then translation will begin. Recognition of Shine-Dalgarno sequence stable binding between 30s subunit & mrna formation of 30s initiation complex formation of the 70s initiation complex starting the translation at the first AUG after Shine- Dalgarno sequence. B. In eukaryotes: - Eukaryotic ribosomes recognize mrnas by binding to the 7- methylguanosine cap at their 5' terminus. - The start codon should be preceded by a sequence called Internal Ribosome Entry Site (IRES). - The IRES is recognized by 1) the 40s ribosome (small subunit) directly. Or 2)eIF4G protein followed by recruitment of the 40S ribosome. * eif4g (eukaryotic initiation factor 4G ) Initiation process: there s no Shine-Dalgarno sequence in eukaryotes however, a similar process takes place. An important factor in initiation of translation in eukaryotes is a protein complex that includes the proteins: eif4g, eif4e and poly-a binding protein (PABP). If you remember we said that post-transcriptional modification is important in translation, but what is their functions in translation? 6 P a g e
7 Caps are important because they are recognized by the small subunit. In other words the small subunit can differentiate between mrna and other types of RNA by finding the Cap. The cap is the place for the eif4e to bind. Poly-A tail are important in initiation even though they are located at the 3' end of the mrna. They participate in the stabilization for initiation by binding to the PABP. eif4g will bind to each of eif4e and poly-a binding protein making a loop. This loop will stabilize the initiation complex. eif4g can also recognize a sequence called internal ribosome entry site (IRES). This sequence has a similar function to the Shine- Dalgarno sequence in prokaryotes. When it recognizes this sequence, it will stimulate the recruitment of the 40S ribosome. However, the 40s subunit can also recognize this sequence by its own. 2. Elongation: This stage consists from 3 steps that are repeated again and again until the termination. Those steps are: A. aminoacyl-trna binding :Aminoacyl-tRNA that has a complementary anticodon for the second codon binds at the A- site. (remember that the first trna is already at the P-site). - Elongation factor EF-Tu an GTP are required. B. peptide bond formation: The first amino acid moves from the first trna and binds to second aminoacyl-trna on the A site leaving the first trna uncharged (inactivated). C. Translocation: the ribosome moves by one codon (3 nucleotides) towards the 3' end, which will make the first trna (the uncharged) at the E-site and it will exit the ribosome, the second trna (peptidyl-trna) is now at the P-site carrying two amino acid chain, leaving an empty A site. 7 P a g e
8 D. Those steps will be repeated over and over until we reach a stop codon. 3. Termination: As we said there is no trna anticodons for the stop codons ( UAA, UAG, UGA), so when we reach the stop codon special proteins recognize it, those are called release factors. The release factor blocks the binding of a new aminoacyl-trna and facilitates the hydrolysis of the bond between the carboxyl end of the peptide and the trna. Then, the whole complex dissociates. Polyribosomes (polysomes) Sometimes the mrna can be translated by multiple ribosomes at the same time making a structure called polyribosome. This applies for prokaryotes and eukaryotes as well. 8 P a g e
9 - The ribosome which is closer to the 3' end of the mrna is the one that attached and started translation first. Some antibiotics work by inhibiting the process of translation such as: Tetracycline: blocks binding of aminoacyl-trna to A-site of ribosome, (Interfere with attachment of trna to mrna-ribosome complex). Streptomycin: Induces binding of wrong t-rna-aa complexes resulting in false proteins by changing the shape of 30S portion. Chloramphenicol: blocks the peptidyl transferase reaction on ribosomes, so it binds to 50S portion. Erythromycin: blocks the translocation reaction on ribosomes, it binds to 50S portion. 9 P a g e
10 Some toxins also affect the process of translation such as diphtheria toxin, which is a protein that interferes with protein synthesis by decreasing the activity of the eukaryotic elongation factor eef2. Cloning: If you remember we said that cloning has many benefits, one of those benefits is that we can make the bacteria synthesize a protein that we need. E.g.: growth hormones and insulin. We can achieve that by introducing a plasmid that contain a promoter and the gene for our protein but without introns as prokaryotic cells don t make splicing. In the case of insulin and because insulin is a dimer linked by disulfide bonds, we use two groups of bacteria, each group will make a chain (A&B) and then the polypeptides are purified from each bacterial group and mixed to form the mature insulin protein(dimer). Regulation of translation: As there is a regulation on the level of transcription and posttranscriptional modification there is a regulation on the level of translation. So the cell might have the mrna but it won't translate it 10 P a g e
11 until it needs that. When the cell needs the proteins it can translate the mrna immediately without the need for transcription. e.g.: globin synthesis: it takes place in reticulocytes (immature erythrocytes), haemoglobin consists from a heme group and a globin protein. So when there isn t enough heme, there is no need for globin synthesis. The cell control this by regulating the eif2, which is responsible for escorting initiator methionyl trna to the ribosome. eif-2 must be bound to GTP to be active. When it is released from the ribosome, GTP is hydrolyzed to GDP, which must be exchanged with GTP for eif-2 to be active again. So we have two situations: A. If the heme level is adequate then the translation will continue normally as the GDP-GTP exchange mechanism won't be affected. B. If the heme level is low then the GDP-GTP exchange mechanism will be inhibited by phosphorylation of the initiating factor. This phosphorylation is done by a kinase protein which is activated when heme levels are low. 11 P a g e
12 Gene editing: Sometimes the same gene can be edited in different cells. That will yield different forms of the protein. e.g.: lipoproteins: lipoproteins are responsible for lipid transport. There are several types of lipoproteins such as: Chylomicrons: those contain ApoB 48 and are produced in the intestines. low-density lipoproteins and very low density lipoproteins (LDL, vldl) : those are produced by the liver and they have the protein ApoB-100 (the number stands for the molecular weight). The special thing here is that both ApoB-48 and ApoB-100 are made from the same gene. And the difference here is a result from gene editing. In the liver there won't be any editing so the final product from translation is the peptide chain in its full-length. In the intestines the mrna gene is edited by changing a cytosine to uracil by deaminatioon, this will change a CAA codon to UAA which resembles a stop codon. The result is a shorter peptide chain. 12 P a g e
13 Regulation by micro-rna: Micro-RNAs usually have a complementary sequence on the mrna. When they bind to this sequence this will induce the degradation of mrn or they maybe just inhibit/block the translation. Those mirna are transcribed by RNA-polymerase II from their own genes into single-stranded, primary mirna (pri-mirna) transcript. Then pri-mirna are processed in the nucleus by Drosha enzyme and exported to the cytoplasm. Then an exonuclease complex containing Dicer will modify it to generate a mature mirna duplex (two-stranded mirna) in the cytoplasm. Then One strand is loaded onto RNA-induced silencing complex (RISC)complex where mirna is targeted to mrna resulting in either translation repression or mrna degradation. Protein folding problems: At this point the cell has finished translation and the result is an unfolded peptide chain, if this chain remained unfolded or was misfolded the cell degrades it by Ubiquitin Proteasome Pathway. Ubiquitinylation which is process where the cell label the protein by ubiquitin. This gives a signal for proteasomes to degrade the protein. - Cells can also degrade proteins by degradative subcellular organelles like lysosomes. 13 P a g e
14 Levels of regulation(this regulation makes us different from all other organisms) Transcription RNA processing RNA transport mrna stability Translation Post-translational modification Protein activity Protein degradation 14 P a g e
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