Translation 1 DONE BY :Maen Faoury 0
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In this lecture and the coming lectures you are going to see how the genetic information is transferred into proteins and how proteins will do their functions. 3
As you can see above this is the structure of mrna to be translated and you saw the different types of processes that took place on mrna which are capping, polyadenylation and splicing. And these are the parts of mrna: 1. 5 end and 3 end. Check them on the image above 4
2. Different sequences. 3. Translation start codon. 4. Ribosome binding site. 5. 5 and 3 untranslated regions. 6.Translation stop codon. There is a difference between the mrna of prokaryotes and eukaryotes, in which the prokaryotic is poly cystronic; it means that one large mrna will be responsible to be translated into different proteins and those proteins are related to each other and this is not the case in eukaryotic. Eukaryotic is mono cystronic : one gene will give one messenger mrna and this mrna will give one protein, but in poly cystronic one large mrna Will give many proteins and the transcription of this large mrna is under the control of one promoter. This phenomena in prokaryotes is called operons Examples of operons ; tryptophan operon and lac operon. Tryptophan operon : is a piece on DNA that one large mrna will be produced under the control of one promoter and all those proteins that are produced from this large mrna are related in function to each other and they are important for the synthesis of tryptophan. 5
The same thing when we are talking about lac operon, many proteins coming from one large mrna under the control of one promoter and those proteins are all related to lac operon metabolism. ومن أحياها Translation 1 6
This is the geneteic code that we are talking about, it has different charestaristics. Codones : 3 letters of nucleotide and these 3 letters represent one amino acid. Ex : phenylalanine : UUU or UUC. For Phenylalaanine there are 2 codons. If we are talking about leucine : CUU CUC CUA CUG UUA UUG. YOU will notice that some of the amino acids have more than one codon, and that s why we have more than 20 codons in the gentic code for amino acids. There are 20 amino acids so logically ther must be 20 codons but there are 61 codons why? because one amino acid could have more than one codon,some will have 6 some 5. 7
Usually the third nucleotide will not determine the genetic code. So if you have the first and second nucleotide and you change the third the amino acid codones will stay the same. The genetic code is universall : not only for humans, if you look at E.COLI you will see that E.COLI uses the same genetice code as humans. Redundant : one amino acid could have more than one codon. Logical : if you take the isoleucine AUU AUC AUA the third codon is pyrimidine not (pyrimidine and purine), If you go to another amino acid you will see the third nucleotide of all codons would be of one category (pyrimidine or purine ). Punctuated : you see 64 codones, 61 of them will read for amino acids 1 will code for the initiation and 3 will code for the stop. AUG : INITIATION. UAA,UAG,UGA : STOP CODONES. These (in the image below) are the steps of the process of translation : initiation,elongation and termination as in trancription and replication, but in addition to these universal steps there is something called amino acid activation. 8
So amino acids when they are inserted into polypeptide will be translating the genetic information in the mrna, they must be activated before. You faced an activation of some molecules before, oxidation and those molecules are fatty acids and the same thing with amino acids. Each amino acid must be combined with energy (ATP) And converted to an adenosine amino acid and that is equivalent to two ATPs because AMP will be produced after the activation of each amino acid. 9
Translation : 10
trna will carry the amino acids according to the anticodon and the result of this translation is the protein. Always remember that codons are found in the mrna and the anticodons are found on the trna and the base pairing is antiparallel : it starts in the 5 to3 in m RNA and the trna will make base pairing in the 3 to5 direction. Each t RNA will get specific amino acid. How many t RNA molecules are needed to transport amino acids to base pair anticodon\codon for protein synthesis? It is less than 61 and it is more than 21. 11
The image above represents the structure of ribosome, it is composed of 2 subunits, one big subunit and one small subunit. 12
The small subunit has a specific site which is 30s And the big subunit has a 50s site,the s stands for sedimentation rate relative to sizes and they are not additive. It means that when the large subunit is assembled to the small one they will not give 80 s but they will give 70 s. There are three important sites in the ribosome : A- site,p-site and E-site. The A-site is the site that receives the incoming trna charged with amino acids. The P-site is the site in which the peptide bond is formed from the incoming amino acid in the A-site and the amino acid in the E-site(not sure if E or P site 26:00). ومن أحياها Translation 1 E-site : the exit site in which the trna after it unloads the amino acid it will exit. In eukaryotic system it is principally the same we have these 3 sites, large and small subunits, The small subunit is 40 s and the large subunit is 60s Also they are not additive (80s). Each subunit (prokaryotic or eukaryotic ) they are composed of RNA and proteins. The following numbers are not for memorization : 13
There are 3 types of RNA molecules in the small subunit in prokaryotic and 4 types in the eukaryotic small subunit, And there are 21 proteins in the large subunit of prokaryotes and 31 proteins in the large subunit in the eukaryotic. The RNA and proteins have functions in the process of translation. Above is the secondary structure of trna, it has modifications and these modifications will cause Double stranded base pairing in the trna. trna is a translator molecule because it transfers amino acids to the ribosome for the process of translation. 14
The anticodon region is very important because it will base pair specifically with the codon region on the mrna. Another important region is the 3 region because of the processing,all types of trna must have a concerned sequence in the 3 prime end which is always CCA. It is the A that is responsible to carry the amino acid. So how the trna carry the specific amino acid on it s A and transfer it to ribosome to be incorporated in the poly peptide chain synthesis? Its according to the codons of the mrna, but how the trna is able to bind to the codon and at the same time select the proper amino acid? 15
There is a system which is very smart,its called the aminoacyl trna synthetase, its an enzyme that could read the anticodon of the t RNA and once it read the anticodon it will link the proper amino acid according to the anticodon, then that charged trna will go to the mrna and it will base pair its codons to the m RNA, if its not the proper one it will go back and another one will come. Its a very highly accurate enzyme. So what is the substrate for this enzyme? trna and proper amino acid,it will bind both in its binding site then it will link the activated amino acid to the A in the CCA of the 3 prime of the trna. Charged trna : its a trna that is linked to a specific amino acid.. 16
Remember that in the A there are 2 hydroxyl groups, one is 3 and the second is 2. ومن أحياها Translation 1 There are 2 types of t RNA : Type 2 - AA on 3 OH Type 1 - AA on 2 OH Charging of trnas : you are not concerned with the structures of these reactions but you should know that each amino acid must be activated by adding ATP to it and AMP will be produced and that means that it was provided with energy which is equivalent to 2 ATP molecules so it will be participating in translation only after is has been activated. 17
The first amino acid to be used in prokaryotic and eukaryotes is methionine AUG but remember that in prokaryotes this methionine must be modified while in eukaryotes there is no need for it to be modified. How it will be modified in prokaryoutes? By this reaction : fmet Synthesis in Prokaryotes In which after the specific trna binds to methionine there is an enzyme called Met-t RNA formyl transferase it will put a formyl group from the N10- formyl-thf(tetrahydrofolate) into the methionine. This formyl group is very important and it prevents this methionine to loop with the second amino acid to be incorporated in prokaryotes so it must be modified (formylated) to prevent this looping and if looping happens all translation will stop. Why its not important in eukaryotes? Because this looping will not happen, why? Because the ribosomes 18
are different in structure, the are large have more proteins and other types of mrna. ومن أحياها Translation 1 Wobble phenomena is very important for the economy of the cell. The doctor asked us before how many trna do we need to transform amino acid; Cell is very wise and does not synthesis 61 t RNA maybe they will synthesis 31 ones, and those will do the job of transferring amino acids specifically to the ribosomes and how? By wobble. Look at the image above : the base pairing between the codon in mrna and the anticodon is antiparallel, so the anticodon is 3 to 5 CGI the 5 nucleotide of the 19
anticodon wobbles ( if it is I it could base pair with any nucleotide ) So instead of synthesizing 4 trna molecules in this case when the 5 is I you synthesis one, I could base pair with the 3 end of m RNA if its A or C or Q. If the 5 of the anticodon is G it could base pair with C or U,if its U it could base pair with A or G, and these ones are still (44:42) in the RNA. ومن أحياها Translation 1 20
Composed of RNA and proteins Highly complex structure 21
The doctor said something that wasn t clear at (45:22) 22
This image represents what happened in the initiation of the protein synthesis. The growing peptide chain comes from the E-site. There will be a translocation of the ribosome from left to right, m RNA will be read from 5 to3,protein will be synthesized from N terminal to C terminal. 23
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