Chapter 9 - Protein Translation

Transcription

1 Chapter 9 - Protein Translation Section 1: Introduction Section 2: The Genetic code! 2.1! The Problem! 2.2! The Solution Section 3: The players in Translation! 3.1! mrna! 3.2! trna! 3.3! The Ribosome Section 4: The Process of Translation! 4.1! Initiation! 4.2! Elongation! 4.3! Termination

2 Section 1: Introduction Translation is the biological synthesis of polypeptides in the ribosome specified by mrna. It is known that DNA contains all of the genetic information that is required for cellular life, and it uses proteins to accomplish many tasks required for cells to proliferate, survive, and other higher order function. translation is that missing step between the information passes along form parent to daughter cell and the proteins that provide this vitality. Protein translation is performed in the ribosome and produces a polypeptide that is later folded and post translational modified to to preform their designed task. There are a number of players and steps involved in translation. The genetic code itself is important to the entire process. Also important are the payers involves, trna, ribosomes, mrna and enzymes and cofactors that facilitate what and when to do.

3 Section 2: The Genetic code 2.1 The Problem Once the structure of DNA was solved, the problem that lay at hand was obvious. "How dose this set of instructions make it to proteins?" "How does this 'alphabet' so simple consisting of only 4 base pairs describe all of the life that we know?" The math is simple there are 20 amino acids. With only 4 bases to choose from we needed at least 3 base pairs 4^1 = 4 4^2 = 16 4^3 = 64 4^4 = 128 too few amino acids almost enough enough options way too much 2.2 the solution The advantage for having 64 possible combinations it that single point mutations can have no effect not the outcome of the polypeptide. This make the process more robust. The genetic code was consolidate to the table shown. this is the rosetta stone that is used to decipher the information in the DNA to the shape of the protein.

4 Section 3: The molecular Components of Translation 3.1 mrna mrna (messenger mrna) contains the genetic information that will be directly translated into amino acids as in the genetic code chart. The DNA is unwound and transcribed into complementary pre-mrna. THis is done by the RNA polymerase enzyme in the nucleus. The pre-mrna is processed into mature mrna. This strand of bases it the line of genetic code that will be directly transcribed into the polypeptide in the ribosome. The mature mrna exists the nucleus and heads toward the ribosome. The mrna contains three parts (figure). The first part is known as the leader sequence. The leader sequence is on the 5' end. These residues are not coded and occur before the start codon. The start codon, if you remember, is a AUG. This also codes for methane. The leader is followed by the coding region. Also known as the open reading frame. The open reading fame starts the start codon and continues for a variable length. The length of the open reading frame varies as does the protein that it codes for. The third part of the mrna is the trailer. The trailer region is a non-coded part that occurs after the start codon.

5 3.2 trna The basic structure of trna (transfer RNA) is shown (figure). It has a clover leaf pattern, 73 to 93 nucleotides, and is attached to an amino acid. The mass is approximately 25 kda, in about one half of the nucleotides are base pared. The amino acid is attached to the 3' end. The figure computer generated model attempts to show the 3d structure of trna. The trna's function is to bring the amino acid to the mrna by means of anti-codon bonding. The trna contains three bases that are complimentary to a codon found in the mrna. Each codon has a unique trna and a unique amino acid that will align in the proper order as instructed by the mrna. The trna will bind to the amino acids on the 3' end by means of an ester linkage on the carboxyl terminus of the amino acid. This is call amino acylation of trna. An enzyme amino acyl adenylate is vital for this process. The two steps of this reaction involve the amino acid activation to the amino acyl adenylate and then transfer to the amino acid of the CCA.

6 3.3 The Ribosome The ribosome is the site in which the actual production of the polypeptide occurs. This is where the mrna and the trna con come together in the right sequence to produce the protein as instructed by the DNA. The ribosome is comprised of two sub-units. The small ribosomal sub-unit is also known as the 30s sub-unit and the large ribosomal sub-unit is know 50s sub-unit. They are determined by their sedimentary separation sizes (Svedburg).

7 4. The Process of Translation 4.1 Initiation Initiation is where the start codon comes in contact with a particular trna molecule. Since the start codon is also the same codon for met there needs to be two kinds of met-trna (trnaimet used exclusively for starting protein chains, trnamet delivers Met to internal sites. In bacteria, a formyl group is added to Met-tRNAiMet). Initation in eukaryotes (eif2 and eif3 have similar counterparts in prokaryotes, eif4 is the cap binding protein, eif1 and 1A scan for initiation codon, eif5 stimulates association between 60S and 48S initiation complex, eif6 binds to 60S to prevent premature association, 60S +40S=80S (4200 kd)). Adapter eif4g (it binds to many proteins and help recruiting 40S to the mrna). (vi) Initiation sites (AUG or GUG preceded by purine-rich bases for 16S pairing, in bacteria called Shine- Dalgarno sequence, for eukaryotes the Kozak sequence -ACCAUGG- defines the initiation site). AUG is the only initiation codon. 40S binds to the cap and searches for AUG, a scanning process powered by helicase and ATP. Many initiation factors are involved. For example, eif4e binds to the 7-mG cap. eif4a is a helicase.

8 4.2 Elongation Elongation is where the polypeptide chain will grow one-by-one with the addition of amino acid residues. it has three steps. First EF-Tu with GTP brings an aa-trna to A site, peptidyl transferase forms a peptide bond, EF-G with GTP translocates the growing peptide and its mrna codon to the P site EF-G (molecular mimicry, the N-terminal region is similar to that of EF-Tu). Second elongation factor Tu,a G-protein family member, binds to aminoacyl-trna when it is in GTP form and then Thirdly delivers the aminoacyl-trna to the A site. EF-Tu cannot bind the fmet- trnaf, but bind Met-tRNAm. Once the complex is at the A site GTP will be hydrolyzed and EF-Ts will join the complex to release GDP. Peptide bond formation is spontaneous. Once formed, mrna must move by a distance of 3 nt and the new peptidyl-trna must move to the P site. This translocation is mediated by EF-G (aka translocase).

9 The amino acid chain needs to be moved along to make rom for the new residue as well as the mrna codons. Translocation mechanism (EF-G/GTP binds to 50S EF-Tu site, GTP hydrolysis induces conformational change and drives the stem of EF-G to A site and pushes trnas and mrna by one codon). 4.3 Termination Termination is where the mrna tells the ribosome to stop producing the polypeptide. It dose this by the use of stop codons that are part o the genetic code. Stop codons (UAA, UGA, or UAG is recognized by RFs, RF1 for UAA or UAG; RF2 for UAA or UGA; RF3 G protein homologous to EF-Tu, mediates interaction of RF1 or 2 with ribosome). The termination is done when the RF brings a H2O molecule to hydrolyze the ester bond in peptidyl-trna. This releases the polypeptide to be brought for posttranslational modification. Termination cocoas before the trailer sequence can be read in the mrna.

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