(6) Cell type with 5s genes (120 nt in length)(a) germcell (oocyte) = 20000 5s genes; 19,000 o-type (95% RNA) and 1,000 s-type (5% RNA) **makes sense(b) somatic = 20,000 5s genes; 19,000 o-type (about O% of RNA) and 1,000 s-type (100% of RNA) **doesn’t make sense(i) the different distribution of RNA gives differential gene expression (same gene expressed differentially in the cell)(ii) 2 types of ribosomal genes (s and o) only a 6 nucleotides different between them, and these are in the ICR. TF3A preferentially binds to the s type gene, not saying that it will not bind to that o type(iii) to alter amount of transcript product that are going to be made, you alter concentration of TF3A, therefore in oocytes there is an excess of TF3A, so it still preferentially binds to s type preferentially, but you have so many that they will bind to the o type as well. In somatic cells, have very limited amounts of TF3A(iv) differential gene expression is caused by altering the concentration of transcription factor.(7) 5s RNA has promoter downstream(a) ICR- is the promoter in this case, in the middle of the gene called internal control region read by RNA polymerase III, and invites– transcription factor 3A(c) Promoter in the middle of the coding region is not a hindrance to the duplication of RNA because we do not compliment the code, we duplicate on the template strand and the factor will be on the coding strand(d) happens in the nucleoplasm (no specific location)- must have an ‘escort’ protein to bind to the 5s RNA called TF3A, the same protein that acts as the transcription factor, and binds probably somewhere between 50 and 83 because it is so similar to the coding strand here to bring it into the nucleus(e) TF3A protein has 2 roles, transcription factor and a factor that moves the RNA making 7sRNP to be escorted to the granular region of the nucleusj) The granular region is where the 60 and 40s subunits are being made(1) then when ready, they are transported to the cytoplasm through large pores, but they are not transported together, there is not ever an 80s when it is not doing work making a protein5. Transfer RNA- smallest of the RNA 75-85nt in lengtha) about 50 different tRNA can be made for the 20 amino acids, therefore an amino acid can correspond to multiple different types of tRNAb) 3D – high number of secondary structure, large number of hairpin loops and looks like an L shape, if flatten out, get the cloverleaf structure, and has 5’ end with close association with the 3’ end.c) all have 3 loops and the last 3 nucleotides on the 3’ end is always CCAd) each loop has specific names:(1) one closest to 5’ end is the D loop, and the nucleotides here are slightly altered, chemically modified, specifically uracil(2) the t(psi)C loop is closest to the 3’ end and the nucleotides here are also partially offered- and this allows us to react with the 5s RNA of the ribosome(3) the loop in between is called the ‘variable loop’ because for each of the 20 amino acid families, there are 3 nucleotides within this loop that make up the anticodon that is complimentary to the codon on the mRNA transcript for protein synthesise) Process of binding the tRNA to an amino acid takes place at the 3’ end (C-C-A-CO-CR—NH2)(1) This process is absolutely critical, there are no mistakes in this process because they are controlled by the family of 20 enzymes called aminoacyl-tRNA-synthase(a) aminoacyl-tRNA-synthase has 2 active sites, so that if by some circumstance something binds wrong, there is a back up that takes care of it(b) 1st active site reaction: aa + ATP  aa-AMP + PP(c) 2nd active site reaction: aaAMP + tRNA  aa-tRNA +AMP(d) Process is VERY costly, needs 2 ATP6. Protein Synthesis (NOT ON TEST 2)a) 3 processes: Initiation, Elongation and Terminationf) Initiation-(1) first the 40s comes in with ribosomal binding region- No 60s yet(2) Initiation factor 1 (IF1) help to escort the tRNA (1st one always carries methionine) so that it sits in there just perfectly(3) Initiation factor 2 (IF2) helps to escort the tRNA (1st one always carries methionine) so that they sit together, anticodon and codon(4) Initiation factor 3 (IF3)- lines up the message on the 40s ribosomal subunit, make sure it is in place, ready to do its job. 1st part of message lines up so 1st codon is correctly oriented (Always AUG)(5) the IFs are all removed and the 60s is lined up with the 40sg) Elogation(1) costly process to make proteins, so you can turn it off by phosphorylating IF2 to inhibit the tRNA attaching to the mRNA(a) phosphorylation is a common regulator(b) this can be regulated by outside sources, a series of signalsBY 330 1st Edition Lecture 12 Outline of Last Lecture 4. RibosomeOutline of Current Lecture 4. Ribosome5. Transfer RNA6. Protein SynthesisCurrent Lecture(6) Cell type with 5s genes (120 nt in length)(a) germcell (oocyte) = 20000 5s genes; 19,000 o-type (95% RNA) and 1,000 s-type (5% RNA) **makes sense(b) somatic = 20,000 5s genes; 19,000 o-type (about O% of RNA) and 1,000 s-type (100% of RNA) **doesn’t make sense(i) the different distribution of RNA gives differential gene expression (same gene expressed differentially in the cell)^^ WHY... answered next time(ii) 2 types of ribosomal genes (s and o) only a 6 nucleotides different between them, and these are in the ICR. TF3A preferentially binds to the s type gene, not saying that it will not bind to that o type (iii) to alter amount of transcript product that are going tobe made, you alter concentration of TF3A, therefore in oocytes there is an excess of TF3A, so it still preferentially binds to s type preferentially, but you haveso many that they will bind to the o type as well. In somatic cells, have very limited amounts of TF3A (iv) differential gene expression is caused by altering the concentration of transcription factor. (7) 5s RNA has promoter downstream These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.(a) ICR- is the promoter in this case, in the middle of the gene called internal control region read by RNA polymerase III, and invites– transcription factor 3A (c) Promoter in the middle of the coding region is not a hindrance to the duplication of RNA because we do not compliment the code, we duplicate on the template strand and the factor will be on the coding strand(d) happens in the nucleoplasm (no specific