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Genetic Code is Unequivocal each codon corresponds to only one amino acid. Genetic Code is degenerate for a given amino acid, there may be more than one codon. First 2 amino acids of a codon play a determining role in which amino acid the codon codes for. Similar Codons often correspond to amino acids with similar properties or chemical structures. Codon Usage Bias Not all codons coding for a given amino acid are used with the same frequency in the genes of an organism. tRNA length varies between 75 and 90 nucleotides tRNA secondary structure the shape of a clover leaf: internal base pairings between complementary bases make the stems and single stranded sequences make the loops. Acceptor Arm "a double-stand stem that ends in a single strand sequence, in which a OH group in position 2' or 3' of the terminal nucleotide can bind the amino acid. " TΨC arm "contains this triplet of bases. Ψ symbolizes pseudo-uridine, a modified base." Anti Codon Arm contains the anti-codon triplet at the center of a loop. This part of the tRNA recognizes the complementary codon on the mRNA. D Loop named because it contains another modified base : dihydrouridine. Variable Loop length varies between 2 and 21 nucleotides. Tertiary Structure takes the shape of the letter « L ». aminoacyl-tRNA synthetase produces an aminoacyl-AMP complex, and then reatcs the aminoacyl-AMP with the tRNA to form an aminoacyl-tRNA. Editing Site when the tRNA is bound to the synthesase, it drags the a.a. to this, which cannot accept the correct a.a. If an incorrect a.a. enters, it is removed. Wobble Hypothesis the identity of the 3rd nucleotide in a codon is variable to a certain degree. tRNAimet the tRNA that encorporates the first methionine from the AUG start codon. Shine-Dalgarno Sequence ribosome binding site, located 10nt upstream of the AUG, sequence is AGGAGGU. IF-3 recognizes the 30s ribosomal subunit and prevents it from binding the 50s unit IF-2 binds a GTP molecule and a tRNAfmet, once all factors come together, GTP is hydrolysed and the 70s subunit is complete. IF-1 binds to 30s subunits and reinforces interactions with IF2 and IF3 Kozak Sequence GCCa/gCC **AUG** G Ribozyme an RNA molecule which catalyzes a chemical reaction. EF-Tu binds to tRNA as it enters A site, temporarily preventing peptide bonding. If the codon, anticodon pair is correct GTP is hydrolysed and peptide bond is formed. EF-G binds to the A site and accelerates movement of the last two tRNAs to the hybrid sites A/P and P/E, by GTP hydrolysis, it recreates the A and P site. Release Factors bind to the A site of a ribosome when a stop codon is reached in the mRNA, and encorporates a H2O, instead of an amino acid, triggers release of chain. Translational Recoding When a stem and loop signal that binds a specific tranlation factor and allows selenocysteine to be incorporated. Tetracyclin blocks binding of aminoacyl-tRNA to the ribosome Chloramphenicol inhibits peptidyl-transferase activity of the ribosome Erythromycin blocks the movement of the ribosome Puromycin binds the A site and prevents translation Negative translational control (Shine-Dalgarno) proteins bind shine-dalgarno sequence, when ribosomal proteins are in excell they bind to their shine sequence. Negative translational control (Eukaryotes) repressors bind to the 5' end or the 3' UTR and interfere with communication of the cap complex Extracellular singal translation control extracellular signal molecules can alter translation of proteins, for example aconitase and iron metabolism. Recognition of DNA template RNA pol binds promoter and dissociates the two strands, forming a transcription bubble. Initiation once RNApol binds DNA it begins to synthesize 2-9 nt long RNAs Elongation RNApol goes beyond 9nt and sysnthesizes the entire mRNA. Termination formation of phosphodiester bonds stops and transctiptional apparatus dissociates. RNA Synthesis PhysChem Reaction is energetically favourable, -deltaG and is irreversible alpha factor enzyme assembly, recognizes promoters and binds to activators. 2 are needed to make RNApol. Beta factor Catalytic centre along with beta prime beta prime factor Catalytic centre along with beta sigma factor reduces the affinity of the core enzyme for sequences that are not promoters and increases the affinity of the core enzyme for sequences that are promoters. TATAAT "-10" consensus sequence for RNApol. TTGACA "-35" consensus seuqnece for RNApol. Intrinsic Terminators form a GC rich hairpin and a stretch of 6 Us at the end of the transcript, both interact with RNApol and terminate transcription. Rho dependent termination Rho protein binds to a C-rich/G-poor RNA sequence and indunce termination. Antitermination A region of DNA that normally enduces termination is not always read as such 100% of the time, thus some times a longer mRNA is produced. Transcriptional Activators proteins that increase transcription by enhancing the ability of the RNA polymerase to bind to a promoter and/or enhance the ability of the RNA polymerase to unwind the DNA. Transcriptional Repressors DNA binding proteins that decrease transcription by inhibiting the ability of RNA polymerase to bind to a promoter region. B-galactosidase (LacZ) cleaves lactose into glucose and galactose B-galactoside permease (LacY) membrane protein that pumps lactose into the cell B-galactoside transacetylase (LacA) enzyme involved in lactose metabolism cAMP levels negatively correlated to glucose levels. CAP only works once cAMP is present binds to its DNA binding region and promotes lac operon expression. Lac Repressor Binds to an operator sequence and loops DNA preventing Lac expresison, is inactivated by lactose. Ribose the sugar in RNA High pH causes the OH of carbon 2 of ribose to react with a phosphorus, cleaving the diester bond B Form the ds form adopted by RNA, different from the DNA helix, it has a narrower major groove, and a shallow minor groove. rRNA Makes peptide bonds during translation grp II self splicing introns are removed in the same way as normal splicing, but does not need any proteins, still needs the important A. grp I self splicing introns are removed without proteins, but requires a free G-nucleotide in any phosphorylated state. Hammerhead Structures RNA sequences that can cleave other RNA by first pairing, then cleaving and then unpairing. RNA pol-1 responsible for rRNA synthesis rRNA modifications methylation and isomerization of uridine into pseudo-uridine snoRNA position themselves through base pairings and attract enzymes responsible for rRNA modification