Finality of Molecular Biology
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66 terms
Terms | Definitions |
|---|---|
 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 |
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