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Eukaryotic DNA
Uni of Notts, Genes, Molecules and Cells, first year
| Term | Definition |
|---|---|
| Histones | Positively charged (basic) octamer proteins which bind ionically to DNA causing it to coil tightly & efficiently. Is used for structural support & gene regulation in eukaryotic cells |
| Nucleosome | DNA wrapped 100-fold around a histone octamer (made from 2 units of H2A, H2B, H3, & H4) with H1 proteins linking the DNA together to form the basic beaded subunit of chromatin |
| Euchromatin & heterochromatin | Euchromatin is loosely packed chromatin with acetylated histones that is more transcriptionally active. Heterochromatin is the opposite |
| Production of pre-mRNA | RNA polymerase II binds to the promotor sequence (TATA box) to transcribe the template strand into pre-mRNA containing introns & exons with a polyadenylation site (AAUAAA) at the end |
| How pre-mRNA is converted to mature mRNA | Introns are spliced out with a spliceosome that recognises intron borders in the sequence & exons are linked seamlessly. A methylated 5' is added for stability & the adenylation site is adenylated with a poly-A-tail |
| Why transcription start & end points don't match the protein coding region | Regulatory Untranslated Regions (UTRs) are added at the 5' end for ribosome binding & the 3' end for removal from ribosomes & degradation, translation start & end codons are added. Protein coding lies in the middle |
| Coupled transcription-translation in prokaryotes | Transcription & translation occur in cytoplasm allowing mRNA to be translated while being synthesised making it a very fast process due to lack of nuclear membrane & introns |
| RNA polymerase I RNA polymerase III | RNA polymerase I: Produces rRNA RNA polymerase III: Produces tRNA, snRNA (small nuclear, involved in mRNA processing), & 5SrRNA (large subunit rRNA) |
| Core promotor Proximal promotor | Core promotor: Transcription starting point, with RNA initiation site & sometimes 25bp TATA box Proximal promotor: Next 100-200bp after core, fine tunes & modulates gene expression |
| General transcription factors & assembly | Transcription factors bind to TATA regions on major grooves of DNA in a specific order to form a pre-initiation complex, opening up the helix & allowing RNA polymerase II to bind |
| Activators, enhancers, & chromatin unpacking | Activators bind to enhancement markers (often far from promotors) to recruit chromatin remodellers & coactivators to unpack the chromatin to expose the promotor & form initiation complexes more easily |
| initiation complexes | Group of proteins such as general transcription factors & RNA polymerase II at major grooves to unwind the helix & allow for the transcription of the gene |
| TATA boxes | DNA sequence rich in T & A bases found in most eukaryotic promotors found 25-35bps upstream of a transcription sequence to allow initiation complex proteins to bind |
| 5' methylated cap | Modified G nucleotide (7-methylguanosine) 2nd from the 5' end (unusual since bases aren't usually added to 5'). Prevents premature RNA degradation, aids transport out of nucleus, & allows certain factors to bind |
| 3' poly-A-tail | After transcription, a protein complex binds to the polyadenylation site & cuts 11-30 bases downstream while 150-250 adenine bases are added to stabilise the mRNA & aid nuclear export & translation efficiency |
| Initiation | Small ribosomal subunit binds to 5' cap & moves along the sequence until it finds AUG. Initiator tRNA binds here through base pairing & begins the peptide sequence at the P site |
| Elongation | The next tRNA binds to the A site bringing the next amino acid forming a peptide bond with the first, the ribosome translocates 1 codon down moving P site to E (exit) site, A to P, & the process repeats |
| Termination | At end end codon, no new tRNA binds & a release factor binds to the A site causing the release of tRNA from the P site & dissociation of the peptide |
| Energetics of peptide bond formation: Part 1 (tRNA charging) | aminoacyl-tRNA is an energetically unfavourable molecule to create so ATP is hydrolysed along its phosphoanhydride bond to form an aminoacyl-AMP intermediate & PPi. This is unstable & substitutes AMP for tRNA |
| Energetics of peptide bond formation: Part 2 | When aminoacyl-tRNA binds to the codon, the bond holding the amino acid is so unstable that it's more favourable for the N terminal to attack the acyl carbonyl nucleophilically to form a bond |
| Benefit & drawback of genetic code being degenerate | Since the code is non-overlapping, less of the protein is impacted by mutations but more space is needed for coding |
| Crick & Brenner reading frame experiment | Deleting a single nucleotide in a gene causes complete loss of function but a second insertion mutations restores gene function |
| Reading frames & their shifts | Grouping of mRNA codons into 3s to be translated into amino acids starting from a fixed point of origin. Addition or deletion of bases not divisible by 3 changes every codon downstream of the mutation. There are up to 3 active reading frames at a time |
| How codons were first discovered: Nirenberg & Leder | Bound ribosomes to nitrocellulose filters (only stick large molecules) & synthesised all 64 possible trinucleotide combinations with radiolabelled tRNAs & only complimentary matches stuck to the filter & transmitted radiation |
| When genetic code isn't universal | Due to losing independence in endosymbiotic relationships, mitochondria don't have the same adaptive pressure as their hosts & limited tRNA (only 22) so they assign codons to fit their limited translation system |
| Structure of tRNA (5) | 2D folded clover shape with acceptor stem (3' modified base bound to specific amino acid), D loop (modified D bases for synthetase recognition), anticodon arm, TΨC arm (fits into ribosome), variable loop (adds flexibility |
| Importance of tertiary structure of tRNA | Rigid L-shaped from base stacking, internal base pairing, tertiary interactions & modified bases. Fits perfectly into A, P, E pockets of ribosome puts amino acid in catalytic centre, & guarantees anticodon matching |
| Base stacking | When flat (aromatic) rings of nitrogenous bases compact together one on top of the other using hydrophobic interactions & Van Der Waals to exclude water & stabilise the structure |
| Modified bases | Post-transcriptionally altered nitrogenous bases (e.g., reducing uracil to dihydrouridine, or deaminating adenine to inosine) to have new properties such as stabilising folding, flexibility, & codon recognition |
| How triplet code degeneracy occurs: "Wobble" pairing | 3rd tRNA anticodon base (1st mRNA base) is flexible & can form non-Watson & Crick pairs or use modified bases (such as inosine) which can pair with A, U, or C. The same tRNA can bind to multiple codons |
| tRNA charging proofreading | tRNA synthetase has an editing domain which can hydrolyse the false amino acid even once it's already been transferred & before the tRNA leaves |
| tRNA proofreading: Valine & isoleucine example | Isoleucine is the methylated form of valine making them very similar molecules & can be substituted for each other every 40,000 amino acids. Isoleucine is just slightly too big to fit in the editing domain so valine is hydrolysed by IleRS |
Created by:
Beech47
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