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Eukaryote - Coggle Diagram

- - - - RNA-pol I-synthesies most rRNA and is sensitive to α-amanitin
      - RNA pol II- synthesies hnRNA(protein coding genes) and is very sensitive to α-amanitin
      - RNA pol III- synthesies tRNA and other small nuclear RNAs and is somewhat sensitive to α-amanitin
  - - - addition of m7Gppp(5') cap
        
        it is bound to 5' end with 3 phosphates
        
        [rotects from degradation and helps with recognition
        
        modified guanosine base
      - 3' cleavage and pol(A) tail addition
        
        it is a run of A and U, then ~20 bases, then a CA, then last bases
        
        tail added by polyA polymerase
        
        the rest is cleaved
      - Intron excision and exon ligation
        
        G is first base and A is the last base in intron, and there is a consensus sequence at start and end of intron
        
        splicing performed by spliceosomes
        
        requires 5 snRNP particles (U1, U2, U4, U5, U6)
        
        The A interacts with guanosine, this leaves an OH at the end of the exon and forms a lasso (lariat formation) which is still attached to the other exon
        
        U1 and U2 assist in finding the cleavage site by adenine, U4 U5 and U6 allow OH to bind to beginning of next exon
    - - it coordinates the activities of splicing
      - the C-terminal domain carries the splicing factors involved
      - the domain is regulated by phosphorylation
    - - because of different splicing factors
      - splice sites can be at different points, exons can be skipped, intron retained
  - - - achieve similar coordination to operons
      - TF binds to CIS or promotor motif on many genes on different chromosomes
      - General transcription facots
        
        they bind to the pre-initiation complex
        
        there are different factors- TFIID, TFIIB, TFIIG, TFIIH
        
        TFIID arrives first encourages other factors
        
        they position RNA pol IIat TATA box
    - - proteins binding leads to bending of the duplex
      - C-terminus domain of protein interacts with TATA box
      - has consensus sequence TATAAA and is located -25 to -30
    - - TFs, GTFs and RNA pol II leads to no transcription so needs cofactors
      - structure
        
        multiprotein complex
        
        tail binds to TF, head binds to RNA Pol II, middle acts as a hinge
      - it recruits RNA pol II to gene
      - different subunits play role in transcription under certain conditions (i.e cold)
  - - - acetylated chromatin is open and transcriptionally active
      - deacetylated chromatin around FLC gene controls flower (produces regulatory protein that inhibits flowering)
      - done by acetyltransferase
  - - - invlove non-coding RNA
      - a dsRNA molecule forms through one or other route
      - DICER enzyme cuts it
    - - come from a ssRNA precursor that forms small hairpins
      - the pre-miRNA is the whole RNA sequence and miRNA is just the hairpin
      - one strand of miRNA combines with proteins to forma an RNA-induced silencing complex
    - - formed from cleavage of mRNA, RNA transposons or RNA viruses
      - dsRNA is cleaved into little pieces by DICER and protein binds to form a RSC which binds to RNA
      - binding is exact and the mRNA is cleaved
      - transcribed by RNA polymerase IV to silence transposons and RNA pol V transcribes siRNA involved in DNA methylation
    - - found in mammalian testes
      - suppress transposable element expression
    - - assist in destruction of foreign DNA
- - - - 70S (30S and 50S)
      - 30S is 16S rRNA and 50S is 23S and 5S rRNA
    - - 80S (60S and 40S)
      - 60S is 28S, 5.8S and 5S rRNA and 40S is 18S rRNA
    - - centrifuging cell layer above sucrose gradient forms bands depending on sedimentation coefficients
      - heavier molecules sink more quickly and travel faster
      - those that travel further get a higher rating with Svedberg unit (S)
  - - - consists of acceptor arm, D arm, anticodon arm, variable loop (sometimes not there), and TC arm
      - acceptor arm always ends with CCA whereas the rest form different bases
      - it is much shorter than rRNA
    - - the A of CCA forms covalent bond with amino acid
      - they join a specific amino acid to the tRNA
      - specific aminoacyl tRNAs are assembled for each different amino acids (amino acid-> amino acid-AMP (using ATP and ejects phosphorylate)-> aminoacyl-tRNA (adds tRNA and ejects AMP)
      - it corrects its own mistakes, by recognising a site and then moved to a different editing site
    - - first codon is AUG for methionine, and its tRNA is different for other mets
      - eukaryotes use Met-tRNAimet
      - bacteria use Met-tRNAfmet because their first met is N-formylmethionine (formyl group or whole met is often removed)
  - - - the start is attached by small IF-3 which helps correctly position ribosome
      - initial tRNA then attached with IF-2 and GTP
      - the large subunit joins with IF1 and the GTP is hydrolysed to move the large subunit and lock it in
      - all IFs and GDP detach
      - binding
        
        prokaryotes- 16S binds to Shine-Dakgarno sequence in mRNA
        
        Eukaryotes- subunits, IFs and Met-tRNAimet find 5' cap and find start codon via Kozak sequence and the polyA tail assists small subunit
    - - first amino acid goes straight into P-site
      - the addition of next amino acid comes with EF-1A-GTP
      - EF-1B regenerates EF-1A has yielded the energy in its attached GTP
      - EF-2 and GTP arrive and deacylated tRNA, EF-2 and GDP detach then amino acid moves out the ribosome
      - in between P and A site the peptidyl transferase makes peptide bond between 2 amino acids
    - - it occurs when the ribosome reaches a stop codon
      - when it reaches the stop codon there is no amino acid to go into the A site and release factor occupies the place
      - RF cannot form a peptide bond, RF1 recognises UAG,UAA; RF2 recognises UGA, UAA and RF3 releases the polypeptide
      - ribosomal release factor separates the ribosomal subunits
  - - - stops cells making useless or toxic versions of proteins
      - nonsense mediated decay- elimination of mRNA with premature stop codons (eukaryotes)
      - tmRNA- stops accumulation of deleterious proteins (prokaryotes)
    - - sometimes mistakes or a break in mRNA mean the stop codon is cleaved off
      - fix
        
        tmRNA with a charged alanine goes into the A site
        
        the mRNA positions it so it is read by the ribosome
        
        the ribosome adds alanine and continues to read 10 more codons
        
        it then reaches a stop codon that enters the A site to release
        
        the cell recognises the additional amino acids and the protein is marked for destruction
- - - - changes are they wrap around the DNA
      - lysine residues can be acetylated or methylated
      - serine residues can be phosphorylated
      - modifications are interactive and summative
      - acetylationis a shift from heterochromatin to euchromatin (methylation is gene silencing)
      - phosphorylation is required for mitosis and meiosis
  - - - tightly condensed
      - genetically inactive
      - found in eukaryotes
    - - less condensed
      - transcribed
      - found in both prokaryotes and eukaryotes