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RNA Metabolism, Protein Metabolism - Coggle Diagram

- - - - Transcription Using RNA Pol II
        
        Initiated
        
        TATA-binding protein (TBP) with the promoter
        
        Helicase
        
        unwinds DNA
        
        Kinase
        
        phosphorylates the polymerase
        
        at the CTD
        
        changing the conformation and enabling RNA Pol II to transcribe
        
        Elongation
        
        Elongation factors bound to RNA Pol II enhance processivity and coordinate posttranslational modifications
        
        Termination
        
        Pol II is dephosphorylated
- - - - promoter sequence
        
        deviating from the consensus sequence
      - activator proteins
        
        CRP
      - repressor proteins
        
        block necessary binding sites
  - - - self-complementary regions in transcript form a hairpin 15−20 nt before the 3’ end
    - - ρ protein processes until
        termination site reached
      - ρ protein is a helicase,
        binds to rut site
- - - - Self-splicing group I introns
      - Hammerhead ribozyme
      - RNase P
  - - - elimination of introns; joining of exons
    - - 3’ end
    - - 5’ end
- - - - govern efficacy of RNA Pol binding and
        therefore affect gene-expression level.
- - - - Group I and group II introns
        
        self-splicing
        
        in nuclear, mitochondrial, and chloroplast genomes
        
        no additional proteins or ATP
        
        Group I
        
        Group II
      - Spliceosomal introns
        
        called spliceosomes
        
        frequent in protein-coding regions of eukaryotic genomes
        
        made up of snRNPs
        
        GU at 5’-end and AU at 3’-end usually mark sites of splicing.
        
        Spliceosome Assembly
      - tRNA introns
        
        spliced by protein-based enzymes.
        
        ATP-dependent ligase
- - - - Step 1 − creation of aminoacyl intermediate
      - Step 2 – transfer of aminoacyl to tRNA
      - The Second Genetic Code
        
        Matching each amino acid with correct tRNA can be viewed as the“second genetic code.”
  - - - The first codon of any peptide is AUG (Met)
      - Eukaryotic protein begins with Met, not fMet, but a
        special tRNA is still used for peptide initiation.
      - two additional amino acids are also found in a few
        proteins and are genetically coded.
        
        Selenocysteine
        
        Pyrrolysine
      - Prokaryotic
        
        Step 2: fMet-tRNAfMet
        joins the complex
        
        Step 3: 50S subunit
        associates
        
        Step 1: The 30S ribosomal subunit binds IF-1, IF-2,
        and IF-3 and mRNA.
      - Eukaryotes
        
        Use more initiation factors
        
        Step 1: 40S subunit
        joins with eIF1A and
        
        Step 2: eIF2 and the
        charged tRNAMet with bound GTP join the 40S
        
        Step 3: mRNA binds
        with eIF4F
        
        Step 4: scanning of
        the mRNA until an AUG codon is
        found
        
        Step 5: 60S subunit
        associates and many of the
        initiation factors are released
  - - - Step 1: binding of the
        incoming aminoacyl-tRNA
      - Step 2: peptide bond forms
      - Step 3: translocation of
        the ribosome
    - - Steps are similar to bacteria
  - - - UAA, UAG, or UGA in the A site will trigger the action of termination factors (release factors) RF-1, RF-2,RF-3.
  - - - removal of formyl group
      - removal of Met
      - acetylation of N-terminal residue
      - Removal of signal sequences or other regions
      - Attaching carbohydratesRemoving sequence to activate an enzyme
      - Removing sequence to activate an enzyme