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Ch.8 nucleotides and nucleic acids - Coggle Diagram

- - - - nitrogeneous base
        
        Derivatives of pyrimidine or purine
        
        Nitrogen-containing heteroaromatic molecules
        
        Planar or almost planar structures
        
        Absorb UV light around 250–270 nm
        
        我們知道的ATCG
        
        Cytosine, adenine, and guanine are found in both
        DNA and RNA.
        
        Thymine is found only in DNA. V
        
        Uracil is found only in RNA.
        
        都是好的H-bond donors and acceptors
        
        Neutral molecules at pH 7
        
        前面的ATUCG彙整，並“注意”層次p.13
        
        Tautomerism（雜環） of Nitrogenous Basesp.18
        
        Prototropic tautomers are structural isomers that differ in the location of protons
        
        . • Keto-enol tautomerism is common in ketones.
        
        • Lactam-lactim tautomerism occurs in some heterocycles.
        
        • Both tautomers exist in solution, but the lactam forms are predominant at neutral pH.
        
        UV Absorption of Nucleobasesp.20
        
        Absorption of UV light at 250–270 nm is due to π→
        
        π* electronic transitions. • Excited states of common nucleobases decay rapidly
        
        via radiationless transitions.
        
        – effective photoprotection of genetic material – no fluorescence from nucleic acids
      - – pentose
        
        Pentose Forms Differ in Some Nucleic acids and Nucleotides
      - – phosphate
        
        Phosphate group
        
        Negatively charged at neutral pH
        
        Typically attached to 5’ position
        
        Nucleic acids are built using the 5’-triphosphates
        version of the nucleotide.
        
        ATP, GTP, TTP, CTP
        
        Two of the three phosphates used for building nucleic acids form a leaving group, and completed nucleic acids contain one phosphate moiety per nucleotide.
        
        May be attached to other positions for specialized
        function
        
        Other Nucleotides: Monophosphate Group in Different Positions
    - - nitrogeneous base
      - pentose
      - 沒有！phosphate
      - Minor Nucleosides in DNA
        
        Modification is done after DNA synthesis. • 5-Methylcytosine is common in eukaryotes and is also found in
        
        bacteria. • N6-Methyladenosine is common in bacteria but not found in
        
        eukaryotes. • Epigenetic marker: • way to mark own DNA so that cells can degrade foreign DNA
        
        (prokaryotes) • way to mark which genes should be active (eukaryotes)
        
        :
      - Minor Nucleosides in RNA
        
        Inosine is sometimes found in the “wobble position” of
        
        the anticodon in tRNA.
        
        – made by de-aminating adenosine – provides richer genetic code
        
        • Pseudouridine (Ψ) is found widely in tRNA and rRNA.
        
        – more common in eukaryotes but found also in
        
        eubacteria – made from uridine by enzymatic isomerization after
        
        RNA synthesis – may stabilize the structure of tRNA – may help in folding of rRNA
  - - - 標號順序
        
        Pyrimidine嘧啶：先選定一個N，再往N的方向數
        
        Purine嘌呤(兩個環)：大環(6單元)：同上。小環(剩下3單元)：反方向
  - - - Conformation around N-Glycosidic Bond
        
        Relatively free rotation can occur around the N-glycosidic bond
        in free nucleotides.
        
        The sequence of atoms chosen to define this angle is O4’-C1’-
        N9-C4 for purine, and O4’-C1’-N1-C2 for pyrimidine derivatives.
        
        Angle near 0° corresponds to syn conformation.
        
        Angle near 180° corresponds to anti conformation.
        
        Anticonformation is found in normal B-DNA.
- - - - storage of genetic info (DNA)
      - – transmission of genetic info (mRNA)
      - – processing of genetic information (ribozymes)
      - – protein synthesis (tRNA and rRNA)
- - - - 有大溝major groove小溝minor
        
        DNA類型 ABZp.38
        
        注意左右轉直徑多少.,39
        
        互補
        
        複製replication
- - - - 當發現迴文的時候，他可以製造出互補股，就可以製造出髮夾
  - - - 有無打開可由up做偵測DNA denaturation is commonly monitored by UV
        spectrophotometry at 260 nm.
        
        當有50%denature被打開可以稱midpoint of melting(Tm)
        
        溫度的影響因素
        
        CG含量
        
        長度：尤其對長度較短的dNA影響更巨
        
        pH and ionic strength
- - - - very slow reactions
      - large number of residues
      - The net effect is significant:
        100 C → U events/day in a mammalian cell.
    - - N-glycosidic（糖甘鍵連接pantose與nitrogenous base） bond is
        hydrolyzed
      - Significant for purines: 10,000 purines lost/day in a mammalian cell
  - - - Oxidative dameage
        
        hydroxylation of guanine
        
        mitochondrial DNA is most susceptible 最常被攻擊
      - Chemical alkylation
        
        methylation of guanine