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Nucleotides and Nucleic Acids, DNA, RNA - Coggle Diagram

- - - - forms differ in some nucleic acids and nucleotides
      - β-d-ribofuranose in RNA
      - β-2’-deoxy-d-ribofuranose in DNA (2'指去氧位置)
      - different puckered conformations of the sugar ring are possible
    - - about
        
        All are good H-bond donors and acceptors --> 可跟彼此形成H-bond ==>DNA雙股螺旋
        
        Neutral molecules at pH 7
        
        Uracil is found only in RNA
        
        Thymine is found only in DNA
        
        Cytosine, Adenine, and Guanine are found in both DNA and RNA
        
        absorb UV light around 250–270 nm --> 可測DNA&RNA 濃度
        
        planar or almost planar structures
        
        nitrogen-containing heteroaromatic molecules
        
        derivatives of pyrimidine or purine
      - Nomenclature
        
        deoxyribonucleotides
        
        ribonucleotides
        
        summary
      - β−N-Glycosidic Bond 醣苷鍵
        
        about
        
        In nucleotides, the pentose ring is attached to the nitrogenous base via a N-glycosidic bond
        
        The bond is formed to the anomeric carbon of the sugar in β configuration
        --is formed to position N1 in pyrimidines
        --is formed to position N9 in purines
        
        quite stable toward hydrolysis, especially in pyrimidines平常非常穩定
        
        bond cleavage is catalyzed by acid 以酸催化來斷鍵
        
        conformation around
        
        relatively free rotation can occur around the N-glycosidic bond in free nucleotides
        
        angle near 0° corresponds to syn conformation同向(朝裡面)
        
        angle near 180° corresponds to anti conformation反向(朝外面)
        
        anticonformation is found in normal B-DNA
      - tautomerism of nitrogenous bases 結構上的H+會跑動
      - UV absorption of nucleobases
        
        excited states of common nucleobases decay rapidly via radiationless transitions
        --effective photoprotection of genetic material 保護遺傳物質
        --no fluorescence from nucleic acids
        
        absorption of UV light (吸收多少光反推濃度)at 250–270 nm is due to π --> π(能量激發) electronic transitions
    - - Typically attached to 5’ position
        
        Nucleic acids are built using the 5’-triphosphates version of the nucleotide.(ATP, GTP, TTP, CTP)
        補充：TP-3*phosphate(α, β, γ)
        
        β, γ常形成leaving group
      - May be attached to other positions for specialized function
      - Negatively charged at neutral pH
      - Other Nucleotides：Monophosphate Group in Different Positions
    - - DNA
        
        N6-Methyladenosine is common in bacteria but not found in eukaryotes.
        
        Epigenetic marker表觀基因學 ：不會改變基因的構造與組成，做表面的改變(epi上) --> 影響許多但不做遺傳
        。prokaryotes: to mark own DNA so that cells can degrade foreign DNA 保護
        。eukaryotes: to mark which genes should be active 標示
        
        5-Methylcytosine is common in eukaryotes and is also found in bacteria
        
        Modification is done after DNA synthesis (DNA出現後才修飾)
      - RNA
        
        pseudouridine (Ψ ) is found widely in tRNA and rRNA
        --> stabilize the structure of tRNA
        --> help in folding of rRNA
        
        Inosine is sometimes found in the “wobble position” of the anticodon in tRNA
        原本沒有那麼豐富的結構，為了有更多的遺傳密碼子 --> inosine
  - - - RNA backbone is unstable (e.g.抽RNA不能講話，因為口水裡有酵素)
      - Linear polymers 本身是一條很直的結構
      - DNA backbone is fairly stable
      - read the sequence from 5’ to 3’
      - Covalent bonds are formed via phosphodiester linkages
        
        negatively charged backbone
        因為phosphate groups都帶負電(跑DNA電泳都是由負-->正)