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Genes & Chromosomes, The Topoisomerases Types in - Coggle Diagram

- - - - In bacteria
        
        they interrupt mainly tRNA sequences,do not interrupt protein-coding sequences
        
        Many bacterial introns encode catalytic RNA sequences that have the ability to insert and reverse transcribe themselves into the genomic DNA.
      - In phage
        
        interrupt protein-coding sequences.
  - - - can move around within the genome of a single cell.
      - the end of transposons: contain terminal repeats,and hybridize with complementary regions
        of target DNA during insertion.
  - - - centromeres 著絲點
        
        Have AT-rich repeated sequences of ~130 bp. Essential for equal distribution of chromosome sets to daughter cells
        
        Region where the chromatids are held together during mitosis.(after DNA replication but before cell division)
      - telomeres 端粒
        
        keep DNA ends from unraveling
        
        Are Associated with Cellular Aging, telomeres are shortened after each round of replication in many tissues.具有保護生物體基因的功能，但無法防止DNA分子因連續多回複製而縮短，只能延緩DNA分子末端基因被侵蝕
        
        Telomerase 端粒酶
        
        真核生物的生殖細胞為避免染色體DNA越來越短，以致其上基因消失，故具有端粒酶以催化端粒延長，以恢復DNA的長度
        
        P.s 一般細胞不具有端粒酶，故細胞複製的次數有限，當DNA過短則使細胞進行凋亡
        
        端粒和癌細胞
        
        癌化的體細胞中發現端粒酶的活性較高，使癌細胞可無限制的進行細胞分裂。
- - - - Positive supercoils(+)
      - Negative supercoils(-)
        
        Note that negatively supercoiled DNA (more compact) travels faster in an agarose gel electrophoresis experiment than relaxed or nicked DNA do.
    - - Plectonemic
        
        involves a right-hand superhelix with terminal loops in plasmids.
      - Toroid/Solenoid
        
        provides more compaction, involves tight left-hand turns, in chromatin
  - - - Expresses change in LK in a quantity independent of DNA length
    - - Lk is an integer for closed-circular DNA and is (+), reflecting a right-handed helix.
      - Formula
        
        Linking number in relaxed DNA:
        Lk = total of bp / (10.5bp/turn)
        
        Underwind by removing two helical turns: if原本的 Lk = 198
        Lk = 198 – 200 = –2
        
        Lk = Tw + Wr
        
        Twist (Tw)
        
        is the # twists or turns of the helix (+)
        
        Writhe(Wr)
        
        is the # coils (-)
        
        Example
        
        若有一個LK=20的 relaxed DNA，remove 4 turns and rejoin，則有兩種可能：
        
        LK=16
        Tw=16
        Wr=0
        
        LK=16
        Tw=20
        Wr=-4
  - - - Function
        
        are required for DNA unwinding and rewinding during transcription and replication,which Change Lk
        
        Reason
        
        超螺旋的發生是因為有結構性張力被引入DNA而導致：為了疏解張力，所以進一步纏繞成為雙螺旋。至於結構性張力被引入的原因，是因為有拓撲異構酶的存在。拓撲酶的作用原理是：對於放鬆狀態的DNA進行切割後，移位，再粘回去，從而將張力引入螺旋之中，導致超螺旋的形成。
        
        Types
        
        Type I
        
        make a transient cut in one DNA strand, changes Lk by 1
        
        Type II
        
        make a transient cut in both DNA strands, change Lk in steps of 2
        
        Topoisomerase Inhibitors used as
        
        Chemotherapy Agents
        
        Eukaryotic Type I topoisomerase inhibitors
        
        captothecin, irinotecan (Campto), topotecan (Hycamtin)
        
        Eukaryotic Type II topoisomerase inhibitors
        
        doxorubicin (Adriamycin), etoposide (Etopophos), ellipticine
        
        Chemotherapy Drugs
        
        Doxorubicin, Etoposide, Ellipticine
        
        Antibiotics
        
        Coumarins(inhibit bacterial Type II topoisomerases from binding ATP), Quinolones(inhibit the last step, which is resealing the DNA strand breaks),Nalidixic acid,Ciprofloxacin,Irinotecan, Topotecan
- - - - In longer DNAs and higher levels of DNA underwinding ,the effect of underwinding is important. Because the hydrogen-bonded base pairs would generally preclude strand separation over such a short distance
- - - - Nucleosomes
        
        Histones(共有8個)
        
        H2A, H2B, H3, H4 各乘以2
        
        DNA
        
        is a “linker” DNA and bound to histone H
        
        Wrapping DNA around the histone core requires removal of one helical turn.
        The underwinding occurs without a strand break, so a compensatory (+) supercoil forms.
        
        H1
        
        Amino-terminal tails of histones stick out, form sites for covalent modification, and form important contacts between nucleosomes.(The amino-terminal tails of one nucleosome extrude from the particle and interact with adjacent nucleosomes, helping to define higher-order DNA packaging.)
        
        It forms a left-hand solenoid.
  - - - S (synthesis) phase
      - G2 (gap) phase
      - G1 (gap) phase
    - - 中期
        
        有些紡錘絲連結於染色體中節的著絲點上、染色體隨意排列在紡錘體中央
      - 後期
        
        個染色體的中節分裂為二、姐妹染色體分離向兩極移動
      - 末期
        
        細胞膜內凹陷、細胞一分為二、染色體變成染色質、核膜核仁出現
      - 前期
        
        染色質變染色體(二分體)、核膜核仁消失、中心粒形成紡錘體
- - - - one strand of double-stranded DNA acts as the molecular template for RNA synthesis (DNA ->messenger RNA).
    - - Proteins (determines its biological function ) are synthesized based on the information stored in ribonucleotide triplets in RNA. the triplets of nucleotides in mRNA bind to complementary triplets in tRNA.