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Genes and Chromosomes, 截圖 2022-06-03 上午3.49.23, 截圖 2022-06-03 上午4.29.55,…

- - - - Normal B-form, relaxed DNA: 10.5 bp/turn (T, twist/turn)
    - - In circular DNA, changing the helical turns requires breaking a strand transiently.
      - Example: Relaxed circular dsDNA of 2100 bp in the
        B form (10.5 bp/turn) has
        
        Lk = 2100 bp 10.5/turn = 200
      - Lk is an integer for closed-circular DNA and is (+), reflecting a right-handed helix.(+)，反映右手螺旋
      - Negative and Positive Supercoils
        
        Linking Number Can Be Broken Down into Twist (Tw) and Writhe (Wr)
        Lk = Tw + Wr
        
        Twist (Tw) is the # twists or turns of the helix 螺旋的曲折
        
        Writhe (Wr) is the # coils 幾個線圈
    - - These enzymes are required for DNA unwinding and rewinding during transcription and replication.
      - Topoisomerases Are Enzymes That Change Lk
        
        Type I topoisomerase
        
        cut in one DNA strand, changes Lk by 1
        
        remove negative supercoils to relax DNA
        
        increase Lk
        
        use single-stranded breaks
        
        Topo I and III are Type I.
        
        Type II topoisomerase
        
        cut in both DNA strands, change Lk in steps of 2
        
        introduces negative supercoils
        
        decreases Lk
        
        uses ATP and double-stranded breaks耗能
        
        Topo II is called DNA gyrase.
        
        Eukaryotic Topoisomerases Include Topo I, II, II, IV
- - - - consists of fibers of
        protein /DNA / a small amount of RNA.
      - DNA associates tightly with proteins called histones.
      - -small proteins with lots of basic (Lys, Arg) residues這些帶正電
      - DNA and protein are packed into discrete units called nucleosomes.核小體
  - - - Wrapping DNA around the histone core requires removal of one helical turn.
        This (+) supercoil is relaxed by a topoisomerase, leaving DNA with net negative supercoil
        已經是nuclesomal的DNA
        儘管有結合histone也是透過topoisomerase去鬆開
      - Histone Binding Depends on DNA Sequence
        
        Histone binding is not random.
        
        It occurs more often at A-T–rich regions.
    - - Higher-Level Structures Depend on Chromosomal Scaffold
      - =Condensed Chromosome Structure Is Maintained by SMC Proteins
        
        SMC = Structural Maintenance of Chromosomes
        
        SMC proteins have five domains
        
        N and C domains form an ATP-binding site.
      - Two major types:
        
        cohesins
        
        help link sister chromatids姐妹染色單體
        
        condensins
        
        help chromosomes to condense; create positive supercoils讓染色質更緊密
- - - - Some Bacterial Genomes Also Contain Introns
        
        bacterial introns encode catalytic RNA sequences that have the ability to insert and reverse transcribe themselves into the genomic DNA細菌內含子編碼具有將自身插入和逆轉錄到基因組 DNA 中的能力的催化 RNA 序列
        
        they interrupt mainly tRNA sequences.
        
        do not interrupt protein-coding sequences;
- - - - -participate in the regulation of gene expression (promoters, termination signals, etc.).
      - -Some DNA encodes for small regulatory RNA with poorly understood functions.
    - - are expressed sequences (translated into amino acid sequence
    - - are regions of genes that are transcribed but not translated.
    - - -Introns are removed after transcription
      - -exon mRNA sequences are spliced together.
    - - Transposons轉座子.跳躍子
      - satellite” DNA
        
        Centromere Sequences
        著絲點
        
        Telomere Sequences
        端粒
        
        Homo sapiens (human) (TTAGGG)n
  - - - Human somatic (non-sex) cells have 46 chromosomes.
      - 22 pairs (diploid) plus X and Y
      - amounts to ~2 m of DNA
  - - - sister chromatid姐妹染色體
- - - - Are Where Proteins Attach During Mitosis有絲分裂
      - after DNA replication but before cell division,Region where the chromatids染色單體
      - are held together during mitosis有絲分裂
      - equal distribution of chromosome
      - Have AT-rich repeated sequences
    - - Cap the Ends of Eukaryotic Chromosomes
      - keep DNA ends from unraveling
      - contain multiple repeats with general sequence
      - added by enzyme telomerase (protein+nucleotides)
      - Homo sapiens (human) (TTAGGG)n
      - Telomeres Are Associated with Cellular Aging
        
        elomeres are shortened after each round of replication.
        
        human cells divide about 52 times before losing the ability to divide again (Hayflick limit).