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cell biology 1st examination_2018.04.10 (Ch12. Endomembrane system (12-4…

- - - - microscope
        
        light
        
        electronic
    - - chemistry
        
        how cell function
        
        enzyme, ATP, pathway
    - - information
      - bioinfomatics
- - - - lipids
        
        define barriers
      - proteins
        
        detect and transduce signals
        
        mediate connection and ahesion
        
        participate communication
        
        produce extracellular matrix
    - - sandwich model:
        Davson and Danielli
        
        more details
        
        discredited
        
        因為用磷酸酶可以分解細胞膜，但是模型說蛋白質應該可以保護好
        
        分離更多膜蛋白的時候發現，用清潔劑就可以分離了，這指出蛋白質應該不是水溶性的，而是疏水性或至少是兩性的
        
        蛋白質跟膜的化學比例有極大的差別
      - Fluid mosaic model:
        Sanger and Nicolson
        
        halobacterium：用電子顯微鏡去看蛋白質組成，發現它是用好幾條alpha-helix來回穿插而成
      - lipids and protein are not randomly distributed
        
        lipid rafts
    - - sterols
        
        cholesterol in animal
        
        phytosterols in plant
        
        not sterols in bacteria but similiar hopanoid
      - fluidity
        
        length
        
        unsaturation
        
        addition of cholesterol
        
        lipi rafts
        
        lipid rafts 是一塊塊比較固定而且比較厚的區塊，已膽固醇被區別開來
      - move
        
        flip-flop
        
        有一些酶是有專一性的，只會送其中一種
        
        asymmetric
    - - classified
        
        Integral
        
        有一個以上的部分是跟膜的內部有親和性(疏水性)
        
        有少數叫做transmembrane protein，是指沒有把蛋白質打到另一端的
        
        Peripheral
        
        表示只有在表層，沒有疏水從進到內部的蛋白質
        
        跟膜的表面用氫鍵結合
        
        Lipid-anchored
        
        跟膜的表面有共價鍵結合
      - function
        
        enzymes
        
        electron carriers
        
        transport molecules
        
        receptor sites
      - glycoproteins
      - methods
        
        SDS-PAGE
        
        molecular biology
        
        X-ray crystalgraphy
        
        affinity labeling
        
        specific antibodies
  - - - transport what: large, polar molecules and ions
      - carrier
        
        alternate two conformational state
        
        examples
        
        anion exchange proteins
        
        antiport
        
        如果任何一方缺少就會停止
        
        Cl-, HCO3-
        
        先抓Cl-，改變並釋放之後再抓CO3-，再改變回去
        
        glucose transporter
        
        uniport
        
        葡萄糖結合T1的蛋白質，造成T1變成T2，然後葡萄糖又因為T2被釋放出來，T2沒有蛋白質再變回T1
        
        可以雙向運輸的
        
        細胞內一直保持低濃度，是因為葡萄糖進去之後馬上被磷酸化(因此不能經過蛋白質
      - channel
        
        classified
        
        single kind: uniport
        
        two or more
        
        same direction: symport
        
        inverse direction: antiport
        
        examples
        
        ion channels
        
        肌肉收縮
        
        鹽分平衡
        
        porins
        
        細菌外膜、粒線體、葉綠體
        
        b barrel穿過細胞膜、極性支鏈在孔的周圍
        
        aquaporins
        
        gated
        
        voltage
        
        ligand
        
        mechanosensitive
    - - power by: ATP, electronchemical potential, ion graient, light
      - type:
        
        P
        
        P1 重金屬離子
        
        P2-維持離子濃度
        
        P3-植物和真菌和細菌，把質子打出細胞膜
        
        P4-把膽固醇跟脂肪酸打出去雙層膜，但是很像flippase
        
        V
        
        把質子打進胞器
        
        F
        
        在細菌、粒線體、葉綠體把質子打出去，重點在於可以雙向運輸
        
        ABC
        
        一些腫瘤細胞裡面有很高濃度的ABC，ABC會把一些抗體跟藥物打出去，造成抗藥性
      - depends on:
        
        sodium(animal cells)
        
        protons (plant, fungal, bacterial)
      - examples
        
        Na+/ K+
        
        Na+/ glucose symporter
        
        Halobacterium
        
        light energy
    - - G<0, spontaneous
      - G>0, energy required
      - G=0, no movement
- - - - secretion
    - - drug detoxification
        
        cytochrome P-450 family
        
        hydroxylation
      - carbohydrate metabolism
        
        it contains glucose-6-phosphatase,
      - calcium storage
        
        calcium-binding proteins
      - steroid biosythesis
        
        Cholesterol, cortisol, and steroid hormones
  - - - N-linked glycosylation
        
        to the nitrogen atom of certain arginine residues
      - O-linked glycosylation
        
        to the oxygen atom on the hydroxyl group of certain serine or threonine residues
  - - - core glycosylation
        
        The initial steps of N-glycosylation on the cytosolic surface of the ER membrane
        
        (1) dolichol phosphate inserted into the ER membrane
        
        (2)GlcNAc and mannose added to the phosphate group
        
        (3)translocated by a flippase
        
        (4) more mannose and glucose are added
        
        (5) transferred to the asparagine
        
        (6) modified
      - folding peptide
        
        calnexin (CNX) and calreticulin (CRT)
        bind to monoglucosylated proteins and promote disulfide bond formation
      - elimination of misfolded
        
        A glucosyl transferase, UGGT
        binds to improperly folded proteins
        adds back a single glucose unit, making the protein a substrate for CNX/CRT binding
      - assembly multimeric proteins
    - - oligosaccharide side chain
      - further glycosylated
        
        N-glycosylated
        
        terminal glycosylations are variable and create great diversity
        removal of a few units of the core oligosaccharide
  - - - ER-specific have retention signals
        
        localized to the ER contain the sequence RXR
        
        also found in some proteins destined for the plasma membrane
      - others have retrieval tags
        
        KDEL (Lys-Asp-Glu-Leu) or KKXX in mammals and HDEL (His-Asp-Glu-Leu) in yeast
        
        returned from the Golgi to the ER,
        protein with this tag binds a receptor, the receptor-ligand complex is packaged into a transport vesicle for return to the ER
    - - short animo acid sequence
      - oligosaccharide side chain
      - other structure
      - Membrane lipids may also be tagged to help vesicles reach their destinations
    - - to lysosome: phosphorylated on mannose residue
      - vesicles with receptors
        
        to lysosome
    - - Constitutive Secretion
        unregulated process is continuous and independent of external signals
      - Regulated Secretion
        only fuse with the plasma membrane in response to specific signals
        
        他們會在vesicle裡面成熟，然後在分泌位置等，如果等到訊號就發出去
  - - - sort receptors, necessary proteins
        
        to lysosome or reuse
      - 受體跟受質結合，之後adapter protein和clathrin包住細胞膜，dynamin把膜收起來。之後是解套，並且跟endosome結合，釋放受體
  - - - from TGN or plasma membrane
      - to endosomes
    - - from ER
      - to Golgi
    - - from golgi
      - back to ER
  - - - phagocytosis or receptor-mediated, early endosomes, lysosomes
        
        fuse with inactive hydrolytic enzyme→ late
    - - lower pH
        
        latent acid hydrolases activate
  - - - hydrolytic enzymes
- - - - Hemicelluloses
        with short side chains in a rigid network
      - Cellulose
        intramolecular hydrogen bonds
      - Pectins
  - - - matrix includes small circular (animal), but
        large (plant) circular/linerar DNA molecules
      - aerobic respiration
    - - especially prominent in the
        liver and kidney cells of animals
        
        Functions:
        
        germinating fat-storing seeds:
        converting the stored fat into carbohydrates
        
        C3 plants: photorespiration
        
        legume plants: conversion of fixed N2 into nitrogen-rich
        organic compound
        
        leaf peroxisomes
        
        close contact with
        mitochondria and chloroplasts
    - - convert stored triacylglycerols to sucrose, β oxidation of fatty acids, and the glyoxylate cycle
      - tissues where fat is stored
        when no longer needed they are converted to peroxisomes
      - glyoxylate cycle
        Two acetate molecules (from acetyl CoA) form succinate, which is converted to PEP
        from stored triacylglycerols to sucrose