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BIOCHEMISTRY (Technical tools (Extraction (Lysis) (Mechanical (bead…

- - - - Pros: native folding for proteins, no need of precise knowledge or method for synthesis :green_cross:
      - Cons: need specific method of purifcation, more easy contamination of products :red_cross:
    - - Pros: very pure and custom-made products :green_cross:
      - Cons: costly and difficult, gives often only low yield :red_cross:
    - - Pros : cheap and very good yield :green_cross:
      - Cons : need cloning, non wanted post-translational modification can occured :red_cross:
  - - - hypotonic solution (deionised water) ==> CYTOLYSIS (or cell rupture)
    - - bead grinding (moudre avec des perles)
      - homogeniser (eg. high pressure applied)
      - French Press
      - sonicator (ultrason waves become mechanical energy)
      - freeze-twaning (as water volume increases of 10% when freezing)
    - - A substance that breaks the membrane structure (eg. Triton)
  - - - Dialysis
        
        size-base separation through a semi-permeable membrane with specific pore size
      - gel electrophoresis
        
        polyacrylamide/agarose gel acting as a net
      - gel filtration chromatography
        
        smaller particles are slowed down by porous beads while bigger particles go through
    - - Precipitation/differential solubilisation
        
        change in ionic strength. To get the precipitate (precipitation) or the particles in solution (diff solubilisation)
    - - Affinity chromatography
        
        the analyte forms a specific non-covalent interaction with a specific ligand. Rest of mobile phase is evacuate and then elution allows to get back the analyte
    - - electrophoresis
        
        particles migrate at different rate in an uniform electric field
      - isoelectric focusing
        
        migration through a pH gradient
      - adsorption
        
        you keep only the adsorbate that stick to the adsorbent thanks to polarity
      - ion exchange chromatography
        
        proteins migrate through a charged solid phase in function of their net charge in the pH used
      - hydrophobic chromatography
  - - - different particles migrate at different rate (retention of the column)
        
        Resolution between 2 peaks : 2delta time/ wA + wB
    - - This machine helps improve the resolution
  - - - Sanger
      - NGS
        
        Illumina
      - Nanopore sequencing : easy to made, quite accurate
    - - Amino acid analysis
        
        A/ion exchange B/reverse-phase
      - Edman degradation
      - separate proteins into smaller subunits (polypeptide chains/ peptides)
        
        eg. using protease
      - Mass spectrometry
- - - - Hydrophobic
        
        Glycine, Alanine, Valine,etc... 9 in total
        
        hydrophilic non-charged
        
        Polar AA : Serine, cysteine, tyrosine,etc... 6 in total
        
        Hydrophilic charged : Basic
        
        Lysine, Arginine, Histine
        
        Hydrophilic charged : Acidic
        
        Aspartic and Glutamic Acid
      - Gene < RNA (exons and introns) < mRNA< Translation in ribosome
        
        Primary structure : chain of AA
        
        Secondary structure : formation of alpha helix and beta sheet
        
        Tertiary Structure : interaction between R group
        
        Quaternary structure : multiple polypeptide chain
        
        peptide chain is a Planar chain
  - - - Neutral side chain : pKa1 and pK2
        
        pI = (pKa1 + pKa2)/2
      - Acidic side chain : pKa1 and pKa3
        
        pI = (pKa1 + pKa3)/2
      - Basic side chain : pKa2 and pKa3
        
        pI = (pKa2 + pKa3)/2
- - - - assemble to give di- and polysaccharides
        
        Disaccharide : Sucrose, Lactose, Maltose
        
        polysaccharides : Glycogen, Starch, Cellulose
        
        Starch is in food
        
        Cellulose is the compounds od plant cell walls
        
        Glycogen is a multibranch polysaccharide of glucose found in liver and muscles
        
        Chitin : fungal cell wall and exoskeleton
        
        The lobster shell is made of twisted chitin fiber layers for resitance
        
        peptidoglycan is the cell wall of bacteria and cyanobacteria
        
        Carbohydrate group + proteins = glycoproteins
        
        sugar attached to the N atom on asparagine = N-linkage
        
        concensus is Asn-X-Thr or Asn-X-Ser with X any residue
        
        sugars attached on the O atoms of Threonine = O-linkage
        
        no consensus for the O-linked glycosilation site
        
        Ketose or aldose
      - Glucose is the most known
        
        Glycolysis
        
        Glucose in more often in a cyclic conformation = more resitant
        
        16 isomers of glucose because of 4 chiral carbons
        
        polarization of light: dextrorotatory or levorotatory
      - sweet taste
      - solid at 25°C and very soluble in water
      - phosphate ester :
- - - - fat and oil
        
        after hydrolysis : fatty acids and glycerol
        
        glycerol COH3 - COH2 - COH3
      - wax
        
        after hydrolysis : fatty acids and long-chain alcohol
        
        from plant leaf or animals (bees)
    - - phospholipids :
        
        bilayer of membrane for cells or micelles
    - - Hydrolysis product of compounds lipids
        
        phenantrene structure : steroids, vitamine
        
        Cholesterol participates in membrane flexibility
- - - - Nucleoside = nitrogenous base + ribose
        
        Nucléotide = nucléoside + phosphate group
      - Purines : 5-m ring and 6-m ring
        
        Adenosine (A); Guanine (G)
      - Pyrimidines : single 6-membered ring
        
        Cytosine (C), Thymine (T in DNA), Uracile (U in RNA)
    - - ribose or deoxyribose
        
        giving name to Ribonucleic Acid (RNA) or Deoxyribonucleic Acid (DNA)
        
        Glycosis bond between nucleotides
        
        A goes wit T (DNA) or U (RNA)
        
        G goes with C
        
        bind with hydrogen bonds
        
        stacking forces : van der waals
        
        hydrophobic nitrogenous bases are inside the helix
        
        charge-charge interactions
        
        DNA is a double helix
        
        RNA : most of the time a single strand
    - - PO4