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3- Organic molecules, 5- Membrane structure, synthesis and transport, 7-…

- - - - Linear sequence of amino acids
      - Encoded by genes
    - - Folding of polypeptide that is caused by hydrogen bond
      - a helix
      - B pleated sheet
      - Random coiled regions
        
        Not helix or pleated sheet
    - - Complex 3D shape
      - Final level of one polypeptide
    - - 2 or more polypeptides
      - Can be formed from one type of polypeptide
      - Or multimeric (different types)
- - - - Saturated
        
        Solid at room temperature
        
        Single bonds only
      - Unsaturated
        
        1 or more double bonds
        
        Liquid at room temperature
        
        Trans formed artiificially and causes disease
        
        Cis formed naturally
  - - - Phosphate head
        
        Polar
      - Fatty acid tail
        
        Non polar
- - - - Pentoses
        
        5 carbon
        
        Ribose and deoxyribose
      - Hexoses
        
        6 carbon
        
        Glucose
    - - Ring
      - Linear
  - - - Starch, moderately branched
      - Glycogen, highly branched
    - - Cellulose, unbranched
- - - - One form
      - Double strand
      - Bases are A,T,C,G
      - Stores genetic information
      - Deoxyribose sugar
    - - Has several forms
      - Single strand
      - Bases are A,U,C,G
      - Decodes DNA to make polypeptide
      - Ribose sugar
- - - - Polar head
      - Non polar tail
  - - - Transmembrane proteins
        
        Physically embedded in the phospholipid bilayer
        
        2 types
        
        Channels
        
        Open passageway for direct diffusion
        
        Mostely gated
        
        Transporters
        
        Passageway for organic molecules
        
        Goes under conformational change to transport
        
        3 types
        
        Uniporter
        
        Single molecule or ion
        
        Symporter
        
        More than one molecule or ion in the same direction
        
        Antiporter
        
        More than one molecule or ion in both directions
      - Lipid anchored proteins
        
        Amino acid is attached to lipid
    - - Bond to integral membrane protein or to polar head of phospholipids
- - - - Move laterally
      - Rotational movement
    - - Flip flop
        
        Done by flippase
        
        Transport lipids to the other side
- - - - It bonds to glycerol-phophate and inserted in the leaflet of ER by acyl transferase
        
        The phosphate is removed
        
        A choline is attached
  - - - Hydrophobic segment is made while the protein is entering through the channel
        
        Synthesis is completed and the hydrophobic segment stays in the membrane
- - - - Carbohydrate to lipid
    - - Carbohydrate to protein
        
        N-linked glycosylation
        
        Adding carbohydrate to nitrogen atom of asparagine
        
        O-linked glycosylation
        
        Adding carbohydrate to oxygen atom of serine or threonine
        
        Happens in Golgi
  - - - Polypeptide synthesis is completed
- - - - Does not require energy
      - Passive diffusion
        
        Moving of molecules without protein help
      - Facilitated diffusion
        
        Moving of molecules with help of protein
    - - Require energy
      - Primary active transport
        
        Uses energy to move solute
      - Secondary active transport
        
        Uses another gradient to drive transport
  - - - The solute is higher on one side of the membrane
    - - Electrical and chemical gradient
    - - Isotonic
        
        Equal concentration of water and solute
      - Hypertonic
        
        Higher solute concentration on one side
      - Hypotonic
        
        Lower solute concentration on one side
  - - - Animal cells
        
        Crenation
        
        In hypertonic solution the cell shrinks
        
        Osmotic lysis
        
        In hypotonic solution the cell swell and burst
      - Plant cells
        
        The cell wall stop big changes in the cell
        
        Plsmolysis
        
        In hypertonic the plasma membrane shrinks
        
        Turgor pressure
        
        In hypotonic the cell becoms turgid
      - Protists
        
        Contractile vacuoles prevent osmotic lysis
        
        Takes water and discharge out of the cell
    - - The tendency for water to move into cells
- - - - Receptor mediated endocytosis
      - Pinocytosis
      - Phagocytosis
- - - - Enters the respiration at different stages
      - Uses metabolism
- - - - 1-3
      - Hydrolysis of 2 ATP to make fructose-1,6 bisphosphate
    - - 4-5
      - Broken down to 2 glyceraldehyde-3-phosphate
    - - 6-10
      - Broken down to 2 pyruvate
      - Produce 2 NADH and 4 ATP
- - - - Provide energy for synthesizing ATP
  - - - Take energy while H+ is entering through
      - Convert the energy to bond energy for ATP
      - Spins while making ATP
  - - - NADH is used in anabolic pathways
      - H+ gradient used for other purposes
- - - - Glycolysis makes a lot of NADH which is dangerous
      - Muscle cells reduces pyruvate to lactate
      - Yeast makes ethanol
- - - - Simple structure
      - No nucleus
      - Bacteria
        
        Abundant in our environment
        
        Mostely unharmful to human
        
        Components
        
        Inside plasma membrane
        
        Cytoplasm
        
        Within plasma membrane
        
        Nucleoid region
        
        DNA location
        
        Ribosomes
        
        Synthesis proteins
        
        Outside plasma membrane
        
        Cell wall
        
        Give protection
        
        Glycocalyx
        
        Trap water and give protection
        
        Appendages
        
        Pili
        
        Help in attachment
        
        Flagella
        
        Help in movement
      - Archaea
        
        Not common
        
        Found in extreme environments
    - - Comlicated cells
      - DNA inside nucleus
      - Membranes form organelles
        
        Each organelle have different function
      - Different shapes and sizes and organization between cells
- - - - Catabolism
        
        Breakdown of molecules
      - Anabolism
        
        Synthesis of molecules
  - - - Microtubules
        
        Hollow cylindrical structure
        
        Dynamic instability
      - Intermediate filament
        
        Twisted ropelike structure
      - Actin filaments
        
        Long thin fibers
    - - Move along cytoskeletal filaments using ATP
      - Head, hinge, tail
      - 3 types of movements
        
        Motor protein carry cargo along filament
        
        Filament moves and motor proteins stays in place
        
        Both stays in place but a force of bending happens
  - - - Separate the cell and extracellular environment
      - Transportation of molecules
      - Cell signaling and adhesion
  - - - Outer membrane is connected to ER membrane
      - Nuclear pores to provide passageway
    - - Ribosome assembly
    - - DNA and protein complex
      - In nuclear matrix
  - - - rough ER
        
        Contains ribosomes
        
        Synthesis of protiens
      - Smooth ER
        
        Synthesis of lipids
  - - - Breaks H2O2
- - - - Breakdown of macromolecules
      - Contains acid hydrolases
      - Part of autophagy
        
        Recycling organelles by endocytosis
    - - Plays a role in cell dvision
      - Where microtubules grow and centrioles
  - - - Cell volume
      - 3 types
        
        Central vacuoles
        
        Storage and support in plants
        
        Contractile vacuoles
        
        Removing excess water in protists
        
        Phagocytic vacuoles
        
        Degradation in protists
- - - - Must eat food
    - - Make organic molecules from inorganic sources
    - - Light is the sorce of energy
      - Green plants, algae, cyanobacteria
- - - - C3 plants ma 3PG
    - - Add O2 to RuBP and release CO2
      - In hot and dry environments
      - When O2 high and CO2 low
  - - - Mesophyll cells
        
        CO2 enters by stomata and 4 carbon molecule formed
      - Bundle sheath cells
        
        4 carbon molecule moving releases CO2
- - - - Light is electromagnetic radiation
      - Travels as waves and behave as photons
      - Pigment absorb light energy and reflect green wavelengths
      - When electron absorb energy it become in excited state
        
        Releases light or heat
    - - O2 in thylakoid lumen from oxidation of water
      - NADPH in stroma from electrons
      - ATP in stroma by ATP synthase using H+ gradient
    - - Photosystem 1 (PSl)
        
        Discovered first
        
        Make NADPH
        
        Depletes H+ to make NADPH
      - Photosystem 2 (PSll)
        
        First step
        
        Electrons travel to PSl
        
        Release energy in ETC and used to make H+ electrochemical gradient
        
        Oxidize water
      - Complexes in the thylakoid membrane
    - - Flow of H+ to stroma by ATP synthase
    - - Increase
        
        Splitting of water
        
        ETC pumping into lumen
      - Decrease
        
        Making NADPH in stroma
  - - - Require energy
    - - Electron from PSll transfer to NADPH in linear process
      - produce ATP, NADPH
    - - Release energy to move H+ into lumen to synthesis ATP
      - Produce ATP
      - PSl electron release energy and return to PSl
    - - 1- carbon fixation
        
        CO2 connected with RuBP by rubisco
        
        Product is 2 3-phosphoglycerate molecules (3PG)
      - 2- reduction and carbohydrate production
        
        Converting 3PG to 1,3-bisphosphoglycerate (1,3-BPG) using ATP
        
        electrons from NADPH reduce it to glyceraldehyde-3-phosphate (G3P)
        
        Products are 12 G3P
        
        2 used for carbohydrates
        
        10 for regenerating RuBP
      - 3- regeneration of RuBP
        
        10 G3P converted to 6 RuBP
- - - - Absorbs photons
      - Resonance energy transfer
    - - Energy transferred quickly because P680* is unstable
      - Electron is captured by primary electron acceptor
      - Oxidation of water replaces the electron on P680*
    - - Removes electrons from pigments to primary electron acceptor