Cycle 3: Energy and Membranes

• Kinetic energy


  From moving particles
• Potential energy


  Stored by position or chemical structure
• Chemical energy


  From chemical reactions
• Open system


  Exchange matter and energy (ex: cells)
• Closed system


  Exchange energy only
• Isolated system


  Neither matter or energy are exchanged
• Energy law 1


  Energy cannot be made or destroyed, can only be converted
• Energy law 2


  Entropy of the universe always increases
• Entropy of cells


  Cells use energy to build ordered molecules, cells are islands of low entropy (energy taken in to replace other things broken down)
• Primary protein (denatured)


  Unfolded, 1 linear chain of amino acids, peptide bonds joining amino acids
• Secondary protein


  1 chain of amino acids (alpha-helix form, beta-barrel form), peptide + hydrogen bonds (disturbed by urea)
• Tertiary protein (functional)


  1 fully folded 3D chain, peptide, hydrogen + any other bond (dipole-dipole, disulfide bridges)
• Quaternary protein (functional)


  Multiple fully folded 3D chains, peptide, hydrogen + any other bond (dipole-dipole, disulfide bridges)
• Most reduced molecules


  More C-H bonds, high free energy, electrons are easy to remove
• Most oxidized molecules


  More C-O bonds, low free energy, electrons are more tightly bound to O
• Heterotrophs consume


  Matter and energy combined through our carbs + fats
• Autotrophs consume


  CO2 = matter, light = energy
• ΔG > 0 is


  Endergonic (requires energy)
• ΔG < 0 is


  Exergonic (spontaneous)
• Free energy


  ΔG = Products - Reactants
• ΔH > 0 is


  Endothermic
• ΔH < 0 is

  Exothermic
• ΔS > 0 is


  More spread out (less order)
• ΔS < 0 is

  Less spread out (more order)
• Can enzymes be used to speed up the rate of an endergonic reaction?

  No, enzymes only work for exergonic reactions
• Activation Energy


  Energy required to get to the activation state, serves as a kinetic barrier (a low activation energy = a faster reaction) 
• How do enzymes lower the activation energy? 

  Precise orientation, charge interactions, conformational strain
• Energy funneling and protein folding


  Protein folding is spontaneous and happens at the same time, the primary sequence dictates the final conformation, a very quick process (just milliseconds)
• Active site


  Area on an enzyme that binds the substrate, discovered by looking at enzyme’s 3D shape, not primary structure, only functional as tertiary structure
• Dealing with very cold temp, enzyme too rigid


  Weaker tertiary structure bonds or arrangements
• Dealing with very hot temp, enzyme too fluid (denatures)


  Stronger tertiary structure bonds or arrangements
• Organism's environment


  Dictates enzyme's optimum temperature
• Phospholipids - primary constituent of the cell membrane


  Hydrophilic (glycerol) and hydrophobic (fatty acids)
• Hydrophilic + hydrophobic


  = Amphipathic
• The plasma membrane is


  A bilayer (2 phospholipids), has a hydrophilic portion on the outer/inner edges, inside is all hydrophobic
• Diffusion


  Molecules go from where there are lots of them to very little (high concentration → low)
• Passive diffusion


  When no proteins are needed to help this process
• Facilitated diffusion 


  When proteins are required
• Do these molecules need help from proteins?

  Nonpolar (no), polar but small (no), polar and big (yes), complete ions (yes)
• Hydropathy plot


  Visualize which amino acids or parts of a protein are hydrophobic