enzymes pt2

• Protein structure


  The four levels are primary, secondary, tertiary, and quaternary
• Primary structure


  Sequence of amino acid chain
• Secondary structure


  Hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern that is of two types
• Tertiary structure


  Side chains interact generating a 3D folding pattern of the whole polypeptide chain
• Quaternary structure


  Comprised of two or more polypeptides that aggregate
• Protein structure is affected by physical and chemical conditions of the environment such as pH, temperature, and salt concentration
• Altering factors beyond the normal and optimum requirement could destroy the bonds in the proteins, a phenomenon called denaturation, where the folded proteins unfold causing it to lose its function
• Protein structure

  Dictates how it will work
• Examples of how protein structure dictates function

  • Fibroin in silk must be very rigid due to β pleated sheet structure
  • Enzymes must assume a shape where grooves along its surface are prominent for binding of specific molecules to active site
• Only some proteins exhibit quaternary structure, such as collagen and hemoglobin
• Enzymes is a large class of proteins that function in catalyzing or speeding up chemical reactions
• Enzymes mediate almost all the biochemical processes taking place in the cells of the body for the other proteins to also fully carry out their functions
• Enzymes

  They bind to ligands called substrates converting them rapidly into different chemically modified molecules called products while remaining unchanged during the entire process
• Enzymes


  • Their ability to catalyze reactions depends on their native conformation
  • They will lose their catalytic activity if they are denatured
• Enzymes are classified according to

  • The reactions they catalyzed
• Enzymes are named by

  Adding the suffix "-ase" to the word that describes their specific activity
• Examples of digestive enzymes

  • Amylase
  • Lipase
  • Protease
• Amylase


  Catalyzes the breakdown of starch into sugars
• Lipase


  Catalyzes the hydrolysis of fats
• Protease


  Cleaves peptide bonds between proteins through hydrolysis to form smaller polypeptides or amino acids
• Enzymes enhance reaction rate by lowering energy barriers called the free energy of activation or activation energy (EA)
• Activation energy

  The amount of energy that separates the reactants and the products or the "energy difference between that of the reactants and a high-energy intermediate that occurs during the formation of the product"
• Reactants must absorb enough thermal energy from the surroundings


  To reach a high-energy unstable condition also known as the transition state which enables them to overcome the energy barrier
• Most of the spontaneous chemical reactions not acted upon by enzymes occur very slowly
• Heat can denature proteins, kill cells, and speed-up reactions that are not needed to proceed
• Enzymes provide an alternative energetically favorable pathway for the specific molecules they catalyze
• Active site


  A region of the enzyme that corresponds to the contours of the reactant molecules (substrates) that it acts on
• The activation energy needed for the conversion of substrates into products significantly lowers down when enzymes bind to the substrates in such a way that would ensure that the transition state can be easily reached
• Simple enzymatic reaction

  1. Substrate binding to the enzyme's active site forming an enzyme-substrate complex

  2. Enzyme slightly changes its conformation for the best snug fit with the substrate

  3. Upon reaching the transition state overcoming the energy barrier, the newly formed product dissociates from the enzyme

  4. The enzyme could readily catalyze another molecule
• Most metabolic reactions are reversible, thus, enzymes could catalyze either forward or reverse reactions
• Metabolism


  The totality of an organism's chemical reactions
• Metabolic pathways


  • A series of defined steps where a specific molecule is altered, each step catalyzed by a specific enzyme
  • Regulate the balance of metabolic supply and demand, like traffic lights controlling traffic flow
• Catabolic pathways


  Degradative processes that release energy by breaking down complex molecules to simpler compounds
• Anabolic pathways


  Consume energy to build complicated molecules from simpler ones; also called biosynthetic pathways
• Catabolic and anabolic pathways are the "downhill" and "uphill" avenues of the metabolic landscape
• Energy released from downhill reactions of catabolic pathways can be stored and then used to drive uphill reactions of anabolic pathways
• Activation energy (EA)


  The initial investment of energy required to start a chemical reaction by contorting the reactant molecules so the bonds can break
• Transition state


  The unstable condition of the reactant molecules when they have absorbed enough energy to break their bonds
• Enzymes catalyze reactions by lowering the activation energy barrier, enabling the reactant molecules to reach the transition state even at moderate temperatures
• Substrate


  The reactant that an enzyme acts on