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3 - Biochemical processes in cells


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3 - Biochemical processes in cells

  1. 1. ENERGY
  2. 2. Organisms obtain their energy by breaking down complex high-energy biomolecules (otherwise known as food) <ul><li>AUTOTROPH </li></ul><ul><li>Can utilize sunlight as an energy source </li></ul><ul><li>Plants and photosynthetic bacteria & protists </li></ul><ul><li>HETEROTROPH </li></ul><ul><li>Must consume organic matter to obtain energy (in the form of chemical energy) </li></ul><ul><li>Animals, fungi and non-photosynthetic bacteria & protists </li></ul>
  3. 3. Energy <ul><li>High energy compounds (ie carbohydrates, fats and alcohols) are broken down to low energy compound (ie water, carbon dioxide and oxygen) </li></ul><ul><li>Chemical reactions in the body can be exergonic (release energy) aka catabolic </li></ul><ul><li>Chemical reactions in the body can be endergonic (require energy) aka anabolic </li></ul><ul><li>Often exergonic and endergonic reactions in the body will be complimentary </li></ul>
  4. 4. Exergonic and Endergonic Reactions
  5. 5. Example of complimentary exergonic and endergonic reactions
  6. 6. Example of complimentary exergonic and endergonic reactions
  7. 7. ENZYMES
  8. 8. Enzyme Structure <ul><li>Some are pure proteins </li></ul><ul><li>Some require COFACTORS to work (usually inorganic metal ions) </li></ul><ul><li>Eg. iron, copper, calcium, zinc, potassium </li></ul><ul><li>Some require COENZYMES to work (an organic substance) </li></ul><ul><li>Eg. a vitamin </li></ul>
  9. 9. Enzyme Structure <ul><li>Enzymes have an active site and a regulatory region </li></ul><ul><li>The active site (formed by folds in the protein) is where substrate binds to the enzyme </li></ul><ul><li>The regulatory region is where cofactors coenzymes or enzyme inhibitors can alter the function of an enzyme </li></ul>Substrate Active site Regulatory region Products Enzyme inhibitor
  10. 10. Some quick facts. Enzymes … <ul><li>Act at both the intra and extracellular level </li></ul><ul><li>Act on SUBSTRATE and yield PRODUCT </li></ul><ul><li>Reduce the ACTIVATION energy required to start a reaction in the body </li></ul><ul><li>Are very specific, each individual type of substrate is acted upon by a specific enzyme </li></ul>
  11. 11. The “Lock and Key” model of enzyme activity <ul><li>The enzyme provides a perfect fit for a particular substrate </li></ul>
  12. 12. The “Induced Fit” model of enzyme activity <ul><li>The substrate induces the enzyme to change shape to create a tighter fit </li></ul>
  13. 13. Factors Affecting Enzyme Activity <ul><li>pH </li></ul><ul><li>Most biological enzymes operate at a neutral pH range of 6-8 </li></ul><ul><li>If enzymes are at a pH outside their optimum range, their shape will change and they will be less efficient. </li></ul>2.0 8.0 7.4 7.6 Opt. pH Stomach Small Intestine Blood Cells Location Pepsin Trypsin Carbonic Anhydrase Enzyme
  14. 14. Factors Affecting Enzyme Activity <ul><li>Temperature </li></ul><ul><li>Most biological enzymes have an optimum temperature of 37° </li></ul><ul><li>If an enzyme is exposed to temperatures higher than optimum, it will permanently denature. </li></ul><ul><li>If an enzyme is exposed to temperatures lower than optimum, it will become inactive until temperature returns to optimum. </li></ul><ul><li>The enzymes of other organisms have optimum temperatures suited to the environment in which they live </li></ul>
  15. 15. Factors Affecting Enzyme Activity <ul><li>Enzyme Concentration </li></ul><ul><li>An increase in enzyme conc. will cause an increase in reaction rate but won’t increase the yield. </li></ul><ul><li>Substrate concentration </li></ul><ul><li>Reaction rate will initially increase as unoccupied enzymes take on substrate but will then plateau. </li></ul><ul><li>Inhibition </li></ul><ul><li>Other molecules can block the active site or regulatory region of an enzyme. </li></ul>
  16. 16. Increasing substrate concentration
  17. 17. Photosynthesis
  18. 18. Photosynthesis <ul><li>The process in which light energy is transformed in to chemical energy </li></ul><ul><li>Performed by </li></ul><ul><ul><li>Plants </li></ul></ul><ul><ul><li>Algae </li></ul></ul><ul><ul><li>Some protists (eg phytoplankton) </li></ul></ul><ul><ul><li>Photosynthetic bacteria </li></ul></ul>
  19. 19. What makes leaves so ideal for photosynthesis? <ul><li>Flat = large surface area to volume ratio </li></ul><ul><li>Many stomata = efficient import of CO 2 and export of O 2 </li></ul><ul><li>Thin with many air chambers = diffusion of CO 2 </li></ul><ul><li>Xylem = transports reactants in </li></ul><ul><li>Phloem = transports products out </li></ul><ul><li>Chloroplasts = photosynthetic pigment concentrated in dedicated organelles </li></ul>
  20. 20. Chloroplasts
  21. 21. The Photosynthetic Equation <ul><li>Photo = light </li></ul><ul><li>Synthesis = put together </li></ul><ul><li>It is a complex series of reactions that can be summarized as: </li></ul><ul><li>12H 2 O + 6CO 2 -> 6O 2 + C 6 H 12 O 6 + 6H 2 O </li></ul><ul><li>6 of the water molecules on either side of the equation cancel each other out to give: </li></ul><ul><li>6H 2 O + 6CO 2 -> 6O 2 + C 6 H 12 O 6 </li></ul>
  22. 23. Photosynthesis Overview <ul><li>6H 2 O + 6 CO 2 --> C 6 H 12 O 6 + 6 O 2 </li></ul>Light Dependent Stage H 2 O --> O 2 requires Light E Light Independent Stage CO 2 --> 2x3C sugars
  23. 24. Light-dependent reaction <ul><li>Inputs: sunlight, water, NADP, ADP & P i </li></ul><ul><li>Outputs: oxygen, ATP & NADPH </li></ul>A not-so-simple explanation of the process
  24. 25. A simplified version of the process
  25. 26. Light-dependent reaction <ul><li>Occurs in the grana </li></ul><ul><li>Light energy is used to split water in to two H + ions and O 2 gas </li></ul><ul><li>The O 2 is released as waste </li></ul><ul><li>With the power of the two free electrons </li></ul><ul><ul><li>One H + ion fuses ADP to P i to form ATP </li></ul></ul><ul><ul><li>One H + ion fuses to NADP to form NADPH </li></ul></ul>
  26. 27. Inputs Outputs Water H 2 O ATP Electron e - NADPH NADP + ADP + P Oxygen (“waste”)
  27. 28. Light-independent stage <ul><li>Occurs in Stroma </li></ul><ul><li>Does not need light, but NADPH and ATP from previous stage </li></ul><ul><li>Needs CO 2 and H + ions </li></ul><ul><li>Sugar molecules are synthesised from CO 2 </li></ul><ul><li>CO 2 = oxidised state (low E compound) </li></ul><ul><li>C(H 2 O)n = reduced state (high E compound) </li></ul><ul><li>NADPH (carrier H + ) is the reducing agent </li></ul><ul><li>ATP is the energy source </li></ul>
  28. 29. Inputs Outputs ATP ADP + P NADPH NADP + 3C -> Glucose
  29. 30. Carbon reduction in C 3 Plants Calvin Cycle Called C 3 plants as the end product is a 3-carbon compound (PGAL), that goes on to form glucose. Photosynthesis occurs in the mesophyll cells,
  30. 31. Carbon reduction in C 4 plants <ul><li>Plants in hot, dry habitats and important crop plants such as corn, sugar cane </li></ul><ul><li>If light independent reaction took place in mesophyll cells, these plants would lose too much water from their open stomata. </li></ul><ul><li>One step occurs (in the mesophyll cells) to transport CO 2 (in the form of oxaloacetate) to the bundle sheath cells, </li></ul>
  31. 32. Carbon reduction in C 4 plants <ul><li>CO 2 combines with the 3-carbon compound PEP (phophoenolpyruvic acid) to form oxaloacetate (4C) </li></ul><ul><li>A further reaction converts oxaloacetate (4C) to malate (4C). </li></ul><ul><li>Then a CO 2 molecule leaves the cycle to nter the Calvin cycle, whilst the remaining 3C pyruvate returns to reform PEP. </li></ul>
  32. 33. C 3 PLANTS C 4 PLANTS
  33. 34. Putting Photosynthesis together 2 x PGAL = fructose fructose = glucose fructose + glucose = sucrose glucose x ∞ = starch
  34. 36. General Info on Cellular Respiration <ul><li>Organisms can’t use glucose (2800 kJ) as energy, needs to be broken down to approx 1/100 th of its size – ATP (30 kJ). </li></ul><ul><li>Breakdown is not 100% efficient (usually 36-38 ATP produced) </li></ul><ul><li>Remainder is lost as heat. Endothermic organisms trap this heat with layers of fat to maintain body temperature. </li></ul>
  35. 37. General Info on Cellular Respiration <ul><li>The rate of respiration depends on the state of activity of the organism </li></ul><ul><li>Respiration involves 2 coupled reactions </li></ul><ul><ul><li>Energy is released by the breakdown of glucose </li></ul></ul><ul><ul><li>Energy is required for the production of ATP </li></ul></ul><ul><li>There are 2 types of respiration </li></ul><ul><ul><li>Aerobic respiration (requires oxygen) </li></ul></ul><ul><ul><li>Anaerobic respiration (does not require oxygen) </li></ul></ul>
  36. 38. Aerobic vs Anaerobic Respiration
  37. 39. Aerobic respiration <ul><li>C 6 H 12 O 6 + O 2 -> CO 2 + H 2 O </li></ul><ul><li>Outside cells, to oxidise glucose need temp of 200° - Entire molecule oxidised simultaneously </li></ul><ul><li>Inside cells, oxidised gradually in small steps </li></ul><ul><li>Steps summarized in to 3 stages </li></ul><ul><ul><li>Glycolysis (produces pyruvate) </li></ul></ul><ul><ul><li>Krebs Cycle (2 required per molecule of glucose) </li></ul></ul><ul><ul><li>Electron transport (harvests H + from carriers) </li></ul></ul>
  38. 40. Glycolysis <ul><li>Occurs in cytosol – uses enzymes and vitamins as coenzymes </li></ul><ul><li>1 glucose (6C) converted to 2 pyruvate (3C) </li></ul><ul><li>Forms 2 ATP & 2 NADH (from NAD – nicotamide adenine dinucleotide ) </li></ul>
  39. 41. Krebs Cycle <ul><li>Occurs in mitochondria </li></ul><ul><li>Pyruvate initially broken down in to CO 2 and Acetyl-coA </li></ul><ul><li>Joins with 4C molecule to form 6 C molecule </li></ul><ul><li>CO 2 to form 5 C molecule, then again to form 4 C molecule </li></ul><ul><li>Further oxidation takes place to reform original 4C </li></ul><ul><li>Throughout cycle, constant oxidation is fusing hydrogen to carrier molecules NAD -> NADH and FAD -> FADH 2 </li></ul>
  40. 42. Electron Transport <ul><li>Occurs in inner membrane of mitochondria </li></ul><ul><li>Produces 2-3 ATP per loaded receptor </li></ul><ul><li>Electrons passed from one cytochrome to next until accepted by O 2- to form water </li></ul><ul><li>Return of released protons through ATP synthase carrier provides energy to produce ATP from ADP & P i ( phosphorylation ) </li></ul>
  41. 43. Summarising Aerobic Respiration <ul><li>Vocabulary </li></ul><ul><ul><li>Oxidation = removal of hydrogen </li></ul></ul><ul><ul><li>Reduction = addition of hydrogen </li></ul></ul><ul><li>A total of 36 ATP are formed except in the cells of heart, liver and kidneys where 38 are formed </li></ul>
  42. 46. Anaerobic respiration (in humans) <ul><li>Occurs in muscles where oxygen supply exceeds demand </li></ul><ul><li>The only stage that can occur is glycolysis </li></ul><ul><li>So 1 glucose produces 2 ATP </li></ul><ul><li>2 NADH convert pyruvate to lactate (lactic acid) </li></ul><ul><li>Lactate build up causes pH to fall and pain & muscle fatigue </li></ul><ul><li>When activity returns to normal and oxygen becomes available, lactate converted back to pyruvate to enter the Krebs Cycle. </li></ul>
  43. 47. Anaerobic respiration (in yeast) <ul><li>Anaerobic respiration in yeast is called fermentation </li></ul><ul><li>Pyruvate is broken down in to CO 2 and ethanol (alcohol) </li></ul>
  44. 48. What happens during starvation? - Autophagia (feeding of self )