Molecular Biology 1-6


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Metabolism and Energy: The images have big font size and reduced background color. Useful for smartphones, classroom and printouts. The rest is standard stuff.

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Molecular Biology 1-6

  1. 1. Molecular Biology 1-6 put together by: Linda Fahlberg-Stojanovska Disclaimer: I put these together for my kid for his smartphone.However, I found most images had very small type and increased the font size. I am posting it because another teacher might find this useful. The sources are given. If I have used anything illegally, write me and I will take it off. 1
  2. 2. Contents• Metabolism• Energy Living organisms exchange energy and matter in order to maintain a dynamic equilibrium separate from changes in its environment.
  3. 3. Metabolism• Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life.• Key biochemicals in metabolism – Amino acids and proteins – Lipids – Carbohydrates – Nucleotides – Coenzymes – Minerals and cofactors 3
  4. 4. Major Types of Reactions in Metabolism• oxidation-reduction (electron transfer)• group transfer reactions (functional group changes from donor to recipient or vice- versa )• hydrolysis (bond cleavage, water released)• nonhydrolytic cleavage (bond cleavage without water)• isomerization/rearrangement (carbon skeleton change)• bond formation reactions using ATP energy Notice that these 6 reaction types directly correspond to the enzyme classification! 4
  5. 5. Metabolism of Heterotrophs vs. AutotrophsAutotrophs - "make their own food“ - photosynthesisThe metabolism of autotrophs is based on their ability togenerate high energy molecules from simplersubstances using the energy of light.Heterotrophs – “eat their food” – cellular respirationThe metabolism of heterotrophs is much simpler and isbased on their ability to break complex molecules downinto simpler substances releasing energy from thischemical breakdown for life processes. 5
  6. 6. Metabolism of Heterotrophs High Energy Biological Nutrients Macromolecules carbohydrates polysaccharides lipids lipids proteins nucleic acids Chemical proteins Energy catabolism anabolism ATP Low Energy NADPH Precursor End Products molecules CO2 monosaccharides H2 O fatty acids NH3 nucleotides amino acidsM. Dolinar, uni-lj 6
  7. 7. Characteristics of a Biological System 7cannot find source
  8. 8. Anabolism – Synthesis – USE ATPAnabolism is the set of metabolic pathways that • construct molecules from smaller units – releases H2O - condensation reaction • requires energy – usually ATP – powered by catabolism (uses ATP made in catabolism)•Anabolic processes “build up” organs and tissues – growth and differentiation of cells and – increase in body size, – synthesis of complex molecules.•Example: growth and mineralization of bone•Example: increases in muscle mass 8
  9. 9. Catabolism – Decomposition – MAKE ATPCatabolism is the set of metabolic pathways that • breaks down large molecules into smaller units – absorbs H2O - hydrolysis reaction • releases energy which is then used to MAKE ATP 9
  10. 10. Catabolism - 2• Catabolic processes include – glycolysis, – Kreb’s cycle, – breakdown of muscle protein to use amino acids as substrates for gluconeogenesis – breakdown of fat in adipose tissue to fatty acids.• Cells use monomers to construct new polymer or further degrade to waste products.• Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia, and urea. 10
  11. 11. ATP → ADP + P + ENERGYSame in both anaerobic and aerobic – breaks phosphoanhydride bond (ATP → ADP) – releases energy (and phosphate) – is an anabolic (condensation) process uses released energy to synthesize 11
  12. 12. ATP – adenosine triphosfateATP - composed of an adenine ring and a ribose sugar and 3 phosphate groups (triphosphate)• 10 C, 16 H, 5 N, 13 O and 3 P. phosphoanhydride bonds adenine ring triphosphate ribose 12
  13. 13. ADP – adenosine diphosfateADP - composed of an adenine ring and a ribose sugar and 2 phosphate groups (diphosphate) adenine ring diphosphate ribose 13
  14. 14. ADP + Pi → ATPDIFFERENT for anaerobic and aerobic – catabolic (hydrolysis) process decomposes food and stores their energy in ATP • ATP is produced and used continuously. • The entire amount of ATP in an organism is recycled once per minute. • Most cells maintain only a few seconds supply of ATP. 14
  15. 15. ADP + Pi → ATP - Anaerobic• Step 1: Glycolysis - Anaerobic or Aerobic 1 glucose → +2ATP (net) + 2 pyruvate acid molecules• Step 2: Fermentation - Anaerobic Yeast Fermentation or Homolactic Fermentation Fermentation → 2ATP + lactate or ethanol + CO2 15
  16. 16. ADP + Pi → ATP - AnaerobicAnaerobic catabolism–Glycolysis–Fermentation 16
  17. 17. ADP + Pi → ATP - AerobicAerobic catabolism = CELLULAR RESPIRATION up to 19 times more efficient than anaerobic Steps –1. Glycolysis –2. Pyruvate decarboxylation –3. Kreb’s Cycle Aerobic –4. ETC (Electron Chain Transport) Chemiosmosis 17
  18. 18. Aerobic Steps in Forming ATP 18
  19. 19. Aerobic Steps in Forming ATP 19
  20. 20. Glycolysis - 1 - Anaerobic or Aerobic• Glycolysis is 1st step in respiration.• It occurs in both aerobic and anaerobic.• Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+.• The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).• We think it is one of the most ancient known metabolic pathways.• It occurs in the cytosol – the intracellular fluid of the cell. 20
  21. 21. Glycolysis: Steps 1-5cannot find source 21
  22. 22. Glycolysis: Steps 6-10-2 ATP +4 ATP = net gain of 2 ATP 22 cannot find source
  23. 23. Glycolysis - 2• Glycolysis is a definite sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis.• Most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates.• The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat. 23
  24. 24. Pyruvate decarboxylation - 1• 2nd step in aerobic respiration (formation of ATP)• Catalyzed by pyruvate dehydrogenase reaction• → 2 pyruvate molecules (from glycolysis) + CoA – 1 C and 2 O atoms are removed, releasing CO2 – a molecule of the coenzyme NAD+ becomes NADH – remaining molecule CH3CO - Acetyl coenzyme A.• occurs in the mitochondria 24
  25. 25. Pyruvate decarboxylation - 2• Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism,• Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production.• Acetyl-CoA is produced during the 2nd step of aerobic cellular respiration, pyruvate decarboxylation, which occurs in the matrix of the mitochondria.• Acetyl-CoA then enters Kreb’s Cycle (3rd step). 25
  26. 26. Acetyl coenzyme A or acetyl-CoA Coenzyme A 26
  27. 27. Kreb’s CycleKreb’s Cycle is the 3rd step in aerobic respirationKreb’s Cycle = Citric Acid CycleKreb’s cycle is amphibolic (both anabolic and catabolic)•Aerobic (requires oxygen)•occurs in the mitochondria•results in the formation of 2 ATP and•results in the formation of other high energy redoxcompounds which undergo further reactions to form moreATP (in the ETC). 27
  28. 28. Kreb’s Cycle→ Acetyl coenzyme A enters binds with oxaloacetic acid (7) 1. citric acid → H2O 2. isocitric acid NAD+→NADH and → CO2 3. α-ketoglutaric acid: NAD+→NADH → CO2 and ATD→ATP ← H2O 4. succinic acid : FAD → FADH2 5. fumaric acid: ← H2O 6. malic acid: NAD+→ NADH 7. oxaloacetic acid 28
  29. 29. 29
  30. 30. Kreb’s Cycle - ATP• Krebs cycle produces 2 ATP directly.• It also produces the high energy redox compounds: 6 NADH and 2 FADH2 – NAD+ →NADH is a redox reaction occurs 3 times in the Kreb’s cycle (and in other reactions). NADH≈2.5 ATP – FAD→FADH2 is another redox reaction. It occurs in step 8 of Kreb’s cycle. FADH2≈1.5 ATP• These are then used to power the formation of additional ≈34 ATP through the electron transport chain (ETC). 30
  31. 31. NAD+ → NADH and FAD→FADH2• Nicotinamide adenine dinucleotide, abbreviated NAD+, is a coenzyme found in all living cells.• In metabolism, NAD+ is involved in redox reactions, carrying electrons from one reaction to another.• NAD+ is an oxidizing agent, i.e. an electron acceptor . It accepts electrons from other molecules and becomes reduced to form NADH.• NADH is thus a reducing agent, i.e. an electron donor.• Similarly FAD is an oxidizing agent that accepts electrons to become the reducing agent FADH2. 31
  32. 32. Electron Transport Chain - ETC• ETC is the 4th and final cellular mechanism in aerobic (oxidative) respiration. (Glycolysis, Pyruvate dehydoxylation, Kreb’s Cycle, ETC) – In the ETC, the 6NADH and 2FADH2 from the Kreb’s cycle are catabolized to produce the energy storing ATP.• Electron transport chain (ETC) couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) and• It uses the movement of these electrons (e-) to pump H+ ions (protons) across a membrane. 32
  33. 33. ETC in Mitochondria 33
  34. 34. ETC – Active Transport System• The transfer of H+ ions (protons) in the ETC in the opposite direction of the concentration gradient is called the active transport system• Example: The NADH (from Kreb’s Cycle) take their 2 electrons (and energy) to Complex I of the ETC.• The electrons are transferred to an electron acceptor and NAD+ is regenerated as the NADH gives up its electrons.• These electrons are now transported along - releasing energy.• This energy is utilized to pump H+ ions (protons) across the inner mitochondrial membrane in the Active Transport S. 34
  35. 35. ETC – Active Transport System 35
  36. 36. Electrochemical Gradient - Chemiosmosis• The energy released by electrons from redox agents such as NADH and FADH2 is used by ETC to pump protons across the inner mitochondrial membrane in the Active Transport System• This generates potential energy in the form of a pH gradient or a proton gradient and an electrical potential across this membrane.• A large enzyme called ATP synthase provides a channel for the protons to flow back across the membrane and down this gradient. This flow is called chemiosmosis.• The energy in this gradient is used to make ATP. 36
  37. 37. Electrochemical Gradient - Chemiosmosis• Hydrogen ions (protons) diffuse from an area of high proton concentration to an area of lower proton concentration creating a gradient of protons (more → less). This process is “similar” to osmosis, (the diffusion of water across a semi-permeable membrane), which is why it is called chemiosmosis. 37
  38. 38. Oxidative Phosphorylation• The ATP synthase enzyme provides a channel for the protons to flow back across the membrane, down this proton gradient and back into the inner mitochondrial space.• This flow is with the concentration gradient.• ATP synthase uses this energy to generate ATP from ADP in a phosphorylation reaction (adding of phospate group).– oxidative phosphorylation is from redox reactions, such as the oxidation of sugars (e.g. glucose) in respiration in heterotrophs.– photophosphorylation from sunlight in photosynthesis in autotrophs and mainly uses a pH gradient. 38
  39. 39. Oxidative Phosphorylation 39
  40. 40. Photophosphorylation - Autotrophs• In photophosphorylation, the energy of sunlight is used to create a high-energy electron donor and an electron acceptor. – Cyclic photophosphorylation (plants and bacteria) – Non-cyclic photophosphorylation (only plants)• In chloroplasts, light drives the conversion of water to oxygen and NADP+ to NADPH with transfer of H+ ions across chloroplast membranes.• NADP+ is a coenzyme with redox agent NADPH (The coenzyme NAD+ is converted into NADP+; the chemistry of this related coenzyme is similar to that of NAD+ but with additional phosphate group.) 40
  41. 41. Photophosphorylation 41
  42. 42. Electron Transport Chain of Photosystems 42