Unit 2 - Metabolism Notes

Unit 2: Metabolism ↹ Energy -​ Energy is the ability to do work/something useful -​ Energy can do something useful once transferred (work) ⇒ Laws of thermodynamics -​ ⇾ 1st law: -​ Energy cannot be created or destroyed, it can only be converted from one form to another form -​ Energy transfer is not 100% efficient, some energy is always lost as waste -​ Thermal heat energy is waste, ultimately all energy in the universe will be transformed into heat energy -​ ⇾ 2nd law: -​ Random arrangement of energy -​ Entropy of an isolated system will always increase, never decreasing -​ Energy must be spent to retain order, however this spending of energy releases heat which increases entropy -​ Loss of energy location = ↑ entropy ⇒ Free energy -​ Called “free” energy because this is the energy that can be used to do work (ΔG) -​ To cause a reaction, energy must be used to strain and break the bonds, this is called activation energy -​ ⇾ Exergonic: -​ Net release of energy -​ Paper doesn’t just ignite when exposed to air, it requires an initial input -​ ⇾ Endergonic: -​ Net storage of energy -​ Most synthesis reactions store energy ⇒ Coupled reactions -​ Endergonic reactions (absorb energy) violate the 2nd law of thermodynamics because it lowers entropy -​ To occur, endergonic reactions must be coupled, use energy released from another reaction, so the 2nd law of thermodynamics is not violated -​ ⇾ ATP: -​ The coupled reaction in biological systems is the hydrolysis of ATP (adenosine triphosphate) -​ When ATP is hydrolyzed, energy is released to power endergonic reactions -​ Some of the released energy will be lost as heat (↑ entropy) -​ Most importantly, the increase in entropy from ATP hydrolysis is always greater than the decrease in entropy of the endergonic reaction -​ ⇒ Redox reactions -​ Transfer of electrons -​ When electrons are transferred, energy is also brought along with -​ ⇾ Oxidation: -​ Lose electrons -​ ⇾ Reduction: -​ Gain electrons ↹ Enzymes -​ Catalysts made of protein (speed up chemical reactions) -​ Reusable (not consumed in reaction) -​ Specific to their substrate (can only catalyse one or two things) ⇒ How -​ Heat provides activation energy for most reactions -​ However, high heat will damage cells -​ Enzymes reduce activation energy -​ Less heat required -​ Faster reactions -​ ⇾ Catabolic -​ Break down -​ Enzyme weakens bonds by pulling or bending -​ ⇾ Anabolic -​ Build up -​ Enzymes holds reactants in close proximity ⇒ Induced-fit model -​ Enzymes are specific to their substrate(s) 1.​ Substrate binds to active sie -​ Substrate and active site must have compatible shape 2.​ Protein of enzyme changes shape to better accommodate substrate -​ Induced fit -​ Creates enzyme-substrate complex 3.​ Substrate is reacted to and leaves ⇒ Temp, pH, salinity -​ Enzymes are sensitive to temperature, pH, and saline concentration -​ There are different optimal levels of temperature, pH, and salinity for all enzymes ⇒ Cofactors -​ Some enzymes have non-protein cofactors (inorganic minerals or coenzymes) to function properly; Zn2+ Mn2+ Fe3+ ⇒ Enzyme inhibition -​ ⇾ Competitive -​ Enters active site and blocks normal substrate from binding -​ Competitive because competing with substrate in active site -​ Irreversible (stops completely) -​ BAD: toxin or poison -​ ⇾ Noncompetitive -​ Interacts with enzyme in some way, causing change in active site -​ Noncompetitive because not competing with substrate -​ Reversible (slows enzyme) or irreversible (stops completely)​ -​ BAD: toxin or poison -​ ⇾ Allosteric enzymes -​ Enzymes that can change their shape (on & off) -​ Allosteric site -​ Binding site other than active site -​ Inhibitors bind to allosteric site and change form -​ Active form -​ Inactive form -​ GOOD: Biologically regulated -​ ⇾ Feedback inhibition -​ Biochemical pathways are series of chemical reactions regulated by enzymes -​ Step-by-step modifying of initial reactant into product -​ Feedback inhibition is when the product of a pathway inhibits the pathway -​ Use of allosteric enzymes -​ Inhibit beginning of pathway so no useless intermediates are produced 1.​ A turns into D 2.​ D inhibits A 3.​ D used by cell 4.​ A uninhibited 5.​ Repeat ↹ Cellular Respiration -​ C6H12O6 + 6O2 → 6CO2 + 6H2O -​ To trap as much free energy from glucose as possible in the form of ATP 1.​ Glycolysis -​ Makes glucose ready for Krebs cycle 2.​ Pyruvate oxidation -​ Locks pyruvate into mitochondria 3.​ Krebs/citric acid cycle -​ Cyclical process that converts remaining glucose molecule into CO2 4.​ Electron transport chain & chemiosmosis -​ Converts coenzyme stored energy into ATP ⇒ Phosphorylation -​ The transfer of a phosphate group -​ ⇾ Substrate-level -​ ATP is formed directly via enzyme -​ ~31kJ/mol of potential energy transferred per mole of ATP -​ ⇾ Oxidative -​ ATP formed indirectly -​ Electron transport chain & chemiosmosis -​ Coenzymes (NAD+ & FAD) oxidise glucose and eventually transfer most free energy into ATP -​ Multiple redox reactions -​ ⇾ NAD+ -​ Oxidizes, taking 2 electrons and 1 proton (H+) -​ Reduced into NADH & other H+dissolved into surroundings -​ ⇾ FAD -​ Oxidizes, taking 2 electrons and 2 protons (H+) -​ Reduced into FADH2 ⇒ Mitochondria -​ Specialised for the production of ATP -​ Where pyruvate oxidation, Krebs cycle, and electron transport chain & chemiosmosis occurs -​ ⇾ Structure -​ Has DNA, RNA, and ribosomes like regular cells -​ Has two membranes (outer and inner) -​ Inner membrane -​ Creates two compartments within the mitochondrion -​ Intermembrane space -​ Matrix -​ Contains proteins that make up electron transport chain and chemiosmosis -​ Have cristae/folds that increase S.A. ​ -​ ⇾ Endosymbiosis hypothesis -​ Mitochondria are evolutionary descendents of prokaryotes ⇒ Glycolysis -​ -​ -​ -​ 6-carbon glucose becomes two 3-carbon pyruvates In cytoplasm Each step catalysed by enzymes Anaerobic -​ ⇾ Glucose Activation 1.​ ATP transfers a phosphate into glucose, turning it into glucose-6-phosphate, while becoming ADP 2.​ Isomerization occurs, forming fructose-6-phosphate 3.​ Another ATP transfers a phosphate, forming fructose-1,6-phosphate -​ ⇾ Sugar Splitting 4.​ Fructose-1,6-phosphate is split into two fragments, forming DHAP and G3P 5.​ DHAP is converted into G3P -​ ⇾ Oxidation 6.​ G3P become oxidised by NAD+, of which becomes NADH and heads toward a mitochondria, releasing enough energy to attach 1 phosphate to form BPG -​ This reaction occurs x2 -​ ⇾ ATP formation 7.​ One of the phosphates of BPG is transferred onto an ADP via substrate-level phosphorylation, forming an ATP. 8.​ The other phosphate of BPG is transferred onto another ADP, forming another ATP. 9.​ This leaves a 3-carbon pyruvate, which heads toward a mitochondria -​ This reaction occurs x2 -​ ⇾ Products -​ 2 ATP (net) -​ 2 pyruvates -​ 2 NADH (converted into 2 FADH2) -​ Heat ⇒ Pyruvate oxidation -​ Two 3-carbon pyruvates into two Acetyl-CoA -​ In matrix -​ Anaerobic -​ ⇾ Pyruvate Oxidation 10.​ Pyruvates enter mitochondria 11.​ A CO2 molecule is removed via decarboxylation, leaving acetyl. 12.​ NAD+ also oxidises, becoming NADH 13.​ CoA is attached to the remaining carbons, creating acetyl-CoA, ⠀⠀which enters the Krebs cycle -​ ⇾ Products -​ 2 Acetyl-CoA -​ 2 NADH -​ Waste CO2 ⇒ Krebs cycle -​ Two Acetyl-CoA into many energy products -​ In matrix -​ Aerobic -​ ⇾ Krebs Cycle 14.​ Acetyl-CoA enters the cycle 15.​ 4-carbon oxaloacetate combines to form 6-carbon citrate 16.​ Citrate is decarboxylated and oxidised by NAD+, which forms ⠀⠀NADH 17.​ It is decarboxylated and oxidised by NAD+ again, forming ⠀⠀another NADH 18.​ Off of what is left, GDP converts into GTP, which is then ⠀⠀converts ADP into ATP 19.​ It is then oxidised by FAD, forming FADH2 20.​ It is oxidised by NAD+ one last time, becoming oxaloacetate to ⠀⠀be used in the next cycle -​ ⠀⠀This reaction occurs x2 -​ ⇾ Products -​ 6 NADH -​ 2 FADH -​ 2 ATP ⇒ Electron transport chain and chemiosmosis -​ -​ -​ -​ Energy products converted into ATP On inner membrane Aerobic Reliant on the electrochemical gradient -​ Higher concentration of H+ in intramembranous space than matrix -​ ⇾ NADH 21.​ NADH goes to NADH reductase, becomes reduced to release 2 electrons, a H+, and turn back into NAD+ 22.​ The electrons fund NADH reductase to move 1 H+ and then gets transported to protein pump 2 by coenzyme Q 23.​ The electrons fund protein pump 2 to move 1 H+ and then gets transported to protein pump 3 by cytochrome C 24.​ The electrons fund protein pump 3 to move 1 H+, donating the last of its energy 25.​ O2 and 4H take the electrons and form 2 H2O. Oxygen is the terminal (last) electron acceptor. -​ Pumps a total of 3 H+ across -​ ⇾ FADH 26.​ FADH2 goes to coenzyme Q, becomes reduced to release 2 electrons, 2 H+, and turn back into FAD 27.​ The electrons are transported to protein pump 2 28.​ The electrons fund protein pump 2 to move 1 H+ and then gets transported to protein pump 3 by cytochrome C 29.​ The electrons fund protein pump 3 to move 1 H+, donating the last of its energy 30.​ O2 and 4H take the electrons and form 2H2O. -​ Pumps a total of 2 H+ across​ -​ ⇾ Chemiosmosis 31.​ Due to high H+ concentration in the intermembrane space, there is high kinetic energy 32.​ H+ diffuses across membrane through ATP synthase 33.​ During diffusion, kinetic energy is turned into chemical potential energy by forming an ATP ⇒ Total ATP formed NADH FADH2 ATP 2 2 2 converted into FADH converted from NADH net Pyruvate oxidation 2 0 0 Kreb’s cycle 6 2 2 Total pre-ETC 8 4 4 8x3 = 24 4x2 =8 Glycolysis Electron transport chain TOTAL ATP 36 ATP ↹ Anaerobic Respiration -​ -​ -​ -​ Cellular respiration without oxygen Some organisms live in oxygen-free environments Many single celled organisms like use only use glycolysis for energy Fermentation is much less efficient at supplying energy ⇒ Lactate Fermentation -​ Occurs when cells are without oxygen temporarily -​ Exercise 1.​ NAD+ reduced very quickly and oxidation of NADH cannot keep up 2.​ Cell will essentially run out of NAD+ 3.​ Without NAD+, glycolysis will stop 4.​ Fermentation allows NAD+ to be oxidised and continue glycolysis, but generates lactate 5.​ Lactate is oxidised back to pyruvate when oxygen becomes available again -​ Oxygen must be deeply breathed in after stopping physical activity because there is a buildup of NADH requiring reoxidation; called the oxygen debt 1.​ Glycolysis produces 2 pyruvates, 2 NADHs, and nets 2 ATP 2.​ Pyruvates will receive 2 hydrogen atoms from 2 NADH, forming lactic acid and reoxidizing 2 NADH back into 2 NAD+ 3.​ The 2 NAD+ will go back to conduct glycolysis ⇒ Ethanol Fermentation -​ Used by yeast, bacteria, etc 1.​ Glycolysis produces 2 pyruvates, 2 NADHs, and nets 2 ATP 2.​ Pyruvates will lose a CO2, creating ethanal 3.​ Ethanal will receive a hydrogen from NADH, forming ethanol and reoxidizing 2 NADH back into 2 NAD+ 4.​ The 2 NAD+ will go back to conduct glycolysis ↹ Related Pathways ⇒ Non-glucose monosaccharides -​ Fructose 1.​ Fructose converted into fructose-1-phosphate by fructokinase 2.​ Enters glycolysis -​ Galactose 1.​ Galactose converted into glucose-6-phosphate through various reactions 2.​ Enters glycolysis ⇒ Protein catabolism 1.​ Protein is digested into amino acids 2.​ Amino groups removed from amino acids 3.​ Remaining portion of amino acid converted into various components of glycolysis or citric acid cycle ⇒ Lipid catabolism 1.​ Triglycerides converted to glycerol and fatty acids 2.​ a.​ Glycerol will be converted into either DHAP or G3P b.​ Fatty acid broken into acetyl groups (β-oxidation) 3.​ Acetyl groups combine with CoA to form acetyl-CoA ↹ Photosynthesis -​ 6CO2 + 6H2O → C6H12O6 + 6O2 -​ To trap as much light energy as possible in the form of glucose 1.​ Light reactions -​ Equivalent to electron transport chain -​ Absorb light energy and transfer to ADP and NADP+ 2.​ Calvin cycle -​ Equivalent to Krebs cycle -​ Combines CO2 into glucose ⇒ Light -​ Form of energy that travels as photons -​ Short wavelength = high energy -​ Long wavelength = low energy -​ Thylakoid membranes can absorb photons in the visible light spectrum ⇒ Pigments -​ Absorbs violet-blue & red -​ Reflects green & yellow -​ Many different pigments as more increases spectrum of light able to be absorbed -​ ⇾ Chlorophyll a -​ Only pigment that can transfer light energy to carbon fixate -​ ⇾ Chlorophyll b -​ Accessory pigment, absorbs photos that chlorophyll A cannot absorb well/at all -​ ⇾ Accessory pigments -​ Transfers energy to chlorophyll A -​ ⇾ Carotenoids -​ Able to absorb light energy that would otherwise damage chlorophyll -​ ⇾ Leaf colour -​ Leaves appear green because of chlorophyll in chloroplasts -​ Leaves appear in different colours in autumn because plants stop producing and disassemble chlorophyll. ⇒ Chloroplast -​ Specialised to conduct photosynthesis -​ Structure -​ Has DNA, RNA, and ribosomes -​ Has 3 membranes (outer, inner, and thylakoid) -​ Inner membrane -​ Creates three compartments within the chloroplast -​ Intermembrane space -​ Stroma -​ Thylakoid lumen -​ An entire stack of thylakoids is called a granum ⇒ Light dependent reactions -​ 1st stage of photosynthesis -​ Involves an electron transport chain -​ Takes place along the thylakoid membrane -​ ⇾ Photoexcitation -​ Electrons in chlorophyll absorb energy from light, moving from ground state to excited state -​ Excited electrons are unstable and return to ground state, releasing energy -​ In plants, the excited electron is captured by the primary electron acceptor (PEA) -​ ⇾ Photosystems -​ Antenna complex -​ Absorbs and transfers energy to chlorophyll A -​ Reaction centre is where an electron in chlorophyll A absorbs transferred energy, becoming excited, and is then transferred to the PEA -​ Energy is officially captured as chemical potential -​ Photosystem I -​ Reaction centre contains P700 and ferredoxin (FD), which is a PEA -​ Photosystem II -​ Reaction centre contains P680 and plastoquinone (PQ), which is a PEA -​ P700 and P680 are identical but their absorption spectra are slightly different because of associated proteins ⇒ Light reactions -​ -​ -​ -​ -​ Light dependent reactions Photon energy converted into NADPH and ATP On thylakoid membrane Anaerobic Reliant on the electrochemical gradient -​ Higher concentration of H+ in lumen than stroma -​ ⇾ Non-cyclic flow 1.​ Photons excite an e- in System II 2.​ The excited e- gets transported to pump by PQ, funding it to move 1 H+ into the lumen, and is depleted 3.​ To replace the depleted e- in System II, protein Z splits water to form oxygen and H+’s, which is what produces the oxygen we need 4.​ The depleted e- is transported into System I 5.​ Photons excite the e- in System I 6.​ The excited e- gets transported to NADPH reductase by FD, combining with a H+, NADP+, and another e- to form NADPH -​ Provides NADPH for Calvin cycle -​ ⇾ Cyclic flow 7.​ Instead of being transported to form NADPH, the excited e- in System I is transported by FD back to pump to fund it to move 1 H+ into the lumen 8.​ The depleted e- is transported into System 1 9.​ Photons excite the e- in System I, allowing it to continue from there -​ Only function is to pump H+ (ATP synthesis) -​ ⇾ Chemiosmosis 10.​ Due to high H+ concentration in the lumen, there is high kinetic energy 11.​ H+diffuses across membrane through ATP synthase 12.​ During diffusion, kinetic energy is turned into chemical -​ Provides ATP for Calvin cycle ⇒ Calvin cycle -​ Light independent reactions -​ Cyclic process that converts CO2 into carbohydrates -​ In stroma -​ ⇾ Carbon fixation 13.​ 3 CO2 combine with 3 RuBP (C5 & P2) with help of enzyme Rubisco, forming an unstable intermediary (C6 & P2) 14.​ The intermediary splits into 6 PGA (C3 & P1) -​ Only way to make inorganic carbon organic -​ ⇾ Reduction reactions 15.​ The 6 PGA combine with 6 ATP to form 6 BPG (C3 & P2) 16.​ The 6 BPG are reduced by 6 NADPH to form 6 G3P 17.​ 1 G3P leaves the cycle as a final product, the cycle must repeat again to form 1 glucose -​ ⇾ RuBP regeneration 18.​ 3 ATP transfers 3 phosphates into the 5 G3P, forming 3 RuBP to repeat the cycle -​ ⇾ Result -​ 18 ATP + 12 NADPH invested = 1 glucose -​ 9 ATP : 6 NADPH -​ Uneven ratio = ATP deficit ↹ C4 and CAM ⇒ Photorespiration -​ O2 competitively inhibits CO2 from rubisco’s active site -​ Rubisco is able to catalyse two reactions 1.​ Addition of carbon to RuBP to form 2 PGA (photosynthesis) 2.​ Addition of oxygen to RuBP to form 1 PGA and 1 glycolate (photorespiration) -​ Photorespiration decreases production of glucose -​ Carbon fixation does not occur -​ Glycolate molecule eventually breaks down and releases CO2, so the plant will lose fixed carbon -​ Earth's atmosphere is 20.95% oxygen and only 0.039% carbon dioxide, so O2 wins the competition for Rubisco’s active site ⇒ C4 Plants -​ Structural adaptation -​ Created a barrier between mesophyll and bundle-sheath cells against O2, but allows CO2 to be carried through -​ Keeps CO2 concentration in the bundle sheath high so CO2 outcompetes O2 -​ Called C4 because the enzyme PEP carboxylase catalyses a CO2 onto a 3-carbon molecule, forming 4-carbon molecule -​ The leaves of C4 plants contains two types of photosynthetic cells -​ Bundle-sheath cells around a vein -​ Mesophyll cells -​ ⇾ C4 pathway 1.​ In mesophyll cells, PEP carboxylase fixes CO2 to PEP, forming an oxaloacetate 2.​ The oxaloacetate becomes a malate 3.​ Malate diffuses into bundle-sheath cells 4.​ A CO2 from malate is removed, forming a pyruvate, and the CO2 enters the Calvin cycle 5.​ Pyruvate diffuses back into mesophyll cells 6.​ Pyruvate is phosphorylated by an ATP to reform a PEP, allowing the cycle to continue -​ There is an ATP cost to move 1 CO2 ⇒ CAM plants -​ Behavioural adaptation -​ Open stomata (CO2 out) at night (no sun) -​ Close stomata (no CO2 out) during day (sun) -​ Closing stomata during day stops transpiration and prevents CO2 loss -​ Occurs in water storing plants, like cacti -​ ⇾ CAM photosynthesis 1.​ During the night, stomata opens to allow CO2 to enter 2.​ CO2 is fixed and stored as C4 molecules (malate) in vacuoles 3.​ When day comes, stomata closes to stop transpiration and CO2 from leaving 4.​ Stored C4 molecules (malate) are broken down, releasing CO2 for Calvin cycle 5.​ Sunlight allows light reactions to occur, powering the Calvin cycle ↹ Environment -​ Rate of photosynthesis is measured by the rate that CO2 is absorbed ⇒ Rate of photosynthesis -​ ⇾ Irradiance -​ Irradiance is the light intensity per unit area of leaf -​ The more light, the more intensity -​ Light compensation point is point on the curve where -​ Rate of CO2 uptake = Rate of CO2 production (from cellular respiration) -​ If you keep on adding light, you will eventually reach the light saturation point where more light won’t have an effect on rate (plateaus) -​ ⇾ CO2 limitation -​ CO2 availability limits overall rate of photosynthesis, not irradiance -​ Max rate is when all enzymes are saturated and cannot convert any faster -​ Like chairs, limit chairs & excess substrates, have to wait until chairs finish converting -​ ⇾ Temperature -​ Light reactions are not affected by temperature, only irradiance -​ Calvin cycle reactions are affected by temperature because of enzyme’s optimal temperature -​ ⇾ Oxygen concentration -​ Oxygen concentration inhibits photosynthesis (rubisco active site) -​ Higher oxygen concentration = lower photosynthesis rate -​ ⇾ Sun vs shade plants -​ Sun: More efficient at harvesting light at high intensity -​ Shade: More efficient at harvest light at low intensity