Respiration 2 PDF

Respiration Mitochondria (plural) Mitochondrion (singular) • The average animal cell has dozens of mitochondria. Electron micrograph (image taken via an electron microscope). Frey & Mannella (2000) Trends in Biochemical Sciences 25: 319-324 Respiration • The mitochondrion is the site of: the lin...

Respiration Mitochondria (plural) Mitochondrion (singular) • The average animal cell has dozens of mitochondria. Electron micrograph (image taken via an electron microscope). Frey & Mannella (2000) Trends in Biochemical Sciences 25: 319-324 Respiration • The mitochondrion is the site of: the linker reaction, the citric acid cycle, the respiratory electron transport chain, and ATP synthase. crista(e) matrix - site of citric acid cycle intermembrane space (“ims”) pyruvate transport protein cytosol -location of glycolysis - pyruvate is the endproduct of glycolysis outer membrane - has porins pyruvate (moves into the matrix) inner membrane -no porins - has specific transport proteins Respiration • Pyruvate (3C) is a product of glycolysis (cytosolic). • Pyruvate is transported into the mitochondrial matrix;  used in the “linker reaction” (links glycolysis to the citric acid cycle) matrix pyruvate Linker Reaction • Pyruvate dehydrogenase (“PDH”; in the mitochondrial matrix). • Links pyruvate (imported via the pyruvate transport protein) with the citric acid cycle. • Generates NADH (= CPE), acetyl CoA (= CPE) and CO2 (= 0 CPE). Glycolysis Pyruvate + NAD+ (3C) CoA CO2 PDH to citric acid cycle Acetyl-CoA + NADH (2C in “acetyl”) • CoA = co-enzyme A; gets removed in the next reaction; -don’t worry about it • For every glucose that enters glycolysis, the linker reaction happens 2x because: 1 glucose 2 pyruvate Respiration – Citric Acid Cycle Modified from OpenStax Biology 2e malate dehydrogenase • A biochemical pathway of 8 enzymes located in the mitochondrial matrix. • Input = acetyl CoA from the linker reaction. • Acetyl CoA (2C) + OAA (4C) produces citrate (6C). • Releases two CO2. • Regenerates NADH (three rxs) and FADH2 (one rx). • Regenerates ATP via SLP (one rx). ATP succinate dehydrogenase matrix ADP + Pi matrix You don’t need to know the details of the various reactions, or the chemical structures. Respiration Summary of the Linker Reaction & Citric Acid Cycle (mitochondrial matrix) CO2 CoA pyruvate + CoA acetyl-CoA (2C) You need to know this summary. (3C) citrate + NADH NAD (6C) OAA (4C) linker reaction; produces CO2 and regenerates NADH 2 CO2 Citric Acid Cycle (8 enzymes) FADH2 ATP SLP ADP + Pi FAD 3 NADH SLP = substrate-level phosphorylation 3 NAD+ Respiration Summary of ACR Energy Transformations So Far (Glycolysis & Citric Acid Cycle) 1 glucose  2 pyruvates  2 turns of the citric acid cycle 1 glucose 2 NADH from glycolysis 2 NADH from the linker reaction 6 NADH from the citric acid cycle 2 FADH2 from the citric acid cycle 2 ATP from glycolysis (SLP) 2 ATP from citric acid cycle (SLP) 6 CO2 waste product (0 CPE) CPE • The 10 NADH represent the majority of the CPE (chemical potential energy). • The job of oxidative phosphorylation is to convert the CPE of the NADH and FADH2 into the CPE of ATP;  will regenerate ~28 ATP • So far have 4 ATP from SLP. Respiration Respiratory Electron Transport Chain (RS ETC) • Located in the inner mitochondrial membrane. • Electrons end up at O2. • Think of O2 as the garbage can for low energy electrons (LEEs). • NADH and FADH2 represent HEEs. • HEEs enter the RS ETC, LEEs leave the RS ETC. • Where did the energy go?  was used to pump H+s against Δ[H+] • The “job” of the RS ETC is to convert the CPE of NADH (and FADH2) into the CPE of a Δ[H+]. higher [H+] in the ims matrix OpenStax Biology 2e lower [H+] in the matrix You don’t need to know the details about this figure. Respiration Respiratory Electron Transport Chain (RS ETC) LEE = low energy electrons higher [H+] nH+ ims H+ Pumping mitochondrial inner membrane HEE 2eLEE RS ETC 2e- NAD+ NADH H2O O2 is a garbage can for LEE nH+ CAC O2 matrix lower [H+] • Energy transformation: CPE of NADH and FADH2 CPE of a Δ[H+] You need to know/understand this diagram. Respiration Respiratory Electron Transport Chain (RS ETC) – Produces a Δ[H+] matrix intermembrane space = ims Zoom in on the NAD+/NADH cycling: NADH ⇌ NAD+ + H+ + 2eThis makes no contribution to the Δ[H+]. Zoom in on this reaction: This is one of the reasons that we “breathe”  Supply O2 as a garbage can for the RS ETC • Energy transformation by RS ETC: CPE of NADH and FADH2 CPE of a Δ[H+] Respiration • Activity of the respiratory electron transport chain creates a Δ[H+] across the mitochondrial inner membrane. • There is a lower [H+] in the matrix and a higher [H+] in the intermembrane space. Δ[H+] across the inner membrane Modified from https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry _Free_and_Easy_%28Ahern_and_Rajagopal%29/02%3A_Energy/2.06%3A_C ellular_Phosphorylations Respiration ATP Synthase • Same membrane as the RS ETC (inner membrane). • Not part of the RS ETC! nH+ matrix ims higher [H+] mitochondrial inner membrane ADP + Pi ATP synthase ATP matrix nH+ lower [H+] OpenStax Biology 2e Respiration Merge two diagrams  Oxidative Phosphorylation • Oxidative phosphorylation = RS ETC + ATP synthase. • Responsible for the majority of ATP regeneration. matrix Respiration Locations of Processes in the Mitochondrion site of RS ETC & ATP synthase cytosol -location of glycolysis - pyruvate is the endproduct of glycolysis crista(e) matrix - site of citric acid cycle higher [H+] (ims) lower [H+] Δ[H+] intermembrane space (“ims”) outer membrane - has porins pyruvate transport protein pyruvate (moves into the matrix) inner membrane -no porins - has specific transport proteins Respiration Mitochondrial Reactions of Aerobic Cellular Respiration OpenStax Biology 2e This figure has more details about the RS ETC than you need to know. outer membrane inner membrane Respiration ATP Synthase Reaction (Complete Reaction and Energy Transformations) ADP + Pi nH+ims ATP nH+matrix ΔG > 0 ΔG < 0 (coupling reaction) ADP + Pi + nH+ims ATP + nH+matrix ΔG < 0 n ≈ 4 H+/ATP The ATP synthase reaction. OpenStax Biology 2e Respiration Oxidative Phosphorylation (Ox Phos) • = the combination of the RS ETC and ATP synthase. CPE of NADH & FADH2 CPE of Δ[H+] CPE of Δ[H+] CPE of ATP RS ETC ATP synthase CPE of NADH & FADH2 CPE of ATP Ox Phos • Ox phos: 28 ATP per glucose • SLP: 4 ATP per glucose (“CPE” = chemical potential energy) OpenStax Biology 2e Energy Conversions During Aerobic Cellular Respiration abbreviation: CPE = chemical potential energy Glycolysis: CPE of Glucose (C6H12O6) CPE of 2 NADH CPE of 2 ATP (via substrate-level phosphorylation) CPE of 2 Pyruvate (= majority of the CEE) heat Pyruvate Oxidation (Linker Reaction) & Citric Acid Cycle: CPE of 2 Pyruvate CPE of 2 ATP (via substrate-level phosphorylation) CPE of 8 NADH (= majority of the CEE) CPE of 2 FADH2 heat Energy Conversions During Aerobic Cellular Respiration continued Respiratory Electron Transport Chain: CPE of 10 NADH (8 are from pyruvate oxidation & citric acid cycle, 2 from glycolysis) CPE of 2 FADH2 CPE of Δ[H+] across the cristae (inner mitochondrial membrane) heat ATP Synthase: CPE of Δ[H+] across the cristae CPE of ~28 ATP (depends on what book you read) heat Respiration Aerobic Cellular Respiration – The Entire Process Glucose 2 Pyruvate CAC (incl. linker rx) By RegisFrey - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=4389845 RS ETC ATP synthase Respiration – Lack of Oxygen What happens if there is no O2 (or insufficient O2) available for ACR? • Can happen in muscles during intense physical exercise. • Drowning. • Happens to yeast during wine- and beer-making. • Happens to plant roots in waterlogged soils. • No RS ETC activity is possible;  no H+ pumping  no Δ[H+]  no ATP synthase activity • In short, no oxidative phosphorylation; -but ox phos represents 28/32 ATP per glucose • Citric acid cycle also shuts down; • Needs NAD+ and FAD;  come from RS ETC activity  lose the ATP from the SLP associated with the citric acid cycle Respiration – Lack of Oxygen NAD+ NADH pyruvate CoA acetyl-CoA (2C) citrate (6C) linker reaction OAA (4C) CO2 Citric Acid Cycle (8 enzymes) FADH2 ATP SLP ADP + Pi FAD 3 NADH = cannot be supplied by the RS ETC in the absence of O2 3 NAD+ Respiration – Lack of Oxygen • All that is left under these circumstances is glycolysis;  2 ATP per glucose via SLP • But glycolysis needs NAD+, just like the citric acid cycle. Fermentation • Running glycolysis in the absence of O2;  regenerate ATP • Substrate-level phosphorylation (2 ATP/glucose) provides the ATP during fermentation. • Specialized biochemical mechanisms to regenerate NAD+ from NADH;  keep glycolysis running Respiration – Glycolysis in the Absence of Oxygen Modified from OpenStax Biology 2e. this is the problem; need NAD+ You don’t need to the biochemical reactions on this slide. Respiration Glycolysis Summary Diagram • Cytosolic pathway. Glucose (6C) 2 NAD+ + 2H+ glycolysis – 10 reactions/enzymes 2 ADP + 2Pi this is the problem (substrate-level phosphorylation) 2 NADH 2 ATP 2 Pyruvate (3C) Respiration - Fermentation Fermentation by Plants & Yeast Glucose 2 NAD+ + 2H+ Fermentation = running glycolysis in the absence of O2. glycolysis 2 ADP + 2Pi (substrate-level phosphorylation) Beer-making: need a 2 NADH 2 ATP 2 Pyruvate (3C) 2 CO2 2 NAD+ + 2H+ 2 Ethanol 2 NADH alcohol dehydrogenase (plants & yeast) 2 Acetaldehyde (2C) https://www.homebrewersassociation.org/how-to-brew/how-toharvest-and-culture-commercial-yeast-for-homebrewers/ pressure relief tube to allow CO2 to escape. Respiration - Fermentation Fermentation by Animals & Some Bacteria Glucose 2 NAD+ + 2H+ Fermentation = running glycolysis in the absence of O2. glycolysis 2 ADP + 2Pi 2 NADH (substrate-level phosphorylation) 2 ATP 2 NAD+ + 2H+ 2 Lactate (3C) 2 NADH 2 Pyruvate (3C) lactate dehydrogenase (animals & some bacteria) By Takeaway - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=36038530 Bacterial lactic acid fermentation is used to make many different food products, including yogurt. Respiration - Fermentation • Some organisms will ferment quite happily for extended periods of time, e.g. yeast. • Mammals aren’t happy with extended fermentation;  inadequate ATP regeneration rate • For mammals, fermentation is usually a short-term response to temporary O2 shortage;  longer term O2 shortage leads to cellular death (because of insufficient ATP) Respiration – Other Energy Sources for Ox Phos • ACR oxidizes the C-H and C-C bonds of organic molecules  regeneration of ATP. • We’ve focused on glucose as the starting point, and glucose is a common starting point. • But there are other potential sources of C-H and C-C bonds (especially fatty acids from fats), and they feed into ACR in different places. • Interesting that the sub-components of fats (fatty acids and glycerol) feed into ACR in different locations. Don’t memorize this diagram; simply understand that glucose is not the only possible input for ACR. OpenStax Biology 2e Glycogen from the liver and muscles, as well as other carbohydrates, hydrolyzed into glucose-1phosphate, together with fats and proteins, can feed into the catabolic pathways for carbohydrates. Respiration – Other Energy Sources for Ox Phos • Fats have a higher energy density than carbohydrates. C-H and C-C bonds represent CPE. Fats have higher proportion of C-H and C-C bonds than do carbohydrates. Modified from OpenStax Biology 2e Respiration – Another Reason for ACR is Biosynthesis From the first slide of the Respiration section • Two major functions for ACR: 1) provide biosynthetic intermediates (carbon skeletons, building blocks) for anabolism 2) regenerate ATP • Let’s very briefly look at provision of biosynthetic intermediates;  also an important role for ACR (ACR intermediates are crucial for biosynthesis) Do not memorize this diagram. Simply understand that respiratory intermediates are used for biosynthesis. Modified from OpenStax Biology 2e The “carbon skeletons” of many amino acids (indicated in boxes) are based on respiratory intermediates. Respiratory intermediates provide many carbon skeletons for many cellular molecules. Important Points About ACR & Oxidative Phosphorylation • When trying to wrap your head around concepts such as ACR & oxidative phosphorylation, it’s better to try to understand what is going on than it is to try to memorize what is going on (i.e. memorizing a diagram ≠ understanding a process). • If you can understand it, then you can probably explain it on a test. I.e. greater understanding leads to less dependence on memorization. • If you truly understand these concepts, and can explain them, then you can probably explain ACR & oxidative phosphorylation. 1) ACR converts the CPE of glucose into the CPE of ATP, via various energy transformations. (self-test: can you explain all of the energy transformations?) 2) The respiratory electron transport chain converts the chemical potential energy of NADH into the chemical potential energy of a Δ[H+]. (self-test: can you explain how this happens?) 3) ATP synthase converts the chemical potential energy of a Δ[H+] into the chemical potential energy of ATP. (self-test: can you explain how this happens?) 4) Parts 2 and 3 (above) are happening in, or in the vicinity of, the mitochondrial inner membrane. (self-test: can you draw a mitochondrion, and clearly indicate where everything is happening, and how it is happening?) Respiration – Mitochondrial Diseases • There are a number of genetic conditions/diseases associated with mitochondria; -genetic diseases = heritable • Estimated that in North America 1/5000 people have a genetic mitochondrial disease. • The primary mitochondrial diseases are the most common of the inherited metabolic disorders, and a common cause of inherited neurological disorders (neurons need a lot of ATP). • The genetic basis of many of the mitochondrial disorders are known. • The mitochondrial disorders are caused by mutations; -mutations = changes in the genetic information (will briefly discuss mutations in the Genetics portion of BIOL 100). • Understanding the genetic basis of mitochondrial disorders is made more complicated by the fact that the mutated genes may be in mitochondrial DNA (mtDNA) or in the nuclear DNA (nDNA); this also affects the inheritance patterns.