326R
Metabolism BIO 2
Carbohydrates Pyruvate
Pyruvate to Acetyl CoA is not considered part of the TCA cycle
NAD+ NADH + H+
Alanine
CO2
2C
Acetyl CoA
Lipids
4C
Oxaloacetate
NADH + H+
Citrate
6C
Malate
NAD+
Isocitrate
NAD+ NADH + H+
Fumarate Succinate Dehydrogenase
FADH2 FAD NAD
+
5C
ketoglutarate
CO2
NADH + H+
Succinate
GTP
Succinyl CoA
4C
CO2
GDP + Pi
TCA (or Krebs) cycle
5 energy producing steps, 12 ATP per cycle
3 NAD NADH + H+
3 ATP equivalent each (9 total) 2 ATP 1 ATP GTP + ADP GDP + ATP
FAD FADH2
1 GDP GTP
12 ATP per cycle means 24 ATP from TCA per molecule of glucose
Chemiosmosis
H+ Extracellular/Outside H+
Electron Transport
Cytoplasm/Inside H+ ADP + Pi H+ ATP
ATPase/ATP synthetase
Electron transport chain
Accepts electron pairs from NADH and FADH
Reminder: Losing a pair of electrons means NADH and FADH are oxidized when they donate them to the electron transport chain
Energy from redox reactions used to move protons across a membrane and create a gradient. ATP can then be made by allowing protons to move back across the membrane.
Redox potentials
-0.4 Substrates (Glyceraldhehyde phosphate) -0.3 NADH, NADH dehydrogenase -0.2 Flavoprotein, Succinate dehydrogenase 0.0 - +0.2 Ubiquinone 0.0 - +0.4 Cytochromes +0.4 NO3, NO2 +0.8 Oxygen
Electron transport - 4 complexes
H+ H+ H+
Outside
I 2eUQ II NADH
NADH dehydrogenase
Cyt c III IV
Inside
O2
bc1 complex Cytochrome Oxidase
FAD
Succinate dehydrogenase
Electron transport
4H+
Outside
2e2eUQ
4H+
2H+
2e- Cyt c 2e
NDH
SDH
2e
-
CytRed
CytOx Complex IV
H2O
Complex III
NADH NAD
FADH2 FAD 2H+ + 1/2O2
4H+ Complex I
Complex II
4H+
2H+
Inside
Abbreviations: NDH: NADH Dehydrogenase SDH: Succinate Dehydrogenase UQ: ubiquinone CytRed: Cytochrome C Reductase CytOx: Cytochrome C Oxidase
ATPase/ATP synthetase
The bucket brigade (again)
Each villager can only hold one bucket each enzyme complex (and ubiquinone) can only hold one pair of electrons.
Unlike the villagers, the electron transport chain isnt really a chain. All the enzymes (and ubiquinone) diffuse back and forth in the membrane. They do not interact with the same exact molecule every time ie, SDH will always donate its electrons to ubiquinone, but not the same ubiquinone every time. If one part of the chain breaks, the whole chain breaks.
Complexes
Each complex is a heteromer of different proteins Up to 26 proteins in complex I (?) I, II and III contain FeS (Iron-Sulfur) proteins IV contains Cu All complexes that pump protons across the membrane (I, III, IV) contain transmembrane proteins The complexes are not physically linked together, but migrate within the membrane Stoichiometry isnt even (if they were linked together, youd find the same number of each enzyme, i.e. a 1:1:1.. Ratio of all enzymes) Complex IV requires oxygen. Without oxygen the entire chain transport will stop for lack of oxidized substrates. This is basis of aerobic respiration.
Succinate dehydrogenase and ubiquinone: a closer look SDH SDH
FAD (ox)
UQred UQox FADH2
(red)
FAD is covalently attached to SDH. FAD is a prosthetic group. SDH is the only TCA enzyme in the electron transport chain.
Succinate
Fumarate
Note that when FADH is oxidized, ubiquinone is reduced. FADH reduces ubiquinone, ubiquinone oxidizes FADH
Ubiquinone is an organic molecule, not a protein. It is hydrophobic and migrates freely within the membrane
Chemiosmosis
Total number of protons translocated is currently thought to be 10 per NAD and 6 per FAD
Complex 1: 4 Complex 3: 4 Complex 4: 2 NAD: 3 ATP/10 protons FAD: 2 ATP/6 protons)
ATP production
Ratio of ~3 protons/1 ATP
ATP synthetase
H+ H+ H+ H H
+ +
H+ H+ H+ H+ H+
Outside : lower pH
H+
OHOH-
OH-
OHOH-
OH-
ADP + Pi
H+
ATP
Fermentation
Fermentation serves to recycle NADH to NAD or maintain the redox balance Allows glycolysis to continue in absence of O2 Note that the fermentation reactions shown do not produce energy, ATP is produced by the glycolysis pathway fermentation allows glycolysis to continue. In E. coli, most fermentation is mixed acid fermentation. This causes the excretion of ethanol and a mixture of many acids, usually strongly acidifying the local environment.
Glucose
NAD NADH NADH NAD NADH NAD
Pyruvate NADH
NAD
Lactate
Ethanol
Anaerobic respiration
Lacking O2 (or the ability to use it), another terminal electron acceptor must be used. Some of these are NO3, SO4, CO2, Fe, etc. etc. Yield of ATP is lower as these molecules are not as oxidative as oxygen (the overall energy change is not as great).
Gluconeogenesis
Glucose
Most reactions in glycolysis are reversible, and are used in both pathways The ones that are different are given here.
ATP
PFK
Fruc 6 phos
Pi
Fructose bisphosphate phosphatase
PFK and Pyruvate Kinase both catalyze reactions that are essentially irreversible: the Keq is extremely high/the free energy change is great/there is a very high -G
ADP
Fruc 1,6 biphos
GDP Phosphoenolpyruvate ADP
Pyruvate kinase Phosphoenolpyruvate carboxykinase
CO2
GTP oxaloacetate ADP ATP
Pyruvate carboxylase
ATP
pyruvate
Left (down): glycolysis, Right (up): gluconeogenesis
Amino Acid catabolism transamination
Alanine transaminase Alanine + ketoglutarate pyruvate + glutamate
amino acid + ketoacid ketoacid + amino acid
Amino Acid Alanine Pyruvate TCA
Keto acid
ketoglutarate ketoglutarate Glutamate
Glutamate
CH3 NH3 - C COOH Alanine
+
CH3 O = C COOH Pyruvate Waste/urea NH3
NADH + H
NAD
Glutamate dehydrogenase
Amino Acid catabolism
pyruvate Fats/Fatty acids Acetyl CoA
Alanine transaminase alanine, glycine, (and others)
glutamine arginine
TCA cycle
glutamate Fumarate phenylalanine Succinyl CoA ketoglutarate