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Biochemistry W9 Metabolism of carbonhydrates II, Cytochrome c - Coggle…
Biochemistry W9
Metabolism of carbonhydrates II
Cellular repiration
Purpose
Provides more energy from glucose than glycolysis,and captures energy stored in lipids and amino acids.
Meaning
Consume O2 and produce CO2
Major stages
acetyl CoA production乙醯輔酶A的生成
(in mitochondrial matrix)
Which can be used to produce acetyl CoA
Fatty acids
Glucose
Carbohydrates release 1/3 of total potential CO2 during Stage 1.
Conversion of Pyruvate to Acetyl-CoA (3C->2C)
Catalyzed by the pyruvate dehydrogenase complex(PDC)
(first carbons of glucose to be fully oxidized)
PDC requires 5 coenzymes
FAD
NAD+
Lipoyllysine
3 more items...
CoA-SH
TTP
PDC
Advantages
3 more items...
Is a large multi enzyme complex
3 more items...
Steps
E1
2 more items...
E2
1 more item...
E3
2 more items...
Structure of Coenzyme A
The function of CoA is to accept and carry acetyl groups
Amino acid s
Generates some ATP,NADH,FADH2
Regulation：
-phosphorylation: inactive
-dephosphorylation: active
PDH kinase and PDH phosphorylase are part of mammalian PDH complex.
Kinase is activated by ATP
high ATP->phosphorylated PDH->less acetyl-CoA
low ATP->kinase is less active and phosphorylase removes phosphate from PDH->more acetyl-CoA
acetyl CoA oxidation 克式循環/檸檬酸循環
(in mitochondrial matrix)
Generates more ATP,NADH,FADH2 and one GTP
electron transfer and oxidative phosphorylation電子傳遞鏈(ETC)
(in the inner membrane)
Generates the vast majority of ATP during catabolism
The Citric Acid Cycle (CAC)
Steps
Oxidation of an Alkane to Alkene by Succinate Dehydrogenase
Succinate Dehydrogenase常考‼️
Reduction of the alkane to alkene requires FADH2.
不用NAD+的原因是因為carbon-hydrogen bond的能力低，不夠於用NAD+
FAD is covalently bound, unusua
Bound to mitochondrial inner membrane‼️
(acts as Complex II in the electron-transport chain)
Near equilibrium/reversible
Hydration Across a Double Bond: Fumarase
Fumarase
Stereospecific
結構的專一性
OH− first adds to fumarate... then H+ adds to the carbanion.
Cannot distinguish between inner carbons, so either can gain –OH
Slightly thermodynamically favorable/reversible
Generation of GTP Through Thioester: Substrate-Level Phosphorylation by Succinyl-CoA Synthetase
Goes through a phospho-enzyme intermediate
Pi取代CoA-SH的位置，enzyme和Pi結合，succinate單獨被釋放出來，而結合在enzyme上的Pi丟給GDP，最後釋放出GTP和Succinylcholine-CoA synthstase
Produces GTP, which can be converted to ATP
Substrate-level phosphorylation(糖解步驟7、10)
Slightly thermodynamically favorable/reversible
The energy of thioester allows for incorporation of inorganic phosphate.
Oxidation of Alcohol to a Ketone and Regeneration of Oxaloacetate by Malate Dehydrogenase
Malate Dehydrogenase
Regenerates oxaloacetate for citrate synthase
Highly thermodynamically UNfavorable/reversible
(oxaloacetate concentration kept VERY low by citrate synthase)
Final Oxidative Decarboxylation by α-Ketoglutarate Dehydrogenase
補充：常見的Dehydrogenase脫氫酶形式
需HS-CoA和NAD+的參與、釋放出CO2和NADH
Classification
Citric acid cycle中的
α-Ketoglutarate dehydrogenase complex
Succinyl-CoA is another higher-energy thioester bond.
Highly thermodynamically favorable/irreversible
Last oxidative decarboxylation
carbons not directly from glucose because carbons lost came from oxaloacetate, not acetate
Oxidation of isoleucine(leucine,valine)
Pyruvate dehydrogenase complex
α-Ketoglutarate
(和氨基酸的分解有關)
α-Ketoglutarate Dehydrogenase Complex
Succinylcholine-CoA
Oxidative Decarboxylation by Isocitrate Dehydrogenase
(先脫氫再脫羧)
Decarboxylation releases CO2
Highly favorable/irreversible and regulated by [ATP] 步驟的調控點之一
Isozymes are specific for
NADP+ (cytosolic)
NAD+ (mitochondrial)
C-C Bond Formation by Condensation of Acetyl-CoA and Oxaloacetate
Rate-limiting step of CAC
Activity largely depends on [oxaloacetate]重要‼️
Uses acid/base catalysis
Highly thermodynamically favorable/irreversible
Use Citrate Synthase
The only reaction with C-C bond formation
Isomerization by Dehydration/Rehydration
Citrate, a tertiary alcohol, is a poor substrate for oxidation.
Isocitrate, a secondary alcohol, is a good substrate for oxidation.
Thermodynamically unfavorable/reversible
Elimination of H2O from citrate gives a cis C=C bond.
Addition of H2O to cis-aconitate is stereospecific.
Aconitase
Iron-Sulfur Center
Water removal from citrate and subsequent addition to cis-aconitate are catalyzed by the iron-sulfur center: sensitive to oxidative stress.
Summary
Acetyl-CoA + 3NAD+ (Step3,4,8)+ FAD(step6)+ GDP (step5)+ Pi (step5)+ 2 H2O(step2,7) -> 2CO2 來自於(oxaloacetate)+ 3NADH + FADH2 + GTP + CoA + 3H+
Energy captured by electron transfer to NADH and FADH2
Energy captured by electron transfer to NADH and FADH2
Intermediates in the citric acid cycle can be used in biosynthetic pathways. Must replenish the intermediates in order for the cycle and central metabolic pathway to continue
特別注意的CAC補充
-pyruvate->oxaloacetate(糖質新生)
-pyruvate->Malate
-phosphoenolpyuvate->oxaloacetate
Regulation：看圖
-inhibitor is NADH and ATP(量多的)
-activator is NAD+ and AMP(量少的)
Oxidative Phosphorylation
electron carriers
Iron-Sulfur Clusters
One-electron carriers
Coordinating by cysteines in the protein
Containing equal number of iron and sulfur atoms
Coenzyme Q or Ubiquinone(mobile)
未接電子-ubiquinone/接2個電子-ubiquinol
Ubiquinol can freely diffuse in the membrane, carrying electrons with protons from one side of the membrane to another side.
Ubiquinone is a lipid-soluble conjugated dicarbonyl compound that readily accepts electrons.
Cytochromes(mobile)
Iron coordinating porphoryin ring derivatives
a, b, or c differ by ring additions
One-electron carrier
Enzyme complex
Complex III(Cytochrome c Oxidoreductase / cytochrome bc1)
The Q cycle
Cycle 1
QH2
(釋出2e- pump2 H+)
其中一個e-傳到iron-sulfur center
最後傳到Cyt c
丟出一個空的Q
其中一個e-傳到額外進來的空的Q
最後形成Q-
QH2+Q+cyt c(oxidized) -> Q+Q- + 2H+ + cyt c(reduced)
Cycle 2
QH2
(釋出2e- pump2 H+)
其中一個e-傳到iron-sulfur center
最後傳到Cyt c
丟出一個空的Q
和cycle 1丟出的Q-結合，並加上額外進來的2H+
QH2
QH2+ Q- + 2H+ +cyt c(oxidized) ->Q+ 2H+ +QH2+cyt c(reduced)
Overall reaction
QH2+2 cyt c(oxidized)+ 2H+(從matrix來的) ->Q + 2cyt c(reduced) + 4H+
Complex IV(Cytochrome Oxidase)
注意電子的數量計算‼️看圖較好理解
2e-(可能是1->3->4或 2->3->4)
從cyt c送到CuA
送到Fe-Cu center
加入1/2的O2 並送到CuB
最後加入額外的2H+,
最後形成H2O丟到matrix
Structure
Contains two heme groups: a and a3
Contains copper ions
CuA
two ions that accept electrons from cyt c
CuB
bonded to heme a3, forming a binuclear center that transfers four electrons to oxygen.
Complex I (ubiquinone oxidoreductase)
NADH binding site in the matrix side
NADH+H+釋放的2e-由FMN接
再傳iron-suffer center(各別接1個)
再傳Ubiquinone(Q)
最後Q加上一開始釋放的2H+形成QH2
One of the largest macro-molecular assemblies in the mammalian cell, Over 40 different polypeptide chains.
NADH + Q + 5H+ = NAD+ + QH2 + 4 H+
Protons are transported by proton wires.
Pump four protons per one NADH
Complex II (Succinate Dehydrogenase)
FADH2釋放出2H+由iron-sulfur center接
再傳Ubiquinone(Q)
最後Q加上一開始釋放的2H+形成QH2
Does not transport protons
P.s：Succinate dehydrogenase is a single enzyme with dual roles:
convert succinate to fumarate in the citric acid cycle.
capture and donate electrons in the electron transport chain.
Summary of the Electron Flow in the Respiratory Chain 看圖‼️‼️
Complex I -> Complex IV(NADH的pathway)
1NADH + 11H+ + 1⁄2 O2 ——> NAD+ + 10H+ + H2O
左側的12H+來自complex I
6,complex III
4,complex IV*2
右側的10H+和左側只差complex IV有2H+給O2形成H2O
Complex II -> Complex IV (FADH2的pathway)
FADH2+6H+ +1⁄2O2 ——>FAD+6H+ +H2O
左側的6H+來自 complex III
2,complex IV
4
右側的6H+來自complex III
4,complex IV
2
Reactive Oxygen Species Can Damage Biological Macromolecules 氧化壓力的影響
Ubiquinone(Q) is naturally “leaky” and facilitates partial reduction of non- Complex III targets.
自由基被釋放出來形成H2O2
故需GSH來還原
(變成GSSG)
而GSSG需要NADH還原
(複習PPP)
Inhibitors of the Electron Transport Chain 看圖
Relationship of ETC and ATP Synthesis
Dinitrophenol(DNP) is an uncouple,allowing respiration to continue without synthesis.
Mitochondrial ATP Synthase Complex
Contains two functional units
and central shaft γ(逆時針轉)
F1
soluble complex in the matrix
individually catalyzes the hydrolysis of ATP
arranged in three αβ dimers
Dimers can exist in three different conformations.
This causes a conformational change within all the three αβ pairs. The conformational change in one of the three pairs promotes condensation of ADP and Pi into ATP.
Loose:binding ADP and Pi
Tight:catalyzes ATP formation and binds product.
Open: empty
F0
integral membrane complex
transports protons from IMS to matrix, dissipating theproton gradient
energy transferred to F1 to catalyze phosphorylation of ADP
Regulation
Inhibitor of F1 (IF1)
prevents hydrolysis of ATP during low oxygen
only active at lower pH, encountered when electron transport it stalled (i.e., low oxygen)
Primarily regulated by substrate availability
— NADH and ADP/Pi
Inhibition of OxPhos leads to accumulation of NADH.
(causes feedback inhibition cascade up to PFK-1 in glycoysis)若氧化磷酸化停止導致NADH太多，則會回去抑制糖解(PFK-1))
Net Production of ATP by Oxidation of Glucose
(and Other Fuels) Varies
NADH生成在細胞質的情況(糖解)
In prokaryotic systems, organelles do not segregate machinery, so all electron carriers can easily feed directly into the electron-transport chain.
In eukaryotic systems, organellar segregation
prevents NADH from the cytosol from directly entering the electron-transport chain at Complex I.
Two methods are used to feed the electrons from NADH
from the cytosol into the mitochondria:
malate-aspartate shuttle 看圖‼️
重點：
NADH進行CAC的step8逆反應，變成Malate即可穿過內膜。
CAC的最終產物oxaloacetate 在matrix可藉由aspartate aminotransferase轉成α-Ketoglutarate或Aspartate，即可穿過內膜至內膜腔
glycerol-3-phosphate shuttle 看圖‼️
(造成最終能量有30,32ATP之差的原因)
此大致為糖解step6的逆反應(但沒有磷酸根的參與)，
而釋出的H2由FAD接並進入complex。
氧化呼吸最終的ATP有30和32的差異就是因為FAD相當於1.5ATP，
和原本會產生的NADH相當於2.5ATP不同。
Cytochrome c
The second mobile electron carrier
Ubiquinone moves through the membrane.
Cytochrome c moves through the intermembrane space.
A soluble heme-containing protein in the intermembrane space.
Cytochrome c carries a single electron from the cytochrome bc1 complex to cytochrome oxidase.
