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Chapter 6 Biological Oxidation. The biochemistry and molecular biology department of CMU. Biological oxidation is the process in which substances (carbohydrate, Lipid, AAs) are oxidized in living organism. Oxidation types: Dehydrogenation Electron lost Oxygenation.

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chapter 6 biological oxidation

Chapter 6Biological Oxidation

The biochemistry and molecular biology department of CMU

slide2

Biological oxidation is the process in which substances (carbohydrate, Lipid, AAs) are oxidized in living organism.

slide3
Oxidation types:

Dehydrogenation

Electron lost

Oxygenation

slide4
Nature of biological oxidation:

1. 37℃, pH 7.4, enzymatic reaction.

2. Energy released gradually.

3. Formation of H2O.

4. Formation of CO2 by decarboxylation.

slide6

§1 Respiratory Chain

§2 Oxidative Phosphorylation

§3 ATP

§4 Shuttle Systems

slide8

A chain in the mitochondria consists of a number of redox carriers for transferring hydrogens removed from the substrate to oxygen to form water. The chain is termed a respiratory chain, also called electron transport chain (ETC).

slide12
Composition of ETC

Hydrogen carrier:NAD +

FMN

FAD

CoQ

electron carrier:Fe-S

Cyt

slide13

1. Nicotinamide coenzymes

  • NAD+/NADH (Nicotinamide Adenine Dinucleotide, CoⅠ)
  • NADP+/NADPH(Nicotinamide Adenine Dinucleotide Phosphate, CoⅡ)

The nicotinamide is the vitamin PP.

slide17

2. Flavin prosthetic groups

FMN: FlavinMononucleotide

FAD: Flavin Adenine Dinucleotide

They contain the riboflavin (Vit B2).

slide18
FMN

Isoalloxazine

ribitol

slide22
NAD+ is a coenzyme, that reversibly binds to enzymes.
  • FAD is a prosthetic group, that remains tightly bound at the active site of an enzyme.
slide23

3. Fe-S

Iron-sulfur centers (Iron-sulfur protein,Fe-S) are prosthetic groups containing 2, 3, 4 or 8 nonheme iron atoms complexed to elemental and cysteine S.

slide25

2 Fe iron-sulfur center of ferredoxin.

2 Fe colored orange; elemental & Cys S yellow.

slide28

4. CoQ

Coenzyme Q (CoQ, ubiquinone) is very hydrophobic. It dissolves in the membrane.

Coenzyme Q functions as a mobile e- carrier within the mitochondrial inner membrane.

slide31

5. Cytochromes

Cytochromes (Cyt)are proteins with heme prosthetic groups. They absorb light at characteristic wavelengths.

  • Hemes in the 3 classes of cytochrome (a, b, c) differ slightly in substituents on the porphyrin ring system.
slide32
Hemes a & a3 are often referred to as cytochromes aa3.
  • Cytochrome c is a small, water-soluble protein with a single heme group.
slide38
The heme iron can undergo an electron transition between ferric and ferrous states:

Fe3+ + e- Fe2+

slide39
The sequence of the components in the respiratory chain has been deduced in several ways.

1. Inhibitor.

2. O2 issuddenly introduced into the system.

3. Standard redox potential.

slide41

Standard reduction potentials for respiratory chain and related electron carriers

slide42
NADHrespiratorychain:
  • Succinaterespiratorychain:
slide44
§2

Oxidative Phosphorylation

slide45
Oxidative phosphorylation:

The phosphorylation of ADP to ATP coupled to electron transfer from a substrate to molecular oxygen.

slide46
Substrate level phosphorylation:

Phosphorylation of ADP or GDP to ATP or GTP coupled to the dehydrogenation of an organic substrate.

slide47
Coupled site:
  • P/O ratio is the number of inorganic phosphates incorporated into ATP per oxygen atom consumed.

(number of ATP / 2H)

slide49

succinate

-hydroxybutyrate

Vit C

E0'

∆E0'

∆G0'

three coupled sites
Three Coupled sites

① NADH → CoQ

② CoQ → Cyt c

③ Cyt aa3→ O2

slide51
NADH ETC has 3 coupled site,

P/O ratio =3,

3mol ATP / 2H.

  • Succinate ETC has 2 coupled site ,

P/O ratio =2,

2mol ATP / 2H.

slide52
Coupled mechanism:

1. Chemiosmotic hypothesis

slide53
The chemiosmotic hypothesis is the concept that a proton concentration gradient serves as the energy reservoir for driving ATP formation and was originally formulated by Peter Mitchell in the early 1960s .
slide55

outer membrane

matrix

inner membrane

cristae

Intermembrane space

  • Respiratory chain is in cristae of the inner membrane.
slide56

Spontaneous electron flowthrough each of complexes I, III, & IV is coupled toH+ ejection from the matrix. 

slide58
A total of 10 H+ are ejected from the mitochondrial matrix per 2 e- transferred from NADH to oxygen via the respiratory chain.
slide60
ATP synthase, embedded in cristae of the inner mitochondrial membrane, includes:
  • F1catalytic subunit, made of 5 kinds of polypeptides α3β3γδε.
  • F0 complex of integral membrane proteins mediates proton transport.
slide64

3H+

3H+

Transport of ATP, ADP, & Pi

summary
summary

2.5 ~P bonds synthesized during oxidation of NADH produced in the matrix. (10 H+ pumped; 4 H+ used up per ATP).

1.5 ~P bonds synthesized during oxidation of FADH2 produced in the matrix.

slide67
The factors affecting ETC

A. Inhibitors of ETC

slide68
B. Uncoupling agent

A compound that disrupts the usual tight coupling between electron transport and phosphorylation of ADP.

slide72
C. Inhibiter of oxidative phosphorylation

A compound that Inhibits electron transport and phosphorylation of ADP.

Oligomycin

slide73
2. ADP

[ADP]↑→ Oxidative phosphorylation↑

[ADP]↓→ Oxidative phosphorylation↓

slide74

pyruvate

ADP

succinate

DNP

Mt.

rotenone

oligomycin

antimycin A ( CN-)

time

Influence of different substrates and inhibitors on quantity consuming oxygen

slide75
3. Thyroxine

Na+,K+-ATPase →ATP catabolism → ADP↑ → Oxidative phosphorylation↑ → formation of ATP↑. Formation and catabolism of ATP↑,consuming of O2↑, Generation of Heat↑.

slide76
4. mtDNA mutation

Free radical → mutation of DNA → inhibition of Oxidative phosphorylation → energy↓

slide79
α bond △ G0′= -14.3KJ

βbond △ G0′= -32.2KJ

γbond △ G0′= -30.5KJ

>30KJ ( 7kcal )-high energy bonds

slide82
Potentially, 2 ~P bonds can be cleaved, as 2 phosphates are released by hydrolysis fromATP.

AMP~P~PAMP~P + Pi

(ATP  ADP + Pi)

AMP~P~PAMP + P~P

(ATP  AMP + PPi)

P~P2Pi

(PPi2Pi)

slide83
Adenylate Kinase:

2 ADP  ATP + AMP

Nucleoside Diphosphate Kinase catalyzes reversible reactions such as:

ATP + GDPADP + GTP,

ATP + UDPADP + UTP, etc.

slide87

The inner membrane of mitochondria is quite impermeable to some molecules and ions.

Permeable to:

Pyr, succinate, α-ketoglutarate, malate, citrite, Glu etc.

Impermeable to:

H+, NADH, NADPH, OAA etc.