Aerobic respiration
• Mitochondrial structure and function
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Visible under light microscope
Universal in aerobic eukaryotes
Have own DNA and ribosomes
Number and shape vary widely in
different cell types
• Number: more in cells with higher E
requirements
• Shape: can undergo fission and
fusion to yield typical ‘cylinder’
shape or more complex tubular
networks
Aerobic respiration
• Mitochondrial structure and function
– Membranes
• Outer: permeable to many things
– Porins, large central pore
• Inner: highly impermeable
– Channels for pyruvate, ATP, etc
Aerobic respiration
• Mitochondrial structure and function
– Membranes
• Outer: permeable to many things
– Porins, large central pore
• Inner: highly impermeable
– Channels for pyruvate, ATP, etc
• Cristae
– Complex invaginations of the
inner membrane
– Functionally distinct
– Joined to inner membrane via
narrow channels
Aerobic respiration
• Mitochondrial structure and function
– Intermembrane space
• Between inner and outer membranes
• Also within the cristae
• Acidified ( high [H+] ) by action of the Electron Transport Chain (ETC)
– H+ are pumped from matrix into this compartment
– ATP synthase lets them back into the matrix
Aerobic respiration
• Mitochondrial structure and function
– Matrix
• Compartment within the inner membrane
• Very high protein concentration ~500mg/ml
• Contains:
– ribosomes and DNA
– Enzymes of TCA cycle, enzymes for fatty acid degradation
NADH enters the mitochondria
by one of two mechanisms:
1. aspartate-malate shuttle
NADH --> NADH
2. glycerol phosphate shuttle
NADH --> FADH2
• Pyruvate to TCA
Oxidation-reduction potentials
• Reducing agents give up electron share
– The lower the affinity for electrons, the stronger the reducing agent
• NADH is strong, H2O is weak
• Oxidizing agents receive electron share
– The higher the affinity for electrons, the stronger the oxidizing agent
• O2 is strong, NAD+ is weak
• Couples
– NAD+ - NADH couple
– O2 - H2O couple
(weak oxidizer, strong reducer)
(strong oxidizer, weak reducer)
strong oxidizing
strong reducing
NADH is a stronger reducing agent than FADH2
G = -nFE
NADH --> H2O
G0’= -52kcal/mol
7ATP(max), ~3ATP(real)
FADH2 --> H2O
G0’= -36kcal/mol
5ATP(max), ~2ATP(real)
The Tricarboxylic Acid (TCA) cycle (Kreb’s cycle)
2Pyruvate + 8NAD+ + 2FAD + 2GDP + 2Pi -->
6CO2 + 8NADH + 2FADH2 + 2GTP
Adding in products of glycolysis,
2NADH + 2ATP
Total yield for both:
10NADH + 2FADH2 + 4ATP
= 38 ATP
How NADH from cytoplasm
are counted changes the
theoretical yield
Formation of a tricarboxylic acid from pyruvate
• In two steps:
– A dehydrogenase step
3C + NAD  2C + CO2
+NADH
– Yields Acetyl group bonded
to CoenzymeA (CoA)
– A synthase step
– 2C + 4C(OA)  6C
(OA)
The Tricarboxylic Acid (TCA) cycle (Kreb’s cycle)
• 2C+4C(OA)  6C
• 6C+NAD  5C+CO2
+NADH
• 5C  4C+CO2
+NADH
• 4C+GDP  4C+GTP
• 4C+FAD  4C+FADH2
• 4C+NAD  4C(OA)
+NADH
Fatty acid catabolism
• Enzymes localized to mitochondrial matrix
– Fatty acids cross inner membrane and become linked to HS-CoA
– Each turn of cycle generates FADH2 + NADH2 + Acetyl-CoA
Amino acid catabolism
• Enzymes in mitochondrial
matrix
– cross inner membrane
via specific transporters
– Enter TCA at various
points
General outline of oxidative phosphorylation
Electron Transport Chain: e- carriers
• Electron carriers
– Flavoproteins (FMN)
– Ubiquinone (Q or UQ)
– Cytochromes (b, c1, c, a)
– Cu atoms
– Fe-S centers
– Proton movement driven
by complexes I, III, IV
coupled to large E
Electron carriers: Ubiquinone
• Lipid soluble
• Dissolved within inner mitochondrial membrane
• Free radical intermediate
Q
• Free radical ‘escape’ from electron transport chain can
damage proteins, lipids, RNA, and DNA in a cell
UQ
Electron Transport Chain
• Complex I passes e- from NADH to Q and pumps 4H+ out of matrix
• Complex II passes e- from FADH2 to Q
• UQ shuttles e- to Complex III
Electron Transport Chain
• Complex III passes e- to Cytochrome c and pumps 4H+ out of matrix
• Cytochrome c passes e- to Complex IV
• Complex IV passes e- to O2 forming H2O and pumps 2H+ out
1 pH
unit diff
ATP synthesis: The ATP Synthase enzyme
• F1 head/sphere (ATPase) catalyzes ADP + Pi <--> ATP
• F0 base embedded in inner membrane (H+ pass through this)
• F0 + F1 = ATP synthase
– Connected via two additional proteins
• Central rod-like gamma subunit
• Peripheral complex (abd) holds F1 in a fixed position
– Location
• Bacteria = plasma mem
• Mitochondria = inner mem
• Chloroplast = thylakoid
ATP
matrix
H+
Intermembrane space
Binding Change mechanism of ATP Synthase
• Each F1 active site progresses through
three distinct conformations
– Open (O)  Loose (L)  Tight (T)
– Conformations differ in affinity for
substrates and products
• Central gamma () subunit rotates
causing conformation changes
Rotational catalysis by ATP synthase
• Central gamma () subunit rotation caused by proton (H+)
translocation drives the conformation changes
1 pH
unit diff
Rotational catalysis by ATP synthase
• If true, should be able to run it backwards (ATP --> ADP + Pi) and
watch gamma spin like a propeller blade
Rotational catalysis by ATP synthase
Other fxns of electrochemical gradient
• E also used for:
– Import of ADP + Pi (+H+) and export of ATP
– Import of pyruvate (+H+)
• Uncoupling sugar oxidation from ATP synthesis
– Uncoupling proteins (UCP1-5)
• UCP1/thermogenin, shuttles H+ back to matrix (endothermy)
– Brown adipose tissue
» Present in newborns (lost with age) and hibernating animals
» Generates heat
– 2,4-dinitrophenol (DNP)
• Ionophore that can dissolve in inner membrane and shuttle H+ across
– 1930’s stanford diet pill trials: overdose causes a fatal fever