Patrishia Luber

4Bio1 Mitochondrial Structure & Function

Glycolysis in the cytosol + 10 reactions:
9: Mitochondrial Structure and Function Glucose pyruvate + NADH
Net synthesis of 2 ATP per molecule of glucose
First organisms were anaerobes
In the presence of oxygen:
Appearance of cyanobacteria 2.4-2.7 BYA which
NADH 30 ATP
produced atmospheric oxygen from
Pyruvate:
photosynthesis (split water to form oxygen)
Pyruvate gets transported to the matrix
Decarboxylated to form 2-carbon acetyl
9.1 Mitochondrial Structure and Function
group
Mitochondria are large enough to be seen Acetyl group is transferred to coenzyme A
under a light microscope and varies in their producing acetyl CoA
overall structure depending on the cell type ** decarboxylation and transfer of acetyl is catalyzed
ranging from 1-4 m in length by pyruvate dehydrogenase **
Fission is induced by contact with thin tubules
from the ER which initiates the constriction
If fusion > fission: elongated and interconnected
mitochondrion
If fission > fusion: more numerous and distinct
mitochondrion
Mitochondria also plays a vital role in the uptake
and regulation of calcium ions
o During high concentrations of calcium in the
cytoplasm, the mitochondria can take in the
excess caclcium

Mitochondrial Membranes
Two membranes:
Outer mitochondrial membrane: 50% lipid by
weight, contains porins (similar to bacterial
membranes)
Inner mitochondrial membrane: devoid of
cholesterol and rich in a phospholipid called
cardiolipin, is highly impermeable
o Inner boundary membrane: rich in
proteins responsible for the import of
mitochondrial proteins
o Cristae: invaginated membranous sheets;
contains large amounts of membrane surface
o Cristae junctions join the two
Matrix is the space within the mitochondria
while intermembrane space exists between ** Mnemonic:
the outer and inner mitochondrial membranes Intermediates: Goodness Gracious, Father Franklin
o Matrix is more viscous, gel-like due to high Did Go By Picking Pumpkins (to) Prepare Pies
protein content Enzymes: Hungry Peter Pan And The Growling Pink
o Intermembrane proteins play a role in Panther Eat Pies **
apoptosis
Mitochondrial matrix also contains ribosomes and Tricarboxylic Acid (TCA) Cycle/Krebs Cycle
circular DNA Substrate is oxidized in the matrix (except
o Nonchromosomal DNA codes for for succinate dehydrogenase)
mitochondrial proteins (13 in humans) Named after Hans Krebs
o Maternal inheritance; egg cell contains
mitochondria Process:
o The RNA polymerase in mitochondria is Acetyl CoA (2C) + oxaloacetate (4C) citrate
different than the ones the nucleus uses; it is (6C)
a single subunit similar to bacteriophages ** Citrate is decreased in chain length one carbon at
(bacterial viruses) a time to recycle the 4C oxaloacetate **
Isocitrate
9.2 Oxidative Metabolism -Ketoglutarate (5)
o CO2
o NAD NADH
1. Glycolysis in cytoplasm Succinyl-CoA (4)
Glucose (6C) 2 pyruvate (3C) o CO2
2. PDC Pyruvate Dehydrogenase o NAD NADH
Complex in matrix Succinate
Pyruvate acetyl-CoA o GDP + P GTP
3. Krebs Cycle in Matrix
Acetyl-CoA NADH +
FADH2
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(NADH + FADH2 are electron carriers)
4. Electron Transport Chain in
inner membrane
Patrishia Luber
4Bio1 Mitochondrial Structure & Function
Fumarate o Chemiosmotic mechanism
o FAD FADH2 o Each pair of electrons transferred from
Malate NADH 3 ATP
o Needs an input of water FADH2 2 ATP
Oxaloacetate (to be recycled) o Net gain is 36 ATP
o NAD NADH
9.2 Role of Mitochondria in ATP Formation
Energy is extracted by the mitochondria from
substrates by generating ionic gradients
Oxidative phosphorylation: ATP formation is
driven by energy released from electrons
removed during oxidation
Substrate-level phosphorylation: ATP is formed
directly by a transfer of phosphate group from a
substrate molecule to ADP

Oxidation-Reduction Potentials
**Reduced = gain electrons, lose H; Oxidized = lose
electrons, gain H**
**Reducing agent = removes e oxidized**
**Oxidizing agent = hoards H reduced**
Reducing agents are ranked according to
electron-transfer potential
Substances with high electron-transfer potential
are strong reducing agents (can lose H, can gain
e) such as NADH
Redox potential: voltage produced by a half-cell
under standard conditions
o G : difference between E0 = (E1 E2)
o (+) G = nonspontaneous
o (-) G = spontaneous
Electron Transport
Dehydrogenase enzyme catalyzes and
transfers pairs of electrons from substrates to
coenzymes
Forming NADH and FADH2
Succinate dehydrogenase FADH2

**Mnemonic: Can I Keep Selling Sex For Money,

Officer?** Types of Electron Carriers
**all four (except ubiquinone) are prosthetic groups, having
a non-amino acid component that are tightly associated
Importance of Reduced Coenzymes in Forming with proteins **
ATP Flavoproteins: polypeptide bound to Flavin
FADH2 and NADH produced from TCA contains adenine dinucleotide (FAD) or Flavin
high-energy electrons produced from oxidation mononucleotide (FMN)
Mitochondria are not able to import the NADH o Derived from riboflavin (vitamin B2)
formed by glycolysis in the cytosol and must o Capable of accepting 2 protons and 2
enter via: electrons
o Malate-aspartate shuttle and reduce NAD o NADH dehydrogenase and succinate
to NADH dehydrogenase
o Transfer electrons to FAD producing FADH 2 via Cytochromes: contain a heme
glycerol phosphate shuttle o Iron atom of heme undergoes a reversible
In forming ATP via Electron Transport Chain: transition from Fe3 Fe2
High-energy electrons are passed from FADH 2 or o Acceptance and loss on single electron
NADH to electron carriers in the electron- o 3 types: a, b, c
transport chain in the inner mitochondrial Three copper atoms
membrane o Located within a single protein complex of
o Releases energy in to form of the inner mitochondrial membrane
electrochemical gradient of protons o Accept and donate a single electron (Cu2
across the membrane Cu1)
o Low-energy electrons are passed to the final Ubiquinone (UQ/Q): lipid-soluble molecule
acceptor, Oxygen which becomes containing a long hydrophobic chains composed
reduced to water of 5-caron isoprenoid units
Controlled movement of protons back across the o Able to accept and donate 2 electrons and
membrane protons
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4Bio1
o Ubiquinone [R] ubisemiquinone [R]
ubiquinol
Iron-sulfur proteins: iron-containing proteins in
which the iron is linked to inorganic sulfide
ions as part of an iron-sulfur center
o ~2 or 4 atoms of iron and sulfur linked to the
protein at cysteine residues
o Capable of donating or accepting a single
electron
o Redox-potential depends on the
hydrophobicity and charge of amino acid
residues
In the ETC, electrons are passed downhill (loses
energy)
Final acceptor is Oxygen Water
Electron-Transport Complexes
In the electron transport chain:
Ubiquinone and cytochrome shuttle
electrons to and from the complexes
Complexes I, II, III, and IV of protein
NADH enters via complex I
FADH2 enters via ubiquinone
NADH Complex I (NADH
Reductase)
Ubiquinone
FADH
2
Complex III
(Cytochrome
Reductase)
Complex II
(Succinate Cytochrome C
dehydrogen
ase)
Cytochrome Oxidase
Complex I, III, IV = coupling sites and are proton
pumps
Complex I: NADH dehydrogenase
Mammalian version is L-shaped and has 45
different subunits
FMN-flavoprotein oxidizes NADH
Electrons are transferred through 7 iron-sulfur
centers
Electrons are transferred to ubiquinone (for
transport)
Movement of electrons is accompanied by 4
protons from the matrix to the intermembrane
space
Membrane embedded domain has -helixes
oriented parallel to the membranes surface
Movement of the electrons to ubiquinone induces
a conformational change causing the lateral
movement of the helices tilting change in
ionic concentration forcing the protons to go
outside
Complex II: Succinate dehydrogenase
Consists of 4 polypeptides: 2 hydrophobic anchor
+ 2 hydrophilic subunits with succinate
dehydrogenase
Pathway for FADH2
Mitochondrial Structure & Function
Contains a heme group which attracts escaped
electrons which prevents the formation of
superoxide radicals
Electron transfer is not accompanied by proton
translocation
Complex III: Cytochrome bc1
Catalyzes the transfer of electrons from ubiquinol
to cytochrome c
4 protons are translocated for every pair of
electrons
Complex IV: Cytochrome c Oxidase
Translocation of 4 protons is coupled to
conformational changes for every 2 molecules of
water
Contains 13 subunits; 3 are encoded by mtDNA
4 protons are also consumed in the reaction to
transfer the electrons
9.4 Translocation and Establishment of PMF
Translocation of the protons is electrogenic
(voltage-producing)
Makes the intermembrane space more acidic and
the matrix more basic
Both the pH and the electric potential contribute
to the proton motive force need of the protons
to go back to the matrix where there is a lower
concentration
Treatment with 2,4-dinitrophenol (DNP) made
cells continuously oxidize substrates without
generating any ATP
o Used as an inhibitor of ATP
o Was prescribed as a diet pill, causing deaths
of patients
o The drug can uncouple oxidation and
phosphorylation because it combines with
the protons and can carry the protons across
the membrane back to the matrix without
passing through the ATP synthase
9.5: The Machinery for ATP Formation
Fernandez-Moran observed a layer of spheres
attached to the inner membrane which was later
isolated by Racker which he called coupling
factor 1 (F1), an ATPase which hydrolyzes ATP
Catalytic portion is the F1 sphere
Structure of ATP Synthase
Mushroom-shaped protein complex with two
components:
o Spherical F1 head
Conserved in bacterial and mitochondrial
ATP synthases
and subunits are arranged alternately
Each F1 contains 3 catalytic sites for
ATP synthesis one on each subunit
subunit connects it to the F0
o Basal F0 embedded in the inner membrane
Contains 3 different polypeptides
Contains a channel through which
protons are conducted from the
intermembrane space to the matrix
Basis of ATP Formation According to the Binding
Change Mechanism
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Patrishia Luber
4Bio1
The energy released by the translocation of
protons is not used to drive ADP phosphorylation
but to change the binding affinity for the active
site for the ATP product
Each active site progresses successively through
3 distinct conformations that have different
affinities for substrates and products
o The 3 catalytic sites has different chemical
properties
o At any given instant, one site is L (loose),
one is T (tight), one is O (open)
ATP is synthesized by rotational catalysis in which
one part of the ATP synthase rotates relative to
another part
o Rotation is driven by the movement of
protons
o Electrical energy in the proton gradient is
transduced to mechanical energy of a
rotating stalk
The apical end of the is asymmetric allowing
different faces of it to interact with the subunits
causing them to adopt L/T/O conformations
Yoshida showed the rotation via a fluorescently
labeled actin filament attached to the subunit
Rotary devices are rare in living organisms and
only occurs in two instances: ATP synthases and
bacterial flagella
12 C subunits of the F 0 base is assembled into a
ring that resides within the inner membrane; C
ring is attached to the stalk
Downhill movement of protons through the
synthase drives the rotation of the C ring which
provides torque that drives the rotation of the
subunit leading to the synthesis and release of
ATP
Proton from the intermembrane space enters
a half-channel within in the stationary a
subunit
Mitochondrial Structure & Function
Proton binds to an acidic residue (Asp61 in E.
coli) on one of the c subunits
Proton binding causes the ring to move 30
Bound proton is carried in a full rotation
before being released to another half-channel
leading to the matrix
9.6 Peroxisomes
Simple membrane-bound organelles that
contains a crystalline core of oxidative enzymes
Multifunctional organelles containing more than
50 enzymes for oxidation of very-long-chain fatty
acids (VLCFA) and synthesis of plasmalogens (a
class of phospholipids where one of the FA is
linked to glycerol by an ether linkage not an
ester) which are abundant in the myelin sheaths
Luciferase is also a peroxisomal enzyme
Form from preexisting organelles and uses the
same proteins as mitochondria
Imports preformed proteins from the cytosol
similar to mitochondria
Site of synthesis and degradation of hydrogen
peroxide, a highly reactive and toxic oxidizing
agent
Plant seedlings contain glyoxisomes which
break down the stored FA for energy and nutrition
into carbohydrate
Diseases
Zellweger syndrome lack peroxisomal enzymes
due to defects in translocation of proteins from
the cytoplasm into the peroxisome.
Adrenoleukodydstrophy is caused by lack of a
peroxisomal enzyme, leading to fatty acid
accumulation in the brain and destruction of the
myelin sheath of nerve cells.
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