Gerry Shadel

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Gerry Shadel Department of Biochemistry office
4129 Rollins Research Center e-mail
gshadel_at_emory.edu office phone [phone]
Real Physician Quotes (I)
Patient has chest pain if she lies on her left
side for over a year Patient's medical history
has been remarkably insignificant with only a 40
pound weight gain in the past three days. On
the 2nd day the knee was better and on the 3rd
day it disappeared completely. The patient has
been depressed ever since she began seeing me in
1993. The patient is tearful and crying
constantly. She also appears to be
depressed. Occasional, constant, infrequent
headaches. Patient was alert and unresponsive.
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ENERGY UTILIZATION

• ANABOLIC (BIOSYNTHETIC) PATHWAYS
• MUSCLE CONTRACTION
• ACTIVE ION TRANSPORT
• GENE EXPRESSION
• HORMONE SECRETION
• CELL DIVISION

ADP P
ATP
i
ENERGY PRODUCTION

• CATABOLIC (BREAK-DOWN) PATHWAYS
• OXIDATIVE PHOSPHORYLATION

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POLYSACCHARIDES (COMPLEX CARBOS)
LIPIDS
PROTEINS
glucose
amino acids
fatty acids
Glycolysis
ATP
pyruvate
acetyl-CoA
FADH2 and NADH (reducing power)
O2
citric acid cycle
oxidative phosphorylation
ATP
ATP
ATP
ATP
ATP
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LIPIDS
CARBOHYDRATES
PROTEINS
fatty acids
pyruvate
amino acids
acetyl-CoA
citric acid cycle
NADH, FADH2
ATP
OXPHOS
energy for anabolic pathways
mitochondrion
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Cristae
(IS)
(OM)
(IM)
OM- 50 lipid / 50protein, relatively few (but
important) enzymes, not a major barrier to
solutes (permeable to molecules lt 5000 mw)
IS- not a well-characterized compartment, but
known to harbor some enzymes (adenylate and
nucleotide diphosphate kinases)
IM- 80 protein, large enzyme complexes involved
in oxidative phosphorylation (ATP production),
many transporter proteins that regulate exchange
of solutes between the matrix and cytosol
(solute shuttles)
Matrix- pyruvate dehydrogenase, citric acid
cycle, many other key metabolic enzymes
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cytosol
matrix
transporter
ADP
adenine nucleotide
ATP
phosphate
phosphate
OH-
pyruvate
monocarboxylate
OH-
malate
tricarboxylate
citrate
Ca
calcium
anion-
some functions of mitochondrial substrate
shuttles
bring in (and concentrate) substrates for
mitochondrial reactions and export products to
cytosol (best example ADP in, ATP out !!! )
transfer of reducing equivalents by exchanging
red-ox pairs
calcium homeostasis
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Entry into oxidative metabolism is the
conversion of pyruvate to acetyl-CoA in the
mitochondria
Glycolysis (catabolism of glucose)
2 ATP
mitochondrion
pyruvate dehydrogenase
Acetyl-CoA
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thiol ester bond
Most energy-generating metabolic pathways lead to
the production of acetyl-CoA
DG hydrolysis of Acetyl-CoA is large and
negative, therefore has a high acetyl
group-transfer potential and acts a carrier of
activated acetyl groups (similar to how ATP is a
carrier of activated phosphate groups)
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target of arsenic poisoning
SH
net pyruvate NAD CoASH
acetyl-CoA CO2 NADH H
coenzyme/vitamin function thiamine
pyrophosphate (TPP) reacts with pyruvate vitamin
B1 lipoamide accepts acetyl group from
TPP lipoic acid as a thio-ester Coenzyme A
(CoA) accepts acetyl group from pantothenate lip
oamide ontransacetylase (E2) FAD accepts
reducing equivilents from riboflavin, vitamin
B2 reduced lipoamide group NAD terminal
acceptor of reducing niacin equivilents from
reduced flavoprotein
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structure of bacterial pyruvate
dehydrogenase complex
E3 dimer 6 total on edges of cube
E2 trimer 8 total form a cubic core
E1 dimer 12 total on edges of cube
E1 pyruvate dehydrogenase
E2 dihydrolipoyl transacetylase
E3 dihydrolipoyl dehydrogenase
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acetyl-CoA
citrate synthase
aconitase
oxaloacetate
citrate
malate dehydrogenase
isocitrate
CITRIC ACID CYCLE (aka., Krebs cycle
or tricarboxylic acid cycle)
malate
isocitrate dehydrogenase
fumarase
fumarate
a-ketoglutarate
succinate dehydrogenase
succinyl-CoA synthase
a-ketoglutarate dehydrogenase
succinate
succinyl-CoA
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Substrate availability levels of acetyl-CoA and
oxaloacetate are regulatory. Acetyl-CoA
dictated by flux through glycolysis and the
pyruvate dehydrogenase complex.
Feedback inhibition 3 TCA enzymes have large
negative DG citrate synthase, isocitrate
dehydrogenase and a-ketoglutarate dehydrogenase.
These enzymes are regulated by end products and
by the level of other cycle intermediates.
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strict regulation of pyruvate dehydrogenase
pyruvate NAD CoASH
acetyl-CoA CO2 NADH H
1. competitive, end-product inhibition
2. inactivation by phosphorylation
NADH, acetyl-CoA
NAD, CoASH

phosphoserine
protein kinase
P
active PDH
inactive PDH
phosphatase
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Respiratory control the ultimate end product of
oxidative metabolism is ATP which is derived by
the stepwise oxidation of NADH and FADH2. Thus,
the TCA cycle is coarsely regulated by oxidative
status read-out through levels NADH, ATP and ADP.
General controls hormonal effects on substrate
availability, Ca
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The TCA cycle has a central position in
metabolism, because of its amphibolic (catabolic
and anabolic) nature. In other words, many of
the intermediates also feed into anabolic
pathways
Heme
red-intermediates used in anabolic pathways
green-intermediates replenished by anaplerotic
filling in reactions
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Clever solutions to traffic problems
Substrate shuttles dont exist for many compounds
(e.g., Acetyl-CoA, NADH and NAD), yet they are
needed in both compartments. The cell can
accomplish this by linking cytoplasmic and
mitochondrial pathways through intermediates
that can be shuttled.
cytosol
mitochondrial matrix
IM
malate
malate

citrate
citrate
acetyl-CoA


acetyl-CoA
TCA cycle
fatty acid, sterol biosynthesis
Acetyl-CoA is needed in the cytoplasm, but is
impermeable to the IM. This is accomplished by
transferring the acetyl group to citrate (citrate
synthase), transporting citrate out, and
then regenerating acetyl-CoA in the cytoplasm
(ATP citrate lyase)
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Stoichiometry of the TCA cycle and where do we go
from here?
one turn of the cycle
1. one acetyl group is oxidized to two
molecules of CO2
2. three molecules of NADH are produced
3. one molecule of FADH2
4. one high-energy phosphate group is
created by substrate-level phosphorylation to
form GTP, which can be converted to ATP
3 ATP
2 ATP
NADH
FADH2
5. total output 12 ATP / turn !!!
electron transport OXPHOS