Russian National Research Medical University
Fundamentals of nutritional biochemistry:
nutrient functions and requirements
Overview of
metabolism and energetic strategies in
human cells
A key cycle for multiple roles: the
tricarboxylic acid cycle
Maxim A. Abakumov
Moscow, 2014
Main paradigm of life
• Live organisms need to spent energy to stop
entropy processes
• Energy can by obtained directly from
surrounding area (autotrophes) or from other
organisms (heterotrophes)
Main paradigm of life
• Metabolism is the set of life-sustaining chemical
transformations within the cells of living
organisms
• Metabolism is divided onto anabolism and
catabolism
• Catabolism is the set of metabolic pathways that
breaks down molecules into smaller units to
release energy
• Anabolism is the set of metabolic pathways that
construct molecules from smaller units
Catabolic and anabolic pathways
Bioenergetics
Energy containing
nutrients
 Carbohydrates
 Proteins
 Fats
Catabolism
ADP+Pi
NAD+
FAD
Cell
macromolecules
 Proteins
 Lipids
 Polysaccharides
 Nucleic acids
Energy depleted
end products
 CO2
 H 2O
 NH3
ATP
NADH2
FADH2
Anabolism
Precursor
molecules
 Aminoacids
 Sugars
 Fatty acids
 Nitrogen bases
Ingestion
Nutrients
• Carbohydrates
• Proteins
• Lipids
• Inorganic
Digestion, transport
Metabolic reaction
Molecular and cellular action
Main nutrients
Carbohydrates
Proteins
Lipids
Digestion
Digestion
Digestion
Sugars
Aminoacids
Fatty acids +
glycerol
Carbohydrates metabolic pathway
Digestion
Glycolysis +TCA
Energy
Glycogenesis
Storage
Liver
Glucose
Absorbtion
Triglycerids
System circulation
VLDL
Adipose tissue
Protein metabolic pathway
Liver
Digestion
Aminoacids
Absorbtion
Oxidation
Oxidation
Peripheral
tissue (muscle)
Protein synthesis
Energy
Energy
Lipid methabolic pathway
Digestion
Triacylglicerids
In chylomicrons
Absorbtion
Lipase
Glycerol
Fatty acid
Liver
Glucose
Muscle
Energy
Adipose
tissue
Fat
(storage)
Nutrients, Organs, and Circulation
Matthews et al 2003 Fig 23.1
Two condition of organism
Fed state
Fasting state
• Overnight fasting
• Prolonged fasting
• Long term physical
• activity
Distihguish them
Fed state
Fasting state
•Blood glucose level is high
•Blood glucose level is low
•Liver glycogen is restored
•Liver glycogen is used
•Energy supply is effecient
•Overall energy supply is
•Storage processes are activated
unsufficient
•Mostly anabolic pathways are
• Action is required
activated
• Mostly catabolic pathways
are activated
Hormonal control
• Insulin and glucagon are two main hormones
controlling glucose methabolism
• Insulin – fed state hormone
• Insuline provides glycolysis, glicogen and fatty
acid synthesis
• Glucagon – fasting state hormone
• Glucagon provides gluconeogenesis, glicogen
and fatty acids decomposition
Major Events: Storage, Retrieval, & Use of “Fuels”
Matthews et al 2003 Fig 23.4
Major metabolic pathways
1.
2.
3.
4.
Fuel oxidation
Fuel storage
Synthetic pathways
Waste-disposal pathway
Energy value of food
Biofuels
Digestion
•Carbonydrates
•Lipids
•Proteins ADP + Pi
ATP
Ready-to-use energy mostly is used as an ATP
Waste products:
CO2
H2O
NH4+
What is ATP?
Adenosine Triphosphate (ATP)
• ATP + H2O  ADP + Pi
G°´ = -30.5 kJ mol-1
• ATP + H2O  AMP + PPi
G°´ = -45.6 kJ mol-1
ATP as an energy equivalent. Energy
coupling
H2N CH
H2N CH
CH2
CH2
O
C OH
COOH
ADP+Pi
ATP
COOH
+
CH2
NH3
CH2
ATP
O
ADP+Pi
NH3
COOH
H2N CH
CH2
CH2
O
C NH
2
ATP provides energy by
the process of group
transfers and not by
simple hydrolysis.
C O
OH
HO P
O
ΔG (kJ/mol)
Reaction
Glu + Pi = Glu-6-P
+14 (unfavorable)
ATP = ADP +Pi
-31 (favorable)
Glu+ ATP=Glu-6-P + ADP
-17 (favorable)
Total reaction
Glu+ ATP + NH3=Gln + ADP + Pi
ATP role in cell
• ATP supplies energy for biosynthesis processes
• ATP supplies energy for movement and muscle
contraction
• ATP provide energy for transmembrane
transport
• ATP used for DNA/RNA synthesis
• ATP used for heat emission
Basal metabolic rate (BMR)
• Rate of energy expenditure by humans and
other animals at rest
• Measured in kJ per hour per kg body mass
Total energy consumption
Activity
Thermogenesis
Basal
metabolic rate
Basal metabolic rate (BMR)
Function
Service
Kidney (Na+ transport)
Heart
Nervous system
Respiration
Repair
Protein resynthesis
Triacylglycerol resynthesis
Transmembrane potential (Na+ transport )
BMR,%
6-7
9-11
15-20
6-7
10-15
1-2
20-25
BMR calculation
The Original Harris-Benedict Equation:
For men
For women
The Mifflin St Jeor Equation:
, where s is +5 for males and −161 for females.
The Katch-McArdle Formula (Resting Daily Energy Expenditure):
, where LBM is the lean body mass in kg
Energy transformation
• Energy of chemical bonds must be transformed
into energy rich compounds (ATP, creatine-P)
• 1) C6H12O6 + O2 = 6CO2 +6H2O +Q → no
cash energy
• 2) C6H12O6 + O2 +36ADP + 36Pi → 6CO2
+H2O +36ATP + Q → 36 ATP cash energy
Energy flow in cell
Energy containing
nutrients
 Carbohydrates
 Proteins
 Fats
Catabolism
ADP+Pi
NAD+
FAD
Cell
macromolecules
 Proteins
 Lipids
 Polysaccharides
 Nucleic acids
Energy depleted
end products
 CO2
 H 2O
 NH3
ATP
NADH2
FADH2
Anabolism
Precursor
molecules
 Aminoacids
 Sugars
 Fatty acids

Nitrogen bases
Lehninger 2002 Fig III.1
Energy flow in cell
• 1) C6H12O6 + O2 = 6CO2 +6H2O +Q
• 2) C6H12O6 + O2 +36ADP + 36Pi = 6CO2
+H2O +36ATP + Q → 36 ATP cash energy
• 1st pathway can be easily realized→ no cash
energy
• 2nd pathway requiers multireaction pathway →
36 ATP cash energy
Energy flow in cell
Glicolysis
Electron transfer chain
Oxidative phosphorilation
TCA cycle
I. Preparation stage
Lipids
Carbohydrates
FA + Glycerol
Glucose
II.
Proteins
Aminoacids
- NH3
Intermediate stage
Pyruvate
AcetylCoenzymeA
III.Terminal stage
TCA
+ О2
Н2О
ADP+ P
СО2
H+ + ē
ETC + ATP
synthase
ATP
Acetyl-CoA (AcCoA)
High energy bond
http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-andbiological/s23-03-overview-of-stage-ii-of-catabo.html
Acetyl-CoA methabolic pathways
Glucose can not be synthesized from AcCoA
http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-andbiological/s23-03-overview-of-stage-ii-of-catabo.html
PDH
COOH
C O
Pyruvate dehydrogenase
+
S-CoA
C O
HS-CoA
CH3
CH3
NAD+
NADH
+
CO2
PDH regulation
Active
PDH
• ATP
+++
PDH kinase
• AcCoA
• NADH
PDH phosphorylase
PDH
Inactive
P
+++
• Insulin
• Ca2+
TCA cycle
• TCA cycle – tricarboxylic acids cycle, Krebs
cycle, citric acid cycle
• Main instrument for fuel transformation into ATP
• Pyruvate (actually acetate) from glycolysis is
degraded to CO2
• Some ATP is produced
• More NADH is made
• NADH goes on to make more ATP in electron
transport and oxidative phosphorylation
TCA cycle
• Anapleurotic pathway (both catabolic and
anabolic pathways)
• Takes place in mitochondria matrix
• Stars from AcCoA obtained from pyruvate or
other sourses
Overall reaction
3NAD+ + FAD + GDP + Pi + acetyl-CoA →
3NADH + FADH + GTP + CoA + 2CO2
TCA cycle
• Pyruvate enters TCA cycle as an AcCoA
• Pyruvate is oxidatively decarboxylated to form
acetyl-CoA by pyruvate dehydrogenase (PDH)
• Pyruvate dehydrogenase uses TPP, CoASH, lipoic
acid, FAD and NAD
• NADH & succinyl-CoA are allosteric inhibitors
Step 1 – Citrate Synthase
• Only step in TCA cycle that involves the formation of a
C-C bond
OH
Acetyl-CoA
O
H3 C
S +
CoA
O
O
H2O
HO
O
O
Oxaloacetate
OH
HS
O HO
CoA
Citrate
OH
O
OH
Step 2 - Aconitase
H2C
COOH
HOOC C OH
HOOC
CH2
Citrate
H2O
H2C
COOH
HOOC C
CH
HOOC
Cis-aconitate
H2O
H2C
COOH
HOOC CH
HOOC
CH
OH
Iso-citrate
Step 2 - Aconitase
Aconitase uses an iron-sulfur cluster
Step 3 – Isocitrate Dehydrogenase
• Classic NAD+ chemistry (hydride removal)
followed by a decarboxylation
• Isocitrate dehydrogenase is a link to the
electron transport pathway because it makes
NADH
Step 3 – Isocitrate Dehydrogenase
NAD+
H2C
COOH
HOOC
H2C
COOH
HOOC CH
HOOC CH
CH
CO2
NADH,H+
OH
Isocitrate
HOOC
C
H2C
COOH
H2C
O
Oxalosuccinate
HOOC
C
O
α-Ketoglutarate
Step 4 -α-Ketoglutarate
Dehydrogenase
• Similar to pyruvate dehydrogenase structurally and mechanistically
• Five coenzymes used - TPP, CoASH, Lipoic
acid, NAD+, FAD
COOH
COOH
CH2
NADH+CO2 CH2
CH2
CH2
O
COOH
α-Ketoglutarate
α-Ketoglutarate
Dehydrogenase
O
S-CoA
Succinyl-CoA
Step 5 - Succinyl-CoA Synthetase
• A nucleoside triphosphate is made
• Its synthesis is driven by hydrolysis of a CoA
ester
COOH
COOH
GDP + Pi → GTP + CoA
H2C
H2C
CH2
CH2
S C
CoA
O
Succinyl-CoA
Succinyl-CoA Synthetase
HO C
O
Succinate
Step 6 - Succinate Dehydrogenase
• Mechanism involves hydride removal by FAD
and a deprotonation
• This enzyme is actually part of the electron
transport pathway in the inner mitochondrial
membrane
• The electrons transferred from succinate to FAD
(to form FADH2) are passed directly to
ubiquinone (UQ) in the electron transport
pathway
Step 6 - Succinate Dehydrogenase
COOH
FAD
COOH
FADH2
HC
H2C
CH
CH2
Succinate dehydrogenase HO
HO C
O
Succinate
C
O
Fumarate
Step 7 - Fumarase
COOH
H2O
HC
CH
HO C
Fumarase
O
Fumarate
COOH
HO CH
CH2
HO C
O
Malate
Step 8 - Malate Dehydrogenase
• This reaction is energetically expensive (ΔGo'
= +30 kJ/mol )
NAD+
NADH2
COOH
COOH
O C
HO CH
CH2
CH2
Malate Dehydrogenase HO C
HO C
O
O
Oxaloacetate
Malate
AcCoA fate in
TCA
TCA total ATP outcome
• Acetyl-CoA + 3 NAD+ + Q + GDP + Pi +2 H20 
HS-CoA + 3NADH + QH2 + GTP + 2 CO2 + 2 H+
•
•
•
•
•
Isocitrate Dehydrogenase
α-ketoglutarate Dehydrogenase
Succinyl-CoA Synthetase
Sunccinate Dehydrogenase
Malate Dehydrogenase
1 NADH=2.5 ATP
1 NADH=2.5 ATP
1 GTP=1 ATP
1 QH2=1.5 ATP
1 NADH=2.5 ATP
• Total of 10 ATPs gained from oxidation of 1 Acetyl-CoA
TCA total ATP outcome
Substrate level
phosphorylation
ATP equivalents
Oxidative
phosphorylation
Glucose
2 ATP
ATP equivalents
2 NADH
5
2 NADH
5
6 NADH
15
2x Pyruvate
2x Acetyl CoA
2 ATP
or GTP
4 ATP
TCA
Total: 32 ATP
28 ATP
Aerobic and anaerobic glycolysis ATP
production
Glucose
Sequence of reactions
+
Aerobic Glycolisis
2x
CoA + CO2
Pyruvate
Anaerobic Glycolisis
Lactate
TCA, ETC, OP
32 ATP
2 ATP
Regulation of the TCA Cycle
• Citrate synthase - ATP, NADH, citrate and
succinyl-CoA inhibit
• Isocitrate dehydrogenase - ATP inhibits, ADP and
NAD+ activate
·
α -Ketoglutarate dehydrogenase - NADH and
succinyl-CoA inhibit, AMP activates
• Pyruvate dehydrogenase: ATP, NADH, acetylCoA inhibit, NAD+, CoA activate
• NADH/NAD+ strongly affects on TCA cycle
Regulation of the TCA Cycle
Oxaloacetate
COOH
COOH
H2C
HOOC C OH
CH2
HOOC
O C
CH2
Malate
COOH
HO CH
CH2
HO C
O
HO C
O
Citrate
H2C
COOH
Isocitrate
HOOC CH
HOOC
COOH
Fumarate
CH OH
NADH
HC
CH
ATP
Ca2+
HO C
O
H2C
COOH
CH2
COOH
HOOC
H2C
CH2
C
O
ADP
α-ketoglutarate
COOH
HO C
H2C
O
CH2
Inhibition
S C
Succinate
CoA
O
Succinyl-CoA
Activation
Irreversible steps of TCA cycle
Pyruvate
1.
2.
3.
4.
1
2
3
4
Pyruvate dehydrogenase
Citrate synthase
Isocitrate dehydrogenase
α-ketoglutarate dehydrogenase
Aminoacids income
into TCA cycle
Serine
Alanine
Tryptophan
Tyrosine
Cysteine
Glycine
Threonine
Pyruvate
Acetyl CoA
Leucine
Lysine
Phenylalanine
Threonine
Tryptophan
Tyrosine
Asparagine
Aspartate
Fumarate
Arginine
Glutamine
Histidine
Proline
α-Ketoglutarate
Glutamate