Fundamentals of nutritional biochemistry: nutrient functions and requirements

Overview of metabolism and energetic strategies in

human cellsA key cycle for multiple roles: the

tricarboxylic acid cycle

Russian National Research Medical University

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

BioenergeticsEnergy containing

nutrients Carbohydrates Proteins Fats

Energy depleted end products

CO2

H2O NH3

Precursor molecules

Aminoacids Sugars Fatty acids Nitrogen bases

Cell macromolecules

Proteins Lipids Polysaccharides Nucleic acids

Catabolism

Anabolism

ADP+Pi

NAD+

FAD

ATPNADH2

FADH2

Ingestion

Nutrients

• Carbohydrates• Proteins• Lipids• Inorganic

Digestion, transport

Metabolic reaction

Molecular and cellular action

Main nutrients

Carbohydrates Proteins Lipids

Digestion DigestionDigestion

Sugars Aminoacids Fatty acids + glycerol

Carbohydrates metabolic pathway

Digestion

AbsorbtionGlucose

Liver

Glycolysis +TCA

Glycogenesis

Triglycerids

Energy

Storage

VLDL

Adipose tissueSystem circulation

Protein metabolic pathway

Digestion

Absorbtion

Aminoacids

Liver

Peripheraltissue (muscle)

Protein synthesis

Energy

Energy

Oxidation

Oxidation

Lipid methabolic pathway

Digestion

Absorbtion

TriacylgliceridsIn chylomicrons

Glycerol

Fatty acid

Lipase

Liver

MuscleEnergy

Adipose tissue

Glucose

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 low

•Liver glycogen is used

•Overall energy supply is

unsufficient

• Action is required

• Mostly catabolic pathways

are activated

•Blood glucose level is high

•Liver glycogen is restored

•Energy supply is effecient

•Storage processes are activated

•Mostly anabolic 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. Fuel oxidation2. Fuel storage3. Synthetic pathways4. Waste-disposal pathway

Energy value of foodBiofuels

•Carbonydrates•Lipids•Proteins

Digestion

Waste products:CO2

H2ONH4

+

ADP + Pi

ATP

Ready-to-use energy mostly is used as an ATP

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

ATP provides energy by the process of group transfers and not by simple hydrolysis.

OH

COOH

CH

CH2

CH2

CO

NH2

+ NH3

ATP ADP+Pi

NH2

COOH

CH

CH2

CH2

CO

NH2

O

COOH

CH

CH2

CH2

CO

NH2

P

O

OHOH

ATP

ADP+Pi NH3

Reaction ΔG (kJ/mol)

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

Basal metabolic

rate

Thermogenesis

Activity

Total energy consumption

Basal metabolic rate (BMR)

Function BMR,%

Service

Kidney (Na+ transport) 6-7

Heart 9-11

Nervous system 15-20

Respiration 6-7

Repair

Protein resynthesis 10-15

Triacylglycerol resynthesis 1-2

Transmembrane potential (Na+ transport ) 20-25

BMR calculationThe Original Harris-Benedict Equation:

For men

For women

The Katch-McArdle Formula (Resting Daily Energy Expenditure):

The Mifflin St Jeor Equation:

, where s is +5 for males and −161 for females.

, 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

Lehninger 2002 Fig III.1

Energy containingnutrients

Carbohydrates Proteins Fats

Energy depleted end products

CO2

H2O NH3

Precursor molecules

Aminoacids Sugars Fatty acids Nitrogen bases

Cell macromolecules

Proteins Lipids Polysaccharides Nucleic acids

Catabolism

Anabolism

ADP+Pi

NAD+

FAD

ATPNADH2

FADH2

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

TCA cycle

Electron transfer chainOxidative phosphorilation

Lipids Carbohydrates Proteins

FA + Glycerol Glucose Aminoacids

Pyruvate

AcetylCoenzymeA

СО2

TCA

H+ + ē ETC + ATP synthase

ADP+ P

ATP

+ О2

I. Preparation stage

II.Intermediate stage

III.Terminal stage

Н2О

- NH3

Acetyl-CoA (AcCoA)

http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s23-03-overview-of-stage-ii-of-catabo.html

High energy bond

Acetyl-CoA methabolic pathways

http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s23-03-overview-of-stage-ii-of-catabo.html

Glucose can not be synthesized from AcCoA

PDH

Pyruvate dehydrogenase

NAD+ NADH

COOH

CH3

O HS-CoA

S-CoA

CH3

O CO2+C C +

PDH regulation

PDH

PDH P

Active

Inactive

PDH phosphorylasePDH kinase+++ • Insulin

• Ca2+

+++• ATP• AcCoA• NADH

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

3NAD+ + FAD + GDP + Pi + acetyl-CoA →

3NADH + FADH + GTP + CoA + 2CO2

Overall reaction

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

CH3S

O

CoA

O

OH

O

O

OHO OH

O

OHOH

O

OH

+

OH2

SH CoA

Acetyl-CoA

Oxaloacetate

Citrate

Step 2 - Aconitase

Citrate Cis-aconitate Iso-citrate

CH2

C

CH2HOOC

OHHOOC

COOHCH2

C

CHHOOC

HOOC

COOH

OH

CH2

CH

CHHOOC

HOOC

COOHOH2

OH2

Step 2 - AconitaseAconitase 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

Isocitrate Oxalosuccinate α-Ketoglutarate

OH

CH2

CH

CHHOOC

HOOC

COOH

O

CH2

CH

CHOOC

HOOC

COOHNAD+ NADH,H+ CO2

O

CH2

CH2

CHOOC

COOH

Step 4 -α-Ketoglutarate Dehydrogenase

• Similar to pyruvate dehydrogenase - structurally and mechanistically

• Five coenzymes used - TPP, CoASH, Lipoic acid, NAD+, FAD

COOH

CH2

CH2

COOH

O

NADH+CO2

COOH

CH2

CH2

S-CoA

Oα-Ketoglutarate Dehydrogenase

α-Ketoglutarate Succinyl-CoA

Step 5 - Succinyl-CoA Synthetase

• A nucleoside triphosphate is made• Its synthesis is driven by hydrolysis of a CoA

ester

GDP + Pi → GTP + CoA

S C

CH2

CH2

COOH

OCoAOH C

CH2

CH2

COOH

OSuccinyl-CoA Synthetase

Succinyl-CoA 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

OH C

CH2

CH2

COOH

O

OH C

CH

CH

COOH

O

Step 6 - Succinate Dehydrogenase

FAD FADH2

Succinate dehydrogenase

Succinate Fumarate

Step 7 - Fumarase

H2O

Fumarase

OH

OH C

CH2

CH

COOH

O

OH C

CH

CH

COOH

O

Fumarate Malate

Step 8 - Malate Dehydrogenase

• This reaction is energetically expensive (ΔGo' = +30 kJ/mol )

OH

OH C

CH2

CH

COOH

O

O

OH C

CH2

C

COOH

O

Malate Oxaloacetate

NAD+ NADH2

Malate Dehydrogenase

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 1 NADH=2.5 ATP

• α-ketoglutarate Dehydrogenase 1 NADH=2.5 ATP

• Succinyl-CoA Synthetase 1 GTP=1 ATP

• Sunccinate Dehydrogenase 1 QH2=1.5 ATP

• Malate Dehydrogenase 1 NADH=2.5 ATP

• Total of 10 ATPs gained from oxidation of 1 Acetyl-CoA

TCA total ATP outcome

Glucose

2x Pyruvate2 NADH 52 ATP

ATP equivalentsATP equivalents

2x Acetyl CoA 2 NADH 5

TCA6 NADH 15

2 ATP or GTP

Substrate levelphosphorylation

Oxidativephosphorylation

Total: 32 ATP28 ATP4 ATP

Sequence of reactions

+ Pyruvate

Glucose

Aerobic and anaerobic glycolysis ATP production

Anaerobic Glycolisis

CoA2x + CO2

Aerobic Glycolisis

TCA, ETC, OP

Lactate

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, acetyl-CoA

inhibit, NAD+, CoA activate

• NADH/NAD+ strongly affects on TCA cycle

Regulation of the TCA Cycle

Inhibition

Activation

Citrate

NADH

Ca2+

Isocitrate

α-ketoglutarate

Succinyl-CoASuccinate

Fumarate

Malate

OxaloacetateO

OH C

CH2

C

COOH

O

CH2

CCH2

HOOC

OHHOOC

COOH

OH

CH2

CH

CHHOOC

HOOC

COOH

O

CH2

CH2

CHOOC

COOH

S C

CH2

CH2

COOH

OCoA

OH C

CH2

CH2

COOH

O

OH C

CH

CH

COOH

O

OH

OH C

CH2

CH

COOH

O

ATP

ADP

Pyruvate 1

2

3

4

Irreversible steps of TCA cycle1. Pyruvate dehydrogenase2. Citrate synthase3. Isocitrate dehydrogenase4. α-ketoglutarate dehydrogenase

Aminoacids income into TCA cycle

SerineAlanineTryptophanTyrosineCysteine

Glycine Threonine

AsparagineAspartate

ArginineGlutamineHistidineProline

FumarateGlutamateα-Ketoglutarate

Acetyl CoA

Pyruvate

LeucineLysinePhenylalanineThreonineTryptophanTyrosine