Download Intro to Metabolism

Introduction to metabolism
Biochemistry, 4th edition, RH Garrett & CM Grisham,
Brooks/Cole (Cengage); Boston, MA: 2010
pp 511-534
Instructor: Kirill Popov
1. Metabolism and metabolic pathways
2. Biochemistry of phosphate compounds
3. Oxidation-reduction reactions
4. Vitamins and co-enzymes
Cycling of carbon dioxide and oxygen
Photosynthesis in plants,
algae, bacteria
CO2
Reduced fuels
and O2
Cellular respiration in
animals, plants, algae, bacteria
Cycling of nitrogen in the biosphere
reduction
by some
anaerobic
bacteria,
most
plants
synthesis in
plants and
microorganisms
Nitrate
NO3−
N2
denitrification
nitrification
by soil bacteria
(e.g., Nitrobacter)
Ammonia
NH4+
nitrogen fixation
by some bacteria
(e.g., Azotobacter, Rhizobium,
Klebsiella)
Nitrite
NO2−
Amino acids
and other
reduced
nitrogen-carbon
compounds
degradation
by animals and
microorganisms
Relationship between catabolic and anabolic pathways
Energycontaining
nutrients
Carbohydrates
Fats
Proteins
Catabolism
ADP+Pi
NAD+
NADP+
FAD
ATP
NADH
NADPH
FADH2
Cell
macromolecules
Proteins
Polysaccharides
Lipids
Nucleic acids
Energy
depleted
end products
CO2
H2O
NH3
Chemical
energy
Precursor
molecules
Anabolism
Amino acids
Sugars
Fatty acids
Nitrogen bases
Chemistry of ATP
Ester
O-
O-
O-
-
O P O P O P O CH2
O
O
O
Anhydride
Adenine
O
Anhydride
ATP
OH
OH
CH3 C O C CH3 CH3 C O CH3
O
O
Acetic anhydride,
a caboxylic acid
anhydride
O
Methyl acetate,
a caboxylic acid
ester
Chemical basis for the large free-energy change associated
with ATP hydrolysis
O
O
O
O P O P O P O
−
−
−
O
O
O
O:
−
H
H
Adenine
ATP4-
hydrolysis, with
relief of charge repulsion
O
O
HO P O P O
−
O−
O
O
O P OH
−
O
−
Pi
Rib
Rib
resonance
stabilization
δ−
δ−
O
O P O δ−
O
δ−
Adenine
ADP2ionization
3−
H+
H+ +
O
O
O P O P O
−
−
O
O
−
Rib
ATP4- + H2O → ADP3- + P2-i + H+
ΔG' = −30.5 kJ/mol
Adenine
ADP3-
Energy coupling in chemical processes
Free energy, G
Reaction 2:
ATP → ADP + Pi
Reaction 1:
glucose + Pi →
glucose 6-phosphate
Reaction 3:
glucose + ATP →
glucose 6-phosphate + ADP
ΔG2
ΔG3
ΔG1
ΔG3 = ΔG1 + ΔG2
Reaction coordinate
ATP hydrolysis in two steps
Written as a one-step reaction
COOH
COOH
ATP ADP + Pi H N CH
H2N CH
2
CH2
CH2 + NH
3
CH2
CH2
C
C
O
NH2
O OH
Glutamate
Glutamine
ATP
NH3
ADP
COOH
H2N CH
CH2
CH2
C
O O O
P
HO OH
Enzyme-bound
glutamyl phosphate
Actual two-step reaction
Pi
Ranking of biological phosphate compounds by standard
free energies of hydrolysis
-70
ΔG’° of hydrolysis (kJ/mol)
-60
-50
O
O P
C
CHOH
CH2 O
COOH
C O P
CH2
Phosphoenolpyruvate
P
P
Creatine
Phosphocreatine
-40
1,3-Bisphosphoglycerate
Adenine
-30
Rib
P
P
P
ATP
Low-energy
compounds
-20
Glucose 6- P
-10
0
High-energy
compounds
Pi
Glycerol- P
The oxidation states of carbon in biomolecules
CH2
CH3
Alkane
CH2
CH2OH
Alcohol
O
CH2
Aldehyde
C
H
O
CH2
Carboxylic acid
C
OH
O
C
O
Carbon dioxide
An oxidation-reduction reaction
2H+ + 2e−
OH
CH3 CH
O
C
CH3 C
OH
Lactate
O
2H+ + 2e−
lactate
dehydrogenase
O
C
OH
Pyruvate
NAD and NADP
H
2e-
O
C
H
O
O P O
CH2
OH
..
N
2H+
O
R
NADH
(reduced)
OH
O
NH2
O P O
O
N
CH2
NAD+
(oxidized)
OH
O
O
C
NH2
+
N
H
N
N
adenine
N
OH
In NADP+ this hydroxyl group
is esterified with phosphate
NH2
+ H+
Structures of oxidized and reduced FAD and FMN
Isoalloxazine ring
H
O
CH3
N
CH3
N
H+ + e-
NH
N
O
CH3
N
CH3
N
FMN
H COH
H COH
FAD
CH 2
O
O P O
O
-
NH2
O P O
N
O
CH2
OH
N
FADH• (FMNH•)
(semiquinnone)
H COH
O
N
N
N
OH
Flavin adenine dinucleotide (FAD) and
Flavin mononucleotide (FMH)
adenine
H
NH
R
CH 2
-
O-
O
H + + e-
O
CH3
N
CH3
N
N
R
H
NH
FADH2 (FMNH2)
(fully reduced)
O
Re-cycling of cytosolic NAD
Glucose
2 NAD+
2 NADH
2 Pyruvate
2 Lactate
Transfer of reducing equivalents via NADP cycle
Reduced
fuel
Catabolism
NADP+
Reductive
biosynthetic
product
Oxidized
product
NADPH
Reductive
biosynthetic
reactions
Oxidized
precursor
General scheme of the pentose phosphate pathway
Nonoxidative
phase
Oxidative
phase
Glucose 6-phosphate
NADP+
2 GSH
glutathione
reductase
GSSG
NADPH
transketolase,
transaldolase
Fatty acids,
sterols, etc
6-Phosphogluconate
NADP+
CO2
reductive
biosynthesis
NADPH
Precursors
Ribulose 5-phosphate
Ribose 5-phosphate
OO P O CH2
O
NADP+
Mg 2+
OH
Nucleotides, coenzymes,
DNA, RNA
OO P O CH2
+
NADPH + H
O
OH
OH
OH
glucose 6-phosphate
glucose 6-phosphate
dehydrogenase
OH
OH
OH
6-phosphoglucono-δ-lactone
O
Three stages of cellular respiration
Amino Fatty
acids acids
Stage 1
Acetyl-CoA
production
Glucose
Glycolysis
ee-
e-
pyruvate
dehydrogenase
complex
CO2
e-
Acetyl-CoA
Stage 2
Acetyl-CoA
oxidation
Citrate
Oxaloacetate
e-
Citric
acid cycle
e-
ee-
CO2
CO2
NADH,
FADH2
(reduced e - carriers)
eRespiratory
(electron transfer)
chain
ADP + Pi
ATP
2H+ + 1/2O2
H2O
Stage 3
Electron transfer
and oxidative
phosphorylation
Types of nonlinear metabolic pathways
Rubber
Phospholipids
Triacylglycerols
Caratenoid
pigments
Isopentylpyriphosphate
Steroid
hormones
Cholesterol
Fatty acids
Mevalonate
Starch
Alanine
Phenylalanine
Glycogen
Glucose
Pyruvate
Sucrose
Serine
Acetate
(acetyl-CoA)
Vitamin K
Cholesteryl
esters
Eicosanoids
Actoacetyl-CoA
Leucine
Fatty acids
Isoleucine
Triacylglycerols
Converging catabolism
Oxaloacetate
CDP-diacylglycerol
Citrate
Phospholipids
Diverging anabolism
CO 2
CO2
Cyclic pathway
Bile
acids
Enzyme-limited and substrate-limited reactions
Enzyme-limited
reaction (far from
equilibrium)
B
A
Substrate-limited
reaction (at or
near equilibrium)
B B
B
B B
B
C
D
E E
E E
E E E
E
E E
E
E
E
E E
F
G
H
H H
H
H H
H
I
J
Feedback inhibition
enzyme 1
A
Threonine
B
C
D
E
F
Isoleucine
Regulation of phosphofructokinase-1
ATP
AMP, ADP
Fructose 6- + ATP
phosphate
citrate
Fructose 1,6- + ADP
phosphate
fructose 2,6bisphosphate
Relative Changes in [ATP] and [AMP] When ATP Is Consumed
Concentration
before ATP
depletion (mM)
Concentration after
ATP depletion (mM)
Relative change
ATP
5.0
4.5
10%
ADP
1.0
1.0
0
AMP
0.1
0.6
600%
Adenine
nucleotide
Role of fructose 2,6-bisphosphate in regulation of PFK-1
PFK-1 activity (% of Vmax)
100
80
+F2,6BP
60
40
-F2,6BP
20
0
0 0.05 0.1
0.2
0.4 0.7
1.0
[Fructose 6-phosphate] (mM)
2.0
4.0
Glycolysis and gluconeogenesis
Glycogen
UDP
UTP
Pi
Third
bypass
Glucose 1-phosphate
Glucose
ATP
ADP
Glucose 6-phosphate
Second
bypass
AMP,
f ructose 2,6bisphosphate
Fructose 6-phosphate
ATP
Pi
ADP
Fructose 1,6-bisphosphate
Glyceraldehyde
phosphate 3-phosphate
f ructose 2,6bisphosphate
Dihydroxyacetone
NAD +
NAD +
NADH
NADH
1,3-Bisphosphoglycerate
ADP
Gluconeogenesis
pathway
ADP
ATP
ATP
3-Phosphoglycerate
2-Phosphoglycerate
Phosphoenolpyruvate
Glycolysis
pathway
Compartmentalization of glycolysis, the citric acid cycle,
and oxidative phosphorylation
Glucose
Glucose
ATP
NADH
Glycolysis
in the cytosol
ATP
Acetyl-CoA
NADH
NADH
ATP
ATP
ATP
ATP
Citric
acid
cycle
Citric acid
cycle and
oxidative
phosphorylation in the
mitochondria
Pyruvate
NADH
ADP
+ P
NAD +
ATP
H2O
O2
CO2
Vitamins and Coenzymes
Vitamin
Coenzyme Form
Water-Soluble
Niacin (nicotinic acid)
Riboflavin (vitamin B2)
Thiamine (vitamin B1)
Pantothenic acid
Pyridoxal, piridoxine (vitamin B6)
Cobalamine (vitamin B12)
Biotin
Lipoic acid
Folic acid
NAD+, NADP+
FAD, FMN
Thiamine pyrophosphate
Coenzyme A
Pyridoxal phosphate
5’-Deoxyadenosylcobalomine
Biotin-lysine
Lipoyl-lysine
Tetrahydrofolate
Fat-Soluble
Retinol (vitamin A)
Cholecalciferol (vitamin D3)
α-Tocopherol (vitamin E)
Vitamin K
Thiamine pyrophosphate and its role in decarboxylation
H+
NH2
CH2
N
CH3
C
N
NH2
S
+
CH2
N
H+
AMP
ATP
CH2
TPP-synthetase
OH
N
CH3
CH3
C
CH2
N
N
CH3
CH3
pyruvate
S
O
N
CH2
O P O P O
O-
H
CH2
CH2
O
O-
Thiamine pyrophosphate (TPP)
H
CH2 N
O
CH3
N
thiazolium
ring
C
S
CH2
Thiamine (vitamin B1)
NH2
Acidic proton
-
Thiamine pyrophosphate
-
O
NH2
O
O P O P O
CH3
CO2
-
O
pyruvate
dehydrogenase CH3
CH2 N
N
C OH
C S
O
CH2
N
active
aldehyde
CH3
CH2
O
-
O P O P O
-
O
Hydroxyethyl thiamine pyrophosphate
-
O
The structure of coenzyme A
NH2
H
HS CH2
CH2
H
N C CH2
O
β-Mercaptoethylamine
CH2
H CH3
N C C C CH2
O OH CH3
Pantothenic acid
-
O
N
-
O
O P O P O CH2
O
O
O
O
N
N
N
OH
-
O P O
-
O
Coenzyme A
3’-Phosphoadenosine diphosphate
(3’-P-ADP)
Enzyme-catalyzed transaminations
COO-
COO-
COO
C O
CH2
+ H2N
CH2
C H
R
-
aminotransferase
CH2
COO
+
CH2
C O
R
-
COO
α-Ketoglutarate
PLP
-
H2N C H
COO
L-Amino acid
L-Glutamate
α-Keto acid
Pyridoxal phosphate, the prosthetic group of
aminotransferases
-
-
O
O
-
-
O P O
O P O
O
O
H2C
H
H2C
H
O C
+
NH
+
H3N C
+
NH
H
HO
CH3
Pyridoxal phosphate
(PLP)
HO
CH3
Pyridoxamine
phosphate
Pyridoxal phosphate is bound to the enzyme
through a Schiff-base linkage
-
O
-
O P O
O
H2C
H
Enz
Lys
NH2
..
+
O C
NH
HO
CH3
-
O
H2O
-
O P O
O
H2C
H H
Enz
Lys
+
N C
NH
+
Schiff base
HO
CH3
Role of biotin in carboxylation reactions
O
O
O
-
O P O P O P O
-
-
O
Rib
Adenine
-
O
O
ATP
O
O
-
O C
OH
NH
HN
Bicarbonate
O
(CH2)4
S
1
C
NH
Biotinyl-enzyme
ADP + Pi
O
Enz
O
C
-
O
NH
N
O
(CH2)4
S
Enz
C
N
H
Carboxybiotinyl-enzyme
O
-
O
O-
O
C C CH2
-
O
C C CH2
O
Pyruvate enolate
2
O
-
O
C C CH2
O
O
+
C
OH
O
NH
HN
Oxaloacetate
O
S
(CH2)4
Enz
C
N
H
Biotinyl-enzyme
Lipoic acid (lipoate) in amide linkage with Lys residue
Oxidized
form
CH2
S
CH2
S
CH
Lipoic
acid
CH2
CH2
CH2
CH2
C O
HN
Lys
residue
of E2
CH2
CH2
CH2
CH2
CH
NH
C
O
Polypeptide chain of
E2 (dihydrolipoyl
transacetylase)
Reduced
form
HS CH2
CH2
HS CH
CH2
O
CH3
Acetylated
form
C S CH2
CH2
HS CH
CH2
Tetrahydrofolate (H4 folate)
H2 N
N
8a
H
N
8
1
2
HN
3
4
O
5
4a
H
7
H
H
6
N
H
6-methylpterin
p-aminobenzoate
10
CH2
9
NH
O
-
COO
C NH CH CH2
CH2
glutamate
Tetrahydrofolate (H4 folate)
-
COO
Conversion of one-carbon units on tetrahydrofolate
Oxidation state
(group transferred)
H
N
CH2
H
N
CH2
CH3
CH3 N
(most reduced)
H
N5,N10-Methyltetrahydrofolate
-
COO
H2N C H
H
N
CH2
H
N
CH2
H
N
H
Tetrahydrofolate
NAD+
GlycineN5,N10-MethyleneCOO tetrahydrofolate
reductase
H2N C H
Serine
H
CH2OH
H2 O
PLP
serine hydroxymethyl transferase
NADH + H+
H
N
CH2
H
N
CH2
H2 C
CH2OH
N
N5,N10-Methylenetetrahydrofolate
NAD+
N5,N10-Methenyltetrahydrofolate
reductase
NADH
+ H+
H
N
CH2
H
N
CH2
C
O
N
H H
N5-Formyletrahydrofolate
O
C H
(most oxidized)
Coenzyme B12 is the cofactor form of vitamin B12
O
1’
5'-Deoxyadenosine
OH
2’
N
4’
HO
3’
N
O
5’
N
N
CH2
C NH2
CH2
NH2
H CH2 C NH2
CH3
H2N C
CH2
H
O C
CH3
3+
N CH3
CH3
CH 2
O C C H2
H
CH2
C
O
NH
Aminoisopropanol
CH2
H2N CH3
N
CH3
N
Dimethylbenzimidazole
ribonucleotide
CH2 C NH
2
Corrin
ring
system
CH2
N
H3C
CH3
Co
O
CH3
H
N
N
C H2
CH2
NH2
O
CH2
O
HC CH3
O
O
O
-
P O
O
OH
CH2OH
The formation of coenzyme B12 occurs in reaction in which
triphosphate is cleaved from ATP
O
1'
OH
O
3'
2'
N
O
N
5'
N
4'
CH2
O
O
-
O P O P O P O
N
-
O
-
O
-
O
ATP
NH2
Co
Cobalamin
O
O
O
-
O P O P O P OO-
O-
O
OH
N
O
Coenzyme B12
N
CH2
N
N
NH2
Co
O-
Coenzyme B12-catalyzed group transfer
H
H
H C
C
O
C
-
H
C
O
O
Coenzyme B12
methylmalonyl-CoA
mutase
S-CoA
H X
H
H C
C
H
C
O
S-CoA
Succinyl-CoA
L-Methylmalonyl-CoA
C C
H
Coenzyme B12
C C
X H
O
C
-
O
Vitamin A1 and its precursors and derivatives
CH3
CH3
CH3
CH3
CH3
CH3
CH3
oxidation CH3
of aldehyde
to acid
CH3
oxidation of
alcohol to
aldehyde
CH3
CH3
CH3
CH3
Hormonal
signal
11
2
6
CH3
12
CH3
CH3
CH3
C
CH3
CH3
C
O
H
cleavage
point of
cleavage
CH3
7
all-trans-Retinal
11
CH3
isomerization/
oxidation of
alcohol to
aldehyde
O
HO
all-trans-Retinoic acid
CH3
CH3
CH3
CH3
15 CH2OH
CH3
CH3
Vitamin A1
(retinol)
CH3
CH3
CH3
CH3
CH3
visible
light
CH3
11
12
H3C
11
12
CH3
C
O
β-Carotene
H
11-cis-Retinal
(visual pigment)
C
H
O
all-trans-Retinal
Vision
Vitamin D3 production and metabolism
H3C
CH3
H3C
CH3
HO
3
1
4
5
CH3
CH3
CH3
25
OH
CH3
CH3
2 steps in skin
7
4
6
6
5
CH2
1 step in the kidney
5
CH2
4
3
UV light
3
1
HO
7-Dehydrocholesterol
7
7
6
8
10
H3C
1 step in the liver
CH3 9
2
CH3
CH3
2
Cholecalciferol (vitamin D 3)
HO
1
OH
2
1,25-Dihydroxycholecalciferol
(1,25-dihydroxyvitamin D 3)
Vitamins E and K and the lipid quinones are
oxidation-reduction cofactors
CH3
HO
CH3
CH2
Vitamin E: an antioxidant
CH3
O
CH3
CH2
CH2
CH3
CH CH2
CH2
CH2
CH3
CH CH2
CH2
CH2
CH CH3
CH3
O
Vitamin K1: a blood-clotting
factor (phylloquinone)
CH3
CH3
CH2
CH2
C CH2
CH3
(CH2
CH2
CH3
CH CH2)2
CH2
CH2
CH CH3
O
O
Warfarin: a blood
anticoagulant
CH
OH
CH2
C CH3
O
O
Ubiquinone: a mitochondrial
Electron carrier (coenzyme Q)
CH3O
CH3
CH3
CH3
CH3O
CH2
O
CH2
C CH2
(CH2
CH2
C CH2)n
CH3
CH2
CH2
C CH3
Vitamin K stimulates the carboxylation of
glutamate residues
O
CH
OH
CH2
C CH3
O
Warfarin
γ-carboxy-Glu
Glu
O
O
N CH C
N CH C
H CH2
H CH2
-
-
H2C C O
O C C C O-
O
O
O
γ-glutamyl
carboxylase
KH2
KO
2
1
vitamin K epoxide
reductase
2
vitamin K
reductase
1
K
warfarin
sensitive
1.
Living cells constantly perform work. They require energy for maintaining
their highly organized structures, synthesizing cellular components,
generating electric currents, and many other processes
2.
ATP is a chemical link between catabolism and anabolism. The exorgonic
conversion of ATP to ADP and Pi, or to AMP and PPi is coupled to many
endergonic reactions and processes. ATP provides the energy for anabolic
processes through the group transfer reactions. In many organisms, a central
energy-conserving process is the stepwise oxidation of glucose, fatty acids,
and amino acids to CO2, in which some of the energy of oxidation is
conserved in ATP as electrons are passed to oxygen
3.
Many biological oxidation reactions are dehydrogenations in which one or
two hydrogen atoms are transferred from a substrate to a hydrogen acceptor
4.
NAD and NADP are the freely diffusible coenzymes of many dehydrogenases.
They accept two electrons and one proton. FAD and FMN, the flavin
nucleotides, serve as tightly-bound prosthetic groups of flavoproteins. They
can accept either one or two electrons and one or two protons
5.
Vitamins are essential nutrients that are required in the diet because they
cannot be synthesized by the organism itself. Often they are components or
precursors of coenzymes