Biochemistry 2/e - Garrett & Grisham Copyright © 1999 by Harcourt Brace & Company Enzyme Kinetics.
Introduction to metabolism Biochemistry, 4 th edition, RH Garrett & CM Grisham, Brooks/Cole (...
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Transcript of Introduction to metabolism Biochemistry, 4 th edition, RH Garrett & CM Grisham, Brooks/Cole (...
Introduction to metabolismBiochemistry, 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
Photosynthesis in plants,algae, bacteria
CO2
Cellular respiration inanimals, plants, algae, bacteria
Reduced fuelsand O2
Cycling of carbon dioxide and oxygen
Amino acidsand otherreduced
nitrogen-carboncompounds
N2NitrateNO3
−Ammonia
NH4+
NitriteNO2
−
nitrogen fixationby some bacteria
(e.g., Azotobacter, Rhizobium,Klebsiella)
degradationby animals andmicroorganisms
synthesis inplants and
microorganisms
nitrificationby soil bacteria
(e.g., Nitrobacter)
denitrification
reductionby some
anaerobicbacteria,
mostplants
Cycling of nitrogen in the biosphere
Cellmacromolecules
ProteinsPolysaccharidesLipidsNucleic acids
Energydepleted
end productsCO2H2ONH3
Catabolism
Anabolism
Chemicalenergy
Energy-containing nutrients
CarbohydratesFatsProteins
Precursormolecules
Amino acidsSugarsFatty acidsNitrogen bases
ADP+PiNAD+
NADP+
FAD
ATPNADH
NADPHFADH2
Relationship between catabolic and anabolic pathways
Chemistry of ATP
Adenine
Ester
AnhydrideAnhydride
Acetic anhydride,a caboxylic acid
anhydride
ATP
Methyl acetate,a caboxylic acid
ester
P O P O P O CH2-O
O
OHOH
O- O- O-
O O O
CH3 C O C CH3
OOCH3 C O
OCH3
ATP4- + H2O → ADP3- + P2-i + H+
ΔG' � = −30.5 kJ/mol
O:H
H
resonance stabilization
O P O P O P OO O O
O O ORib Adenine
−−
−
−
Rib AdenineP O P OO O
O OOH
−−O P
O
OOH
−
−
Rib AdenineP O P OO O
O OO
−
−
−
3−δ−
δ−
δ−
δ−O P OO
OH+ +H+
hydrolysis, withrelief of charge repulsion
ionization
ATP4-
ADP2-Pi
ADP3-
Chemical basis for the large free-energy change associated with ATP hydrolysis
Reaction coordinate
Free
ene
rgy,
G
Reaction 1:glucose + Pi →
glucose 6-phosphate
Reaction 3:glucose + ATP →
glucose 6-phosphate + ADP
Reaction 2:ATP → ADP + Pi
ΔG1
ΔG2 ΔG3
ΔG3 = ΔG1 + ΔG2
Energy coupling in chemical processes
COOHCHCH2
H2N
CH2COHO
+ NH3
NH3
Pi
Glutamine
ATP
ATP
ADP + Pi
ADP
Glutamate
Enzyme-boundglutamyl phosphate
Written as a one-step reaction
Actual two-step reaction
COOHCHCH2
H2N
CH2CNH2O
COOHCHCH2
H2N
CH2COO P
OOHHO
ATP hydrolysis in two steps
-70
1,3-BisphosphoglyceratePhosphocreatine
ATPHigh-energycompounds
Low-energycompounds
ΔG’°
of h
ydro
lysis
(kJ/
mol
)
-60
-50
-40
-30
-20
-10
0
Phosphoenolpyruvate
Pi
Glycerol- PGlucose 6- P
CCHOHOO
CH2 O
P
P P Creatine
COOHCCH2
O P
Adenine Rib PP P
Ranking of biological phosphate compounds by standard free energies of hydrolysis
Alkane
CH2 CH2OH
CH2 CH3
O C O
CCH2HO
O
CH2
O
HC
Alcohol
Aldehyde
Carboxylic acid
Carbon dioxide
The oxidation states of carbon in biomolecules
CH CHO
OCH3
OH O
C CHO
OCH3
Lactate Pyruvatelactate
dehydrogenase
2H+ + 2e−
2H+ + 2e−
An oxidation-reduction reaction
N
HC
O
NH2
CH2O
OH OH
O
PO O-
O
O
OHOH
CH2
N
N
N
N
NH2PO O-
O
+N
C
R
H H O
NH2..
2e-
2H+
NADH(reduced)
NAD+
(oxidized)
adenine
+ H+
In NADP+ this hydroxyl groupis esterified with phosphate
NAD and NADP
N
N N
NH
O
OCH2
COHCOHCOHCH2
OPOPO
O
OHOH
CH2
N
N
N
N
NH2
O
O
-O
-O
CH3
CH3
HHH
N
N N
NH
O-
ROCH3
CH3
HN
N N
NH
R
O
OCH3
CH3
H
H
Isoalloxazine ring
FAD
FMN
H+ + e- H+ + e-
FADH• (FMNH•)(semiquinnone)
FADH2 (FMNH2)(fully reduced)
Flavin adenine dinucleotide (FAD) andFlavin mononucleotide (FMH)
adenine
Structures of oxidized and reduced FAD and FMN
Glucose
2 Pyruvate 2 Lactate2 NADH
2 NAD+
Re-cycling of cytosolic NAD
Transfer of reducing equivalents via NADP cycle
NADP+ NADPH
Reductivebiosynthetic
reactions
Catabolism
Reductivebiosynthetic
product
Oxidizedprecursor
Reducedfuel
Oxidizedproduct
Glucose 6-phosphate
6-Phosphogluconate
Ribulose 5-phosphate
Ribose 5-phosphate
Nucleotides, coenzymes,DNA, RNA
Fatty acids,sterols, etc
NADPH
NADPH
NADP+
NADP+
CO2
GSSG
2 GSH
Precursors
reductivebiosynthesis
Nonoxidativephase
Oxidative phase
glutathionereductase
transketolase,transaldolase
General scheme of the pentose phosphate pathway
OH OHOH
OH
CH2OPO
O-
-O
OHOH
OH
CH2OPO
O-
-O
O
glucose 6-phosphate
glucose 6-phosphatedehydrogenase
6-phospho-glucono-δ-lactone
NADP+ NADPH + H+
Mg2+
Acetyl-CoA
CO2
NADH,FADH2
(reduced e- carriers)
ATPADP + Pi
Respiratory(electron transfer)
chain
Citricacid cycle
Glycolysis
Stage 3Electron transfer
and oxidativephosphorylation
Stage 2Acetyl-CoAoxidation
Stage 1Acetyl-CoAproduction
CO2
e-
e-
e-
e-
e-
e-
e- e-
e-
Aminoacids
Fattyacids Glucose
2H+ + 1/2O2
H2O
CO2
pyruvatedehydrogenasecomplex
OxaloacetateCitrate
Three stages of cellular respiration
Phospholipids
Triacylglycerols
Starch
Pyruvate
Sucrose
Isoleucine
LeucineSerine
Phenyl-alanine
Bileacids
Steroidhormones
Caratenoidpigments
Rubber
Isopentyl-pyriphosphate
Cholesterylesters
Vitamin K
Cholesterol
Triacylglycerols
Eicosanoids
Mevalonate
Fatty acids
CDP-diacylglycerol
Diverging anabolism
Converging catabolism
CO2
OxaloacetateCitrate
CO2
Cyclic pathway
Acetate(acetyl-CoA)
Alanine
GlucoseGlycogen
Fatty acids
Actoacetyl-CoA
Phospholipids
Types of nonlinear metabolic pathways
A
BB B
BB
B B
Enzyme-limitedreaction (far from
equilibrium)
C
Substrate-limitedreaction (at ornear equilibrium)
D
EEE
EE
EE
E
E
EEE E
EE
F G
H
H
HH
HH
H
I J
Enzyme-limited and substrate-limited reactions
enzyme 1
IsoleucineThreonineC D E FA B
Feedback inhibition
Fructose 6- + ATPphosphate
Fructose 1,6- + ADPphosphate
ATP AMP, ADP
citrate fructose 2,6-bisphosphate
Regulation of phosphofructokinase-1
Relative Changes in [ATP] and [AMP] When ATP Is Consumed
Adenine nucleotide
Concentration before ATP
depletion (mM)
Concentration after ATP depletion (mM)
Relative change
ATP 5.0 4.5 10%ADP 1.0 1.0 0AMP 0.1 0.6 600%
[Fructose 6-phosphate] (mM)
PFK
-1 a
ctiv
ity (%
of V
max
)
-F2,6BP
+F2,6BP
100
80
60
40
20
00 0.05 0.1 0.2 0.4 0.7 1.0 2.0 4.0
Role of fructose 2,6-bisphosphate in regulation of PFK-1
Glyceraldehyde3-phosphate
Fructose 1,6-bisphosphate
Dihydroxyacetonephosphate
Glycolysispathway
Gluconeogenesispathway
Fructose 6-phosphate
2-Phosphoglycerate
Phosphoenolpyruvate
3-PhosphoglycerateATP ATP
ADP ADP
NADH
NAD+
NADH
NAD+
1,3-Bisphosphoglycerate
Thirdbypass
Secondbypass
ATP
ADP
Pi
Glucose 6-phosphate
ATP
ADP
Pi
Glycogen
GlucoseGlucose 1-phosphate
UTP
UDP
AMP,fructose 2,6-
bisphosphate
fructose 2,6-bisphosphate
Glycolysis and gluconeogenesis
Compartmentalization of glycolysis, the citric acid cycle, and oxidative phosphorylation
ATP
ATP
ATP
P
NADHNADH
NADHNAD+
ADP
H2O
O2 CO2
NADH
Acetyl-CoA
Glucose
Citricacidcycle
Citric acidcycle andoxidativephosphoryla-tion in the mitochondria
Glycolysisin the cytosol
Glucose
Pyruvate
ATP
ATP
ATP
ATP
+
Vitamins and Coenzymes
Vitamin Coenzyme Form
Water-SolubleNiacin (nicotinic acid)Riboflavin (vitamin B2)Thiamine (vitamin B1)Pantothenic acidPyridoxal, piridoxine (vitamin B6)Cobalamine (vitamin B12)BiotinLipoic acidFolic acid
NAD+, NADP+
FAD, FMNThiamine pyrophosphateCoenzyme APyridoxal phosphate5’-DeoxyadenosylcobalomineBiotin-lysineLipoyl-lysineTetrahydrofolate
Fat-SolubleRetinol (vitamin A)Cholecalciferol (vitamin D3)α-Tocopherol (vitamin E)Vitamin K
N
N
NH2
CH2
CH3
SN
C
CH3
CH2 CH2 O P O P O-OO
O- O-
H+
N
N
NH2
CH2
CH3
SN
C
CH3
CH2 CH2 OH
H+
ATP+
AMP
TPP-synthetase
Thiamine (vitamin B1) Thiamine pyrophosphate (TPP)
Acidic proton
Thiamine pyrophosphate
thiazoliumring
activealdehyde
Hydroxyethyl thiamine pyrophosphate
pyruvate CO2
pyruvatedehydrogenase
N
N
NH2
CH2
CH3
SN
C
CH3
CH2 CH2 O P O P O-OO
O- O-
H
N
N
NH2
CH2
CH3
SN
C
CH3
CH2 CH2 O P O P O-OO
O- O-
C
H
OHCH3
Thiamine pyrophosphate and its role in decarboxylation
The structure of coenzyme A
Pantothenic acidβ-Mercaptoethylamine
3’-Phosphoadenosine diphosphate(3’-P-ADP)
Coenzyme A
O
OHO
CH2
N
N
N
N
NH2
P O-
O-O
OPOPOCH2CCCNCH2CH2CNCH2CH2HSH
O
H
O
H CH3
CH3OH
O- O-
O O
COO-
C
CH2
CH2
COO-
O COO-
C HH2N
R
COO-
C
CH2
CH2
COO-
HH2N COO-
C
R
O
α-Keto acidL-Amino acid L-Glutamateα-Ketoglutarate
aminotransferase+ +
PLP
Enzyme-catalyzed transaminations
NH
H2C
C
HO CH3
O
P
O-
-O O
H
O
Pyridoxal phosphate(PLP)
+NH
H2C
C
HO CH3
O
P
O-
-O O
H3N
H
H
Pyridoxaminephosphate
+ +
Pyridoxal phosphate, the prosthetic group of aminotransferases
NH
H2C
C
HO CH3
O
P
O-
-O O
N
HH
NH
H2C
C
HO CH3
O
P
O-
-O O
H
OLys NH2
LysEnz
Enz
Schiff base
+
+
+
H2O
..
Pyridoxal phosphate is bound to the enzyme through a Schiff-base linkage
HN NH
S(CH2)4 C
N
O
O
H
Enz
Enz
HN NH
S(CH2)4 C
NH
O
O
Enz
-O P O P O P O
O- O- O-
O O O
AdenineRib
Bicarbonate
ATP
Pyruvate enolate
Carboxybiotinyl-enzyme
Biotinyl-enzyme
Biotinyl-enzyme
Oxaloacetate
+
ADP + Pi
1
2
-O CO
OH
H
C
O
-O N NH
S(CH2)4 C
N
O
O
C C-O
O O-
CH2C C-O
O O
CH2-
CO
OHC C
-O
O O
CH2
Role of biotin in carboxylation reactions
CHCH2
CH2
CH2
S
HS
CCH3
O
Polypeptide chain ofE2 (dihydrolipoyltransacetylase)
Lipoicacid
Acetylatedform
Reducedform
Oxidizedform
Lysresidue
of E2
CHCH2
CH2
CH2
HS
HS
S
S CHCH2
CH2
CH2
CH2
CH2
CH2
C O
HNCH2
CH2
CH2
CH2
CHNH C
O
Lipoic acid (lipoate) in amide linkage with Lys residue
Tetrahydrofolate (H4 folate)6-methylpteringlutamate
p-aminobenzoate1
23
4 5 6
78
9
8a
104aN
N N
N
H2N
O
H
CH2
H
H
NH C
O
NH CH
COO-
CH2 CH2 COO-H
H
H
Tetrahydrofolate (H4 folate)
COO-
C HH2N
H
NADH
NADH
+ H+
NAD+
NAD+
PLP
Serine Glycine
TetrahydrofolateN5,N10-Methylenetetrahydrofolate
N5,N10-Methyltetrahydrofolate
N5-Formyletrahydrofolate
(most reduced)
(most oxidized)
Oxidation state(group transferred)
N5,N10-Methylene-tetrahydrofolate
reductase
N5,N10-Methenyl-tetrahydrofolate
reductase
+ H+
H2O
serine hydroxymethyl transferaseN
CH2N
CH2
H
NH
H
H
COO-
C HH2NCH2OH
N
CH2N
CH2
H
NC
H
H2
N
CH2N
CH2
H
NCH3
H
H
CH3
CH2OH
N
CH2N
CH2
H
NCO H
H
H
CO
H
Conversion of one-carbon units on tetrahydrofolate
O
OH O
CH2N
N N
N
NH2
H
N
N
N
N
CH2
CH2NO
CH3
CH2
CH2
CO
NH2
H CH2
CH3
C
O
NH2
CH2
H
H CO
NH2
CH3
H2CH2C
C
H3C
CH3
O
H2N
H
H2CH2C
CO
NH2
CH3CH3 Co3+
CH2
CH2
CNHCH2
HC CH3
OP O-
OO
N
NCH3
CH3
O
CH2OHOH
O
5'-Deoxy-adenosine
Amino-isopropanol
Corrinringsystem
Dimethyl-benzimidazoleribonucleotide
1’
2’ 3’
4’
5’
Coenzyme B12 is the cofactor form of vitamin B12
-O P O P O P O-O O O
O- O-O-
Co
Coenzyme B12
Cobalamin
1'
2' 3'
4'
5'
ATP
O
OH O
CH2 O P O P O P O-O O O
O- O-O-N
N N
N
NH2
Co
O
OH O
CH2N
N N
N
NH2
The formation of coenzyme B12 occurs in reaction in which triphosphate is cleaved from ATP
Coenzyme B12-catalyzed group transfer
methylmalonyl-CoAmutase
Coenzyme B12 C
H
H C
H
CO-
O
HCO S-CoA
C
H
H C
H
H
CO
CO-
O
S-CoA
L-Methylmalonyl-CoA Succinyl-CoA
Coenzyme B12C C
H X
CC
HX
all-trans-Retinoic acid
C
CH3
CH3
CH3
CH3
CH3
OHO
β-Carotene
CH3
CH3CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
point ofcleavage
oxidation ofalcohol toaldehyde
oxidationof aldehyde
to acid
visiblelight Vision
Hormonalsignal
Vitamin A1(retinol)
CH2OH
CH3
CH3
CH3
CH3
CH3
26
7
11
15
cleavage
isomerization/oxidation ofalcohol toaldehyde
11-cis-Retinal(visual pigment)
CH3
CH3
CH3
CH3
C
H3C
O H
11
12
all-trans-Retinal
11
12
C
CH3
CH3
CH3
CH3
CH3
OH
all-trans-Retinal
11
12
C
CH3
CH3
CH3
CH3
CH3
OH
Vitamin A1 and its precursors and derivatives
7-Dehydrocholesterol
UV light
2 steps in skin
Cholecalciferol (vitamin D3)
1 step in the liver
1 step in the kidney
1,25-Dihydroxycholecalciferol (1,25-dihydroxyvitamin D3)
H3C CH3
CH3CH3
CH3
HO
12
34
56
7
8
9
10
H3CCH3
CH3CH3
HO
CH2
12
3
45
67
H3CCH3
CH3CH3
HO
CH2
OH
OH
25
12
3
45
67
Vitamin D3 production and metabolism
O
CH
CH2 C CH3
O
OH
Warfarin: a bloodanticoagulant
Vitamin E: an antioxidantO
CH2
CH3
CH2 CH2 CH CH2
CH3
CH2 CH2 CH
CH3
CH2 CH2 CH2 CH
CH3
CH3
CH3
CH3
CH3
HO
Vitamin K1: a blood-clottingfactor (phylloquinone) CH2 CH2 CH
CH3
CH3CH2 C CH2
CH3
(CH2 CH2 CH
CH3
CH2)2CH2
O
O
CH3
Ubiquinone: a mitochondrialElectron carrier (coenzyme Q)
CH2 C CH3
CH3
CH2CH2 C CH2)n
CH3
(CH2
CH3
CH2 C CH2
CH3
CH2CH3O
CH3O
O
O
Vitamins E and K and the lipid quinones are oxidation-reduction cofactors
Vitamin K stimulates the carboxylation of glutamate residues
N CH C
H CH2
H2C C O-
O
O
N CH C
H CH2
C C O-
O
O
C-O
O
KH2 KO
K
Glu γ-carboxy-Glu
Warfarin
warfarinsensitive
O
CH
CH2 C CH3
OOH
γ-glutamylcarboxylase
vitamin K epoxide reductase
vitamin K reductase
12
2
1
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