catabolism and anabolism

1. Chapter 1
Introduction
1 / 573

2. Significance of metabolism in medicine
◮ hereditary enzyme defects
◮ diabetes, atherosclerosis, gout
◮ antimetabolites in the chemotherapy of cancers and infections
◮ inactivation and elimination of xenobiotics and drugs
2 / 573

3. Catabolic and anabolic reactions
Foodstuffs Small intermediates
Small intermediates CO2 + H2O
Complex
biomolecules
NADP+
NADPH + H+
ADP + Pi
ATP
O2
3 / 573

4. Diversity of metabolism: pathways in plants and bacteria
Pathway Organisms
photosynthesis plants and cyanobacteria
nitrogen fixation specialized soil bacteria
oxidation or reduction of
inorganic minerals
archaebacteria
acid- and gas-producing
fermentations
anaerobic bacteria
4 / 573

5. Types of foodstuffs
◮ carbohydrates
◮ protein
◮ fat
◮ nucleic acids
5 / 573

6. Breakdown of foodstuffs: Overview
Glycogen
Carbohydrates
Glucose
Pyruvate
Proteins
Amino acids
Acetyl-CoA
CO2 + H2O
Triacylglycerol (fat)
Fatty acids
Ketone bodies
ADP + Pi
ATP
6 / 573

7. Functional anatomy of the digestive system
Stomach
Liver
Small intestine Large intestine
Pancreas
Liver
Pancreatic duct
Duodenum
Bile bladder
Bile duct
7 / 573

8. Intestinal organs: functional overview
Organ Function
stomach killing of microbes contained in the food;
protein denaturation
small intestine breakdown of macromolecules to small
molecules, uptake of the latter
large intestine fluid and ion reuptake
pancreas production of digestive enzymes and of
hormones
liver production of bile; metabolic homeostasis
8 / 573

9. The portal circulation
9 / 573

10. Liver tissue structure
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
B
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
Central vein
Sinusoid
Portal vein branch
Bile duct tributary
Liver artery branch
A–C reproduced with permission from pathorama.ch.
10 / 573

11. Blood flow and bile flow within the liver lobule
Liver artery branch
Portal vein branch
Bile duct tributary
Liver vein tributary
11 / 573

12. The stomach: functions of gastric acid
◮ HCl, pH 1–2
◮ secreted by specialized cells in the mucous membrane (parietal cells)
◮ kills germs contained in food; patients with lack of gastric acid are at increased
risk of intestinal infection
◮ denatures food proteins and makes them accessible to cleavage by proteases
12 / 573

13. Gastric acid and pepsin in protein digestion
13 / 573

14. Function of the exocrine pancreas
◮ secretion of digestive enzymes
◮ amylase
◮ proteases, peptidases
◮ lipases
◮ DNAse, RNAse
◮ secretion of sodium bicarbonate to neutralize gastric acid
14 / 573

15. Roles of bile in digestion
◮ Bile acids solubilize triacylglycerol and make it accessible to pancreatic lipase
◮ Bicarbonate contributes to the neutralization of gastric acid
15 / 573

16. The small intestine
16 / 573

17. Microscopic structure of the small intestine
Left panel with permission from pathorama.ch. Right panel with permission from
http://www.udel.edu/Biology/Wags/histopage/histopage.htm.
17 / 573

18. Amylose and amylopectin are polymers of α-d-glucose
O. . .
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
. . .
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
. . .
18 / 573

19. Amylase breaks down starch to maltose and isomaltose
OH
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
H
OH
OH
OH
CH2O
OH
OH
CH2OH
O
O
H
O
O
H
Maltose Isomaltose
19 / 573

20. Mechanism of glucose uptake from the gut
Gut lumen Cytosol Interstitial fluid
Glucose Glucose Glucose
2 Na+
2 Na+
SGLT1 GLUT2
20 / 573

21. The large intestine
◮ Anaerobic milieu—99% of all bacteria in the large intestine are strict anaerobes
◮ Bacteria degrade non-utilized foodstuffs, reducing osmotic activity of gut
content
◮ Mucous membrane recovers water and electrolytes
◮ Bacterial metabolism releases potentially toxic products (e.g. ammonia), which
are taken up and inactivated by the liver
21 / 573

22. A metabolic map for
Chem 333
UDP-Galactose UDP-Glucose Glycogen
Galactose Galactose-1-P Glucose-1-P 6-P-Gluconate Ribulose-5-P
Lactose Glucose Glucose-6-P
Sucrose Amylose Fructose-6-P Erythrose-4-P Xylulose-5-P
Fructose Fructose-1,6-bis-P Sedoheptulose-7-P
Fructose-1-P Glyceraldehyde Glyceraldehyde-3-P Ribose-5-P
1,3-bis-P-Glycerate
3-P-Glycerate
2-P-Glycerate
Phosphoenol-
pyruvate
Pyruvate
Acetyl-CoA
CO2
Oxaloacetate
Malate
Fumarate
Succinate
Citrate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
HMG-CoA
Acetoacetate
Malonyl-CoA
Fatty acyl-CoA
Glycerol-P
Hydroxybutyrate
Triacylglycerol
Fatty acids
Glycerol
Cholesterol
Glutamate
Glutamine
Arg
His
Pro
Leu
Lys
Phe
Trp
Tyr
Ile
Met
Thr
Val
Ala
Cys
Ser
Gly
Phe
Tyr
H2
CO2
CO2
H2O
O2 ADP + Pi
ATP
Citrulline Asp
Argininosuccinate
Arginine
Ornithine
Carbamoyl-P
CO2
NH3
22 / 573

23. A more realistic metabolic map
23 / 573

24. Chapter 2
Refresher
24 / 573

25. The “catalytic triad” in the active site of chymotrypsin
O
H
N
N
H ⊖
O O
Asp102
His57
Ser195
25 / 573

26. The catalytic mechanism of chymotrypsin
N′
R1
C
O
H
N
R2
C′
O⊖
Ser195
N′
R1
C
O⊖
O
Ser195
H
N
R2
C′
N
Asp102
O
H
O
His57
N
H
H
N
Asp102
O⊖
O
His57
N
N′
R1
C
O H2N
R2
C′
O
Ser195
26 / 573

27. IUBMB classification of enzymes
Enzyme class Catalyzed reactions
oxidoreductases catalyze redox reactions, frequently involving one
of the coenzymes NAD+
, NADP+
, or FAD
transferases transfer functional groups between metabolites,
e.g. a phosphate from ATP to a sugar hydroxyl
group
hydrolases catalyze hydrolysis reactions, such as those in-
volved in the digestion of foodstuffs
lyases perform elimination reactions that result in the
formation of double bonds
isomerases facilitate the interconversion of isomers
ligases form new covalent bonds at the expense of ATP
hydrolysis
27 / 573

28. A simile: the Walchensee–Kochelsee hydroelectric power system
28 / 573

29. Analogies in the simile
Hydroelectric system Metabolic pathway
altitude energy
difference in altitude between
lakes
energy difference between
metabolites (∆G)
height of ridge between lakes ∆G∗
of uncatalyzed reaction
tunnels enzymes
tunnel barrages regulatory switches of
enzymes
29 / 573

30. Discrepancies in the simile
Hydroelectric system Metabolic pathway
all tunnels work the same way enzymes have different catalytic
mechanisms
potential energy determined
by one parameter: altitude
free energy of metabolites depends
on two parameters: ∆H and ∆S
water always collects at the
bottom
molecules partition between lower
and higher energy levels
30 / 573

31. The catalytic mechanism of glutamine synthetase
O
C
−O
C
H
NH2
C
H2
C
H2
C
O
O⊖
Adenosine
O
P
O
O−
O
P
O
O−
O
P
O
O−
−O
ADP
O
C
−O
C
H
NH2
C
H2
C
H2
C
O
O P
O
O−
O−
O
C
−O
C
H
NH2
C
H2
C
H2
C
O
NH2
NH3
Pi
Glutamate
Glutamyl-5-phosphate Glutamine
31 / 573

32. The phosphofructokinase reaction
O
P
O O−
O−
O
OH
O
H
OH
CH2OH O
P
O O−
O−
O
OH
O
H
OH
O
P
O O−
O−
ATP
ADP
Fructose-6-phosphate Fructose-1,6-bisphosphate
32 / 573

33. The adenylate kinase reaction equilibrates AMP, ADP and ATP
2ADP ATP + AMP
K =
[ATP] [AMP]
[ADP]2 ⇐
⇒ [AMP] = [ADP]2 K
[ATP]
[AMP]
[ADP]
33 / 573

34. Allosteric regulation of phosphofructokinase by AMP
34 / 573

35. How allosteric regulation works
35 / 573

36. Enzyme regulation by protein phosphorylation
36 / 573

37. Oligomeric enzymes behave cooperatively
0
25
50
75
100
0 25 50 75 100
Reaction
velocity
Ligand concentration
37 / 573

38. Substrate cycles can amplify molecular regulation mechanisms
A
B
C
A
B
C
A
B
C
E
A
B
C
E
(a) (b)
38 / 573

39. Regulation of enzyme molecule abundance
◮ transcriptional induction
◮ accelerated mRNA degradation
◮ ubiquitin ligation, followed by proteolytic degradation
39 / 573

40. Chapter 3
Glycolysis
40 / 573

41. Overview of glucose metabolism
Pathway Function
glycolysis, citric acid
cycle, respiratory chain
complete degradation of glucose for ATP
production
hexose monophosphate
shunt
degradation of glucose for regeneration
of NADPH
glycogen synthesis and
degradation
short-term glucose storage
gluconeogenesis synthesis of glucose from amino acids,
lactate, or acetone
41 / 573

42. The place of glycolysis in glucose degradation
glucose pyruvate
acetyl-CoA fatty acids
triacylglycerol
“H2”
H2O
mitochondrion
glycolysis
CO2
pyruvate
dehydrogenase CO2
citric acid cycle
O2 ADP + Pi
ATP
respiratory chain
42 / 573

43. Alternate structures of d-glucose
OH
OH
OH
CH2OH
O
O
H
O
OH
OH
CH2OH
OH
O
H
OH
OH
OH
CH2OH
O
O
H
α-d-Glucose Aldehyde form β-d-Glucose
43 / 573

44. Reactions in glycolysis
OH
OH
OH
CH2OH
O
O
H OH
OH
OH
O
P
O O−
O−
O
O
H
O
P
O O−
O−
O
OH
O
H
OH
CH2OH O
P
O O−
O−
O
OH
O
H
OH
O
P
O O−
O−
1
ATP ADP
2
ATP ADP
3
4
Glucose Glucose-6- P Fructose-6- P Fructose-1,6-bis- P
OH
O
O P
O
O−
O−
O
OH
O P
O
O−
O−
5
O
P
O O−
O−
O
OH
O P
O
O−
O−
6
Pi
NAD+
NADH+H+
COO−
OH
O P
O
O−
O−
ADP
ATP
7
3-Phosphoglycerate
1,3-Bisphosphoglycerate Glyceraldehyde-3- P Dihydroxyacetone- P
8
COO−
O P
O
O−
O−
OH
H2O
9
COO−
O P
O
O−
O−
CH2
ADP ATP
10
COO−
O
CH3
NADH+H+
NAD+
11
COO−
OH
CH3
2-Phosphoglycerate Phosphoenolpyruvate Pyruvate Lactate
44 / 573

45. The phosphate groups in ATP are shielded from nucleophilic
attack
O
OH
N N
N
NH2
N
OH
P
O
⊖O
O
P
O
⊖O
O
⊕
P
O
⊖O
⊖
O
X⊖
R
. . . and therefore, phosphate group transfer needs assistance from enzymes.
45 / 573

46. The catalytic mechanism of hexokinase
O Adenosine
P
O
O
⊖
⊕
NH2
H
N
H
N
Arg
O
P
O
O
⊖
Mg2+
O
P
O
X⊖
R
O
⊖
O
⊖
⊕
H3N
Lys
R X P
O
O−
O− −O P
O
O−
O P
O
O−
Adenosine
46 / 573

47. Hexokinase envelopes its substrates to prevent ATP hydrolysis
OH
OH
OH
H2C OH
O
O
H
Glucose
OH
OH
OH
H OH
O
O
H
Xylose
47 / 573

48. Phosphohexose isomerase performs acid-base catalysis
O
P
O
H
OH H
OH
O H ⊖OH
⊕NH3
Lys
H
⊕
N
His
N
OH
P
O
H
OH H
OH
O H OH
⊕NH3
Lys
N
His
N
OH
P
O
H
OH
OH
H ⊖O O
Glu
O
H⊕
OH
P
O
H
OH
O
H
H O O
Glu
OH
OH
P
O
H
OH
O
H
C
H
OH
O
P
O
H
OH
OH
CH2OH
48 / 573

49. Glyceraldehyde-3-phosphate dehydrogenase carries out covalent
catalysis
Cys
S
H
N
His
N
Cys
S⊖ O H
⊕
H
R
Cys
S
H
⊕NAD
R
O H B
Cys
S
⊕
H O
⊖O P
O
O−
O−
R
Cys
S
H
O
R
O P
O
O−
O−
NADH
49 / 573

50. Structure and redox chemistry of NAD+
and NADP+
O O
OH
⊕
N
NH2
O
OH
P O
−O
O
P O
−O
O O
O X
N N
N
NH2
N
OH
P
O
O−
O−
NAD: X = H NADP: X =
R
⊕
N
NH2
O
R
H
O
H
S
Cys
R
N
NH2
O
H
H
R
O
H⊕
S
Cys
50 / 573

51. Pyruvate Kinase
O
OH
N N
N
NH2
N
OH
O
P
O
O−
O
P
O
O−
O
⊖
O−
P
O
−O
O
⊕H
O
O−
CH2
H
O
O
O−
CH2
⊕H
O
O
O−
CH3
51 / 573

52. Energy-rich functional groups in substrates of glycolysis
◮ the enolphosphate in PEP
◮ the carboxyphosphate in 1,3-bisphosphoglycerate
◮ the thioester in the active site of glyceraldehyde-3-dehydrogenase
52 / 573

53. Regeneration of cytosolic NAD+
under aerobic conditions
Glyceraldehyde-3- P 1,3-Bis- P -glycerate
NAD+
NADH + H+
Carrier
Carrier-H2
1/2 O2 H2O Mitochondrion
53 / 573

54. Under anaerobic conditions, NAD+
is regenerated by lactate
dehydrogenase
Glyceraldehyde-3- P 1,3-Bis- P -glycerate
NAD+
NADH + H+
COO−
H OH
CH3
COO−
O
CH3
Lactate Pyruvate
54 / 573

55. Ethanolic fermentation in yeast serves a dual purpose
Glyceraldehyde-3- P 1,3-Bis- P -glycerate
NAD+
NADH + H+
H2C OH
C
CH3
HC O
C
CH3
COO−
O
CH3
Ethanol Pyruvate
CO2
Acetaldehyde
55 / 573

56. Kinetics of glucose transport by facilitated diffusion
Vtransport = Vmax
[S]
KM + [S]
56 / 573

57. GLUT transporters in different tissues vary in their affinity for
glucose
0
25
50
75
100
0 2 4 6 8 10
Transport
rate
(%
of
max)
Glucose (mM)
GLUT2 (liver)
GLUT4 (muscle, fat)
GLUT3 (brain)
57 / 573

58. Reaction velocities of hexokinase and glucokinase
0
25
50
75
100
0 2 4 6 8 10
Reaction
velocity
(%)
Glucose (mM)
Glucokinase (liver)
Hexokinase (other tissues)
58 / 573

59. Chapter 4
Catabolism of sugars other than glucose
59 / 573

60. Dietary sugars other than glucose
Trivial name Composition Source
lactose (milk sugar) disaccharide of glucose
and galactose
milk
sucrose disaccharide of glucose
and fructose
sugar cane, sugar
beet, other fruits
fructose monosaccharide various fruits
sorbitol sugar alcohol fruits; semisyn-
thetic
ribose, deoxyribose monosaccharides nucleic acids
60 / 573

61. Degradation of fructose and sucrose
CH2OH
O
OH
O
H
OH
CH2OH O
OH
OH
CH2OH
O
O
H
CH2OH
O
OH
O
H
CH2OH
fructose α-d-glucosyl-(1,2)-β-d-fructoside (sucrose)
61 / 573

62. The fructolysis pathway
CH2OH
O
OH
O
H
OH
CH2OH
CH2OH
O
OH
O
H
OH
CH2
O
P
O O−
O−
O P
O
O−
O−
O
OH
O
OH
OH
O
OH
O P
O
O−
O−
ATP ADP
ATP ADP
Fructose Fructose-1- P
Dihydroxyacetone- P
Glyceraldehyde Glyceraldehyde-3- P
1 2
3
4
62 / 573

63. Fructose intolerance
Fructose Fructose-1- P Glyceraldehyde
ATP ADP
Dihydroxyacetone- P
Glyceraldehyde-3- P
3- P -glycerate 1,3-Bis- P -glycerate Pi
Fructokinase Aldolase B
PG-kinase
NADH+H+
NAD+
63 / 573

64. Lactose and galactose
OH
OH
OH
CH2OH
O
HO OH
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
HO
β-d-galactose β-d-galactosyl-(1 4)-d-glucoside (lactose)
64 / 573

65. The Leloir pathway for galactose utilization
Lactose Galactose
Glucose Galactose-1- P UDP-Glucose
Glucose-6- P Glucose-1- P UDP-Galactose
Gal-1- P uridyltransferase
. . .
Lactase
Galactokinase
UDP-Gal epimerase
Phosphogluco-
mutase
Glycolysis
65 / 573

66. Mechanism of UDP-galactose epimerase
O
OH
OH
CH2OH
O
HO
P
O
O−
O P
O
O−
O
O
OH
N O
NH
O
O
OH
OH
CH2OH
O
O
P
O
O−
O P
O
O−
O
O
OH
N O
NH
O
O
OH
OH
CH2OH
O
HO P
O
O−
O P
O
O−
O
O
OH
N O
NH
O
UDP-Galactose
UDP-Glucose
66 / 573

67. Lactose intolerance
67 / 573

68. Galactosemia
Type Enzyme deficiency Accumulating metabolites
I galactose-1-phosphate-
uridyltransferase
galactose, galactose-1-phosphate,
galactitol, galactonate
II galactokinase galactose, galactitol
III UDP-galactose epimerase galactose-1 phosphate, UDP-
galactose
sorbitol pathway
68 / 573

69. Sorbitol is an intermediate of the polyol pathway
aldose
reductase
sorbitol
dehydrogenase
O
OH
O
H
OH
OH
OH
OH
OH
O
H
OH
OH
OH
OH
O
O
H
OH
OH
OH
NADPH+H+
NADP+
NAD+
NADH+H+
glucose sorbitol fructose
69 / 573

70. Chapter 5
Pyruvate dehydrogenase and the citric acid cycle
70 / 573

71. Pyruvate degradation occurs in the mitochondria
Glucose Pyruvate
Pyruvate
Cytosol
Mitochondria
Acetyl-CoA
CO2
Oxaloacetate
Malate
Fumarate
Succinate
Citrate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
H2
CO2
CO2
H2O
O2 ADP + Pi
ATP
H+
H+
71 / 573

72. The PDH reaction occurs in three successive steps that are
catalyzed by three different subunits
O OH
O
C
H3
CoA
S
O
C
H3
CO2
E1
CoA–SH
E2
NAD+
NADH + H+
E3
72 / 573

73. The structural organization of the E. coli PDH complex
E2 E2 + E1 E2 + E1 + E3
73 / 573

74. A lipoamide tether guides the substrate from one active site to
the next
NH
O
S
O
S
H
E2
E1 E3
74 / 573

75. The pyruvate dehydrogenase reaction involves multiple
coenzymes
Coenzyme Subunit Role in catalysis
thiamine pyro-
phosphate
E1 provides a carbanion for nucleophilic
attack on the substrate
lipoamide E2 transfers substrate to coenzyme A,
retains hydrogen
flavin adenine di-
nucleotide (FAD)
E3 transfers H2 from lipoamide to NAD+
75 / 573

76. Thiamine pyrophosphate forms a carbanion
Asp
O
O
H
N
H
N
H
⊕
N
H
S P
P
N
Asp
O
O⊖
N N
H
⊕
N
H
S P
P
N
H
N NH2
⊕
N
⊖ S P
P
N
76 / 573

77. Decarboxylation of pyruvate by E1
R1
⊕
N
⊖
C
O
H⊕
CH3
C
⊖O
O
S
R2
R1
⊕
N
C
O
H
CH3
C
O
⊖
O
S
R2
R1
⊕
N
⊖C
O
H
CH3
C
O
O
S
R2
77 / 573

78. Release of acetyl-CoA and disposal of hydrogen
R1
⊕
N
C
⊖
O
H
CH3
S
S
⊕
H
S
R2
S
CH3
O
H
S
S
C
H3 O
S⊖
A
Co
H
⊕
SH
H
S
H
S
S
O
C
H3
CoA
FAD
FADH2
NADH+H+
NAD+
E1
E2
E3
78 / 573

79. Alternate metabolic destinations of pyruvate
1. Conversion to acetyl-CoA by PDH for complete degradation or for synthesis of
fatty acids and cholesterol
2. Carboxylation to oxaloacetate, for use in gluconeogenesis or in the citric acid
cycle
3. Synthesis of amino acids, e.g. transamination to alanine
4. Reduction to lactate
79 / 573

80. Regulation of PDH by allosteric effectors and by phosphorylation
Fructose-1,6-bis- P CoA-SH, NAD+
, pyruvate Acetyl-CoA, NADH
PDH
PDH- P
kinase phosphatase
Ca++
in E. coli
Catalysis
Activation
Inhibition
80 / 573

81. The overall reaction of the TCA cycle: does it add up?
CH3COOH 2 CO2 + 4 H2
2 H2O + CH3COOH 2 CO2 + 4 H2
cycle
81 / 573

82. The citrate synthase reaction
Citrate Citryl-CoA
Oxaloacetate
Acetyl-CoA
CoA
S O H
⊕
N
N
His274
H
H
H
⊖
O
O
Asp375
CoA
S O H N
N
His274
CH2
O
H
N
⊕
N
His320
COO−
H2
C
−OOC
CoA
S O
CH2
COO−
OH
C
H2
−OOC
HO O
CH2
COO−
OH
C
H2
−OOC
H2O
CoA-SH
82 / 573

83. Reactions in the TCA cycle: from citrate to succinyl-CoA
Citrate
H2C COO−
C
O
H COO−
H2C COOH
H2O H2C COO−
C COO−
HC COOH
H2O
Isocitrate
H2C COO−
HC COO−
C
H
O
H COOH
NAD+
NADH+H+
H2C COO−
HC COO−
C
O COOH
H+
CO2
α-Ketoglutarate
H2C COO−
CH2
C
O COOH
CoA-SH
NAD+
CO2
NADH+H+
Succinyl-CoA
H2C COO−
CH2
C
O S
CoA
83 / 573

84. Reactions in the TCA: from succinyl-CoA to oxaloacetate
Succinyl-CoA
H2C COO−
CH2
O S
CoA
Pi
CoA-SH
H2C COO−
CH2
O O
P O
−O
O−
Succinate
H2C COO−
CH2
O O−
GDP GTP
Fumarate
H COO−
H
−OOC
FAD
FADH2
H2O
O
H COO−
H
−OOC
Malate
NAD+
NADH+H+
O COO−
H
−OOC
Oxaloacetate
84 / 573

85. α-Ketoglutarate dehydrogenase resembles PDH
E1
E2
E3
Pyruvate
CO2
CoA-SH
Acetyl-CoA
NAD+
NADH+H+
E1
E2
E3
α-Ketoglutarate
CO2
CoA-SH
Succinyl-CoA
NAD+
NADH+H+
85 / 573

86. Regulation of the citric acid cycle
◮ ATP and NADH inhibit isocitrate dehydrogenase
◮ NADH inhibits α-ketoglutarate dehydrogenase
◮ High levels of NADH will lower the oxaloacetate concentration, which limits
citrate synthase activity
86 / 573

87. Chapter 6
The respiratory chain
87 / 573

88. Overview of the respiratory chain
I
II
Q
III
C
IV
ADP + Pi
ATP
H⊕ H⊕ H⊕
H⊕
⊖
⊖ ⊖
⊖
NADH
NAD⊕+H⊕
FADH2
FAD+2H⊕
2H⊕+ 1
2 O2
H2O
AS
88 / 573

89. Functional stages in the respiratory chain
1. H2 is abstracted from NADH+H+
and from FADH2
2. The electrons obtained with the hydrogen are passed down a cascade of carrier
molecules located in complexes I–IV, then transferred to O2
3. Powered by electron transport, complexes I, III, and IV expel protons across the
inner mitochondrial membrane
4. The expelled protons reenter the mitochondrion through ATP synthase, driving
ATP synthesis
89 / 573

90. Uncoupling proteins dissipate the proton gradient
H⊕ H⊕ H⊕
H⊕
⊖
⊖ ⊖
⊖
90 / 573

91. The uncoupling action of dinitrophenol
O⊖
NO2
NO2
H⊕
OH
NO2
NO2
O⊖
NO2
NO2
H⊕
OH
NO2
NO2
Cytosol Mitochondrial matrix
91 / 573

92. The Racker experiment: bacteriorhodopsin can drive ATP
synthase
H⊕ H⊕
H⊕ H⊕
ADP+Pi
ATP
H⊕
H⊕
H⊕
H⊕
H⊕
92 / 573

93. Molecules in the electron transport chain
Complex I Complex II Complex III Complex IV
cytochrome C
Q
Cytoplasmic side
Mitochondrial matrix
93 / 573

94. Iron-containing redox cofactors
Fe2⊕
N
N⊖
O
O
H
N
O
O
H
⊖
N
Heme Iron-sulfur cluster
94 / 573

95. Flavin-containing redox cofactors
H3C N
O
NH
O
N
N
OH
OH
OH
OH
O P
O
O−
O X
C
H3
H3C N
H
O
NH
O
H
N
N
R
C
H3
H3C N
O
NH
O
H
N
N
R
C
H3
X = H : FMN
X = AMP : FAD
FMNH/FADH
FMNH2/FADH2
95 / 573

96. The respiratory chain generates reactive oxygen species as
by-products
N
O
NH
O
H
N
N
R
N
O
NH
O
N
N
R
O2 O2
–•
H+
O
O
. . .
O−
O
O
O
. . .
O
O
O2 O2
–•
FAD/FMN
coenzyme Q
96 / 573

97. Redox reactions can be compartmentalized to produce a
measurable voltage
V
1
2 H2 H⊕
e⊖
Q Q⊖
e⊖
V
H2 2H⊕
2e⊖
H⊕
+NAD⊕ NADH
2e⊖
∆E > 0 ∆E < 0
97 / 573

98. Energetics of electron transport
◮ Each electron transfer step along the chain is a redox reaction: the first cofactor
is oxidized and the second one is reduced
◮ In a redox reaction, electrons flow spontaneously if the reduction potential
increases in the forward direction (∆E > 0)
◮ Redox reactions, like other reactions, proceed spontaneously if their free energy
is negative (∆G < 0)
How is the reduction potential of a redox reaction related
to its free energy?
98 / 573

99. The redox potential (∆E) is proportional to the free energy (∆G)
∆G ≡
energy
moles (number of molecules)
∆E ≡
energy
charge transferred
∆G =
energy
charge transferred
×
charge transferred
moles
∆G = ∆E ×
charge transferred
moles
therefore
∆G = −∆E × n × F
99 / 573

100. Redox potentials and free energies in the respiratory chain
I
III
IV
NADH FMN
(Fe-S)N-2
CoQ
Heme c1 CytC
Heme a3
O2
FADH2
−0.4
0
0.4
0.8
75
0.0
−75
−150
∆E
′
0
(V)
∆G
(
KJ
/
2
mol
electrons
)
100 / 573

101. The first two redox steps in complex I
NADH + H+
+ FMN NAD+
+ FMNH2
FMNH2 + FeIII
– S FMNH•
+ H+
+ FeII
– S
FMNH•
+ FeIII
– S FMN + H+
+ FeII
– S
101 / 573

102. The reduction of coenzyme Q involves protons and electrons
O
O
O
O
e⊖
O
O
. . .
O⊖
O
2H⊕
e⊖ O
OH
. . .
OH
O
2H⊕ 2e⊖
Q
Q⊖ QH2
102 / 573

103. The Q cycle (criminally simplified)
QH2
Q e⊖
–
Q
Q
QH2
cytochrome C
to complex IV
2H⊕
QH2
Q⊖
2H⊕
–
Q
QH2
to complex IV
2H⊕
B
A
B
A
B
A
B
A
103 / 573

104. Reduction of oxygen by cytochrome C oxidase (complex IV)
O
2+
O
1+
O−
3+
O−
2+
e⊖
H⊕
O2−
4+
OH−
2+
H⊕
e⊖
OH−
3+
OH−
2+
2H⊕
H2O
3+
2+
2e⊖
2+
1+
O2
104 / 573

105. How is electron transport linked to proton pumping?
◮ Some redox steps in the ETC are coupled to proton binding and dissociation,
which may occur at opposite sides of the membrane. Example: Coenzyme Q
cycle at complex III
◮ Redox steps that do not involve hydrogen directly need a different mechanism
in order to contribute to proton pumping. Example: Sequence of iron-sulfur
clusters and hemes in complex IV
105 / 573

106. Linking electron movement to proton pumping: A conceptual
model
106 / 573

107. Proton pumping creates both a concentration gradient and a
membrane potential
∆Gconcentration = RT × ln K = 6
kJ
mol
∆Gpotential = ∆ψ × n × F = 15
kJ
mol
107 / 573

108. Structure of ATP synthase
α β
γ
c c
a
b1
δ
F0
proton flow
Rotation of γ
and F0 subunits
108 / 573

109. The binding-change model of ATP synthase catalysis
ADP Pi
ATP
ATP
γ γ
γ
109 / 573

110. How does proton flux drive ATP synthase?
110 / 573

111. Proton flux causes c chains to rotate within the F0 disk
111 / 573

112. A hypothetical malate-oxaloacetate shuttle
cytosol mitochondrial matrix
malate malate
oxaloacetate oxaloacetate
NAD+
NADH+H+
NAD+
NADH+H+
shuttles overview
112 / 573

113. The malate-aspartate shuttle
cytosol
H+
glutamate
aspartate
α-ketoglutarate
malate
oxaloacetate
NAD+
NADH+H+
mitochondrial matrix
H+
glutamate
aspartate
α-ketoglutarate
malate oxaloacetate
NADH+H+
NAD+
1 1
2 2
113 / 573

114. The glycerophosphate shuttle
outer membrane inner membrane
Glycerophosphate Glycerophosphate
DHAP DHAP
NAD+
NADH+H+
FADH2
FAD QH2
Q
GPD
114 / 573

115. The two mitochondrial isocitrate dehydrogenases
Isocitrate
α-Ketoglutarate
NADP+
NADPH+H+
CO2
NAD+
NADH+H+
CO2
115 / 573

116. Nicotinamide nucleotide transhydrogenase couples hydrogen
transfer with proton transport
H+
NADP+
NADPH + H+
NAD+
NADH + H+
116 / 573

117. At rest, transhydrogenase and the two isocitrate dehydrogenases
form a futile cycle
transhydrogenase
H+
NAD-dependent
dehydrogenase
α-ketoglutarate + CO2
NAD+
NADH
NADP-dependent
dehydrogenase
isocitrate
NADP+
NADPH
117 / 573

118. When ATP demand is high, transhydrogenase turns into an
auxiliary proton pump
transhydrogenase
H+
NAD-dependent
dehydrogenase
α-ketoglutarate + CO2
NAD+
NADH
NADP-dependent
dehydrogenase
isocitrate
NADP+
NADPH
respiratory
chain
118 / 573

119. Theoretical ATP yield per molecule of glucose completely
oxidized
Quantity Intrinsic value Per glucose
Accrued hydrogen 10 NADH, 2 FADH2
Protons ejected 10 per NADH, 6
per FADH2
112
Proton-powered ATP
synthase revolutions
10 protons per
revolution
11.2
ATP from ATP synthase 3 per revolution 33.6
ATP from glycolysis 2
GTP from TCA cycle 2
Total 37.6
119 / 573

120. Processes other than ATP synthesis that are powered by the
proton gradient
◮ Nicotinamide nucleotide transhydrogenase
◮ Uncoupling proteins; proton leak
◮ Secondary active transport:
◮ ATP4 –
/ADP3 –
antiport
◮ phosphate/H+
symport
◮ amino acid/H+
symport
◮ pyruvate/H+
symport
120 / 573

121. Chapter 7
Gluconeogenesis
121 / 573

122. Glucose is an indispensable metabolite
◮ The brain requires at least ~50% of its calories in the form of glucose
◮ Red blood cells exclusively subsist on glucose
◮ Glucose is a precursor of other sugars needed in the biosynthesis of
nucleotides, glycoproteins, and glycolipids
◮ Glucose is needed to replenish NADPH, which supplies reducing power for
biosynthesis and detoxification
122 / 573

123. Overview of
gluconeogenesis
Glucose
Glucose-6- P
Fructose-6- P
Fructose-1,6-bis- P
Glyceraldehyde-3- P
P -enolpyruvate
Pyruvate
Acetyl-CoA
α-Ketoglutarate
Succinyl-CoA
Fumarate
Oxaloacetate
Lactate
Acetone
Glycerol
Amino acids
123 / 573

124. The pyruvate carboxylase reaction
H3C C
O
C
O
OH
C
O
O
H
CH2 C
O
C
O
OH
CO2
ATP ADP + Pi
124 / 573

125. The active site of E. coli biotin carboxylase
Biotin
Arg338 Glu296
HCO–
3 Mg2+
Arg292
ADP
125 / 573

126. Activation of bicarbonate
O
H2N⊕
N
H
Arg
NH2
N
H
R S
N H O P
O
O
H
⊖O O
ADP
⊖O
O
H
⊖O O
Glu
O
H2N⊕
N
H
Arg
NH2
N
H
R S
N H O P O
OH
O⊖
⊖O
O
HO O
Glu
126 / 573

127. The carboxylation of biotin
O
H2N⊕
N
H
Arg
NH2
N
H
R S
N H O P O
OH
O⊖
⊖O
O
HO O
Glu
O⊖
H2N⊕
N
H
Arg
NH2
N
H
R S
N O P O
OH
O⊖
O
H
O
HO O
Glu
O
NH2⊕
N
H
Arg
NH2
N
H
R S
N ⊖O
O
O
H
Glu
P
OH
O
O⊖
O
OH
127 / 573

128. The carboxylation of pyruvate
O O
⊖O
O
H
O
N
O
NH
O
⊖O O
O
OH
R
S
O
H
CH2
⊖O O H⊕
CH2
H
128 / 573

129. The phosphoenolpyruvate carboxykinase reaction
O
O
⊖
O
O
OH
CO2
H2C
⊖O
O
P
O
H
O⊖
O GDP
O
OH
GDP
H2C
O
P
⊖O
OH
O
O
OH
129 / 573

130. Fructose-1,6-bisphosphatase and glucose-6-phosphatase
Fructose-1,6-bisphosphate + H2O Fructose-6-phosphate + Pi
Glucose-6-phosphate + H2O Glucose + Pi
130 / 573

131. Energy balance of gluconeogenesis
Reaction ATP/GTP input
2 pyruvate 2 oxaloacetate 2
2 oxaloacetate 2 PEP 2
2 3- P -glycerate 2 1,3-bis- P -glycerate 2
Total 6
131 / 573

132. Mitochondrial substrate transport in gluconeogenesis
ATP
ADP
Pi
malate
oxaloacetate
pyruvate
ATP
ADP
Pi
malate
oxaloacetate
pyruvate
CO2 ATP
ADP+Pi
NADH+H+
NAD+
NADH+H+
NAD+
H+
H+
Cytosol Mitochondria
pyruvate
carboxylase
malate
dehydrogenase
dicarboxylate
transporter
ATP synthase
132 / 573

133. Ethanol degradation inhibits gluconeogenesis
ethanol
acetaldehyde
acetate
acetyl-CoA
malate
lactate
oxaloacetate
pyruvate
glucose
NADH+H+
NAD+
133 / 573

134. Simultaneous activity of glycolysis and gluconeogenesis creates
futile cycles
glucose
glucose-6- P
ATP
ADP
Pi
H2O
fructose-6- P
fructose-1,6-bis- P
ATP
ADP
Pi
H2O
ADP
ATP
ADP+Pi
ATP+CO2
GDP + CO2
GTP
oxaloacetate PEP
pyruvate
134 / 573

135. Glucose phosphorylation cycling involves two separate
compartments
Glucose Glucose
Glucose-6- P Glucose-6- P
Hexokinase
Glucose-6-
phosphatase
Cytosol
Endoplasmic reticulum
ATP
ADP+Pi
H2O
Pi
135 / 573

136. Allosteric regulation limits fructose-6-phosphate phosphorylation
cycling
Fructose-6- P
ATP
AMP
Fructose-2,6-bis- P
Fructose-1,6-bis- P
Pi
H2O
ATP
ADP
Phosphofructokinase
Fructose-1,6-
bisphosphatase
substrate cycling
136 / 573

137. The level of fructose-2,6-bisphosphate is controlled by hormones
Epinephrine, glucagon Insulin
Adenylate cyclase Phosphodiesterase
ATP cAMP AMP
Protein kinase A
PFK 2/F-2,6-bis-P’ase PFK 2/F-2,6-bis-P’ase
Fructose-2,6-bis- P
Fructose-6- P
137 / 573

138. The secondary messengers cAMP and fructose-2,6-bisphosphate
O
O
OH
N N
N
NH2
N
P
O
O−
O
O
P
O O−
O−
O
OH
O
H
O P
O
O−
O−
CH2OH
cyclic 3′,5′-AMP (cAMP) fructose-2,6-bisphosphate
138 / 573

139. Regulation of pyruvate kinase
◮ allosteric activation by fructose-1,6-bisphosphate
◮ allosteric inhibition by ATP and alanine
◮ inhibition by PKA-mediated phosphorylation
139 / 573

140. Chapter 8
Glycogen metabolism
140 / 573

141. Why store glucose in polymeric form?
◮ The osmotic pressure is governed by the gas equation:
pV = nRT ⇐
⇒ p =
n
V
RT
◮ Glycogen amounts to 10% of the liver’s wet weight, equivalent to 600 mM
glucose
◮ When free, 600 mM glucose would triple the osmotic activity of the
cytosol—liver cells would swell and burst
◮ Linking 2 (3, . . . ) molecules of glucose divides the osmotic effect by 2 (3, . . . ),
permitting storage of large amounts of glucose at physiological osmolarity
141 / 573

142. Covalent structure of glycogen
O Glycogenin
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
. . .
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
. . .
142 / 573

143. The size of glycogen particles is limited by crowding in the outer
layers
0 5 10 15
Layer
volume
Layer generation
available
required
143 / 573

144. Glycogen is more loosely packed and more soluble than amylose
Glycogen Amylose
144 / 573

145. Life cycle of glycogen
Synthesis:
1. synthesis of an activated precursor, UDP-glucose, by UTP:glucose-1-phosphate
uridylyltransferase
2. initiation of glycogen synthesis by glycogenin
3. introduction of branches by branching enzyme
4. chain elongation by glycogen synthase
5. repeat steps 3 and 4
Degradation:
1. depolymerization of linear strands by phosphorylase
2. removal of branches by debranching enzyme
3. repeat steps 1 and 2
145 / 573

146. Activation of glucose for glycogen synthesis
OH
OH
OH
O
P
O O−
O−
O
O
H O P
O
O−
O−
OH
OH
CH2OH
O
O
H
O
P
O
O−
O
P
O
O−
O
P
O
O−
−O
O
OH
N O
NH
O
OH
O
P
O
O−
O
P
O
O−
O
OH
OH
CH2OH
O
O
H
O
OH
N O
NH
O
OH
O−
P
O
O−
O
P
O
O−
−O
Glucose-6-phosphate
Glucose-1-phosphate
UTP
Pyrophosphate
UDP-glucose
1
2
146 / 573

147. Overview of glycogen synthesis
Glycogenin
Branching enzyme
Glycogen synthase
HO Gg
UDP-Glc
UDP
UDP-Glc
UDP
UDP-Glc
UDP
. . .
O Gg
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
O Gg
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
UDP-Glc
UDP
. . .
UDP-Glc
UDP
. . .
147 / 573

148. A hypothetical reaction mechanism of glycogen synthase
O
P
O O−
O
P
O O−
O
O
⊖ O
Glu
O
H
OH
CH2OH
O
O
H
O
OH
N O
NH
O
OH
O O
Glu
O
H
OH
CH2OH
O
O
H
. . .
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
⊖
UDP
. . .
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
H
148 / 573

149. An alternative glycogen synthase mechanism
O
P
O O−
O
P
O O−
O
O
H
OH
CH2OH
O
O
H
O
OH
N O
NH
O
OH
X
P
O O−
O
P
O O−
O⊖
δ+
O
H
OH
CH2OH
Oδ+
O
H
O
OH
N O
NH
O
OH
. . .
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
H
. . .
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
H
UDP
149 / 573

150. Overview of glycogen degradation
O Gg
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Pi
Glc-1- P Pi
Glc-1- P
O Gg
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
O Gg
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
Glc
H2O
Glc
phosphorylase
debranching enzyme
150 / 573

151. The reaction mechanism of phosphorylase
HO
O
H
OH
O
Glycogen
H
O
P
−O
O−
O
H
O
P
O
O
N
OH
N
−O
O
OH
HO
O
H
OH
δ+
H
O
Glycogen
O
P O−
−O
O
H
O−
P O
O
N
OH
N
−O
O
δ+
OH
HO
O
H
OH
O
P
O−
O−
O
H
O
P O
O
N
OH
N
−O
O
OH
151 / 573

152. Lysosomal glycogen disposal
◮ concerns a minor fraction of glycogen
◮ key enzyme: acid maltase; enzyme defect causes slow but inexorable glycogen
accumulation
◮ possible role: disposal of structurally aberrant glycogen particles that have
become “tangled up” during repeated cycles of glucose accretion and depletion
152 / 573

153. Allosteric regulation of glycogen synthase and phosphorylase
Glycogen
ATP
AMP
Glucose-6- P
Glucose-1- P
UDP-glucose
Phosphorylase
Glycogen synthase
153 / 573

154. Hormonal control of glycogen metabolism
Epinephrine, glucagon Insulin
Adenylate cyclase Phosphodiesterase
ATP cAMP AMP
Protein kinase A
Glycogen
synthase
Glycogen
synthase- P
Phosphorylase
kinase
Phosphorylase
kinase- P
Phosphorylase Phosphorylase- P
154 / 573

155. Regulatory differences between liver and muscle phosphorylase
Liver enzyme Muscle enzyme
Inhibition by glucose + −
Activation by Ca2+
− +
Activation by AMP even when
unphosphorylated
− +
155 / 573

156. Liver glycogen utilization
Glycogen
Glucose-1- P
Glucose-6- P
Glucose-6- P
Glucose Glucose
Glucose
glucose-6-phosphatase glucokinase
endoplasmic reticulum
extracellular space
cytosol
156 / 573

157. Muscle glycogen utilization
Glycogen
Glucose-1- P
Glucose-6- P
Glucose-6- P Pyruvate
Glucose Glucose
Glucose
Lactate
Lactate
CO2, H2O
glucose-6-phosphatase hexokinase LDH
ADP + Pi
ATP
endoplasmic reticulum
157 / 573

158. The Cori cycle
Glucose
Pyruvate Lactate
2 ATP
2 ADP
NADH+H+
NAD+
Pyruvate
Glucose
NAD+
NADH+H+
6 ATP
6 ADP
158 / 573

159. Glucose-6-phosphatase deficiency (von Gierke disease)
Biochemical defect:
◮ glucose-6-phosphate formed in gluconeogenesis or glycogen degradation
cannot be converted to free glucose
◮ glucose cannot be exported from liver and kidney cells
Clinical manifestations:
◮ glycogen builds up in liver and kidneys (organ enlargement and functional
impairment)
◮ severe hypoglycemia
◮ lactic acidosis
◮ hyperlipidemia
◮ hyperuricemia
159 / 573

160. Acid maltase deficiency (Pompe disease)
Infant chest X-ray,
normal heart
Infant with Pompe
disease, distended heart
Normal skeletal muscle
(transverse section)
Glycogen aggregates
in Pompe disease
160 / 573

161. Muscle phosphorylase deficiency (McArdle’s disease)
◮ Deficient glycogen breakdown inhibits rapid ATP replenishment
◮ Patients experience rapid exhaustion and muscle pain during exertion
◮ Liver phosphorylase and blood glucose homeostasis remain intact
muscle glycogen utilization
161 / 573

162. Lafora disease
◮ deficiency for laforin, a glycogen phosphatase
◮ accumulation of hyper-phosphorylated glycogen (Lafora bodies)
◮ patients develop epilepsy, dementia
162 / 573

163. Chapter 9
The hexose monophosphate shunt
163 / 573

164. The hexose monophosphate shunt: Overview
Glucose-6- P
Ribulose-5- P
Ribose-5- P
RNA, ribonucleotides
Ribo-, deoxyribonucleotides
2 NADP+
CO2
2 NADPH+H+
164 / 573

165. Reactions in the oxidative stage
OH
OH
OH
O
P
O O−
O−
O
O
H
O
OH
OH
O
P
O O−
O−
O
O
H
NADP+
NADPH+H+
1
H2O
2
OH
O
OH
O
H
OH
OH
O P
O
O−
O−
OH
O
OH
O
OH
OH
O P
O
O−
O−
OH
O
OH
OH
O P
O
O−
O−
NADP+
NADPH+H+
CO2
3 3
Glucose-6- P
6- P -Gluconolactone
6- P -Gluconate
Ribulose-5- P
165 / 573

166. Reactions in the sugar shuffle stage
OH
O
OH
OH
O P
OH
O
OH
OH
O P
OH
O
OH
OH
O P
OH
O
O
H
OH
O P
O
OH
OH
OH
O P
OH
O
O
H
OH
O P
O
OH
O P
OH
O
O
H
OH
OH
OH
O P
O
OH
OH
O P
OH
O
O
H
OH
OH
O P
O
OH
O P
OH
O
O
H
OH
OH
O P
RE
RI
RE
TK
TA
TK
Ribulose-5- P Xylulose-5- P Glyeraldehyde-3- P Fructose-6- P
Ribose-5- P Sedoheptulose-7- P Erythrose-4- P
166 / 573

167. Ketoses and aldoses in the HMS
OH
O
OH
OH
O P
OH
O
O
H
OH
O P
OH
O
O
H
OH
OH
O P
OH
O
O
H
OH
OH
OH
O P
O
OH
OH
OH
O P
O
OH
OH
O P
O
OH
O P
TK TK TK
TA TA
RE
RI
Ribulose-5- P
Ribose-5- P Erythrose-4- P Glyceraldehyde-3- P
Xylulose-5- P Fructose-6- P Sedoheptulose-7- P
167 / 573

168. The mechanism of transketolase
⊕
N
R
⊖
O H⊕
OH
O
H
OH
O P
S
R
⊕
N
R
OH
OH
O
H OH
O P
S
R
⊕
N
R
OH
OH
⊖
O
OH
O P
S
R
O
H⊕
OH
OH
OH
O P
⊕
N
R
O H
OH
O
H
OH
OH
OH
O P
S
R
OH
O
O
H
OH
OH
OH
O P
168 / 573

169. The mechanism of transaldolase
NH2
Lys O
OH
O
H
OH
OH
OH
O P
N
H
⊕
Lys
OH
O
H
O H
OH
OH
O P
N
H
Lys
OH
O
H
O
OH
OH
O P
O
H⊕
OH
O P
N
H
⊕
Lys
OH
O
H
OH
OH
O P
NH2
Lys O
OH
O
H
OH
OH
O P
OH–
OH–
169 / 573

170. Why do we need both NADH and NADPH?
O O
OH
N
NH2
O
H
H
OH
P O
−O
O
P O
−O
O O
OH
N N
N
NH2
N
OH
O O
OH
N
NH2
O
H
H
OH
P O
−O
O
P O
−O
O O
O
P O
−O
O−
N N
N
NH2
N
OH
170 / 573

171. NADPH generation by malic enzyme
Pi
malate
pyruvate
Pi
malate
oxaloacetate
pyruvate
CO2 ATP
ADP+Pi
NADH+H+
NAD+
NADPH+H+
NADP+
CO2
H+
H+
Cytosol Mitochondria
pyruvate
carboxylase
malate
dehydrogenase
dicarboxylate
transporter
malic
enzyme
171 / 573

172. NADPH generation by transhydrogenase and NADP-linked
isocitrate dehydrogenase
nicotinamide nucleotide
transhydrogenase
isocitrate
dehydrogenase
citrate/isocitrate
carrier
oxoglutarate
carrier
Mitochondria
NADH+H+
NAD+
NADPH+H+
NADP+
H+
α-ketoglutarate
isocitrate
CO2
malate
Cytosol
malate
α-ketoglutarate isocitrate
NADPH+H+
NADP+
CO2
172 / 573

173. Uses of NADPH
1. synthesis of fatty acids and cholesterol
2. fixation of ammonia by glutamate dehydrogenase
3. oxidative metabolism of drugs and poisons by cytochrome P450 enzymes
4. generation of nitric oxide and of reactive oxygen species by phagocytes
5. scavenging of reactive oxygen species that form as byproducts of oxygen
transport and of the respiratory chain
173 / 573

174. The nitric oxide synthase reaction
O
O
H
NH2
N
N
H2 NH2
NADPH + H+
O2
NADP+
H2O
O
O
H
NH2
N
N
H2 NH
OH
1/2(NADPH+H+
)
O2
1/2NADP+
H2O
O
O
H
NH2
NH
N
H2 O
+
N−
−O
arginine N-hydroxyarginine citrulline
174 / 573

175. Signaling effects of nitric oxide
175 / 573

176. Phagocytes use NADPH to generate reactive oxygen species
2O2 + NADPH 2O–
2 + NADP+
+ H+
2O–
2 + 2H+
H2O2 + O2
H2O2 + Cl–
OCl–
+ H2O
NADPH oxidase
Superoxide dismutase
Myeloperoxidase
176 / 573

177. Scavenging of reactive oxygen species requires NADPH, too
H
S
O
NH
O
HO
N
H
O
2N
O
HO
H S
O
N
H
O
OH
NH
O
NH2
O
OH
S
O
NH
O
HO
N
H
O
H2N
O
HO
S
O
N
H
O
OH
NH
O
NH
O
OH
R – OOH ROH + H2O
NADPH+H+
NADP+
glutathione
peroxidase
glutathione
reductase
G – SS – G
2 G – SH
177 / 573

178. Glucose-6-phosphate dehydrogenase deficiency
◮ most patients are healthy most of the time—hemolytic crises occur upon
exposure to drugs or diet components that cause enhanced formation of ROS
◮ manifest in red blood cells because these cells lack protein synthesis—no
replacement of deficient protein molecules
◮ affords partial protection against malaria—similar to sickle cell anemia and
other hemoglobinopathias
◮ X-chromosomally encoded—males more severely affected
178 / 573

179. Vicia faba and favism
H2N N
H
O
NH
O
H2N N
H
O
NH
O
HO
Divicine Isouramil
179 / 573

180. Redox cycling of isouramil
HN N
H
O
NH
O
O
H2N N
H
O
NH
O
HO
NADPH
NADP+
4
GSSG
2 GSH
1
O2
H2O2
2
2 H2O
2 GSH
GSSG
3
NADP+
NADPH
4
180 / 573

181. Malaria parasites detoxify heme by crystallization
181 / 573

182. Primaquine and glucose-6-phosphate dehydrogenase deficiency
N
NH
N
H2
O
N
NH
N
H2
O
OH
N
N
N
H2
O
O
Primaquine
CYP450
H2O2
O2
GSSG 2 GSH
182 / 573

183. Chapter 10
Triacylglycerol metabolism
183 / 573

184. Foodstuffs and their energy contents
Foodstuff Energy (kcal/g)
protein 4
carbohydrates 4
triacylglycerol 9
alcohol 7
184 / 573

185. Carbon pools in carbohydrate and fat metabolism
Triacyl—glycerol
Fatty acids Glycerol- P
Glucose
Glycogen
Ketone bodies
Acetyl-CoA
Glyceraldehyde- P
Pyruvate
185 / 573

186. Triacylglycerol and its cleavage products
O
O
O
O
O
O
OH O
O
OH
HO
O
HO
O
HO
O
HO
O
Triacylglycerol Monoacylglycerol Fatty acids
C16:0 C18:0 C18:1 C18:2
186 / 573

187. Solubilization of fat by detergents
187 / 573

188. Uptake and re-packaging of digested fat in the small intestine
188 / 573

189. The lymphatics drain excess fluid from the interstitial space
artery
vein
interstitial
space
blood fluid filtration
osmotic reuptake
lymph drainage
capillary
lymph
vessel
189 / 573

190. Chylomicrons are drained from the intestine through the
lymphatics, bypassing the liver
190 / 573

191. Lipoprotein lipase extracts triacylglycerol from chylomicrons
191 / 573

192. Medium-chain fatty acids
◮ contain less than 12 carbon atoms
◮ low content in most foods, but relatively high (10–15%) in palm seed and
coconut oil, from which they are industrially prepared
◮ triglycerides with medium chains are more soluble and more rapidly
hydrolyzed by gastric and pancreatic lipase
◮ not efficiently re-esterified inside intestinal cells; systemic uptake mostly as free
fatty acids
◮ reach mitochondria by diffusion, without prior activation to acyl-CoA and
acyl-carnitine
192 / 573

193. Two activated forms of fatty acids
O
S
N
H
O
N
H
O
OH
O
P O
−O
O
P O
−O
O O
OH
N N
N
NH2
N
OH
O
O
N+
O
−O
Acyl-CoA
Acyl-carnitine
193 / 573

194. Activation of fatty acids and transport to the mitochondrion
Outer membrane Inner membrane
CoA-SH
Acyl-CoA Acyl-CoA
CoA-SH
Acyl-carnitine Acyl-carnitine
Acyl-CoA
Carnitine
Carnitine
ATP
AMP + PPi
Fatty acid
CoA-SH
194 / 573

195. Reactions in β-oxidation
β
β′
CoA
S
O
CoA
S
O
CoA
S
O OH
CoA
S
O O
CoA
S
O
CoA
S
O
FAD
FADH2
1
H2O
2
NAD+
NADH+H+
3
4
CoA−SH
195 / 573

196. Shared reaction patterns in β-oxidation and TCA cycle
Enzyme Reaction Cosubstrate TCA cycle pendant
acyl-CoA dehydro-
genase
dehydrogenation of
CH2 – CH2 bond
FAD succinate dehydro-
genase
enoyl-CoA hy-
dratase
hydration of
CH2 –
– CH2 bond
H2O fumarase
hydroxyacyl-CoA
dehydrogenase
dehydrogenation of
CH – OH bond
NAD+
malate dehydroge-
nase
196 / 573

197. The reaction mechanism of thiolase
CoA
S
O O
Enzyme
BH+
S−
CoA
S
O
Enzyme
B
H+
S
O
−S CoA
CoA
S
O
197 / 573

198. Utilization of propionate
CoA
S
O
CoA
S
O O
OH
CoA
S
O O
OH
CoA
S
O
O
OH
ATP
CO2
ADP
1
2
3
Propionyl-CoA S-methylmalonyl-CoA
R-methylmalonyl-CoA
Succinyl-CoA
198 / 573

199. Organ relationships in triacylglycerol utilization
triacylglycerol
glycerol fatty acids
acetyl-CoA
ketone bodies
gluconeogenesis glucose
acetyl-CoA
acetyl-CoA
glycolysis
199 / 573

200. Brown fat tissue
200 / 573

201. Ketone body metabolism
fatty acids acetyl-CoA
acetoacetate
β-hydroxy-
butyrate
β-hydroxy-butyrate
acetoacetate
acetoacetyl-CoA
acetyl-CoA
FADH2
FAD
NADH+H+
NAD+
succinyl-CoA
succinate
citrate
201 / 573

202. Synthesis of acetoacetate and β-hydroxybutyrate
CoA
S
O
CoA
S
O
CoA
S
O O
CoA-SH
1
2 acetyl-CoA acetoacetyl-CoA
CoA
S
O OH
O
OH
O
O
OH
O
H
O
OH
2 O
S
CoA
CoA-SH
H2O
3
CoA
S
O
NADH+H+
NAD+
4
HMG-CoA
acetoacetate
β-hydroxybutyrate
202 / 573

203. Decarboxylation of acetoacetate
0
20
40
60
80
0 20 40 60 80 100 120
Acetone
produced
(A.U.)
Incubation time (min)
serum ultrafiltrate
washed serum proteins
O O
OH
O
CO2
Acetoacetate
Acetone
203 / 573

204. Acetone can serve as a precursor for gluconeogenesis
CH3
C O
CH3
H2C OH
C O
CH3
H2C OH
CH
HO
CH3
NADPH+H+
O2
NADP+
H2O
NADH+H+
NAD+
NAD+
NADH
HC O
CH
HO
CH3
OH
C O
CH
HO
CH3
OH
C O
C O
CH3 H2O
NAD+
NADH+H+
NAD+
NADH+H+
acetone acetol 1,2-propanediol
pyruvate l-lactate l-lactaldehyde
carbon pools
204 / 573

205. Anticonvulsant effects of acetone and acetol
40
80
120
1 10 100
PTZ
threshold
(mg/kg)
Metabolite injected (mmol/kg)
acetone
acetol
none
H2N
O
OH
N
N
N
N
γ-Aminobutyric acid (GABA)
Pentylenetetrazole (PTZ)
205 / 573

206. Fatty acid synthesis
◮ carried out mostly by one large cytosolic enzyme (fatty acyl synthase)
◮ uses acetyl-CoA, which is activated by carboxylation
◮ reducing power provided by NADPH
◮ final product: palmitate (hexadecanoate)
◮ elongation and desaturation carried out by dedicated enzymes in the ER
206 / 573

207. The acetyl-CoA carboxylase reaction
CoA
S
O ATP
CO2
ADP+Pi
CoA
S
O O
OH
Acetyl-CoA Malonyl-CoA
207 / 573

208. The structure of fatty acid synthase
ACP
TE
1
2
3
4
5
6
N′ KS MAT HD ER KR ACP TE C′
208 / 573

209. Phosphopantetheine acts as a flexible tether in
acyl carrier protein
OH
O
S
N
H
O
N
H
O
OH
O
P
O
O−
O
ACP
acyl-CoA
209 / 573

210. Fatty acid synthase reactions (1)
FAS
ACP S−
KS S−
acetyl-CoA CoA-S-
MAT
FAS
ACP S
O
KS S−
KS
FAS
ACP S−
KS S
O
malonyl-CoA
CoA-S-
MAT
FAS
ACP S
O O
O⊖
KS S
O
CO2
KS
FAS
ACP S
O O
KS S−
NADPH+H+
NADP+
KR
FAS
ACP S
O OH
KS S−
ATP
CO2
ADP+Pi
acetyl-CoA
210 / 573

211. Fatty acid synthase reactions (2)
FAS
ACP S
O OH
KS S−
H2O
HD
FAS
ACP S
O
KS S−
NADPH+H+
NADP+
ER
FAS
ACP S
O
KS S−
KS
FAS
KS S
O
ACP S−
CoA-S-
MAS
malonyl-CoA
FAS
KS S
O
ACP S
O O
O⊖
CO2
KS
FAS
ACP S
O O
KS S−
ATP
CO2
ADP+Pi
acetyl-CoA
211 / 573

212. Mitochondrial export of acetyl-CoA via citrate
mitochondria
citrate
oxaloacetate
malate
cytosol
citrate
oxaloacetate
malate
NADH+H+
NAD+
NAD+
NADH+H+
acetyl-CoA
CoA-SH ATP
ADP+Pi
CoA-SH
acetyl-CoA
212 / 573

213. Mitochondrial export of acetyl-CoA via acetoacetate
cytosol
mitochondria
2 acetyl-CoA acetoacetyl-CoA
HMG-CoA
acetoacetate
2 acetyl-CoA
acetoacetyl-CoA
acetoacetate
CoA-SH
acetyl-CoA
CoA-SH
acetyl-CoA ATP CoA-SH
AMP+PPi
CoA-SH
213 / 573

214. Elongation and desaturation of fatty acids
◮ elongases reside in mitochondria and endoplasmic reticulum
◮ chemistry of elongation similar to β-oxidation in mitochondria, similar to fatty
acid synthase in the ER
◮ desaturases occur in the ER, introduce double bonds at various positions
◮ double bonds are created at least 9 carbons away from the ω end—ω-3 fatty
acids cannot be formed in human metabolism and are therefore essential
214 / 573

215. Cerulenin, an antibiotic that irreversibly inhibits fatty acid
synthase
O O
OH
O
O
H⊕
O
NH2
S
⊖ Cys FAS
O
O
H
O
NH2
S
Cys FAS
β-keto acid
cerulenin
covalent adduct
215 / 573

216. Fatty acid synthase inhibition slows tumor growth in mouse
experiments
O
OH
OH
OH
O
O O
O
H
OH
OH
0
0.1
0.2
0.3
0.4
0.5
0 10 20 30 40
avg.
tumor
volume
(cm
3
)
days of treatment
untreated
compound 7
compound 7
216 / 573

217. The glyoxylate cycle
Citrate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Oxaloacetate
Acetyl-CoA
Glyoxylate
Acetyl-CoA
Glucose
217 / 573

218. Reactions in the glyoxylate cycle
Glyoxylate
Succinate
H2C COO−
HC COO−
C
H
O
H COOH
H2C COO−
H2C COO−
C
H
O COOH
Isocitrate lyase
H2C
O
OH
C
H
COO−
HO
H3C
O
S CoA
C
H
COO−
O
H2O
CoA-SH
Malate synthase
Acetyl-CoA
218 / 573

219. Chapter 11
Cholesterol metabolism
219 / 573

220. Biological significance of cholesterol
◮ Cholesterol is an essential lipid constituent of cell membranes
◮ Cholesterol is a precursor of steroid hormones and of bile acids
◮ Intermediates of cholesterol biosynthesis are required to make vitamin D and
for posttranslational modification of membrane proteins
◮ High plasma cholesterol promotes atherosclerosis
220 / 573

221. Processes that determine the cholesterol balance
◮ intestinal uptake of dietary cholesterol
◮ de novo cholesterol synthesis
◮ synthesis of steroid hormones from cholesterol
◮ synthesis of bile acids from cholesterol, and their biliary secretion
◮ biliary secretion of surplus cholesterol in unmodified form
221 / 573

222. Overview of cholesterol synthesis
acetyl-CoA HMG-CoA mevalonate
activated C5
activated C10
activated C15
squalene (linear C30) lanosterol cholesterol
HMG-CoA
reductase
222 / 573

223. Initial activation steps in cholesterol synthesis
CoA
S
O
CoA
S
O
CoA
S
O O
CoA-SH
1
CoA
S
O
H2O CoA-SH
2
CoA
S
O OH
O
OH
O
⊖
O OH
OH
3ATP
3ADP
4
2NADPH + 2H+
2NADP+
H2O + CoA-SH
3
O
⊖
O O
P
O P P
O P P
CO2
P ⊖
5
HMG-CoA
mevalonate
isopentenyl-
pyrophosphate
223 / 573

224. Formation of a C10 intermediate
O P P
O P P ⊕ O P P
⊕
O P P
O P P
PPi
H⊕
geranyl-pyrophosphate
dimethylallyl-pyrophosphate
isopentenyl-pyrophosphate
224 / 573

225. Formation of C15 and C30 intermediates
O P P O P P
H⊕
PPi
O P P
P P O
NADPH + H+
2 PPi
NADP+
farnesyl-pyrophosphate
squalene
isopentenyl-pyrophosphate
geranyl-pyrophosphate
225 / 573

226. Squalene cyclization yields the first sterol intermediate
O
⊕H
HO
⊕
HO
NADPH+H+
O2
NADP+
H2O
H+
lanosterol
squalene
squalene epoxide
226 / 573

227. Demethylation, desaturation and saturation steps convert
lanosterol to cholesterol
HO HO HO
lanosterol 7-dehydrocholesterol cholesterol
227 / 573

228. UV-dependent synthesis of cholecalciferol
HO
HO
OH
O
H OH
7-Dehydrocholesterol Cholecalciferol 1,25-Dihydroxycholecalciferol
hν 25-OH 1-OH
228 / 573

229. Sterol metabolism occurs in the smooth endoplasmic reticulum
reproduced from medcell.med.yale.edu/histology, with
permission
229 / 573

230. Transcriptional regulation of cholesterol synthesis starts in the
endoplasmic reticulum
230 / 573

231. When cholesterol is low, SREBP is sorted to the Golgi apparatus
231 / 573

232. Proteolytic cleavage in the Golgi releases SREBP
232 / 573

233. Lipoprotein structure
apolipoproteins
phospholipids,
free cholesterol
triacylglycerol,
cholesterol esters
233 / 573

234. Classification of plasma lipoproteins
Chylomicrons VLDL LDL HDL
Density (g/ml) 0.95 0.95–1.0 1.02–1.06 1.06–1.12
Origin small intestine liver liver liver
Function distribute di-
etary TAG and
cholesterol
distribute
TAG from
liver
distribute
cholesterol
from liver
return excess
cholesterol to
liver
Predominant
lipid species
TAG TAG cholesterol phospholipids,
cholesterol
234 / 573

235. Two membrane proteins control the uptake of sterols from the
intestine
Chylomicron drainage
235 / 573

236. Plant sterol structures
HO
tail
ring
ring
ring
ring
ring
cholesterol
avenasterol
brassicasterol
campesterol
stigmasterol
236 / 573

237. Structures of ABC transporters in the inward-open and
outward-open conformations
ATP
237 / 573

238. ABC transporters induce substrate “flip-flop” across the
membrane
238 / 573

239. Transport of cholesterol between the liver and peripheral tissues
chylomicrons
chylomicron remnants
cholesterol
Liver
VLDL
HDL
nascent HDL
LDL
cholesterol
Other tissues
LPL
LPL
LDL receptor
ABCA1
LCAT
239 / 573

240. Stages of cholesterol transport
Dietary cholesterol
◮ Packaged into chylomicrons, which turn into chylomicron remnants through
triacylglycerol extraction by lipoprotein lipase
◮ Chylomicron remnants are taken up by the liver
Liver cholesterol (from diet, or endogenously synthesized)
◮ Packaged into VLDL
◮ Lipoprotein lipase turns VLDL into IDL and then LDL
◮ LDL is taken up through receptor-mediated endocytosis in peripheral tissues
240 / 573

241. Cholesterol transport (ctd.)
Cholesterol in peripheral tissues
◮ HDL is produced in liver and intestines as an empty carrier for cholesterol
(containing mainly phospholipid and apo A-1)
◮ HDL binds to cells in periphery (including in vascular lesions) and takes up
surplus cholesterol
◮ Cholesterol-laden HDL is taken up into the liver by endocytosis, cholesterol is
recycled
241 / 573

242. The lecithin-cholesterol acyltransferase (LCAT) reaction
N⊕
O
P
O
O⊖
O
O
O
O
O
OH
lecithin
cholesterol
N⊕
O
P
O
O⊖
O
O
H
O
O
O
O
lysolecithin
cholesterol ester
LCAT
242 / 573

243. Cholesterol esters can be stored inside lipoprotein particles
243 / 573

244. Bile acids are derived from cholesterol
OH
O
O−
OH
O
H
OH
O
H OH
O
H
N
S O−
O
O
cholate taurocholate
244 / 573

245. Bile acids undergo enterohepatic cycling
245 / 573

246. Bile acid cycling involves multiple transport proteins
246 / 573

247. A deficient ABCC2 transporter causes Dubin-Johnson syndrome
◮ impaired excretion of bile acids cholesterol precipitates in the bile bile
stones
◮ impaired excretion of bilirubin jaundice
◮ impaired excretion of many drugs potential drug toxicity
247 / 573

248. Is atherosclerosis a metabolic disease?
. . . it is important to remember that the best documented
initiating factor is still hypercholesterolemia . . . additional
factors should be considered in the context of how they relate
to the processes initiated by hypercholesterolemia.
Daniel Steinberg, “Atherogenesis in perspective: Hypercholesterolemia and
inflammation as partners in crime”, Nature Medicine 8:1211 (2002).
248 / 573

249. Macroscopic appearance of atherosclerotic lesions
249 / 573

250. Microscopic appearance of atherosclerotic lesions
Normal artery Foam cells in early lesion
Detritus, fibrosis in advanced lesion High-grade stenosis, thrombus
A B
C D
250 / 573

251. Development of an atherosclerotic lesion
A B C D
Thrombocyte
Foam cell
Macrophage
Endothelial cell
Cholesterol crystals
Modified LDL
Native LDL
251 / 573

252. Metabolic aspects of atherosclerosis
◮ cholesterol uptake, synthesis and degradation
◮ cholesterol transport in the circulation: LDL (low density lipoprotein) and HDL
(high density lipoprotein)
◮ biochemical changes that turn physiological, benign LDL into an atherogenic
agent
252 / 573

253. Two modes of uptake of cholesterol into macrophages
253 / 573

254. Modification of LDL is essential for excessive uptake by
macrophages via the scavenger receptor
◮ LDL receptor is down-regulated once the cell is full up with cholesterol—no
further LDL will be taken up
◮ Covalently modified LDL will be taken up by macrophages via scavenger
receptors
◮ Various modifications have similar effects
◮ Modifications can affect both lipid and apolipoprotein components of LDL
254 / 573

255. Experimental protein modifications that turn LDL into a ligand
for the scavenger receptor
protein
NH2
protein
H
N
O
protein
H
N
O
NH2
protein
N
OH
OH
OH
OH
OH
unmodified amine (native LDL)
acetylated amine
carbamylated amine
glucosylated amine
255 / 573

256. Which modifications of LDL are significant in vivo?
Modification Possible causes
acetylation easily achieved in vitro, but not plausible in
vivo
carbamylation promoted by urea, which is enhanced in
kidney disease; also promoted by smoking
glucosylation promoted by high blood glucose (diabetes)
partial proteolysis proteases released from macrophages
oxidation of lipids and
apolipoproteins
reactive oxygen species released from ma-
crophages
256 / 573

257. How does LDL become oxidized?
◮ Phagocytes produce reactive oxygen species
◮ Transition metals (Fe, Cu) exacerbate ROS activity
◮ Lipoxygenases convert fatty acids to radicals that can bind to LDL and induce
lipid peroxidation
257 / 573

258. Self-sustained lipid peroxidation induced by peroxy radicals
N⊕
P
O
O
O
O
X
Y
•
X
Y
O O•
X
Y
O OH
X
Y
H
X
Y
•
HOO•
HOOH
O2
258 / 573

259. α-Tocopherol intercepts lipid peroxidation
R1
R2
O O•
HO
O
R1
R2
O OH
O
O
R1
R2
•
R1
R2
O
O
259 / 573

260. Experimental evidence implicating LDL oxidation in the
pathogenesis of atherosclerosis
◮ Vitamin E reduces the severity of atherosclerosis in animal models—but not in
clinical studies on humans
◮ Antibodies against oxidized LDL are found in blood; among these, IgG promotes
atherosclerosis, whereas IgM inhibits it
◮ Haptoglobin alleles differ in the efficiency of hemoglobin clearance, which
correlates inversely with susceptibility to atherosclerosis
◮ Production of HOCl by myeloperoxidase: chlorotyrosine residues detectable in
oxLDL ex vivo—but myeloperoxidase k.o. mice have increased susceptibility to
atherosclerosis
260 / 573

261. Lowering LDL cholesterol: therapeutic principles
◮ inhibition of cholesterol synthesis
◮ inhibition of cholesterol uptake
◮ inhibition of cholesterol ester transfer protein
◮ inhibition of bile acid reuptake
◮ LDL apheresis
261 / 573

262. “Statins” inhibit HMG-CoA reductase
F
N
O
H
O
H
O
OH
O
N
H
Atorvastatin
Mevastatin
Mevalonate
HO
O
O
O
O
HO
OH
OH
O
262 / 573

263. Inhibitors of intestinal cholesterol uptake
F N
OH
O
OH
F
HO F
F
F
O
N
H
N
NH
F
F
F
O
S
S
N
N
H
O
S
ezetimibe sitosterol
lomitapide
CP-113,818
intestinal uptake
263 / 573

264. Cholesterol ester transfer protein (CETP) short-circuits
cholesterol transport by lipoproteins
LDL
HDL
CETP
cholesterol
cholesterol
esters
triacylglycerol
O
NH
S
O
dalcetrapib
264 / 573

265. Cholestyramine particles absorb bile acids
OH
O
⊖O
O
H OH
N
⊕
N
⊕
cholestyramine cholic acid
265 / 573

266. LDL apheresis
◮ Blood is diverted through an extra-corporeal filtration device
◮ cells are separated from plasma
◮ LDL is removed from plasma by affinity methods or size-based filtration
◮ The remaining plasma and cells are returned to the circulation
◮ The procedure is repeated in weekly or biweekly intervals
266 / 573

267. More . . .
◮ triparanol—an old drug, inhibits some CYP450 enzymes in the conversion from
lanosterol to cholesterol; withdrawn due to toxicity
◮ bezafibrate—a PPARγ agonist
◮ nicotinic acid—activates hormone-sensitive lipase through a G protein coupled
receptor named HM74A; 5 likely additional mechanisms
◮ probucol and succinobucol—supposedly antioxidants that prevent LDL
oxidation, but also cause unrelated changes in other laboratory parameters
◮ guar gum and other carbohydrate fibers —absorb and prevent intestinal uptake
of cholesterol and bile acids with variable efficiency
◮ thyroid hormone analogs—promote LDL utilization
267 / 573

268. Familial hypercholesterolemia is due to a gene defect in the LDL
receptor
chylomicrons
chylomicron remnants
cholesterol
Liver
VLDL
HDL
nascent HDL
LDL
cholesterol
Other tissues
LPL
LPL
LDL receptor
ABCA1
LCAT
268 / 573

269. Tangier disease: Disruption of cholesterol transfer to HDL
chylomicrons
chylomicron remnants
cholesterol
Liver
VLDL
HDL
nascent HDL
LDL
cholesterol
Other tissues
LPL
LPL
LDL receptor
ABCA1
LCAT
269 / 573

270. A defective plant sterol exporter causes sitosterolemia
270 / 573

271. Chapter 12
Amino acid metabolism
271 / 573

272. Metabolic uses of amino acids
◮ building blocks for protein synthesis
◮ precursors of nucleotides and heme
◮ source of energy
◮ neurotransmitters
◮ precursors of neurotransmitters and hormones
272 / 573

273. Outline of amino acid degradation
◮ The liver is the major site of degradation for most amino acids, but muscle and
kidney dominate the degradation of specific ones
◮ Nitrogen is removed from the carbon skeleton and transferred to
α-ketoglutarate, which yields glutamate
◮ The carbon skeletons are converted to intermediates of the mainstream carbon
oxidation pathways via specific adapter pathways
◮ Surplus nitrogen is removed from glutamate, incorporated into urea, and
excreted
273 / 573

274. Amino acid breakdown pathways join mainstream carbon
utilization at different points of entry
Arg, Gln, Glu, His, Pro
Ile, Met, Thr, Val
Phe, Tyr
Asn, Asp
Ala, Cys, Gly, Ser
Leu, Lys, Phe, Trp, Tyr
propionyl-CoA
acetoacetate
α-ketoglutarate
succinyl-CoA
fumarate
oxaloacetate
pyruvate
acetyl-CoA
glucose
glucogenic
ketogenic
274 / 573

275. Transamination of amino acids
COOH
CH
H2N
CH3
COOH
C O
CH2
CH2
COOH
COOH
C O
CH3
COOH
CH
H2N
CH2
CH2
COOH
l-alanine α-ketoglutarate pyruvate l-glutamate
275 / 573

276. The reaction mechanism of transamination
H3C C
H
COOH
NH2
O
CH
⊖O
⊕
N
H
P
H2O
H3C C
H B
Enzyme
COOH
N
⊕ CH
⊖O
H
⊕
N
H
P
H3C
H⊕
C
O⊖
H
BH⊕
Enzyme
COOH
N
⊕ CH
⊖O
H
N
H
P
H3C
H⊕
C
O
H
COOH
N⊕
H CH
⊖O
H
N
H
P
H3C C
O
COOH
H3N⊕
CH
⊖O
N
H
P
276 / 573

277. The ping pong bi bi mechanism of transamination
R1 C
H
COOH
NH2
R1 C COOH
O
R2 C COOH
O
R2 C
H
COOH
NH2
O
CH
⊖O
⊕
N
H
P
H2N
CH
⊖O
N
H
P
O
CH
⊖O
⊕
N
H
P
277 / 573

278. Nitrogen disposal and excretion
◮ Nitrogen accruing outside the liver is transported to the liver as glutamine or
alanine
◮ In the liver, nitrogen is released as free ammonia
◮ Ammonia is incorporated into urea
◮ Urea is released from the liver into the bloodstream and excreted through the
kidneys
278 / 573

279. The urea cycle, part 1: carbamoylphosphate synthetase
HO
O
O−
HO
O
H3
N
O P
O
O−
O−
O
−O NH2
O
O
P
O
O−
−O NH2
ATP ADP Pi ATP ADP
279 / 573

280. The urea cycle, part 2: subsequent reactions
2 3
3
4
5
NH2
O
NH2
O P
NH2
COOH
Pi
NH2
O NH
NH2
COOH
ATP
PPi
NH
O
P
M
A
NH2
C
O
O
H
C
O
O
H
NH
NH2
COOH
AMP
NH
N
H
C
O
O
H
C
O
O
H
NH
NH2
COOH
C
O
O
H
C
O
O
H
NH
N
H2
O
NH2
N
H2
NH
NH2
COOH
H2O
carbamoyl- P
citrulline
aspartate
arginino-
succinate
fumarate
arginine
urea
ornithine
280 / 573

281. The urea cycle in context
amino acid α-keto acid
α-KG Glu
NH3
carbamoyl- P
HCO–
3, ATP
AS
Cit
Orn
Arg
urea
Asp
oxaloacetate
malate
fumarate
amino acid α-keto acid
α-KG Glu
transaminases
glutamate dehydrogenase
urea cycle
TCA cycle
malate aspartate shuttle
281 / 573

282. The urea cycle spans mitochondria and cytosol
mitochondria cytosol
citrulline
ornithine
H+
H+
citrulline
ornithine
argininosuccinate
arginine
carbamoyl-
phosphate
NH3 + HCO–
3
2 ADP
2 ATP
aspartate
ATP AMP
fumarate
urea
282 / 573

283. The glucose-alanine cycle
amino acid
α-keto acid
α-KG
Glu
1
Ala
pyruvate
glucose
1
Ala
pyruvate
glucose
α-KG
Glu
1
NH3
H2O
2
urea
283 / 573

284. Nitrogen transport by glutamine
amino acid
α-keto acid
α-KG
Glu
1
NH3
H2O
2
Glu
Gln
3
Glu
Gln
NH3
H2O
4
urea
284 / 573

285. The central role of glutamate in nitrogen disposal
HO
O
H2N
O
NH2
HO
O
H2N
O
OH
HO
O
O
O
OH
H2O
NH3
glutaminase
NH3 + ATP
ADP + Pi
glutamine
synthetase
NAD+
+ H2O
glutamate
dehydrogenase
NADH + H+
+ NH3
urea
amino acid
α-keto acid
oxaloacetate aspartate
transaminases
285 / 573

286. Control of ammonia levels in the liver lobule
blood from portal vein
blood from liver artery
blood to systemic circulation
glutamate dehydrogenase,
glutaminase: NH3
urea cycle runs at speed
glutamine synthetase: NH3
before blood leaves liver
liver tissue
286 / 573

287. Regulation of the urea cycle
glutamine
glutamate
N-acetyl-glutamate
NH3
carbamoyl- P
urea
ornithine
aspartate
oxaloacetate
α-ketoglutarate
287 / 573

288. Hereditary enzyme defects in the urea cycle
◮ may affect any of the enzymes in the cycle
◮ urea cannot be synthesized, nitrogen disposal is disrupted
◮ ammonia accumulates, as do other metabolites depending on the deficient
enzyme
◮ treatment
◮ protein-limited diet
◮ arginine substitution
◮ alternate pathway therapy
glutamine conjugation
288 / 573

289. Asparagine degradation
HO
O
H2N
O
NH2
HO
O
H2N
O
OH
HO
O
O
O
OH
H2O
NH2
1
α-KG
Glu
2
asparagine aspartate oxaloacetate
289 / 573

290. Serine dehydratase
HO
O
H2N
HO
HO
O
H2N
HO
O
O
H2O
H2O
NH3
serine aminoacrylate pyruvate
290 / 573

291. Serine-pyruvate transaminase
HO
O
H2N
O
H
HO
O
O
O
H
HO
O
O
H
O
H
HO
O
O
H
O
P
pyruvate
alanine
1
xxNADH+H+
NAD+
xxx
2
ATP
ADP
3
serine hydroxypyruvate glycerate 3- P -glycerate
dhfr
291 / 573

292. Degradation of leucine
1 2 3
4
5
6
HO
O
H2N
α-KG
Glu
HO
O
O
CoA-SH
NAD+
CO2
NADH+H+
CoA
S
O
CoA
S
O
CoA
S
O
O
HO
H2O
CoA
S
O
O
H
O
HO
CoA
S
O
O
O
HO
ATP
ADP+Pi
CO2
FAD FADH2
292 / 573

293. Degradation of phenylalanine and tyrosine
HO O
N
H2
O2 + BH4
H2O + BH2
HO O
N
H2
OH
α-Ketoglutarate
Glutamate
HO O
O
OH
O2
CO2
HO O
OH
OH
Phenylalanine Tyrosine Hydroxyphenylpyruvate Homogentisate
1 2 3
4
5
6
O2
HO O
O
O
O
OH
HO
O O O
O
OH
Maleylacetoacetate
Fumarylacetoacetate
H2O
HO
O O
HO
O
O
OH
Acetoacetate Fumarate
F
F F
N
O
O
O
O
O
NTBC
293 / 573

294. Phenylketonuria (PKU)
◮ homozygous defect of phenylalanine hydroxylase
◮ affects one in 10,000 newborns among Caucasians; frequency differs with race
◮ excess of phenylalanine causes symptoms only after birth; intrauterine
development normal
◮ cognitive and neurological deficits, probably due to cerebral serotonin deficit
◮ treatment with phenylalanine-restricted diet
◮ some cases are due to reduced affinity of enzyme for cofactor THB, can be
treated with high dosages of THB
294 / 573

295. The Guthrie test for diagnosing phenylketonuria
Grow E. coli Phe– on
rich medium
Spread on minimal
medium
Cells persist, but do
not grow
Place patients’ blood sam-
ples onto inoculated agar—
bacteria will grow around
samples containing excess
phenylalanine
295 / 573

296. Ochratoxin A inhibits phenylalanyl-tRNA synthetase
OH
O
NH2
OH
O
H
N
OH
O
Cl
O
O
OH
ATP AMP + PPi
Phe-tRNA synthetase
OH
O
NH2
296 / 573

297. Tyrosinemia
◮ homozygous defect of fumarylacetoacetate hydrolase
◮ fumarylacetoacetate and preceding metabolites back up
◮ fumaryl- and maleylacetoacetate react with glutathione and other nucleophiles,
causing liver toxicity
◮ the drug NTCB inhibits p-hydroxyphenylpyruvate dioxygenase, intercepting the
degradative pathway upstream of the toxic metabolites
◮ dietary restriction of tyrosine required to prevent neurological deficit
Phe degradation
297 / 573

298. Chapter 13
Hormonal regulation of metabolism
298 / 573

299. Hormones that affect energy metabolism
Hormone Message
insulin glucose and amino acids available, more sub-
strates on the way
glucagon glucose and amino acids in short supply,
need to mobilize internal reserves
epinephrine prepare for imminent sharp rise in substrate
demand
glucocorticoids prepare for extended period of high demand
thyroid hormones increase basal metabolic rate
299 / 573

300. Langerhans’ islets in the pancreas produce insulin and glucagon
300 / 573

301. A little bit of history: The purification of insulin—the problem
301 / 573

302. The purification of insulin—Banting’s solution
apply ligature,
reseal abdomen
pancreatic juice backs
up, exocrine tissue
self-destroys
obtain protease-free
homogenized extract
302 / 573

303. Historical side note: Norman Bethune, Banting’s famous
classmate
“Comrade Bethune’s spirit, his utter devotion to others without any thought of self, was
shown in his great sense of responsibility in his work and his great warmheartedness
towards all comrades and the people. Every Communist must learn from him.”
Mao Zedong, “In Memory of Norman Bethune”
303 / 573

304. Structure of insulin and its precursors (1)
G
I
V
E Q C C T S I C S L Y Q L E N Y C N
F V N Q H L C G S H L V E A L Y L V C G E R G F
F
Y
T
P
K
T
304 / 573

305. Structure of insulin and its precursors (2)
preproinsulin proinsulin C peptide insulin
305 / 573

306. Sequences of human, swine, and bovine insulins
GIVEQCC
C
L
H
Q
N
V
F GSHLVEALYLVCGERGFFYTPKT
TSICSLYQLENYCN
GIVEQCC
C
L
H
Q
N
V
F GSHLVEALYLVCGERGFFYTPKA
TSICSLYQLENYCN
GIVEQCC
C
L
H
Q
N
V
F GSHLVEALYLVCGERGFFYTPKA
ASVCSLYQLENYCN
306 / 573

307. Insulin secretion in the β-cell is controlled by glucose and
triggered by membrane depolarization
H2O, CO2
ADP + Pi
ATP
Ca2+
K+
K+
Ca2+
ATP
ATP
Insulin
Insulin
Glucose
Glucose
Membrane
potential
Sulfonylurea receptor
307 / 573

308. The sulfonylurea receptor controls an associated potassium
channel
308 / 573

309. KATP channels also regulate the tone of smooth muscle cells
309 / 573

310. Tolbutamide promotes closing of the KATP channel
HN
O
HN
S O
O
Cl
S
O
O
N
NH
H
N
O−
S
O
O
O
+
N NH2
N
N
H2
N
Tolbutamide Diazoxide Iptakalim
Minoxidil sulfate
310 / 573

311. The insulin receptor is a receptor tyrosine kinase
311 / 573

312. Insulin receptor first phosphorylates itself and then a number of
insulin receptor substrate proteins
312 / 573

313. Insulin effects on glycogen synthesis
PDE
313 / 573

314. The role of insulin in glucose transport
Active transport Facilitated transport
insulin-
independent
small intestine,
kidney tubules
brain, β-cells, red blood cells,
cornea and lens of the eye
insulin-
dependent
never muscle, fat, most other tis-
sues
314 / 573

315. Insulin promotes glucose uptake by increasing the surface
exposure of GLUT 4 transporters
Glc
Glc
high insulin low insulin
315 / 573

316. Transcriptional regulation by insulin
316 / 573

317. Other hormones
Epinephrine Cortisol Triiodothyronine
HO
OH
O
H
N
H
O
O
OH
OH
O
H
I
O
O
H
N
H2
I
O I
OH
Glucagon
N′ C′
H S Q G T F T S D Y S K Y L D S R R A Q D F V Q W L M N T
317 / 573

318. Glucagon and epinephrine act via G-protein-coupled receptors
318 / 573

319. The glucagon and epinephrine receptors activate adenylate
cyclase and protein kinase A
319 / 573

320. Metabolic effects of protein kinase A
Target Effect Metabolic consequence
glycogen synthase glucose is not locked up in glyco-
gen, remains available
phosphorylase kinase phosphorylase is activated, glucose
is released from glycogen storage
PFK-2 / Fructose-2,6-
bisphosphatase
/ Fructose-2,6-bisphosphate drops;
glycolysis is inhibited, gluconeoge-
nesis is activated
hormone-sensitive
lipase
fatty acids are mobilized for β-
oxidation and ketogenesis
320 / 573

321. Glucocorticoids and thyroid hormones act on nuclear hormone
receptors to activate transcription
enzymes,
receptors,
transporters
nuclear hormone
receptor
321 / 573

322. DNA binding by thyroid hormone receptors
A G G T C A
5′ 3′
A
G
G
T
C
A
3′ 5′
A G G T C A A G G T C A
5′ 3′ 5′ 3′
322 / 573

323. Thyroid hormones induce respiratory chain uncoupling proteins
I
II
Q
III
C
IV
ADP + Pi
ATP
H⊕ H⊕ H⊕
H⊕
⊖
⊖ ⊖
⊖
NADH
NAD⊕+H⊕
FADH2
FAD+2H⊕
2H⊕+ 1
2 O2
H2O
H⊕
323 / 573

324. Metabolic effects of glucocorticoid hormones
◮ induction of enzymes for glycogen synthesis, glycogen breakdown, as well as
gluconeogenesis
◮ induction of enzymes for protein breakdown, which supplies substrates for
gluconeogenesis
◮ induction of adrenergic receptors
. . . overall, glucocorticoids increase blood glucose
324 / 573

325. Glucocorticoid receptor agonists and antagonists
0
25
50
75
100
Effect
(%
dexamethasone)
Prednisolone
RU 24858
Mifepristone
IL-1β↓
TAT ↑
O
F
O
OH
OH
O
H
O
O
OH
OH
O
H
Dexamethasone Prednisolone
O
F
O
H
O
O
OH
N
Mifepristone RU 24858
325 / 573

326. Control of food intake by leptin
326 / 573

327. Chapter 14
Diabetes mellitus
327 / 573

328. Diabetes mellitus
What’s in a name?
1. diabetes: “marching through”—urine is produced incessantly
2. mellitus: honey-sweet—as opposed to diabetes insipidus (insipid—without
flavor)
What does the adjective tell us about a traditional method of diagnosis?
328 / 573

329. Forms and causes of diabetes mellitus
Form Cause
type 1 lack of insulin due to destruction of β-cells
in pancreas islets
type 2 lack of functional response to insulin
secondary excess activity of hormones antagonistic to
insulin
329 / 573

330. Overview of kidney function
Urine is “distilled” from blood plasma in several stages:
1. ultrafiltration: 10-20% of the blood plasma volume that passes through the
kidneys is squeezed across a molecular sieve; small solutes are filtrated,
macromolecules are retained
2. solute reuptake: glucose, amino acids, salts etc. are recovered from the
ultrafiltrate through active transport
3. water reuptake: driven by osmotic gradient
4. solute secretion: some substrates are actively secreted into the nascent urine
330 / 573

331. The nephron
Macula densa
Glomerulus
Proximal
tubule
Distal
tubule
Loop of Henle
Collecting duct
331 / 573

332. Kidney tissue structure and function: Glomeruli and tubules
From pathorama.ch with permission
332 / 573

333. Primary filtration occurs in the glomerulus
333 / 573

334. Reuptake and secretion occur in the tubular segments
334 / 573

335. The capacity for glucose reuptake is saturated slightly above the
physiological plasma concentration range
Reabsorption
maximum (~10 mM)
normal
range
Glucose
filtrated
or
excreted
Plasma glucose level
Glucose
filtrated
Glucose
excreted
335 / 573

336. Lack of insulin drives up cAMP
glucacon
glucagon receptor
epinephrine
β-adrenergic receptor
adenylate cyclase
ATP cAMP
phosphodiesterase
AMP
insulin
insulin receptor
protein kinase B
336 / 573

337. Lack of insulin promotes gluconeogenesis
Epinephrine, glucagon Insulin
Adenylate cyclase Phosphodiesterase
ATP cAMP AMP
Protein kinase A
PFK 2/F-2,6-bis-P’ase PFK 2/F-2,6-bis-P’ase
Fructose-2,6-bis- P
Fructose-6- P
337 / 573

338. Lack of insulin promotes gluconeogenesis (2)
Fructose-6- P
ATP
AMP
Fructose-2,6-bis- P
Fructose-1,6-bis- P
Pi
H2O
ATP
ADP
Phosphofructokinase
Fructose-1,6-
bisphosphatase
338 / 573

339. Lack of insulin induces breakdown and inhibits synthesis of
glycogen
Epinephrine, glucagon Insulin
Adenylate cyclase Phosphodiesterase
ATP cAMP AMP
Protein kinase A
Glycogen
synthase
Glycogen
synthase- P
Phosphorylase
kinase
Phosphorylase
kinase- P
Phosphorylase Phosphorylase- P
339 / 573

340. Lack of insulin induces triacylglycerol breakdown in fat tissue
epinephrine, glucagon insulin
adenylate cyclase phosphodiesterase
ATP cAMP AMP
protein kinase A
hormone-sensitive lipase
triacylglycerol
fatty acids,
glycerol
340 / 573

341. Lack of insulin induces protein breakdown in muscle tissue
protein
amino acids keto acids
α-ketoglutarate
glutamate
malate
pyruvate
alanine alanine
pyruvate glucose
TCA
cycle
glutamate
α-ketoglutarate
341 / 573

342. Substrate overload in the liver leads to ketogenesis and
lipoprotein synthesis
glucose fatty acids
amino acids
amino acids
glucose pyruvate
acetyl-CoA
cholesterol
fatty acids
triacylglycerol
lipoproteins
lipoproteins
ketone bodies
ketone bodies
342 / 573

343. Laboratory findings in untreated or under-treated diabetes
Observation Cause
increased blood glucose excessive gluconeogenesis, lack of utilization
glucose excreted in
urine
capacity for renal reuptake exceeded
acidosis (low blood pH) high plasma levels of ketone bodies
increased urea levels accelerated muscle protein breakdown
increased blood
lipoproteins
increased synthesis and packaging of chol-
esterol and triacylglycerol in the liver
343 / 573

344. Typical symptoms and history in a new case of type 1 diabetes
Symptom Cause
dehydration osmotic diuresis due to glucose excretion
acetone smell acetone forms from acetoacetate, is ex-
haled
coma both acidosis and blood hyperosmolarity
impair brain function
loss of body weight dehydration, breakdown of proteins and
fat
recent flu-like disease,
possibly myocarditis
coxsackievirus infection
344 / 573

345. The role of coxsackieviruses in the pathogenesis of type 1
diabetes
345 / 573

346. Outline of T lymphocyte function in antiviral immune responses
346 / 573

347. Structure of a T cell receptor bound to its cognate peptide
presented by an HLA molecule
presented peptide
T cell receptor
HLA molecule
HLA residues that
interact with the
T cell receptor
347 / 573

348. HLA alleles influence the risk of developing type 1 diabetes
HLA-DQ Haplotype Relative risk Absolute risk
A1: 0301-0302 / B1: 0501-0201 21 6%
B1: 0602 0.03 0.01%
348 / 573

349. How to treat a fresh case of acute diabetes
1. Severely sick, possibly comatose patient
◮ infusion therapy for fluid replacement, pH and electrolyte adjustment
◮ parenteral nutrition with proportional insulin substitution
◮ frequent monitoring of lab parameters (glucose, salts, pH) to adjust therapy
2. Upon stabilization
◮ reversal to oral nutrition
◮ train patient to adhere to a stable, regular diet and inject themselves with
insulin
◮ teach patient to monitor blood glucose and to recognize symptoms of
hyper- and hypoglycemia
349 / 573

350. Kinetics of physiological insulin secretion
time
plasma
insulin
level
meal big meal
sustained
secretion
postprandial
peak
350 / 573

351. The reversible aggregation of insulin delays its diffusion from
tissue into the circulation
Capillary wall
Hexamer Dimer Monomer
351 / 573

352. Delayed release of insulin from protamine complexes
protamine MARYRCCRSQSRSRYYRQRQRSRRRRRRSCQTRRRAMRCCRPRYRPRCRRH
352 / 573

353. Biphasic insulin preparations
plasma
insulin
time
short-acting
long-acting
combination
353 / 573

354. Short-term complications of insulin-requiring diabetes
Deviation Symptoms
insulin too low hyperglycemia, acidosis, . . . , coma
insulin too high hypoglycemia, coma
354 / 573

355. Long-term complications of insulin-requiring diabetes
Biochemical deviation Clinical manifestation
accumulation of sorbitol in the
lens of the eye
cataract polyol pathway
increased conversion of glucose
to lipids
increased blood fats, atherosclero-
sis
glucosylation of proteins? sor-
bitol accumulation?
damage to nerve fibres, kidneys,
other organs
355 / 573

356. HbA1C as a parameter of long-term glucose control
N
H2
O
H
C
Glc COOH
HbA1
N
H
C
Glc COOH
HbA1C
H2O
356 / 573

357. Intensive insulin therapy
◮ rationale: prevent long term complications through tight control of blood
glucose
◮ means: frequent glucose sampling and injections, or continuous insulin
application with pump, such that the rate of insulin infusion is controlled by
the current glucose level
◮ challenge: avoid hypoglycemia through insulin overdose—we need to minimize
the delay between insulin application and effect
357 / 573

358. Nerdy intermission: delayed feedback causes signal oscillation
Signal
Time
delayed reaction
immediate reaction
358 / 573

359. Mutant insulins optimized for rapid dissociation and uptake
◮ Insulin lispro: Proline B28 switched with lysine B29
◮ Insulin aspart: Proline B28 replaced with aspartate
359 / 573

360. Structural basis for proline B28 mutations
Dimer 1
Dimer 2 Dimer 3
Gly B23
Glu B21
Pro B28
360 / 573

361. Oral antidiabetic drugs
N
N
O
O
NH
O
S
O
S
O
H
N
O
H
N
NH
N
N
N
H2
NH2
Acarbose Metformin
Rosiglitazone Tolbutamide
OH
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH2OH
O
O
OH
OH
CH3
O
N
H
OH
OH
CH2OH
O
H
361 / 573

362. Action modes of oral antidiabetics
Drug Action mechanism
tolbutamide sulfonylurea receptor agonist
rosiglitazone peroxisome proliferator-activated receptor γ ag-
onist; inhibition of mitochondrial pyruvate trans-
port
acarbose inhibition of the brush border enzymes sucrase
and maltase—reduced or delayed glucose uptake
tolrestat aldose reductase inhibitor (withdrawn)
metformin NADH dehydrogenase inhibition ?
362 / 573

363. Hypothetical mode of action of metformin
NAD+
NADH
NAD+
Lactate
Pyruvate
2 H+
2 e– 1
2 O2
H2O
H+
H+
ADP
ATP
Pi
ADP
ATP
AMP
AMP-activated
protein kinase
1
4
3
2
Metformin
363 / 573

364. Inhibition of complex I of the respiratory chain by metformin
50
75
100
125
respiration
rate
(%
of
control)
50µM 100µM 50µM 100µM metformin
glutamate + malate succinate
24 hours
60 hours
364 / 573

365. Chapter 15
Biosynthetic pathways using tetrahydrofolate and
vitamin B12
365 / 573

366. The role of tetrahydrofolate in biosynthetic reactions
amino acids2 urea, H2O, CO2
THF THF−C1
Cn+1 products Cn precursors
carbon sources
C1–tetrahydrofolate pool
biosynthetic pathways
366 / 573

367. Folic acid is reduced by dihydrofolate reductase (DHFR)
H2N N N
HN
O
N
H
O OH
O
OH
N
OH
N
n
pteridine moiety
p-aminobenzoate polyglutamate
H2N N N
NR
H
N
OH
N
H2N N N
H
NR
H
N
OH
N
H2N N N
H
NR
H
H
N
OH
N
NADPH+H+
NADP+
NADPH+H+
NADP+
folate dihydrofolate tetrahydrofolate
367 / 573

368. Sources and destinations of C1 units transferred by
tetrahydrofolic acid
Sources:
1. serine, glycine
2. histidine, tryptophan
Biosynthetic destinations:
1. purine bases
2. thymine
3. S-adenosylmethionine choline phospholipids, creatine, epinephrine, DNA
methylation
368 / 573

369. The serine hydroxymethyltransferase reaction: release of CH2O
HO CH2 C
H
COOH
NH2
O
CH
⊖O
⊕
N
H
P
H2O
H
B
Enzyme
O CH2 C
H
COOH
N
⊕ CH
⊖O
H
⊕
N
H
P
O CH2
⊕B H
Enzyme
C
H
COOH
N
⊕ CH
⊖O
H
N
H
P
O CH2
B
Enzyme
H C
H
COOH
N
⊕ CH
⊖O
H
⊕
N
H
P
369 / 573

370. Capture of formaldehyde by THF yields N,N′
-methylene-THF
HO CH2 CH
NH3
COOH O CH2 H2C
NH3
COOH
H2N N N
H
N
H
R
H
N
O
H
N
H2N N N
H
N
R
H2C
N
O
H
N
H2O
serine glycine
tetrahydrofolate N,N-methylene-tetrahydrofolate
370 / 573

371. N,N′
-methylene-THF production by the glycine cleavage system
NH
O
S
S
N
H
O
S
H
S
N
H2
HN
O
H
S
H
S
H2N
O
OH
CO2
THF
NH3 + N,N’-CH2-THF
NAD+
NADH + H+
371 / 573

372. Histidine degradation produces N,N′
-methenyl-THF
N,N′-methenyl-THF
histidine urocanate
imidazolone-
propionate
formimino-
glutamate
HO
O
N
H2
N NH
HO
O
N NH
HO
O
O
N NH
HO
O
O
O
H NH
NH
glutamate
THF
H2N N N
H
NHR
N
NH
O
H
N
H2N N N
H
NR
⊕N
O
H
N
NH3
H2O H2O
H+
NH3
372 / 573

373. Redox transitions between various forms of C1-THF
R
N
H
H
N
N
H
R
N
C
H
O
H
N
N
H
R
N
⊕
N
C
H
N
H
HCOOH
ATP ADP+Pi
NADP+
CO2
NADPH
H2O
H+
NADPH
NADP+
R
N
N
C
H2
N
H
R
N
N
CH3
N
H
NADH
NAD+
THF N10-formyl-THF N,N ′-methenyl-THF
N,N ′-methylene-THF
N5-methyl-THF
373 / 573

374. Overview of flux through the C1-THF pool
tryptophan
formic acid
N10-formyl-THF
purine bases
histidine
formimino-THF
N,N ′-methenyl-THF
serine
glycine
N,N ′-methylene-THF
thymine
N5-methyl-THF
methionine
B12
HC
N N
CH
H
N
N
CH3
O
HN
O N
H
CH3
S
N
H2
O
OH
374 / 573

375. Folate antimetabolites as antimicrobials
H2N
NH2
N
N S
O
NH2
O
H2N S
O
NH2
O
H2N
OH
O
Sulfamidochrysoidine (Prontosil)
Sulfanilamide
p-Aminobenzoic acid
NH2
N
N
H2
N
O
O
O
Trimethoprim
Pyrimethamine
H2N N NH2
Cl
N
375 / 573

376. Structure of methylcobalamin
NH2
O
N
N
N
N
H2
O
N
H2
O
N⊖
Co3+
N
H2
O
NH2
O
NH2
O
O
HN
O
P
O−
O
O
O
H
N
N
O OH
376 / 573

377. The S-adenosylmethionine (SAM) cycle requires vitamin B12
THF−CH3
THF
B12
B12−CH3
homocysteine
ymethionine S-adenosylmethionine (SAM)
S-adenosylhomocysteine (SAH)
ATPi 3 Pi
H2O
adenosine
precursor
methylated product
377 / 573

378. Structures of S-adenosylmethionine and S-adenosylhomocysteine
O
OH
N
H3
S⊕
C
H3 O
OH
N N
N
NH2
N
OH
O
OH
N
H3
S
O
OH
N N
N
NH2
N
OH
SAM SAH
378 / 573

379. SAM-dependent methylation reactions
1. methylation of phosphatidylethanolamine (PE) to phosphatidylcholine (PC)
2. guanidinoacetate creatine
3. norepinephrine epinephrine
4. acetylserotonin melatonin
5. DNA methylation
6. methylation of drugs (e.g. mercaptopurine)
379 / 573

380. Phosphatidylethanolamine methylation
O−
P
O
O
O
O
O
O
O
NH2
O−
P
O
O
O
O
O
O
O
NH
O−
P
O
O
O
O
O
O
O
N
O−
P
O
O
O
O
O
O
O
N
⊕
SAM SAH SAM SAH SAM SAH
PE methyl-PE dimethyl-PE PC
380 / 573

381. Sphingomyelin acquires its phosphocholine headgroup from PC
O
P
O
N+
O
O−
O
O
O
O
HO
OH
H
N
O
HO
O
O
O
O OH
H
N
O
O
P
O
N+
O
O−
PC ceramide diacylglycerol sphingomyelin
381 / 573

382. Major nerve fibers are myelinated
382 / 573

383. Creatine metabolism
NH2
CH2
COO−
NH+
2
C NH2
NH
CH2
COO−
arginine ornithine
NH+
2
C NH2
N CH3
CH2
COO−
SAM SAH
NH+
2
C NH P
N CH3
CH2
COO−
H3C
N
O
NH
HN
ADP
ATP
P
glycine guanidinoacetate creatine
creatine phosphate
creatinine
creatine kinase
383 / 573

384. Uptake, transport and storage of folic acid
◮ contained in vegetables (Latin folium = leaf)
◮ synthesized by bacterial flora in the large intestine
◮ active transport mediates intestinal uptake and renal reuptake, as well as
accumulation in the liver
◮ 50% of all folate is stored in the liver
384 / 573

385. Causes of folate deficiency
◮ malnutrition
◮ inflammatory bowel diseases
◮ surgical bowel resection (short intestine syndrome)
◮ cytochrome P450-inducing drugs
◮ excessive alcohol consumption—contentious
385 / 573

386. Folate deficiency causes macrocytic anemia
normal red cells macrocytic red cells
C1-pool
386 / 573

387. Intestinal uptake of vitamin B12
387 / 573

388. Various causes of B12 deficiency
Disease Pathogenetic mechanism
autoimmune
gastritis
destruction of the gastric parietal cells that pro-
duce gastric acid, haptocorrin, and intrinsic factor
pancreatic
insufficiency
failure to digest haptocorrin
inflammatory
bowel disease
disrupted uptake of B12 bound to intrinsic factor
receptor
deficiencies
disrupted binding and cellular uptake of intrinsic
factor or transcobalamin
C1 pool
388 / 573

389. Vitamin B12 deficiency causes disruption of folate-dependent
metabolism: the methyl trap ‘hypothesis’
formyl-THF
methenyl-THF methylene-THF methyl-THF
methionine
S-adenosyl-methionine
purine synthesis thymidine synthesis
histidine serine
B12
389 / 573

390. Chapter 16
Nucleotide metabolism
390 / 573

391. Functions of nucleotides in biochemistry
◮ Building blocks of nucleic acids
◮ Cosubstrates and coenzymes
◮ Signaling
391 / 573

392. Structures of PAPS, acetyl-CoA, and NAD
NAD+
O O
OH
⊕
N
NH2
O
OH
P O
−O
O
P O
−O
O O
OH
N N
N
NH2
N
OH
PAPS
O S
O−
OH
O P
O−
O
O O
OH
N N
N
NH2
N
O
P O
−O
O−
coenzyme A
HS N
H
O
N
H
O
OH
O
P O
−O
O
P O
−O
O O
OH
N N
N
NH2
N
OH
cobalamin structure
392 / 573

393. The RNA world hypothesis
393 / 573

394. Why have cosubstrates become fossilized, whereas enzymes have
not?
Me substrate 1
cosubstrate
substrate 2
Me enzyme 4
enzyme 3
enzyme 2
enzyme 1
. . .
. . .
. . .
. . .
. . .
. . .
. . .
. . .
An enzyme’s world . . .
. . . and a cosubstrate’s world
394 / 573

395. Metabolic routes and pathways of nucleotides
◮ De novo synthesis
◮ Intestinal uptake of nucleosides
◮ Endogenous turnover (partial degradation/salvage)
◮ Degradation and excretion
395 / 573

396. Overview of purine synthesis
O
P
O
O−
−O
O
OH OH
O P
O
O−
O P
O
O−
O−
O
P
O
O−
−O
O
OH
N N
NH
O
N
OH
PRPP
IMP
ring synthesis
ring modification
GMP
ring modification
AMP
396 / 573

397. IMP synthesis (1)
ribose-5-phosphate PRPP
O
P
O
O−
−O
O
OH OH
OH
O
P
O
O−
−O
O
OH OH
O P
O
O−
O P
O
O−
O−
ATP
AMP
glutamine
glutamate + PPi
O
P
O
O−
−O
O
OH OH
NH2
O
P
O
O−
−O
O
OH OH
HN O
N
H2
glycine + ATP
ADP + Pi
phosphoribosylamine
glycinamide ribotide (GAR)
397 / 573

398. IMP synthesis (2)
R
HN O
N
H2
R
HN O
H
N
O
R
HN NH
H
N
O
R
N NH2
N
R
N NH2
O
OH
N
R
N NH2
O
N
H
O OH
O OH
N
R
N NH2
O
NH2
N
CAIR
SAICAR
AICAR
asp + ATP
ADP + Pi
fumarate
GAR FGAR FGAM AIR
N10
-formyl-THF
THF
gln + ATP
glu + ADP + Pi
ATP
ADP + Pi
CO2
398 / 573

399. IMP synthesis (3)
R
N NH2
O
NH2
N
R
N N
H
O
O
NH2
N
R
N N
O
NH
N
N10-formyl-THF
THF H2O
AICAR FAICAR IMP
399 / 573

400. A bifunctional enzyme combines AIR carboxylase and SAICAR
synthetase activities
substrate substrate
product
400 / 573

401. Synthesis of AMP from IMP
O
P
O
O−
−
O O
OH
N N
N
NH2
N
OH
O
P
O
O−
−
O O
OH
N N
NH
O
N
OH
O
P
O
O−
−
O O
OH OH
N N
N
N
H
O
OH
OH
O
N
GDP + Pi
GTP + aspartate
fumarate
adenylosuccinate
adenylosuccinate lyase
adenylosuccinate
synthetase
AMP
IMP
H2O
NH3
AMP deaminase
401 / 573

402. Synthesis of GMP from IMP
O
P
O
O−
−
O
O
OH
N N NH2
NH
O
N
OH
O
P
O
O−
−
O
O
OH
N N
NH
O
N
OH
O
P
O
O−
−
O
O
OH OH
N N
H
O
NH
O
N
NAD+
+ H2O
NADH + H+
glutamine + ATP + H2O
glutamate + AMP + PPi
XMP
GMP synthetase
IMP dehydrogenase
GMP
IMP
NADPH
NADP+
+ NH3
GMP reductase
402 / 573

403. Feedback regulation in purine synthesis
Ribose-5-phosphate
PRPP
PRA
IMP
XMP
GMP
GDP
GTP
Adenylosuccinate
AMP
ADP
ATP
403 / 573

404. Overview of digestion and utilization of nucleic acids
nucleic acids
nucleotides
nucleosides
nucleosides nucleotides
sugar phosphates bases
CO2 and H2O uric acid, β-amino acids
nucleotides
degradation
salvage
phosphorylase
intestinal uptake
phosphatase
DNAse, RNAse
Na+
Pi
H2O
H2O
Pi
404 / 573

405. Utilization of ribose and deoxyribose
O
H
O
OH OH
O P
O
O−
O−
O
P
O
O−
−O
O
OH OH
OH
phosphopentomutase
hexose monophosphate
shunt
5/6 glucose-6-phosphate
O
H
O
OH
O P
O
O−
O−
O
P
O
O−
−O
O
OH
OH
glyceraldehyde-3-phosphate +
acetaldehyde
deoxyribose phosphate
aldolase
405 / 573

406. Degradation of endogenous purine nucleotides (overview)
GMP
XMP
IMP
AMP
guanosine
xanthosine
inosine
adenosine
guanine
xanthine
hypoxanthine
adenine
uric acid
5
2
1
3
4
5
deamination
oxidation
dephosphorylation
phosphorolysis
406 / 573

407. Adenine nucleotide degradation
N N
Ribose-P
N
NH2
N
N
H
N
Ribose-P
N
O
N
O N
H
N
Ribose-P
N
O
HN
O N
H
N
Ribose
N
O
HN
O N
H
N
H
N
O
HN
O N
H
N
H
O
H
N
O
HN
H2O
NH3
NAD+
+H2O
NADH
H2O
phosphate
phosphate
Ribose-1-P
NAD+
NADH+H+
AMP IMP XMP
xanthosine
xanthine
uric acid
1 2
3
4
5
407 / 573

408. The guanase and xanthine dehydrogenase/oxidase reactions
N
H
N
H
N
O
N
O N
H
N
H
N
O
HN
N
H2 N
H
N
H
N
O
HN
O N
H
N
H
O
H
N
O
HN
O2 + H2O
H2O2
O2 + H2O
H2O2
H2O
NH3
xanthine
oxidase
uric acid
guanase
guanine
xanthine
hypoxanthine
408 / 573

409. Renal urate elimination: tubular reuptake and secretion
urate
organic acid
URAT1
urate
MRP4
urate
organic acid
?
urate
ATP?
Interstitial fluid /
blood plasma
Tubule epithelial cell Tubule lumen
(nascent urine)
409 / 573

410. Non-primates break down uric acid to allantoin
O N
H
N
H
O
H
N
O
HN
O2+H2O H2O2
O N N
H
O
H
N
OH
O
HN
H2O
HO
O OH
N
H
O
N
H2
N
O
H
N
CO2
O
N
H
O
N
H2
N
H
O
H
N
urate oxidase (uricase)
hydroxyisourate
hydrolase
OHCU decarboxylase
spontaneous
spontaneous
uric acid
allantoin
2-oxo-4-hydroxy-
4-carboxy-5-ureido-
imidazoline (OHCU)
410 / 573

411. Overview of purine salvage reactions
GMP
XMP
IMP
AMP
adenylo-
succinate
Guanosine
Xanthosine
Inosine
Adenosine
Guanine
Xanthine
Hypoxanthine
Adenine
Uric acid
3
2
1
4 5
5
nucleoside kinases
phosphoribosyltransferases
shared with biosynthesis
degradation
411 / 573

412. Enzyme defects in purine degradation and salvage
Enzyme Biochemical effects Clinical symptoms
adenosine
deaminase
accumulation of dA
and dATP
severe combined im-
munodeficiency (SCID)
HGPRT defective purine sal-
vage, increased de
novo synthesis and
degradation
gout; impeded cerebral
development and self-
mutilation (Lesch-Nyhan
syndrome)
412 / 573

413. Gout
◮ Genetic or dietary factors cause chronically increased urate production or
retention
◮ Urate has limited solubility and may form crystalline deposits, preferentially in
joints and soft tissue
◮ Urate crystals activate inflammation and lead to arthritis that is painful and, in
the long run, destructive
413 / 573

414. Diets and drugs that may promote gout
◮ too much food, too rich in purines
◮ excessive fructose or sucrose
◮ alcoholic beverages—but not all kinds: beer yes, wine no
◮ anorexia nervosa (!)
◮ drugs that interfere with uric acid secretion: pyrazinamide, salicylic acid
◮ drugs that contain purines: dideoxyadenosine
renal urate elimination
414 / 573

415. Gout: the fructose connection
fructose fructose-1- P glyceraldehyde
ATP ADP
dihydroxyacetone- P
glyceraldehyde-3- P
3- P -glycerate
1,3-bis- P -
glycerate
Pi
fructokinase aldolase B
PG-kinase
NADH+H+
NAD+
adenylate
kinase
1/2 ATP
1/2 AMP
purine
degradation
1/2 urate
415 / 573

416. Drugs that affect purine degradation and elimination
O
N
N N
H
NH
O
S
O
N
O
OH
Br
OH
Br
O
O
HO
O OH O NH2
N
N
O OH
N
N
O OH
N
O
N
allopurinol probenecid benzbromarone
salicylic acid pyrazinamide pyrazinoate 5-hydroxy-
pyrazinoate
416 / 573

417. Acute urate nephropathy in tumor lysis syndrome
◮ Occurs during chemotherapy of malignancies, particularly with lymphomas and
leukemias
◮ Chemotherapy causes acute decay of large numbers of tumor cells
◮ Degradation of nucleic acids from decaying cells produces large amounts of
uric acid
◮ Uric acid in nascent urine exceeds solubility and precipitates, clogging up and
damaging the kidney tubules
◮ Clinically manifest as acute kidney failure with high fatality rate
417 / 573

418. Rasburicase, a better preventive treatment for urate nephropathy
Adenine Hypoxanthine
Guanine Xanthine
Uric acid
Allantoin
Urine
Allopurinol
Rasburicase
418 / 573

419. Synthesis of pyrimidines (1)
HCO–
3 O
NH2
O P
O
O−
O−
O
N
H2
N
H
O
OH
O
OH
O N
H
O
OH
O
HN
O N
H
O
OH
O
HN
P
O
OH OH
N
O
OH
O
HN
O
gln + 2ATP
glu + 2ADP + Pi
1
aspartate
Pi
2
H2O
3
NAD+
NADH+H+
4
PRPP
PPi
5
bicarbonate carbamoylphosphate carbamoylaspartate
dihydroorotate
orotate
orotidine mono-
phosphate
419 / 573

420. Synthesis of pyrimidines (2)
P O
OH OH
N
O
OH
O
HN
O
P O
OH OH
N
O
HN
O
P O
OH OH
N
NH2
N
O
CO2
gln + ATP
glu + ADP + Pi
OMP UMP CMP
420 / 573