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Chapter 24
Biosynthetic Pathways
Chemistry 203
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Catabolic reactions:
Anabolic reactions: Biosynthetic reactions
Complex molecules Simple molecules + Energy
Simple molecules + Energy (in cell) Complex molecules
Metabolism
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Biosynthetic pathways
Anabolic and catabolic reactions have different pathways.
1. Flexibility: if a normal biosynthetic pathway is blocked, the organism can often use the reverse of the catabolic pathway for synthesis.
Complex Molecule Simple MoleculesCatabolic
Biosynthetic
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(Glucose)n +Pi
Glycogen
phosphorylase(Glucose)n-1
Glycogen(one unit smaller)
+Glucose 1-phosphate
(Glucose)n-1 +UDP-glucose (Glucose)nGlycogen
(one unit larger)
+ UDP
2. Overcoming Le Chatelier’s principle:
Biosynthetic pathways
If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to counteract the change.
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Biosynthetic pathways
Anabolic and catabolic reactions need different energy.
Anabolic and catabolic reactions take place in different locations.
Catabolic reactions
Anabolic reactions
Mitochondria
Cytoplasm
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Biosynthetic pathways
1. Biosynthesis of Carbohydrates
2. Biosynthesis of Lipids
Biosynthesis of Fatty acids
Biosynthesis of Membrane Lipids
3. Biosynthesis of Amino acids
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Glycolysis
Glucose is converted to two molecules of pyruvate.
An anaerobic reaction in cytoplasm.
10 Reactions
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Glycolysis
Steps [1] – [5] energy investment phase:
The 6-carbon glucose molecule is converted into two 3-carbon segments.
2 ATP molecules are hydrolyzed.
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Glycolysis
Steps [6] – [10] energy-generating phase:
producing 1 NADH and 2 ATPs for each pyruvate formed.
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Glycolysis
Enzymes:
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Step [1] begins with the phosphorylation of glucose into glucose 6-phosphate, using an ATP and a kinase enzyme.
Glycolysis
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Step [2] isomerizes glucose 6-phosphate to fructose 6-phosphate with an isomerase enzyme.
Glycolysis
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Step [3] is the phosphorylation of fructose 6-phosphate into fructose 1,6-bisphosphate with a kinase enzyme.
Glycolysis
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Glycolysis
Overall, the first three steps of glycolysis:
1.2 phosphate groups is added.
2.A 6-membered glucose ring is isomerized into a 5-membered fructose ring.
3. The energy stored in 2 ATP molecules is utilized to modify the structure of glucose
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Glycolysis
Step [4] cleaves the fructose ring into a dihydroxy-acetone phosphate and a glyceraldehyde 3-phosphate.
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Step [5] isomerizes the dihydroxyacetone phosphate into another glyceraldehyde 3-phosphate.
Glycolysis
Thus, the first phase of glycolysis converts glucose into 2 glyceraldehyde 3-phosphate units and 2 ATP is used.
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In step [6] the aldehyde end of the molecule is oxidized and phosphorylated by a dehydrogenase enzyme and NAD+;this produces 1,3-bisphospho-glycerate and NADH.
Glycolysis
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Glycolysis
In step [7], the phosphate group is transferred onto an ADP with a kinase enzyme, forming 3-phosphoglycerate and ATP.
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In step [8], the phosphate group is isomerized to a new position in 2-phosphoglycerate.
Glycolysis
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In step [9], water is lost to form phosphoenol-pyruvate.
Glycolysis
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Glycolysis
In step [10], the phosphate is transferred to an ADP,yielding pyruvate and ATP with a kinase enzyme.
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The 2 glyceraldehyde 3-phosphate units are converted into 2 pyruvate units in phase two of glycolysis.
Overall, the energy-generating phase forms 2 NADHs and 4 ATPs.
Glycolysis
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Glycolysis
Overall of glycolysis
2 ATPs are used in phase one of glycolysis, and 4 ATPs are made in phase two of glycolysis.
The net result is the synthesis of 2 ATPs from glycolysis.
The 2 NADHs formed are made in the cytoplasm and must be transported to the mitochondria to join the electron transport chain and make ATP.
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under aerobicconditions
under anaerobicconditions
in fermentationby microorganisms
The fate of pyruvate
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Aerobic conditions
The NADH formed needs O2 to return to NAD+, so without O2 no additional pyruvate can be oxidized.
Pyruvate must diffuse across the outer and inner membrane of mitochondria into the matrix.
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Fermentation is the anaerobic conversion of glucose to ethanol and CO2 by yeast and other microorganisms.
Fermentation
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1. Biosynthesis of Carbohydrates
6H2O 6H2O C6H12O6 6H2O+ +energy chlorophyll +(from
sun light)Glucose(from sun)
In plants
6CO2
Photosynthesis
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1. Biosynthesis of Carbohydrates
In animals
When both glucose and stored glycogen are depleted, glucose can be synthesis by gluconeogenesis.
Intermediates of Glycolysis and Citric acid cycle are used to produce glucose.
Gluconeogenesis is not the exact reversal of glycolysis: pyruvate to glucose does not occur by reversing the steps of glucose to pyruvate.
(in liver)
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1. Biosynthesis of Carbohydrates
Only four enzymes are unique.
(compare to glycolysis)
ATP is produced in glycolysis and used up in gluconeogenesis.
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Lactate from glycolysis in muscle is transported to the liver,
where gluconeogenesis converts it back to glucose.
Cori Cycle
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Gluconeogenesis
Glucose is the main source of energy for cells and the only source of energy used by the brain.
Gluconeogenesis is a mechanism that ensures that the brain has a supply of glucose when a diet is low in carbohydrates.
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Conversion of glucose to other Carbohydrates (in animals)
Conversion of glucose to other hexoses (isomers) and synthesis ofdi- or polysaccharides.
Activation of glucose by Uridine Triphosphate (UTP) to form UDP-glucose.
OH
HO
H
O-P-O-P-OCH2
H
OHH
OH
CH2OH
H
O-
O
O-
O
HHHO OH
H HO
HN
N
O
O
Uridine diphosphate glucose (UDP-glucose)
(Similar to ATP)
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UTP
UTP
UDP
UDP
pyrophosphate
pyrophosphate
Glucose 1-phosphate + UDP-glucose +
(Glucose)n +UDP-glucose (Glucose)n+1 +
Glucose 1-phosphate + + (Glucose)n
(Glucose)n+1 + +
OH
HO
H
O-P-O-P-OCH2
H
OHH
OH
CH2OH
H
O-
O
O-
O
HHHO OH
H HO
HN
N
O
O
Uridine diphosphate glucose (UDP-glucose)
OH
HO
H
O-P-O-P-OCH2
H
OHH
OH
CH2OH
H
O-
O
O-
O
HHHO OH
H HO
HN
N
O
O
Uridine diphosphate glucose (UDP-glucose)
- -
OH
HO
H
O-P-O-P-OCH2
H
OHH
OH
CH2OH
H
O-
O
O-
O
HHHO OH
H HO
HN
N
O
O
Uridine diphosphate glucose (UDP-glucose)
OH
HO
H
O-P-O-P-OCH2
H
OHH
OH
CH2OH
H
O-
O
O-
O
HHHO OH
H HO
HN
N
O
O
Uridine diphosphate glucose (UDP-glucose)
- -
Enzyme
Conversion of glucose to other Carbohydrates (in animals)
Glycogenesis: conversion of glucose to glycogen.
Exess glucose is stored in form of glycogen.
Same process to produce di- and polysaccharides.
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2. Biosynthesis of Fatty acids
Our body can produce all the fatty acids except essential fatty acids.
Acetyl CoA
Fatty acids synthesis: in cytoplasm
Degeradation of fatty acids: in mitochondria
They build up two C at a time.
Excess food Acetyl CoA Fatty acids Lipid (fat)
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2. Biosynthesis of Fatty acids
ACP has a side chain that
carries the growing fatty acid
ACP rotates counterclockwise,
and its side chain sweeps over
the multienzyme system (empty spheres).
Acyl Carrier Protein (ACP)
At each enzyme, one reaction of chain is catalyzed.
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CH3C-SCoAO
+ HS-ACP
+ HS-synthase
+ HS-synthase
CH3C-S-ACPO
CH3C-SCoAO
CH3C-S-ACPO
CH3C-S-synthaseO
CH3C-S-SynthaseO
+ HS-CoA
+
+ HS-ACP
HS-CoA
Acetyl-CoA Acetyl-ACP
Acetyl-ACP Acetyl-synthase
Acetyl-synthaseAcetyl-CoA
2. Biosynthesis of Fatty acids
Step 1: ACP picks up an acetyl group from acetyl CoA and delivers to the first enzyme:
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2. Biosynthesis of Fatty acids
Step 2: ACP-malonyltransferase reaction:
Step 3: condensation reaction:
CH2C-SCoA
COO-
O+ HS-ACP CH2C-S-ACP
COO-
O+ HS-CoA
Malonyl-CoA Malonyl-ACP
CH3C-S-synthaseO
+ CH2C-ACPCOO-
O
CH3C-CH2-C-S-ACPO O
+ CO2 + HS-synthase
Acetyl-synthaseMalonyl-ACP
Acetoacetyl-ACP
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Step 4: the first reduction:
Step 5: dehydration:
2. Biosynthesis of Fatty acids
CH3C-CH2-C-S-ACP
O
Acetoacetyl-ACP
+ NADPH + H+
D--Hydroxybutyryl-ACP
C
OH
CH2-C-S-ACPHH3C
O+ NADP+
O
D--Hydroxybutyryl-ACP
OH
C CC-S-ACP
H3C H
+ H2O
Crotonyl-ACP
C
OH
CH2-C-S-ACPHH3C
O
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CH3-CH2-CH2-C-S-ACP
O
Butyryl-ACP
+ NADPH + H+
OH
C C
C-S-ACP
H3C HCrotonyl-ACP
+ NADP+
Step 6: the second reduction:
2. Biosynthesis of Fatty acids
One cycle of merry-go-round.
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Maximum 16C (Palmitic acid). For 18C (Stearic acid) another system and enzyme.
+ CH2C-S-ACPCO2
-
Malonyl-ACP
CH3CH2CH2C-S-ACPO
CH3CH2CH2CH2CH2C-S-ACP
Butyryl-ACP
Hexanoyl-ACP
3. condensation4. reduction
6. reduction5. dehydration
O
O
2. Biosynthesis of Fatty acids
Second cycle:
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3. Biosynthesis of Membrane Lipids
1- Glycerophospholipid
2- Cholesterol
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3. Biosynthesis of Membrane Lipids
Glycerol 1-phosphate, which is obtained by reduction of
dihydroxyacetone phosphate (from glycolysis).
CH2-OHC=OCH2-OPO3
2-NADH + H+
CH2-OHCHCH2-OPO3
2-HO NAD+
Dihydroxyacetonephosphate
Glycerol1-phosphate
+ +
A vehicle for transporting electrons in and out of mitochondria.
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3. Biosynthesis of Membrane Lipids
CH2-OHCHCH2-OPO3
2-HO 2RC-S-CoA
O CH2-OCR
CH
CH2-OPO32-
RCOO
O
2CoA-SH+ +
Acyl CoA A phosphatidateGlycerol1-phosphate
Fatty acids are activated by CoA, forming Fatty Acyl CoA.
An amino alcohol is added to phosphate by phosphate ester bond.
Is activated by CTP (like UTP but cytosine instead of uracil)
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3. Biosynthesis of Membrane Lipids
Cholesterol is made of acetyl CoA (all of the C atoms).
3CH3CSCoAO
-O SCoA
OO OH
Acetyl CoA 3-Hydroxy-3-methylglutaryl-CoA
-O OH
O OH
Mevalonate
HMG-CoAreductase
First reaction of three acetyl CoA to form the six-carbon compound
3-hydroxy-3-methylglutaryl CoA (HMG-CoA).
-2CoA-SH
-1CoA-SH
In Liver
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Mevalonate undergoes phosporylation and decarboxylation to give the C5 compound, isopentenyl pyrophosphate.
3. Biosynthesis of Membrane Lipids
-CO2
ATP ADP-O OH
O OH
MevalonateOP2O6
3-
Isopentenylpyrophosphate
Isoprene
Building block
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Isopentenyl pyrophosphate (C5) is the building block for the synthesis of
geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15).
3. Biosynthesis of Membrane Lipids
OP2O63-
OP2O63-
Geranyl pyrophosphate Farnesyl pyrophosphate
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3. Biosynthesis of Membrane Lipids
HOCholesterol
Two farnesyl pyrophosphate (C15) units are joined to form squalene (C30) and, in a series of at least 25 steps, squalene is converted to cholesterol (C27).
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4. Biosynthesis of Amino Acids
All 20 amino acids are found in a normal diet.
Essential amino acids: cannot be synthesis in our body.
Nonessential amino acids: can be synthesis in our body.
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Most nonessential amino acids are synthesized from
intermediates of either glycolysis or the citric acid cycle.
4. Biosynthesis of Amino Acids
-O-C-CH2-CH2-C-COO-
-Ketoglutarate
+ NH4+
-O-C-CH2-CH2-CH-COO-
NH3+
Glutamate
NADPH + H+
NADP+
O
O O
Amination and reduction
Reverse of oxidative deamination reaction (degradation in catabolism).
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4. Biosynthesis of Amino Acids
Glutamate in turn serves as an intermediate in the synthesis of
several amino acids by the transfer of its amino group by transamination.
COO-
C=OCH3
COO-
CH-NH3+
CH2CH2COO-
COO-
CH-NH3+
CH3
COO-
C=OCH2CH2COO-
-KetoglutaratePyruvate
+
AlanineGlutamate
+