[Christina Smolke] the Metabolic Pathway Engineeri(BookFi.org)
Chapter 19 & 20 Metabolic pathway & Energy production
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Transcript of Chapter 19 & 20 Metabolic pathway & Energy production
Chapter 19 & 20
Metabolic pathway & Energy production
Chemistry 20
Metabolism
Chemical reactions in cells that break down or build molecules. It produces energy and provide substances to cell growth.
Catabolic reactions:
Anabolic reactions:
Complex molecules Simple molecules + Energy
Simple molecules + Energy (in cell) Complex molecules
Metabolism in cell
CarbohydratesPolysaccharides
Proteins
Lipids
GlucoseFructose
Galactose
Amino acids
Glycerol
Fatty acids
Step 1: Digestion and hydrolysis
Glucose Pyruvate Acetyl CoACitricAcidcycle
CO2 & H2O
UreaNH4
+
Step 2: Degradationand some oxidation
Step 3: Oxidation to CO2,H2O and energy
e
e
Mitochondria
Cell Structure
Membrane
Nucleus
Cytoplasm
(Cytosol)
Mitochondria
Nucleus: consists the genes that control DNA replication and protein synthesis of the cell.
Cytoplasm: consists all the materials between nucleus and cell membrane.
Cytosol: fluid part of the cytoplasm (electrolytes and enzymes).
Mitochondria: energy producing factories.
Cell Structure
Enzymes in matrix catalyze the oxidation of carbohydrates, fats , and amino acids.
Produce CO2, H2O, and energy.
ATP and Energy
- Adenosine triphosphate (ATP) is produced from the oxidation of food.
- Has a high energy.
- Can be hydrolyzed and produce energy.
-N-glycosidic bondHH
HO
-O-P-O-P-O-P-O-CH2
HO OH
N
N
N
N
NH2
phosphoric anhydrides
phosphoricester
-D-ribofuranose
adenine
O-O- O-
H
O O O
Ribose
3 Phosphates
ATP and Energy
-O-P-O-P-O-AMPO
O--O
OH2O
ATP ADP
-O-P-O-AMP-O
OH2PO4
-+ + + 7.3 kcal/mol
Pi
(adenosine triphosphate) (adenosine diphosphate) (inorganic phosphate)
- We use this energy for muscle contraction, synthesis an enzyme, send nerve signal, and transport of substances across the cell membrane.
- 1-2 million ATP molecules may be hydrolysis in one second (1 gram in our cells).
- When we eat food, catabolic reactions provide energy to recreate ATP.
ADP + Pi + 7.3 kcal/mol ATP
Step 1: Digestion
Carbohydrates Lipids (fat) Proteins
Convert large molecules to smaller ones
that can be absorbed by the body.
Digestion: Carbohydrates
+
+
Polysaccharides
Dextrins
Maltose Glucose
Mouth
Salivaryamylase
Stomach pH = 2 (acidic)
Maltose +Maltase
Glucose Glucose
Lactose +Lactase
Galactose Glucose
Sucrose +Sucrase
Fructose Glucose
Small intestinepH = 8
Dextrins
Bloodstream Liver (convert all to glucose)
α-amylase (pancreas)
Digestion: Lipids (fat)
Intestinal wall
Monoacylglycerols + 2 Fatty acids → Triacylglycerols
Small intestine
Bloodstream
Glycerol + 3 Fatty acids
H2C
HC
H2C
Fatty acid
Fatty acid
Fatty acid
+ 2H2O
H2C
HC
H2C
OH
Fatty acid
OH
+ 2 Fatty acids
lipase(pancreas)
Triacylglycerol Monoacylglycerol
Protein
Lipoproteins
Chylomicrons
Lymphatic system
Cells Enzymes hydrolyzes
liver Glucose
Digestion: Proteins
Intestinal wall
Small intestine
Bloodstream
Cells
Stomach
Pepsinogen Pepsin
Proteins Polypeptides
HCl
Polypeptides Amino acids
TypsinChymotrypsin
denaturation + hydrolysis
hydrolysis
Some important coenzymes
2 H atoms 2H+ + 2e-
oxidation Coenzyme + Substrate Coenzyme(+2H) + Substrate(-2H)
Reduced Oxidized
NAD+
FAD
Coenzyme A
Coenzymes
NAD+
Nicotinamide adenine dinucleotide
HH
H
O
HO OH
N
CNH2
-O-P-O-CH2
O
O
AMP H
O
a -N-glycosidic bond
+
The plus sign on NAD+
represents the positivecharge on this nitrogen
Nicotinamide;derivedfrom niacin
ADP
(vitamin)
Ribose
- Is a oxidizing agent.
- Participates in reactions that produce (C=O) such as oxidation of alcohols to aldehydes and ketones.
NAD+
CH3-CH2-OH + NAD+ CH3-C-H + NADH + H+
NAD+ + 2H+ + 2e- NADH + H+
NAd
CNH2
OH
H+ 2e-
NAd
CNH2
OH H
+ +
NAD+
(oxidized form)NADH
(reduced form)
:+
O
FAD
Flavin adenine dinucleotide
O=P-O-AMP
O-
CH2
C
O
C
C
CH2
N
H OH
OHH
H
N
N
NH3C
H3C O
HO
OH Ribitol
Flavin
Riboflavin
ADP
(Vitamin B2)
(sugar alcohol)
FAD
- Is a oxidizing agent.
- Participates in reaction that produce (C=C) such as dehydrogenation of alkanes.
R-C-C-R + FAD R-C=C-H + FADH2
H H
H H H H
AdN
N
N
NHH3C
H3C O
O
+ 2H+ + 2e-H3C
H3C O
OH
HAdN
N
N
NH
FAD FADH2
Coenzyme A (CoA)
Aminoethanethiol
( vitamin B5)
Coenzyme A
HS-CoA
Coenzyme A (CoA)
CH3-C- + HS-CoA CH3-C-S-CoA
O O
Acetyl group Coenzyme A Acetyl CoA
- It activates acyl groups, particularly the acetyl group.
Metabolism in cell
CarbohydratesPolysaccharides
Proteins
Lipids
GlucoseFructose
Galactose
Amino acids
Glycerol
Fatty acids
Step 1: Digestion and hydrolysis
Glucose Pyruvate Acetyl CoACitricAcidcycle
CO2 & H2O
UreaNH4
+
Step 2: Degradationand some oxidation
Step 3: Oxidation to CO2,H2O and energy
e
e
Mitochondria
Step 2: Glycolysis
- We obtain most of our energy from glucose.
- Glucose is produced when we digest the carbohydrates in our food.
- We do not need oxygen in glycolysis (anaerobic process).
C6H12O6 + 2 NAD+ 2CH3-C-COO- + 2 NADH + 4H+
O
PyruvateGlucose
2 ADP + 2Pi 2 ATP
Inside of cell
Pathways for pyruvate
Aerobic conditions: if we have enough oxygen.
Anaerobic conditions: if we do not have enough oxygen.
- Pyruvate can produce more energy.
Aerobic conditions
- Pyruvate is oxidized and a C atom remove (CO2).
- Acetyl is attached to coenzyme A (CoA).
- Coenzyme NAD+ is required for oxidation.
CH3-C-C-O- + HS-CoA + NAD+ CH3-C-S-CoA + CO2 + NADH
O O
pyruvate Coenzyme A Acetyl CoA
O
Important intermediate productin metabolism.
Anaerobic conditions
- When we exercise, the O2 stored in our muscle cells is used.
- Pyruvate is reduced to lactate.
- Accumulation of lactate causes the muscles to tire and sore.
- Then we breathe rapidly to repay the O2.
- Most lactate is transported to liver to convert back into pyruvate.
CH3-C-C-O- CH3-C-C-O-
O O
pyruvate Lactate
O HO
H
Reduced
NADH + H+ NAD+
Glycogen
- If we get excess glucose (from our diet), glucose convert to glycogen.
- It is stored in muscle and liver.
- We can use it later to convert into glucose and then energy.
- When glycogen stores are full, glucose is converted to triacylglycerols and stored as body fat.
Metabolism in cell
CarbohydratesPolysaccharides
Proteins
Lipids
GlucoseFructose
Galactose
Amino acids
Glycerol
Fatty acids
Step 1: Digestion and hydrolysis
Glucose Pyruvate Acetyl CoACitricAcidcycle
CO2 & H2O
UreaNH4
+
Step 2: Degradationand some oxidation
Step 3: Oxidation to CO2,H2O and energy
e
e
Mitochondria
Step 3: Citric Acid Cycle
- Is a central pathway in metabolism.
- Uses acetyl CoA from the degradation of carbohydrates, lipids, and proteins.
- Two CO2 are given off.
- There are four oxidation steps in the cycle provide H+ and electrons to reduce FAD and NAD+ (FADH2 and NADH).
8 reactions
Reaction 1
Formation of Citrate
CH3-C-S-CoA
O
Acetyl CoA
COO-
C=O
CH2
COO-
Oxaloacetate
COO-
CH2
CH2
COO-
CHO COO-
Citrate
+ CoA-SH
Coenzyme A
+
H2O
Reaction 2
Isomerisation to Isocitrate
COO-
CH2
CH2
COO-
CHO COO-
Citrate Isocitrate
COO-
CH2
C
COO-
CH COO-
HO H
Isomerisation
- Because the tertiary –OH cannot be oxidized. (convert to secondary –OH)
Reaction 3
First oxidative decarboxylation (CO2)
Isocitrate
COO-
CH2
C
COO-
CH COO-
HO H
- Oxidation (-OH converts to C=O).- NAD+ is reduced to NADH.- A carboxylate group (-COO-) is removed (CO2).
C-COO-H
CH-COO-
CH2-COO-
HOIsocitrate
C-COO-H
C-COO-
CH2-COO-
C-HH
C-COO-
CH2-COO-
NADH + H+NAD+
-Ketoglutarate
CO2
isocitratedehydrogenase
O O
Oxalosuccinate
COO-
CH2
C
COO-
CH COO-
O
α-Ketoglutrate
COO-
CH2
C
COO-
CH2
O
CO2
Reaction 4
Second oxidative decarboxylation (CO2)
α-Ketoglutrate
COO-
CH2
C
COO-
CH2
O CH2
C-COO-
CH2-COO-
-Ketoglutarate
O
CoA-SH
NADHNAD+
-ketoglutaratedehydrogenase
complex
CH2
C
CH2-COO-
SCoAOSuccinyl-CoA
+ CO2
Succinyl CoA
COO-
CH2
C
S-CoA
CH2
O + CO2
- Coenzyme A convert to succinyl CoA.- NAD+ is reduced to NADH.- A second carboxylate group (-COO-) is removed (CO2).
Reaction 5
Hydrolysis of Succinyl CoA
Succinyl CoA
COO-
CH2
C
S-CoA
CH2
O
- Energy from hydrolysis of succinyl CoA is used to add a phosphate group (Pi) to GDP (guanosine diphosphate).
- Phosphate group (Pi) add to ADP to produce ATP.
+ H2O + GDP + Pi
COO-
CH2
CH2
COO-
Succinate
+ GTP + CoA-SHFAD FADH2
CH2-COO-
CH2-COO-
Succinate
succinatedehydrogenase
C
CH
H
COO-
-OOC
Fumarate
ADP + Pi ATP
Reaction 6
Dehydrogenation of Succinate
- H is removed from two carbon atoms.- Double bond is produced.- FAD is reduced to FADH2.
COO-
CH2
CH2
COO-
Succinate
FAD FADH2
CH2-COO-
CH2-COO-
Succinate
succinatedehydrogenase
C
CH
H
COO-
-OOC
Fumarate
COO-
CH
CH
COO-
Fumarate
Reaction 7
Hydration
- Water adds to double bond of fumarate to produce malate.
COO-
C
CH2
COO-
HO H
Malate
H2O
COO-
CH
CH
COO-
Fumarate
Reaction 8
Dehydrogenation forms oxaloacetate
- -OH group in malate is oxidized to oxaloacetate.
- Coenzyme NAD+ is reduced to NADH + H+.
COO-
C
CH2
COO-
HO H
Malate
COO-
C=O
CH2
COO-
Oxaloacetate
C-COO-
CH2-COO-
Oxaloacetate
NAD+ NADH
malatedehydrogenase
CH-COO-HO
CH2-COO-
L-Malate
O+ H+
Summary
Pyruvate
-KetoglutarateSuccinyl-CoA
Fumarate
Oxaloacetate
Fatty AcidsProteins
Acetyl-CoA
Carbohydrates
Malate
intermediatesof the citric acid cycle
The catabolism of proteins, carbohydrates, and fatty acids
all feed into the citric acid cycle at one or more points:
Summary
FAD
FADH2
NAD+
NADH
NAD+
NADHCO2
NAD+
NADHCO2
Acetyl-CoA
GDPGTP
Citric acidcycle
(8 steps)
CoA
+ H+
+ H+
H+ +
CoA
CH3C-SCoAO
+ GDP +Pi + 3NAD++ FAD + 2H2O
2CO2 + GTPCoA + 3NADH + FADH2 + 3H++
12 ATP produced from each acetyl-CoA
Electron Transport
H+ and electrons from NADH and FADH2 are carried by an electron carrieruntil they combine with oxygen to form H2O.
FMN (Flavin Mononucleotide)
Fe-S clusters
Coenzyme Q (CoQ)
Cytochrome (cyt)
Electron carriers
FMN (Flavin Mononucleotide)
O=P-O-AMP
O-
CH2
C
O
C
C
CH2
N
H OH
OHH
H
N
N
NH3C
H3C O
HO
OH Ribitol
Flavin
Riboflavin
(Vitamin B2)
(sugar alcohol)
-
2H+ + 2e-
O=P-O-AMP
O-
CH2
C
O
C
C
CH2
N
H OH
OHH
H
N
N
NH3C
H3C O
HO
OH Ribitol
Flavin
Riboflavin
-
H
H
FMN + 2H+ + 2e- → FMNH2
Reduced
Fe-S Clusters
Fe3+
SS
SS
Cys
Cys
Cys
Cys
Fe2+
SS
SS
Cys
Cys
Cys
Cys
+ 1 e-
Fe3+ + 1e- Fe2+
Reduced
Coenzyme Q (CoQ)
OH
OH
2H+ + 2e-
Reduced Coenzyme Q (QH2)Coenzyme Q
Q + 2H+ + 2e- → QH2
Reduced
Cytochromes (cyt)
- They contain an iron ion (Fe3+) in a heme group.
- They accept an electron and reduce to (Fe2+).
- They pass the electron to the next cytochrome and they are oxidized back to Fe3+.
Fe3+ + 1e- Fe2+
ReducedOxidized
cyt b, cyt c1, cyt c, cyt a, cyt a3
Electron Transfer
Mitochondria
Electron Transfer
Complex I
NADH + H+ + FMN → NAD+ + FMNH2
FMNH2 + Q → QH2 + FMN
NADH + H+ + Q → QH2 + NAD+
Complex II
FADH2 + Q → FAD + QH2
Electron Transfer
Complex III
QH2 + 2 cyt b (Fe3+) → Q + 2 cyt b (Fe2+) + 2H+
Complex IV
4H+ + 4e- + O2 → 2H2O
Oxidative Phosphorylation
Transport of electrons produce energy to convert ADP to ATP.
ADP + Pi + energy → ATP
Chemiosmotic model
- H+ make inner mitochondria acidic.- Produces different proton gradient. - H+ pass through ATP synthase (a protein complex).
ATP synthase
Total ATP
Glycolysis: 6 ATP
Pyruvate: 6 ATP
Citric acid cycle: 24 ATP
36 ATPOxidation of glucose
C6H12O6 + 6O2 + 36 ADP + 36 Pi → 6CO2 + 6H2O + 36 ATP
Metabolism in cell
CarbohydratesPolysaccharides
Proteins
Lipids
GlucoseFructose
Galactose
Amino acids
Glycerol
Fatty acids
Step 1: Digestion and hydrolysis
Glucose Pyruvate Acetyl CoACitricAcidcycle
CO2 & H2O
UreaNH4
+
Step 2: Degradationand some oxidation
Step 3: Oxidation to CO2,H2O and energy
e
e
Mitochondria
Oxidation of fatty acids
CH3-(CH2)14-CH2-CH2-C-OH
O α
oxidation
- Oxidation happens in step 2 and 3.
- Each beta oxidation produces acetyl CoA and a shorter fatty acid.
- Oxidation continues until fatty acid is completely break down to acytel CoA.
Oxidation of fatty acids
Fatty acid activation
- Before oxidation, they activate in cytosol.
R-CH2-C-OH
O
+ ATP + HS-CoA R-CH2-C-S-CoA
O
+ H2O + AMP + 2Pi
Fatty acyl CoAFatty acid
-Oxidation: 4 reactions
Reaction 1: Oxidation (dehydrogenation)
R-CH2-C-C-C-S-CoA
O
Fatty acyl CoA
H H
H H
+ FAD R-CH2-C=C-C-S-CoA + FADH2
OH
H
Reaction 2: Hydration
R-CH2-C=C-C-S-CoA + H2O
OH
H
R-CH2-C-C-C-S-CoA
O
H H
HHO
Reaction 3: Oxidation (dehydrogenation)
Reaction 4: Cleavage of Acetyl CoA
R-CH2-C-C-C-S-CoA + NAD+
O
H H
HHO
R-CH2-C-CH2-C-S-CoA + NADH+ H+
OO
R-CH2-C-CH2-C-S-CoA + CoA-SH
OO
R-CH2-C-S-CoA
O
CH3-C-S-CoA
O
+
Acetyl CoAFatty acyl CoA
Oxidation of fatty acids
One cycle of -oxidation
R-CH2-CH2-C-S-CoA + NAD+ + FAD + H2O + CoA-SH
O
R-C-S-CoA
O
CH3-C-S-CoA + NADH + H+ + FADH2
O
+
Acetyl CoAFatty acyl CoA
# of Acetyl CoA =# of fatty acid carbon
2= 1 + oxidation cycles
Ketone bodies
- If carbohydrates are not available to produce energy.
- Body breaks down body fat to fatty acids and then Acetyl CoA.
- Acetyl CoA combine together to produce ketone bodies.
- They are produced in liver.
- They are transported to cells (heart, brain, or muscle).
CH3-C-S-CoA
O
Acetyl CoA
CH3-C-S-CoA
OCH3-C-CH2-C-O-
O O CH3-C-CH3 + CO2 + energy
O
Acetoacetate
Acetone
-Hydroxybutyrate
CH3-CH-CH2-C-O-
OH O
Ketosis (disease)
- When ketone bodies accumulate and they cannot be metabolized.
- Found in diabetes and in high diet in fat and low in carbohydrates.
- They can lower the blood pH (acidosis).
- Blood cannot carry oxygen and cause breathing difficulties.
Fatty acid synthesis
- When glycogen store is full (no more energy need).
- Excess acetyl CoA convert to 16-C fatty acid (palmitic acid) in cytosol.
- New fatty acids are attached to glycerol to make triacylglycerols. (are stored as body fat)
Metabolism in cell
CarbohydratesPolysaccharides
Proteins
Lipids
GlucoseFructose
Galactose
Amino acids
Glycerol
Fatty acids
Step 1: Digestion and hydrolysis
Glucose Pyruvate Acetyl CoACitricAcidcycle
CO2 & H2O
UreaNH4
+
Step 2: Degradationand some oxidation
Step 3: Oxidation to CO2,H2O and energy
e
e
Mitochondria
Degradation of amino acids
- They are degraded in liver.
Transamination:
- They react with α-keto acids and produce a new amino acid and a new α-keto acid.
-OOC-C-CH2-CH2-COO-
O
alanine
CH3-CH-COO-
NH3
+
+
α-ketoglutarate
-OOC-CH-CH2-CH2-COO-
O
pyruvate
CH3-C-COO-
NH3
+
+
glutamate
Degradation of amino acids
Oxidative Deamination
-OOC-CH-CH2-CH2-COO-
NH3
+
glutamate
+ H2O + NAD+
-OOC-C-CH2-CH2-COO-
O
α-ketoglutarate
glutamatedehydrogenase
+ NH4+ + NADH + H+
Urea cycle
- Ammonium ion (NH4+) is highly toxic.
- Combines with CO2 to produce urea (excreted in urine).
- If urea is not properly excreted, BUN (Blood Urea Nitrogen) level in blood becomes high and it build up a toxic level (renal disease).
- Protein intake must be reduced and hemodialysis may be needed.
H2N-C-NH2 + 2H+ + H2O
O
urea
2NH4+ + CO2
Energy from amino acids
- C from transamination are used as intermediates of the citric acid cycle.
- amino acid with 3C: pyruvate- amino acid with 4C: oxaloacetate- amino acid with 5C: α-ketoglutarate
- 10% of our energy comes from amino acids.
- But, if carbohydrates and fat stores are finished, we take energy from them.