Download Metabolism - UPM EduTrain Interactive Learning

Why Study Metabolism?
• Classification of bacteria
– Oxygen Tolerance
– Biochemical reactions
• Acids, Ammonia, Gases
• Fermentation Products
– Food Products
• Yogurt, Sour Cream, Bread, Alcohol
– Commercial Products
• Citric Acid, Plastics
• Environmental Cleanup
Metabolism?
● Metabolism Is the Sum of Cellular Reactions - the
entire network of chemical reactions carried out by
living cells
● Arises from interactions between molecules
● Metabolism = Anabolism + Catabolism
● Catabolic reactions - degrade molecules to create
smaller molecules and energy
● Anabolic reactions - synthesize molecules for cell
maintenance, growth and reproduction
● Metabolites - small molecule intermediates in the
degradation and synthesis of polymers
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Organization of the Chemistry of Life into
Metabolic Pathways
• A metabolic pathway has many steps
– That begin with a specific molecule and end with
a product
– That are each catalyzed by a specific enzyme
Enzyme 1
A
Enzyme 3
D
C
B
Reaction 1
Starting
molecule
Enzyme 2
Reaction 2
Reaction 3
Product
Organization of the Chemistry of Life into
Metabolic Pathways
• Catabolic pathways
– Break down complex molecules into
simpler compounds
– Release energy
• Anabolic pathways
– Build complicated molecules from simpler
ones
– Consume energy
Metabolism
Breakdown
Proteins to Amino Acids, Starch to Glucose
Synthesis
Amino Acids to Proteins, Glucose to Starch
Overview of Metabolism
 Source of Energy (Photo- vs. Chemotroph)




Source of Electrons
Carrier of Electrons
Final Electron Acceptor
Source of Carbon (Auto- vs. Heterotroph)


Auto- : Carbon Dioxide
Hetero- : Organic Compounds
Classification based on Metabolism
 Where microbes get their energy?
◊ Sunlight vs. Chemical
◊ Photo- vs. Chemo- trophs
 How do they obtain carbon?
◊ Carbon Dioxide (or inorganic compounds) vs.
Organic Compounds (sugars, amino acids)
◊ Auto- vs. Hetero- trophs

Examples
◊ Photoautotrophs vs. Photoheterotrophs
◊ Chemoautotrophs vs. Chemoheterotrophs
Types of -trophs
Type
PhotoautoPhotoheteroChemoauto-
Energy C-Source
Example
Purple & Green
sulfur bacteria
Sun
CO2
Sun
Organic
Purple & Green
compounds Non-sulfur bacteria
Chemical
CO2
bonds
H, S, Fe, N bacteria
Most bacteria,
Chemical Organic
Chemoheterofungi, protozoa,
bonds Compounds
animals
Source of Electrons
 Autotrophs
◊ Photosynthesis
◊ H2O, H2S
 Chemotrophs
◊ Organic Compounds
◊ Carbohydrates (C H2O)
 Glucose, Lactose, Sucrose, Mannitol, Citrate
◊ Amino Acids
Electron Carriers
• Photosynthesis
 NADP + H to NADPH
• Respiration
 NAD + H to NADH
 FAD + H to FADH
• Contain Niacin and Riboflavin
 Vitamins, not stable
 Can’t store these molecules
Final Electron Acceptor
 Photosynthesis


CO2 + H’s to CH2O
Stores energy
 Respiration

Aerobic

½O2 + H 2 to H2O
 Anaerobic

Fermentation
Movement of Electrons
•
•
•
•
Chemical reactions
Oxidation Reactions
Reduction Reactions
Reactions Coupled
– Redox reactions
Comparison of oxidation and reduction
Oxidation
Reduction
Loss of electron (A)
gain of electrons (B)
Gain of oxygen
Loss of oxygen
Loss of Hydrogen
Gain of Hydrogen
Loss of energy
(Liberates energy)
Exothermic; exergonic
(gives off heat energy)
Gain of energy (stores
energy in the reduced
compound)
Endothermic; endergonic
(requires energy, such As
heat)
Oxidation
Reduction
Example of Redox Equations
Example of Redox Equations
Example of Redox Equations
Examples
• ATP  ADP + P
◊
Oxidation, release energy
• ADP + P  ATP
◊
Reduction, stores energy
• NAD + H  NADH
• FADH  FAD + H
• NH4 + 1½O2 NO2- +H2O + 2H + ATP
• 2H2 + O2  2H2 O
Examples
 Cellular Respiration

C6H12 O6 + 6O2 6H2O + 6CO2 + 38 ATP
 Photosynthesis

6H2O + 6CO2 + light  C6H12 O6 + 6O2
 Nitrification

NH4  NO2 to NO3
• Ammonia to Nitrite to Nitrate
 Ammonification

N2  NH4
Forms of Energy
• Energy
– Is the capacity to cause change
– Exists in various forms, of which some can
perform work
• Kinetic energy

Is the energy associated with motion
• Potential energy


Is stored in the location of matter
Includes chemical energy stored in molecular
structure
Energy can be converted From one form to another
Concept : The free-energy change of
a reaction tells us
whether the reaction
occurs spontaneously
Free-Energy Change, DG

The change in free energy, ∆G during a
biological process is related directly to the
enthalpy change (∆H) and the change in
entropy (DS)
∆G = ∆H – T∆S
Free-Energy Change, DG
Free-Energy Change
● A living system’s free energy = energy that can do
work under cellular conditions
● Free-energy change (G) is a measure of the
chemical energy available from a reaction

G = Gproducts - Greactants
● The free energy change (G) of a reaction
determines its spontaneity
● A reaction is spontaneous if ∆G is negative (if the
free energy of products is less than that of
reactants).
Bioenergetics and Thermodynamics
Enthalphy
● A thermodynamic function of a system
● The heat content of a chemical system
= sum of the internal energy of the system + the
product of its volume multiplied by the pressure
exerted on it by its surroundings
Bioenergetics and Thermodynamics
Entrophy
● Entropy is the quantitative measure of disorder in a
system
● In any closed system, the entropy of the system will
either remain constant or increase
● E.g. adding heat to a system causes the molecules
and atoms to speed up
Relationship between energy and entropy
● The change in free energy, ∆G during a biological
process Is related directly to the enthalpy change
(∆H) and the change in entropy
∆G = ∆H – T∆S
DH = change in enthalpy
DS = change in entropy ; T = degree Kelvin
◘ -DG = a spontaneous reaction in the direction
written
◘
+DG = the reaction is not spontaneous
◘ DG = 0 the reaction is at equilibrium
Standard Free-Energy Change (DGo)

Reaction free-energy depends upon conditions

Standard state (DGo) - defined reference conditions
Standard Temperature = 298K (25oC)
Standard Pressure = 1 atmosphere
Standard Solute Concentration = 1.0M

Standard transformed constant = DGo’
Standard H+ concentration = 10-7 (pH = 7.0)
H2O concentration = 55.5 M
Mg2+ concentration = 1 mM
For a reaction A + B  C + D
G = Go' + RT ln
[C] [D]
[A] [B]
DGo' = standard free energy change (at pH 7, 1M
reactants & products); R = gas constant; T =
temp)
At equilibrium DG = 0.
K'eq, the ratio [C][D]/[A][B]
at equilibrium, is the
equilibrium constant.
An equilibrium constant
(K'eq) greater than one
indicates a spontaneous
reaction (negative DG').
[C] [D]
[A] [B]
G = Gº' + RT ln

 = Gº' + RT ln
Gº' = - RTln
[C] [D]
[A] [B]
[C] [D]
[A] [B]
[C] [D]
defining K'eq =
[A] [B]
Gº' = - RT ln K'eq
DGo' = - RT ln K'eq
Variation of equilibrium constant with DGo‘ (25 oC)
K'eq
G º'
kJ/mol
104
- 23
proceeds forward (spontaneous)
102
- 11
proceeds forward (spontaneous)
100 = 1
0
Starting with 1 M reactants &
products, the reaction:
is at equilibrium
10-2
+ 11
reverses to form “reactants”
10-4
+ 23
reverses to form “reactants”
• ATP hydrolysis
–
Can be coupled to other reactions
Endergonic reaction: ∆G is positive, reaction
is not spontaneous
NH2
Glu
NH3
+
Glutamic
acid
Ammonia
∆G = +3.4 kcal/mol
Glu
Glutamine
Exergonic reaction: ∆ G is negative, reaction
is spontaneous
ATP
+
H2O
ADP
+
Coupled reactions: Overall ∆G is negative;
together, reactions are spontaneous
P
∆G = - 7.3 kcal/mol
∆G = –3.9 kcal/mol
Other examples of high energy compounds
Phosphocreatine
Other examples of high energy compounds
Phosphoenolpyruvate (PEP)
Other examples of high energy compounds
1, 3-bisphosphoglycerate
• At maximum stability
– The system is at equilibrium
• More free energy (higher G)
• Less stable
• Greater work capacity
In a spontaneously change
• The free energy of the system
decreases (∆G<0)
• The system becomes more stable
• The released free energy can
be harnessed to do work
.
• Less free energy (lower G)
• More stable
• Less work capacity
(a)
Gravitational motion. Objects
move spontaneously from a
higher altitude to a lower one.
(b)
Diffusion. Molecules
in a drop of dye
diffuse
until they are
randomly dispersed.
(c)
Chemical reaction.
In a
cell, a sugar
molecule is
broken down into
simpler
molecules.
Free Energy and
Metabolism
Exergonic and Endergonic Reactions in Metabolism
• An exergonic reaction
– Proceeds with a net release of free energy and is
spontaneous
Free energy
Reactants
Amount of
Energy released
(∆G <0)
Energy
Products
Progress of the reaction
(a) Exergonic reaction: energy released
Exergonic and Endergonic Reactions in Metabolism
• An endergonic reaction
– Is one that absorbs free energy from its
surroundings and is nonspontaneous
Free energy
Products
Energy
Reactants
Progress of the reaction
(b) Endergonic reaction: energy required
Amount of
Energy released
(∆G>0)
Equilibrium and Metabolism
• Reactions in a closed system
– Eventually reach equilibrium
∆G < 0
∆G = 0
(a) A closed hydroelectric system. Water
flowing downhill turns a turbine that drives a
generator providing electricity to a light bulb,
but only until the system reaches equilibrium.
Cells in our body
– Experience a constant flow of materials in and
out, preventing metabolic pathways from
reaching equilibrium
(b) An open hydroelectric
system. Flowing water
keeps driving the generator
because intake and outflow
of water keep the system
from reaching equlibrium.
∆G < 0
• An analogy for cellular respiration
∆G < 0
∆G < 0
∆G < 0
(c) A multistep open hydroelectric system. Cellular respiration is
analogous to this system: Glucoce is broken down in a series
of exergonic reactions that power the work of the cell. The product
of each reaction becomes the reactant for the next, so no reaction
reaches equilibrium.
•
Concept :ATP powers cellular work by coupling
exergonic reactions to endergonic reactions
•
A cell does three main kinds of work
– Mechanical
– Transport
– Chemical
• Energy coupling
– Is a key feature in the way cells manage their
energy resources to do this work
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OBJECTIVE –Learning outcome
1. learn essentially all of the reactions in the glycolytic
pathway (substrates and products)
2. understand where the free energy changes come from
which allow production of ATP in glycolysis
3. Know the activators and inhibitors of the major
regulated enzymes in glycolysis and understand the
metabolic logic of their function.
4. What is "substrate level" phosphorylation?
5. Understand the connection between glycolysis and
glycogen synthesis & gluconeogenesis
6. relationship between glycolysis, gluconeogenesis and
the pentose pathway.
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METABOLISM
● Summation of all chemical reactions in an organism in
order to maintain life
● These processes allow organisms to grow and
reproduce, maintain their structures, and respond to
their environments
● Metabolism is usually divided into two categories.
a.
Catabolism breaks down large molecules, for
example to harvest energy in cellular respiration.
b.
Anabolism, uses energy to construct components
of cells such as proteins and nucleic acids.
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METABOLISM
● The chemical reactions of metabolism are organized
into metabolic pathways, in which one chemical is
transformed into another by a sequence of enzymes.
● Enzymes are crucial to metabolism because they
allow organisms to drive desirable but
thermodynamically unfavorable reactions by
coupling them to favorable ones.
●
Enzymes also allow the regulation of metabolic
pathways in response to changes in the cell's
environment or signals from other cells.
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CARBOHYDRATE METABOLISM
● All organisms obtain energy from the oxidation of
glucose and other carbohydrates
● In some cells and organisms, glucose is the major or
sole source of energy

Brain

Erythrocytes

Many bacteria
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CARBOHYDRATE METABOLISM
Major pathways
1. Glycolysis
● Main pathway for glucose oxidation
● Forms pyruvate anaerobically
2. Phosphogluconate pathway
● an auxillary route for glucose oxidation in
animals
● Produces ribose-5-phosphate
3. Gluconeogenesis
● Pathway for the synthesis from pyruvate
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Energy metabolism of glucose
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GLYCOLYSIS
● First stage of CHO metabolism
● Simple sugars are broken down to pyruvate
● Anaerobic process – no oxygen required
● All life use this process
● Requires






Glucose
2ADP
2ATP
2NAD+
2PO4=
10 different enzymes
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Overall Glycolysis
● Net energy produced is 2ATP
● The two pyruvate can go on the citric acid cycle to
produce more energy
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Glycolysis = two phases
1. a preparatory phase
2. payoff or energy-yielding phase.
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Preparatory phase
Energy-yielding
phase
Overall Glycolysis
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6-Carbon
Stage Requires
Energy
GLUCOSE
ADP
ATP
Glucose-6-phosphate
Fructose-6-phosphate
ADP
ATP
Fructose-1,6-diphosphate
Glyceraldehyde-3-P
Dihydroxyacetone -P
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Glyceraldehyde -3-phosphate
NAD
Pi
NADH + H
1-3-Dihosphoglycerate
ADP
ATP
3-Carbon Stage
– Double this
because 2piruvate are
produced
3-phosphoglycerate
2-dihosphoglycerate
3-phosphoenolpyruvgate
ADP
ATP
PYRUVATE
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Overall Glycolysis
Glucose + 2ATP + 2ADP + 2PO42- + 2NAD+
10 enzymes
2 Pyruvate + 2NADH + 2H2O + 4ATP
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Regulation of Glycolysis
AS with all metabolic pathways, glycolysis is under
constant control by the body
Glycolysis is regulated by 3 enzymes
1.
Hexokinase
Inhibited by glucose-6-phosphate
2.
Phosphofructokinase
Inhibited by glucose-6-phosphate
3.
Pyruvate kinase
Inhibited by ATP
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Feedback inhibition
GLUCOSE
Hexokinase
Glucose-6-phosphate
Fructose-6-phosphate
Phosphofructokinase
Fructose-1,6-diphosphate
Phosphophenolpyruvate
Pyruvate kinase
PYRUVATE
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OVERVIEW OF GLYCOLYSIS
68
Glycolysis pathway is similar in all organisms
What happens to pyruvate?
What happens to pyruvate will vary significantly
1. In animal, plant and many microbial cells, under
aerobic conditions – pyruvate is converted to acetylCoA in mitochondria
2. Under anaerobic conditions – fermentation to
produce lactate/ethanol
69
FERMENTATION
 Processing of pyruvate under anaerobic
conditions
 2 types – lactate and alcohol fermentations
70
Lactate fermentation
 Lactate produced by muscles when the
body cannot supply enough O2
 Anaerobic conversion of pyruvate to lactate
permits regeneration of NAD+
 Body can then make more ATP – but at a
cost- creates an oxygen debt
 Must use extra O2 to oxidise lactate later
71
Lactate fermentation
72
Alcohol fermentation
73
Alcohol fermentation
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What happens to Pyruvate?
 Pyruvate is the final product of the 10 step
pathway of glycolysis.
 The next step in the oxidation of glucose is the
conversion of pyruvate to acetyl-CoA, and the
subsequent oxidation of this two carbon compound
to CO2
 The metabolic pathway in which this occurs is a
cyclic one known as the Citric Acid Cycle (CAC) or
Krebs Cycle or TCA Cycle
 Acetyl CoA comes from multiple sources including
carbohydrates, fats and many amino acids
76
The citric acid cycle
 Also known as Krebs cycle after the founder, Hans
Kreb
 Final stage for the metabolism of carbohydrates
 Requires oxygen – aerobic process
77
Conversion of pyruvate to acetyl-CoA
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How?
Where?
Energy extracted???
How much
OXIDATIVE PHOSPHORYLATION
85
OXIDATIVE PHOSPHORYLATION
 Oxidative phosphorylation is the process in which ATP
is formed as a result of the transfer of electrons from
NADH or FADH2 to O2 by a series of electron carriers –
Electron transport system
 The NADH and FADH2 formed in glycolysis, fatty acid
oxidation, and the citric acid cycle are energy-rich
molecules because each contains a pair of electrons
having a high transfer potential
 takes place in mitochondria
 the major source of ATP in aerobic organisms
86
Electron Transport Schematic
87
Electron Transport Schematic
1. Citric acid cycle  NADH and FADH2 - energy-rich
molecules because each contains a pair of electrons
having a high transfer potential = electron motive
force
2. The flow of electrons from NADH or FADH2 to O2
through protein complexes located in the
mitochondrial inner membrane leads to the
pumping of protons out of the mitochondrial oxidoreductase, Q-cytochrome c oxidoreductase, and
cytochrome c oxidase
3. These large transmembrane complexes contain
multiple oxidation-reduction centers, including
quinones, flavins, iron-sulfur clusters, hemes, and
copper ions
88
Flavin adenine dinucleotide
89
Electron Transport Schematic
90
Electron Transport Schematic
4. The final phase of oxidative phosphorylation is
carried out by ATP synthase, an ATP-synthesizing
assembly that is driven by the flow of protons back
into the mitochondrial matrix
91
ELECTRON TRANSPORT CHAIN
 NADH and FADH2 carry protons (H+) and electrons (e-) to
the electron transport chain located in the membrane
 The energy from the transfer of electrons along the chain
transports protons across the membrane and creates an
electrochemical gradient.
 As the accumulating protons follow the electrochemical
gradient back across the membrane through an ATP
synthase complex, the movement of the protons provides
energy for synthesizing ATP from ADP and phosphate
 At the end of the electron transport system, two protons,
two electrons, and half of an oxygen molecule combine to
form water.
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ATP synthase and the F1 complex
In this step, the H+ concentration difference between the
mitochondrial matrix and the intermembrane space is
what provides the energy to produce ATP
Steps consist of
H+ transport – movment of H+
F1 event = production of ATP
96
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GLUCONEOGENESIS
 Process where glucose is synthesised
 Occurs primarily in the liver
 Common materials used as starting materials are
o
o
o
Lactate
All amino acids except leucine and lysine
Glycerol from fats
 Sometimes referred to as “reverse glycolysis” but not
true because glycolysis is not reversible
 Only used under starvation conditions
99
100
Gluconeogenesis appears to be the exact reverse of
glycolysis but why is it not the reverse of glycolysis?
Because there 3 reactions in glycolysis that are not
reversible
1. Phosphoenol pyruvate to pyruvate – catalysed by
piruvate kinase
2. Fructose 6 phosphate to fructose 1,6-biphosphate –
catalysed by phospho fructokinase-1
3. Glucose 6-phosphate to glucose 6-phosphate –
catalysed by hexokinase
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These 3 reactions must be bypassed in gluconeogenesis
By pass 1- Pyruvate to Phosphoenolpyruvate
 Pyruvate in cytoplasm is transported into the
mitochondria where it converted to oxaloacetate
by pyruvate carboxylase
 OAA is transported back to the cytoplasm where it
is converted to PEP (phosphoenolpyruvate) by PEP
carboxykinase
103
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By pass 2 – Fructose 1,6-Biphosphate to Fructose 6phosphate
Reaction catalysed by fructose 1,6-biphosphatase
Fructose 1,6-biphosphate + H2O  fructose 6phosphate + Pi
By pass 3 – Glucose 6-phosphate to glucose
Reaction catalysed by glucose 6-phosphatase
Glucose 6-phosphate + H2O  glucose + Pi
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PENTOSE PHOSPHATE PATHWAY
 The major catabolic fate of most glucose is oxidation
via the TCA cycle.
 However, some can undergo the pentose pathway.
The pentose pathway has several names-the
phosphogluconate pathway, or the hexose
monophosphate pathway.
 Importance?
1. yields the five carbon sugars used in
biosynthesis of RNA, DNA, and coenzymes such
as ATP, NAD+, FAD, and coenzyme A - required
by rapidly growing cells such as those of bone
marrow, skin and intestinal mucosa.
108
2. To produce NADPH which are required
a. for reductive biosynthetic reactions - fatty acid
biosynthetic reactions in liver, adipose tissue and
lactating mammary glands, cholesterol and
steroid hormones
b. for protection of tissues from damage due to
reactive oxygen species. Erythrocytes and the cells
of the cornea are exposed to high concentrations
of oxygen and are therefore prone to oxidative
damage from a variety of oxygen radicals.
NADPH is required to reduce glutathione which is
one of the prime defenses from oxidative damage.
109
PENTOSE PHOSPHATE PATHWAY
The pentose pathway is logically divided into two
components,
1. an oxidative component in which 2 moles of NADPH
are produced for each mole of glucose 6-phosphate
that enters the pathway.
2. The second portion of the pentose pathway is the
nonoxidative phase in which the product of the
oxidative phase is reorganized into glucose 6phosphate.
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OVERVIEW OF GLYCOLYSIS
116
Glycolysis –Steps 1-6
117
Glycolysis –Steps 6-10
118
Pyruvate Pathways
119
Pyruvate Oxidation
120
Krebs Cycle Overview
121
Krebs Cycle begins
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ELECTRON TRANSPORT CHAIN
Chemiosmosis
Overview of ATP Synthesis
ATP Theoretical Yield
Catabolism of other Organic Molecules