Week 2 Notes

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Transcript Week 2 Notes

Week 2 Lecture Material
October 2001
Metabolism
Metabolism
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Chemical processes taking place in the
cell
Chemicals from which cells are built are
called nutrients
Metabolism generates the essential
elements of the cell and the energy to
put them together in an organized
fashion
Why Does Metabolism Take Place?
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For metabolism to take place, there has
to be a chemical which is willing to give
up electrons.
This chemical is called the electron
donor
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organic: carbohydrates, lipids, aromatics, etc.
inorganic: ammonia, sulfide, ferrous iron, etc.
If there is an electron donor, then there
must be an electron acceptor
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oxygen, nitrate, sulfate, ferrous iron, pyruvic acid,
etc.
What Types of Reactions Occur
During Metabolism?
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Oxidation/Reduction Reactions with Chemical
as Donor
 carbon oxidized to CO2
 ammonia oxidized to nitrate
 sulfur oxidized to sulfate
Oxidation/Reduction Reactions with Chemical
as Acceptor
 carbon dioxide reduced to CH4
 nitrate reduced to nitrogen gas
Where is Metabolism Important in
Environmental Management
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Agriculture waste management
Domestic wastewater treatment
Protection of drinking water from pathogens
and taste and odors
Bioremediation of contaminated
groundwater, soil, and air
Biological corrosion of structures
Fresh and marine ecosystem productivity
Ecosystem Management
Wastewater Treatment
Treatment of Air Emissions
Airplane Deicing
Sludge Land Application and Spills
Bioremediation of Gas Spills
Composting Explosives
Metabolism Basics
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Energetics
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Enzyme Function
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Oxidation/Reduction Half Reactions
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Electron Carriers
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Energy Carriers
Energetics
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Chemical energy is released when
compounds are oxidized
The amount available for useful work is
defined as free energy (G) kCal or kJ
Go’ is negative: energy is released and
reaction is spontaneous as written
(exergonic)
Go’ is positive: the reaction is not
spontaneous as written and is referred to as
endergonic
Change in Free Energy
A + B
C + D
Go’ = Gof [C + D] - Gof [A + B]
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Go’ = free energy of reaction at standard
conditions, all reactants and
products at 1 molar, and pH 7
Gof = free energy of formation
need to make sure the reaction is balanced
Free Energy of Reaction Example
H2S + 8 Fe3+
H2S + 8 Fe3+
8 Fe2+ + SO428 Fe2+ + SO42- + 10H+
H2S + 8 Fe3+ + 4 H20
8 Fe2+ + SO42- + 10H+
Go’ = Gof [C + D] - Gof [A + B]
Go’ = ?
Enzymes
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Free energy does not tell us how fast a
spontaneous reaction proceeds
Many spontaneous biological reactions are
slow because of the activation energy of
reactions
Enzymes reduce the activation energy of a
reaction
Activation energy is the energy required to
bring all reactants to the reactive state
Activation Energy
Reaction Progress
Enzyme Catalyzed Reactions
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Enzymes are specific to reaction classes or a
specific reaction
The reactant is called the substrate (S)
The binding of the enzyme to the substrate is
called the enzyme/substrate complex (ES)
The binding site is called the active site
The product is called the product (P)
E + S
ES
E + P
Aldolase
Oxidation/Reductions
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catalysis is a series of oxidation/reduction
reactions that liberate energy
many substrates can serve as either electron
donors or acceptors
in most reactions, electrons are given up to
intermediate electron carriers
Electron Carriers
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During metabolism electrons are
transferred from the primary electron
donor (Substrate) to the terminal
electron donor via an electron carrier
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In catabolism, nicotinamide adenine
dinucleotide (NAD) is most often used
½ NAD+ + ½ H+ + e-
½ NADH
NAD+ as an Electron Carrier
NADH as an Electron Carrier
Reduction Potential
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the degree to which substrates can serve as
e donors or acceptors is related to their
reduction potential, Eo’
Eo’ measured relative to H2 in volts
 Eo’ values given for the reduction
¼ O2 + H+ + e½ H20
Eo’ = 0.82 v
o
 the lower the E ’, the greater the ability to
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donate electrons
thus glucose/CO2 (-0.43v) has a higher ability
to donate electrons than oxygen/ H20 (0.82v)
Coupled Half Reactions
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as stated earlier, in catabolic reactions,
there are a series of oxidation/reduction
reactions
thus one substrate is oxidized and
another is reduced
these are written as coupled half
reactions
Example of Coupled Half Reaction
Oxygen as Terminal Acceptor
½ NAD+ + ½ H+ + e¼ O2 + H+ + e-
½ NAD
½ H20
½ NADH
½ NAD+ + ½ H+ + e¼ O2 + H+ + e½ H20
¼ O2 + ½ NADH + ½ H+
Eo’ = 1.12 v
Eo’ = - 0.32 v
Eo’ = 0.82 v
Eo’ = 0.32 v
Eo’ = 0.82 v
½ NAD+ + ½ H20
Electron Tower
Half reactions with lower Eo’ values
can reduce half reactions with higher
Eo’ values.
Eo’
-0.50
NAD+/NADH
SO4/S2-
Accordingly, the higher the half
reaction is on the tower, the more
likely it is to be an electron donor for
cell metabolism.
To gain the most energy, the cell will
try to maximize the full extent of the
tower
NO3- /NO2+ 0.90
½ O2/H20
High Energy Phosphate Bonds
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Energy liberated from oxidation/reductions must
be converted to usable form
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Typically energy transferred to high energy
phosphate compounds, the most common of
which is ATP
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ATP is characterized by the presence of high
energy anhydride bonds
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Other examples include phosphoenolpyruvate,
ADP
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High energy bonds designated by ~Pi
Summary of Basics
Energy for Cell
Synthesis and
Maintenance
Carbon Electron Donor
Energy investment as
NADH or ATP
Metabolism Intermediate
Often these initial reactions are
preparatory reactions to get other
things going
Electrons from oxidation
are “carried” by electron
carriers primary NADH
Oxidized Carbon
oxygen
Electrons in NADH
are transferred to
terminal electron
acceptors. This
process results in
energy captured as
ATP which can be
used in cell for a
variety of purposes
Reduced
Terminal
Acceptors
water
Aerobic Metabolism of Common
Organics
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Carbohydrates
Lipids
Saturated Hydrocarbons
Alcohols, Aldehydes, and Ketones
Amino Acids
Oxidation of Carbohydrates (Glucose)
glucose
NAD+
ADP
ATP
glycolysis
NADH
pyruvate
CoA-SH
Acetyl CoA
CoA-SH
½ O2
GDP
GTP
Citric
Acid
Cycle
CO2
e-
Electron Transport System
Electrons flow in the
form of reduced
dinucleotides (NADH
and FADH)
H20
Steps in Glucose Glycolysis
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Stage I: Preparatory reactions
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glucose to glyceraldehyde-3-P
Stage II: Oxidation reactions
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glyceraldehyde-3-P to pyruvate-
Stage 1: Preparation
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glucose is
phosphorylated
ATP is used
Fructose-1,6diphosphate is
cleaved to G-3-P
and
Dihydroxyacetone
phosphate
State 2: Oxidation
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glyceraldehyde is
converted to pyruvic
acid
NADH is formed
during oxidation of
glyceraldehyde-3-P
ATP is formed
during conversion of
1,3-DPGA to 3-PGA
and PEP to pyruvic
acid
Carbon
Flow During
Respiration:
Citric Acid
Cycle
Citric Acid
Cycle
Summary of Glucose Oxidation
water and hydrogen left out of balance
glycolysis:
C6H12O6 + 2ADP + 2NAD+
2 pruvate- + 2ATP + 2NADH
Preparatory Step:
pruvate- + CoA-SH + NAD+
acetyl CoA + CO2 + NADH
CAC:
Acetyl-CoA + 4NAD+ + FAD+ + GDP
3 CO2 + 4NADH + FADH + GTP
Summary of glucose oxidation
C6H12O6 + 2ADP + 2GDP + 10NAD+ + 2FAD+
6 CO2 + 2ATP + 2GTP + 10NADH + 2FADH
Regeneration of Reduced
Nucleotides and Energy Production
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After oxidation in CAC, a large number
of NADH formed and some FADH
formed
These must be reoxidized so that they
can be recycled
In addition, energy production is
necessary
Electron transport accomplishes these
tasks.
Electron Transport
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NADH is oxidized and
donates its electrons and
protons to a flavoprotein
This flavoprotein is
oxidized and pumps out
H+ across membrane
This process continues
until electrons are passed
to final acceptor, O2
a gradient established
across membrane
this gradient used to drive
energy production (ATP)
ATPase
Enzyme
Summary of Basics
Energy for Cell
Synthesis and
Maintenance
Carbon Electron Donor
Energy investment as
NADH or ATP
Metabolism Intermediate
Often these initial reactions are
preparatory reactions to get other
things going
Electrons from oxidation
are “carried” by electron
carriers primary NADH
Oxidized Carbon
oxygen
Electrons in NADH
are transferred to
terminal electron
acceptors. This
process results in
energy captured as
ATP which can be
used in cell for a
variety of purposes
Reduced
Terminal
Acceptors
water
Acetic Acid, Volatile Acids, Lipids
fatty acid
CH3 - (CH2)n - COOH
Lipids
b oxidation
glycerol
CO2
pyruvic acid
acetyl CoA,
NADH, FADH
fatty acid oxidized in
two carbon
increments
acetyl CoA,
NADH, FADH
Straight Chain Aliphatic
Hydrocarbons
CH2OH
CH3
CHO
O2 MMO H2O
H 2O
NAD+ NADH
NADH
COOH
NAD+ NADH
NAD
alcohol
aldehyde
b oxidation
acid
Amino Acids and Proteins
peptide bond
cleavage
proteins
amino acids
NH3
pyruvic acid,
oxalacetic acid
ketoglutaric acid
CAC
CO2
CO2