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Week 2 Lecture Material October 2001. Metabolism. Metabolism. 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. - PowerPoint PPT Presentation
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Week 2 Lecture MaterialOctober 2001
Metabolism
Metabolism
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? 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 organic: carbohydrates, lipids, aromatics, etc. inorganic: ammonia, sulfide, ferrous iron, etc.
If there is an electron donor, then there must be an electron acceptor oxygen, nitrate, sulfate, ferrous iron, pyruvic acid,
etc.
What Types of Reactions Occur During Metabolism?
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
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
Energetics
Enzyme Function
Oxidation/Reduction Half Reactions
Electron Carriers
Energy Carriers
Energetics 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
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
A + B C + D
Go’ = Gof [C + D] - Go
f [A + B]
Free Energy of Reaction Example
H2S + 8 Fe3+ 8 Fe2+ + SO42-
H2S + 8 Fe3+ 8 Fe2+ + SO42- + 10H+
H2S + 8 Fe3+ + 4 H20 8 Fe2+ + SO42- + 10H+
Go’ = Gof [C + D] - Go
f [A + B]
Go’ = ?
Enzymes
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
Fre
e E
nerg
y
Enzyme Catalyzed Reactions
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 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
During metabolism electrons are transferred from the primary electron donor (Substrate) to the terminal electron donor via an electron carrier
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
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+ + e- ½ H20 Eo’ = 0.82 v the lower the Eo’, the greater the ability to donate
electrons thus glucose/CO2 (-0.43v) has a higher ability to
donate electrons than oxygen/ H20 (0.82v)
Coupled Half Reactions
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 ReactionOxygen as Terminal Acceptor
½ NAD+ + ½ H+ + e- ½ NAD Eo’ = - 0.32 v
¼ O2 + H+ + e- ½ H20 Eo’ = 0.82 v
½ NADH ½ NAD+ + ½ H+ + e- Eo’ = 0.32 v
¼ O2 + H+ + e- ½ H20 Eo’ = 0.82 v
¼ O2 + ½ NADH + ½ H+ ½ NAD+ + ½ H20
Eo’ = 1.12 v
Electron TowerEo’
-0.50
+ 0.90
Half reactions with lower Eo’ values can reduce half reactions with higher Eo’ values.
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
NAD+/NADH
SO4/S2-
½ O2/H20
NO3- /NO2
-
High Energy Phosphate Bonds Energy liberated from oxidation/reductions must be
converted to usable form
Typically energy transferred to high energy phosphate compounds, the most common of which is ATP
ATP is characterized by the presence of high energy anhydride bonds
Other examples include phosphoenolpyruvate, ADP
High energy bonds designated by ~Pi
Summary of Basics
Carbon Electron Donor
Metabolism Intermediate Often these initial reactions are preparatory reactions to get other things going
Energy investment as NADH or ATP
Oxidized Carbon
Electrons from oxidation are “carried” by electron carriers primary NADH
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
Energy for Cell Synthesis and Maintenance
wateroxygen
Aerobic Metabolism of Common Organics
Carbohydrates Lipids Saturated Hydrocarbons Alcohols, Aldehydes, and Ketones Amino Acids
Oxidation of Carbohydrates (Glucose)
CitricAcid Cycle
Electron Transport System
CO2
e-
½ O2
H20
glycolysis
Electrons flow in the form of reduced dinucleotides (NADH and FADH)
GDPGTP
glucose
pyruvate
ADPATP NADH
NAD+
Acetyl CoACoA-SH
CoA-SH
Steps in Glucose Glycolysis
Stage I: Preparatory reactions glucose to glyceraldehyde-3-P
Stage II: Oxidation reactions glyceraldehyde-3-P to pyruvate-
Stage 1: Preparation
glucose is phosphorylated
ATP is used Fructose-1,6-
diphosphate is cleaved to G-3-P and Dihydroxyacetone phosphate
State 2: Oxidation
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 Oxidationwater and hydrogen left out of balance
C6H12O6 + 2ADP + 2NAD+ 2 pruvate- + 2ATP + 2NADH
Acetyl-CoA + 4NAD+ + FAD+ + GDP 3 CO2 + 4NADH + FADH + GTP
C6H12O6 + 2ADP + 2GDP + 10NAD+ + 2FAD+
6 CO2 + 2ATP + 2GTP + 10NADH + 2FADH
glycolysis:
CAC:
Summary of glucose oxidation
Preparatory Step:
pruvate- + CoA-SH + NAD+ acetyl CoA + CO2 + NADH
Regeneration of Reduced Nucleotides and Energy Production
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 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
Carbon Electron Donor
Metabolism Intermediate Often these initial reactions are preparatory reactions to get other things going
Energy investment as NADH or ATP
Oxidized Carbon
Electrons from oxidation are “carried” by electron carriers primary NADH
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
Energy for Cell Synthesis and Maintenance
wateroxygen
Acetic Acid, Volatile Acids, Lipids
Lipids
pyruvic acid
glycerol
acetyl CoA,NADH, FADH
fatty acidCH3 - (CH2)n - COOH
acetyl CoA,NADH, FADH
CO2
oxidation
fatty acid oxidized in two carbon increments
Straight Chain Aliphatic Hydrocarbons
CHO COOH
aldehyde acid
CH3
NADH NAD
O2 H2O
CH2OH
alcohol
MMO
oxidation
NAD+ NADH NAD+ NADH
H2O
Amino Acids and Proteins
proteinspeptide bond cleavage
amino acids
pyruvic acid, oxalacetic acid
ketoglutaric acid
CACCO2
NH3
CO2