week 2 lecture material october 2001

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