chapter 9 introduction to metabolism. an overview of metabolism metabolism is the total of all...

Chapter 9

Introduction to Metabolism

An Overview of Metabolism

Metabolism is the total of all chemical reactions in the cell and is divided into two partscatabolism – energy-conserving reactions that

also generate a ready supply of electrons (reducing power) and precursors for biosynthesis E.g break down of glucose to release energy in the form of ATP in the mitochondria.

anabolism – the synthesis of complex organic molecules from simpler ones e.g formation of starch from carbondioxide

Anabolism

Anabolism are reaction which requires energy E.g Photosynthesis in chloroplast

Catabolism are reaction where energy is released E,g Cellular respiration in mitochondria

Energy and Work

Energy is defined as the capacity to do work or to cause particular changes

Types of Work Carried out by Organisms

Chemical work Synthesis of complex molecules from simpler

precursors (i.e anabolism). Here energy is needed to increase the complexity of a cell.

Transport work Take up of nutrients, elimination of wastes, and

maintenance of ion balances i.e energy is needed to transport molecules and ions across a cell membrane against a gradient.

Mechanical work Energy is needed for cell motility and movement of

structures within cells

The Laws of Thermodynamics

To understand how energy is conserved in ATP and how ATP is used to do work in a cell, one has to understand the law of Thermodyanamics.

Thermodynamicsa science that analyzes energy changes

in a collection of matter called a system (e.g., a cell or a plant)

all other matter in the universe is called the surroundings

….The Laws of Thermodynamics

Thermodynamics focuses on the energy difference between the initial state and final state of a system and not the rate of the process from one state to another

e.g boiling of water: cold liquid–hot-vapor i.e energy moves from one state to another ( thermodyanmics is not concerned with the rate at which the water is boiling.

First Law of Thermodynamics

Two laws of Thermodynamics:First Law: energy can be neither

created nor destroyed total energy in universe remains

constant however, energy may be redistributed either within a system or between the system and its surroundings

..First Law of Thermodynamics

Example in some reaction energy is released and in some it is absorbed..Why?

We need the second Law of Dynamics to explain why?

Second Law of Thermodynamics

Entropy is a condition of matter and the amount of randomness (disorder) in a system

The second law of Thermodynamics state that physical and chemical processes proceed in such a way that the disorder of the universe ( the system and its surroundings) increases to the maximum possible.

The greater the disorder the greater is the entropy of the universe, however, the entropy of a system varies: increases, decreases or remain constant.

Energy Units

calorie (cal)amount of heat energy needed to raise 1

gram of water from 14.5 to 15.5°Cjoules (J)-amount of energy can also

be expressed in joulesunits of work capable of being done 1 cal of heat is equivalent to 4.1840 J of

workRefer pg 170 for Kilo joule and Kilo

calorie

Free Energy and Reactions

The first and Second Law of Thermodynamics can be combined as

follows:Free energy change, G = H - TS

to expresse the change in energy that can occur in chemical reactions and other processes

to indicate if a reaction will proceed spontaneously

Where,

G = H - TS

G free energy changeamount of energy that is available to do

work at constant temperature and pressure H

change in enthalpy (heat content)/change in the total energy during the reaction

T temperature in Kelvin (0C +273)

Schange in entropy occurring during the

reaction ( entropy is randomness/disorder)

Chemical Equilibrium

The change in the free energy has a definite and concrete relationship to the direction of chemical reactions.

Equilibrium:consider the chemical reaction

A + B ↔ C + D reaction is at equilibrium when rate of forward reaction

= rate of reverse reaction

Equilibrium constant (Keq)expresses the equilibrium concentrations of products

and reactants to one another. No further changes occur in the products or reactants

Chemical Equilibrium

Equilibrium Constant:(Keq) = (C) (D)/(A)(B)

The equilibrium constant (Keq) of a reaction is directly related to its change in free energy.

Standard Free Energy Change (Gº)

Standard Free Energy Change is when free energy change is determined at standard conditions of concentration, pressure, temperature, and pH

Gº symbol used to indicate standard free energy change at pH 7 (close to pH of living cells) and is directly related to Keq

(equilibrium constant)

Relationship between Gº & Keq :

Gº´ = -2.303RT•logKeq

Where, R is the gas constant(1.9872 cal/mole-degree) 7 T is absolute temperature

Types of energy driven reactions

Exergonic reaction- reactions in a cell when energy is released from energy source and standard free energy change (G´) is negative & Equilibrium constant (Keq) is greater than one.

Endergonic reactions-reactions in a cell when energy is trapped and the energy captured by cell is used to drive reactions to completion, hence standard free energy change (G´) is positive & (Keq) is less than one.

The Relationship…

Figure 9.1 Relationship between Equilibrium constant and Free Energy Change.

Assignment on Adenosine 5’ triphosphate (ATP) (SL.19-27)

for next lecture!!Adenosine 5’ triphosphateFor all metabolic reactions (exergonic

& endergonic) energy in the form of ATP drives the processes in a cell

Some reactions earn ATP and some process spend ATP

ATP serves as a link between exergonic & endergonic reactions

ATP also referred as Energy Currency of the Cell.

..Role of ATP in Metabolism

Endergonic e;g reactant (A+b) to give product (C+D)

Exergonic breakdown of ATP to ADP is aiding an endergonic reactions to make them more favorableFigure 9.3 ATP as a coupling agent

..Adenosine-5'-triphosphate (ATP)

Adenosine-5'-triphosphate (ATP) is a multifunctional nucleotide

"molecular unit of currency" of intracellular energy transfer

In this role, ATP transports chemical energy

….Adenosine-5'-triphosphate (ATP)

ATP is made from adenosine diphospahate (ADP) or adenosine monophosphate (AMP), and its use in metabolism converts it back into these precursors.

ATP is therefore continuously recycled in organisms, with the human body turning over its own weight in ATP each day

..Adenosine-5'-triphosphate

This conversion of ATP to ADP is an extremely crucial reaction for the supplying of energy for life processes.

Just the breaking of one bond with the accompanying rearrangement is sufficient to liberate about 7.3 kilocalories per mole = 30.6 kJ/mol.

This is about the same as the energy in a single peanut!!

Adenosine-5'-triphosphate Living things can use ATP like a battery.

The ATP can power needed reactions by losing one of its phosphorous groups to form ADP

One can use food energy (cellular respiration) in the mitochondria to convert the ADP back to ATP so that the energy is again available to do needed work

In plants, sunlight energy can be used to convert the less active compound (CO2) and water back to the highly energetic form ( to starch )

..Structure of Adenosine 5’-triphosphate (ATP)

Energy Currency of the Cell

Figure 9.2- Pyrimidine ring with carbon atoms in a ribose attached to 3 phosphate group, adenine and an amino group.

..Adenosine 5’ triphosphate

Structure of ATP has a carbon compound as a backbone

Part which is really critical is the phosphorous part - the triphosphate.

Three phosphorous groups are connected by oxygens to each other, and there are also side oxygens connected to the phosphorous atoms.

Each of these oxygens has a negative charge & the negative charges repel each other.Highly charged

These bunched up negative charges, want to escape - to get away from each other, so there is a lot of potential energy here.

The Cell’s Energy Cycle

Figure 9.4 Cell Energy Cycle

Oxidation-Reduction Reactions and Electron

Carriersmany metabolic processes involve

oxidation-reduction reactions (electron transfers)

electron carriers are often used to transfer electrons from an electron donor to an electron acceptor

Oxidation-Reduction (Redox) Reactions

can result in energy release, which can be conserved and used to form ATP

E.g Acceptor + e- =donor

The acceptor and the donor makes a couple and called a redox couple

In a reversible reaction, the acceptor becomes the donor until an equilibrium is reached called Standard Reduction Potential (E0)

..REDOX..REDOXThe termThe term redox redox comes from the two concepts comes from the two concepts

of of redreduction and uction and oxoxidation. It can be explained idation. It can be explained in simple terms:in simple terms:

OxidationOxidation describes thedescribes the lossloss of of electrons electrons / / hydrogen or hydrogen or gaingain of oxygen of oxygen

ReductionReduction describes the describes the gaingain of electrons / of electrons / hydrogen or a hydrogen or a lossloss of oxygen of oxygen

……RedoxRedox

This can be either a simple This can be either a simple redoxredox process such as the process such as the oxidationoxidation of of carboncarbon to yield to yield carbon dioxide carbon dioxide or or

the the reductionreduction of of carboncarbon by hydrogen by hydrogen to yield to yield methanemethane (CH(CH44),),

or it can be a complex process such or it can be a complex process such as the oxidation of as the oxidation of sugarsugar in the in the human body through a series of very human body through a series of very complex electron transfer processes.complex electron transfer processes.

Standard Reduction Potential (E0) Equilibrium constant for an oxidation-reduction

reaction and is measured in volts (unit of electric potential)

Hence redox couples are a potential source of energy

A measure of the tendency of the reducing agent to lose electrons

Redox couple with more negative E0 (Std reduction potential) better electron donor i.e reducing agent has tendency to lose more electrons

Redox couple with more positive E0 (Std reduction potential) better electron acceptor

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Electron Transport ChainsElectron Transport Chains(ETC)(ETC)

Also known as electron transport system Also known as electron transport system (ETS)(ETS)

ETC comprises of electron carriers such ETC comprises of electron carriers such as co-enzymes, as co-enzymes, NADNAD ( Nicotinamide ( Nicotinamide adenine dinucleotide), or adenine dinucleotide), or FADFAD (Flavin (Flavin adenine dinucleotide) and othersadenine dinucleotide) and others

E.g when glucose ( CE.g when glucose ( C6 6 H H 12 12 O O 66) is ) is oxidisedoxidised during cellular respiration, many during cellular respiration, many electrons are released and these are electrons are released and these are accepted by accepted by NAD NAD which is which is converted/reduced to converted/reduced to NADHNADH

..ETC..ETC

During During Cellular RespirationCellular Respiration::

CC66HH1212OO66 + 6O + 6O22 ––> 6CO ––> 6CO2 2 + 6H+ 6H22O + energy O + energy ATP), ATP),

NADH transfers electrons to Oxygen via a NADH transfers electrons to Oxygen via a series of electron carriers with varying series of electron carriers with varying redox potential (redox potential (E0) which is organised into which is organised into a system called a system called electron transport system.electron transport system.



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Electron CarriersElectron CarriersNADNAD

nicotinamide adenine dinucleotidenicotinamide adenine dinucleotide

NADPNADPnicotinamide adenine dinucleotide nicotinamide adenine dinucleotide

phosphatephosphate



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……Electron CarriersElectron Carriers

FADFADflavin adenine dinucleotideflavin adenine dinucleotide

FMNFMNflavin mononucleotideflavin mononucleotide

Figure 9.8



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cytochromescytochromesuse iron to transfer electronsuse iron to transfer electrons

iron is part of a heme groupiron is part of a heme group



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coenzyme Q (CoQ)coenzyme Q (CoQ)a quinonea quinonealso called ubiquinonealso called ubiquinone

Figure 9.9



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nonheme nonheme iron proteinsiron proteinse.g., ferredoxine.g., ferredoxinuse iron to transport electronsuse iron to transport electrons



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EnzymesEnzymesEnzymes are critically important Enzymes are critically important

for cells to speed up reactions. for cells to speed up reactions. They act as They act as catalystscatalysts

catalystcatalystsubstance that increases the rate of a substance that increases the rate of a

reaction without being permanently reaction without being permanently alteredaltered

substratessubstratesreacting moleculesreacting molecules

productsproductssubstances formed by reactionsubstances formed by reaction



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Enzyme StructureEnzyme Structure

Many enzymes are composed of only Many enzymes are composed of only proteins. However many enzymes are proteins. However many enzymes are composed ancomposed an

Apoenzyme Apoenzyme which is which is protein component of an enzyme protein component of an enzyme and aand a

Cofactor Cofactor nonprotein component of an enzymenonprotein component of an enzyme

prosthetic group prosthetic group – firmly attached– firmly attachedcoenzymecoenzyme – loosely attached – loosely attached

HoloenzymeHoloenzyme is a complete enzyme i.e is a complete enzyme i.e Holoenzyme= apoenzyme + cofactorHoloenzyme= apoenzyme + cofactor



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CoenzymesCoenzymes

Coenzymes Coenzymes often act as often act as carriers, carriers, transporting transporting substances substances around the around the cellcell

Figure 9.11- Coenzyme as a carrier



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The Mechanism of Enzyme The Mechanism of Enzyme ReactionsReactions

a typical exergonic reactiona typical exergonic reaction

A + B A + B AB AB‡‡ C + D C + D

transition-state complex transition-state complex – – resembles both the substrates and resembles both the substrates and

the productsthe products

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Activation energy (EActivation energy (Ea)a)– energy – energy required to form transition-state required to form transition-state complexcomplex

enzyme speeds up reaction by enzyme speeds up reaction by lowering lowering EEaa



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How Enzymes Lower How Enzymes Lower AActivation energy (ctivation energy (EEa)a)

by increasing concentrations of by increasing concentrations of substrates at substrates at active site active site of enzymeof enzyme

by orienting substrates properly with by orienting substrates properly with respect to each other in order to respect to each other in order to form the transition-state complexform the transition-state complex

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Lock and Key Model of Enzyme Function

Figure 9.13 Lock and Key Model of Enzyme Function



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The Effect of Environment The Effect of Environment on Enzyme Activityon Enzyme Activity

Rate of enzyme activity is Rate of enzyme activity is significantly impacted by substrate significantly impacted by substrate concentration, pH, and concentration, pH, and temperaturetemperature



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Effect of [substrate]Effect of [substrate]

rate rate increasesincreases as [substrate] as [substrate] increasesincreases

no further no further increase increase occurs after all occurs after all enzyme enzyme molecules are molecules are saturated saturated with with substratesubstrateFigure 9.15



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Effect of pH and Effect of pH and TemperatureTemperature

Each enzyme has Each enzyme has specific pH specific pH and and temperature optimatemperature optima

DenaturationDenaturationloss of enzyme’s structure and activity loss of enzyme’s structure and activity

when temperature and pH rise too much when temperature and pH rise too much above optimaabove optima



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Enzyme InhibitionEnzyme Inhibition

Competitive inhibitor Microorganisms can be poisoned with enzyme inhibitors/ competitive inhibitor which directly competes with binding of substrate to active siteNoncompetitive inhibitor

–binds enzyme at site other than active site; changes enzyme’s shape so that it becomes less active



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Metabolic ChannelingMetabolic Channeling

Metabolic Channeling-Metabolic Channeling-differential differential localization of enzymes and metaboliteslocalization of enzymes and metabolites

compartmentationcompartmentation differential distribution of enzymes and differential distribution of enzymes and

metabolites among separate cell structures metabolites among separate cell structures or organellesor organelles



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ChemotaxisChemotaxis

An example of a complex behavior An example of a complex behavior that is regulated by altering enzyme that is regulated by altering enzyme activityactivity

system involves a number of system involves a number of enzymes and other proteins that are enzymes and other proteins that are regulated by covalent modification regulated by covalent modification e.g Chemotaxis response of e.g Chemotaxis response of E. coliE. coli

BibliographyBibliography

Lecture PowerPoints Prescott’s Principles Lecture PowerPoints Prescott’s Principles of Microbiology-Mc Graw Hill Co.of Microbiology-Mc Graw Hill Co.

http://en.wikipedia.org/wiki/http://en.wikipedia.org/wiki/Scientific_methodScientific_method

https://files.kennesaw.edu/faculty/https://files.kennesaw.edu/faculty/jhendrix/bio3340/home.htmljhendrix/bio3340/home.html

http://hyperphysics.phy-http://hyperphysics.phy-astr.gsu.edu/Hbase/biology/atp.htmlastr.gsu.edu/Hbase/biology/atp.html

chapter 9 introduction to metabolism. an overview of metabolism metabolism is the total of all...

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