Princípios Físicos Aplicados à Fisiologia (PGF5306-1)fge.if.usp.br/~aalencar/adriano/Produtividade/... · Princípios Físicos Aplicados à Fisiologia (PGF5306-1) Prof. Adriano

Princípios Físicos Aplicados à Fisiologia (PGF5306-1)

Prof. Adriano Mesquita AlencarDep. Física Geral

Instituto de Física da USP

EnergiaAula 11

B02

calorimeter9 (Fig. 1.11) is used to measure the heat given off in theoxidation of a combustible substance like food, and nutritionistsrefer to tables of combustion heats in planning a diet.

The study of energy transformations is called thermodynamics.It is a hierarchical science – the more advanced concepts assumeknowledge of the more basics ones. To be ready to tackle the moredifficult but more interesting topics in later chapters, let’s use thismoment to develop an understanding of what is being measured inthe bomb calorimeter. We know from experience that the oxidation(burning) of wood gives off heat. Some types of wood are useful forbuilding fires because they ignite easily (e.g. splinters of dry pine);others are useful because they burn slowly and give off a lot of heat(e.g. oak). The amount of heat transferred to the air per unit volumeof burning wood depends on the density of the wood and its struc-ture. The same is true of food. Fine, but this has not told us whatheat is.

It is the nature of science to define terms as precisely as possibleand to formalize usage. Accepted definitions are importantfor minimizing ambiguity of meaning. What we need now is a

Fig. 1.11 Schematic diagram of a bomb calorimeter. A sample is placed in the reaction

chamber. The chamber is then filled with oxygen at high pressure (>20 atm) to ensure

that the reaction is fast and complete. Electrical heating of a wire initiates the reaction.

The increase in water temperature resulting from the combustion reaction is recorded,

and the temperature change is converted into an energy increase. The energy change is

divided by the total amount of substance oxidized, giving units of J g!1 or J mol!1.

Insulation helps to prevent the escape of the heat of combustion, increasing the accuracy

of the determination of heat released from the oxidized material. Based on diagram on

p. 36 of Lawrence et al. (1996).

9 But one of many different kinds of calorimeter. The instrument used to measure theenergy given off in an atom smasher is called a calorimeter. In this book we discuss abomb calorimeter, isothermal titration calorimeter, and differential scanningcalorimeter.

14 ENERGY TRANSFORMATION

sábado, 5 de outubro de 13

Princípios Físicos Aplicados à Fisiologia (PGF5306-1)


Entalpia, H

R, é uma constante universal, 8.3145 J/K mol

calorimeter9 (Fig. 1.11) is used to measure the heat given off in theoxidation of a combustible substance like food, and nutritionistsrefer to tables of combustion heats in planning a diet.

The study of energy transformations is called thermodynamics.It is a hierarchical science – the more advanced concepts assumeknowledge of the more basics ones. To be ready to tackle the moredifficult but more interesting topics in later chapters, let’s use thismoment to develop an understanding of what is being measured inthe bomb calorimeter. We know from experience that the oxidation(burning) of wood gives off heat. Some types of wood are useful forbuilding fires because they ignite easily (e.g. splinters of dry pine);others are useful because they burn slowly and give off a lot of heat(e.g. oak). The amount of heat transferred to the air per unit volumeof burning wood depends on the density of the wood and its struc-ture. The same is true of food. Fine, but this has not told us whatheat is.

It is the nature of science to define terms as precisely as possibleand to formalize usage. Accepted definitions are importantfor minimizing ambiguity of meaning. What we need now is a

Fig. 1.11 Schematic diagram of a bomb calorimeter. A sample is placed in the reaction

chamber. The chamber is then filled with oxygen at high pressure (>20 atm) to ensure

that the reaction is fast and complete. Electrical heating of a wire initiates the reaction.

The increase in water temperature resulting from the combustion reaction is recorded,

and the temperature change is converted into an energy increase. The energy change is

divided by the total amount of substance oxidized, giving units of J g!1 or J mol!1.

Insulation helps to prevent the escape of the heat of combustion, increasing the accuracy

of the determination of heat released from the oxidized material. Based on diagram on

p. 36 of Lawrence et al. (1996).

9 But one of many different kinds of calorimeter. The instrument used to measure theenergy given off in an atom smasher is called a calorimeter. In this book we discuss abomb calorimeter, isothermal titration calorimeter, and differential scanningcalorimeter.

14 ENERGY TRANSFORMATION

�H = �U +RT�n

Em um experimento dessa bomba de calorímetro com

Etanol, a 298K e volume constante, 1368 kJ/mol de

calor é liberado

C2H5OH(`) + 3O2(g) ! 2CO2(g) + 3H2O(`)


Entalpia, H�H = �U +RT�n

�H = �U + 298 · 8.3145�n

�H = �U + 2478�n

�n = 2� 3 = 1

�H = �1368000� 2478

Se a variação de entalpia é negativo o processo é exotérmico. Caso contrario o processo é

endotérmico

C2H5OH(`) + 3O2(g) ! 2CO2(g) + 3H2O(`)

(J/mol)


Entalpia, H

C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

Liquido para Gas = 277

((5*415+346+358+464)+277)+3*498

C = O ! 1077 em Monoxido

C = O ! 805 em Dioxido

C �O ! 358

O �H ! 464

H � Cl ! 432

C � C ! 346

C = C ! 602

C �H ! 415

H �H ! 436

O = O ! 498

Liquido para Gas = 41

(2*2*805+6*464+(3*41))

ΔHο= -1113 (saindo do estado liquido)

C2H5OH(`) + 3O2(g) ! 2CO2(g) + 3H2O(`)

ΔHο= -1267 (estado gasoso para todos)

ΔHο= -1368 kJ/mol (Valor de Tabela)


C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

C2H5OH(`) + 3O2(g) ! 2CO2(g) + 3H2O(`)En

talp

ia

C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

liquidogás

C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

gásgás

+277

+4737

6H + 2C + 7O

átomos

C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

gás gás

-6004

C

H

H

H

C

H

H

O

H

+ 3 ( OO )�H

+ 2 ( CO O ) + 3 ( O H

H

)

1

1

gás liquido

-123


Bioquímica

• Aproximadamente 1/2 da massa seca do corpo humano é de proteinas• O estado nativo das proteínas é “folded”, empacotado - uma espécie de cristal orgânico• Mesmo nesse estado existe flutuação na estrutura do caroço central.• Estado empacotado - parecido com solido• Estado desempacotado - parecido com liquido


ideal case all amino acid side chains are completely exposed tosolvent (Table 2.4).

The non-covalent interactions that stabilize folded protein struc-ture (or double-stranded DNA or folded RNA structure) can be“broken” in a number of ways. One is by adding heat. If all the non-covalent bonds break simultaneously, in an all-or-none fashion(“cooperative” unfolding), then there are in essence just two states ofthe protein: the folded state and the unfolded state. The transitionfrom the folded state to the unfolded state is like melting. Soinducing the unfolding of protein by heat or some other means issomething like melting a solid. This is true even if one is workingnot with a mass of freeze-dried protein but with folded proteinsdissolved in aqueous solution. The cooperativity of the transition, theall-or-none character of going from being folded to being unfolded,

Table 2.3. Characteristics of hydrogen bonds of biological importance

Bond typeMean bonddistance (nm) Bond energy (kJ mol!1)

O–H . . .O 0.270 !22O–H . . .O! 0.263 !15O–H . . .N 0.288 !15 to !20N"–H . . .O 0.293 !25 to !30N–H . . .O 0.304 !15 to !25N–H . . .N 0.310 !17HS–H . . .SH2 — !7

The data are from Watson (1965).

Table 2.2. Energetics of non-covalent interactions betweenmolecules

Type of interaction Equation

Approximatemagnitude(kcal mol!1)

Ion–ion E# q1q2/Dr 14Ion–dipole E# q„!/Dr2 !2 to "2Dipole–dipole E#„1„2!

0/Dr3 !0.5 to "0.5Ion–induced dipole E# q2fi/2Dr2r4 0.06Dispersion E# 3h”fi2/4r6 0 to 10

a Charge q1 interacts with charge q2 at a distance r in medium of dielectric D.b Charge q interacts with dipole „ at a distance r from the dipole in medium of dielectric D. !and !0 are functions of the orientation of the dipoles.

c Dipole „1 interacts with dipole „2 at an angle q relative to the axis of dipole „2 and adistance r from the dipole in medium of dielectric D.

d Charge q interacts with molecule of polarizability at fi distance r from the dipole in mediumof dielectric D.

e Charge fluctuations of frequency ” occur in mutually polarizable molecules of polarizabilityfi separated by a distance r.

The� data� are� from� Table� 1.1� of� van� Holde� (1985).

SOME EXAMPLES FROM BIOCHEMISTRY 43

1 kcal = 4.18 kJ


Bioquímica

ideal case all amino acid side chains are completely exposed tosolvent (Table 2.4).

The non-covalent interactions that stabilize folded protein struc-ture (or double-stranded DNA or folded RNA structure) can be“broken” in a number of ways. One is by adding heat. If all the non-covalent bonds break simultaneously, in an all-or-none fashion(“cooperative” unfolding), then there are in essence just two states ofthe protein: the folded state and the unfolded state. The transitionfrom the folded state to the unfolded state is like melting. Soinducing the unfolding of protein by heat or some other means issomething like melting a solid. This is true even if one is workingnot with a mass of freeze-dried protein but with folded proteinsdissolved in aqueous solution. The cooperativity of the transition, theall-or-none character of going from being folded to being unfolded,

Table 2.3. Characteristics of hydrogen bonds of biological importance

Bond typeMean bonddistance (nm) Bond energy (kJ mol!1)

O–H . . .O 0.270 !22O–H . . .O! 0.263 !15O–H . . .N 0.288 !15 to !20N"–H . . .O 0.293 !25 to !30N–H . . .O 0.304 !15 to !25N–H . . .N 0.310 !17HS–H . . .SH2 — !7

The data are from Watson (1965).

Table 2.2. Energetics of non-covalent interactions betweenmolecules

Type of interaction Equation

Approximatemagnitude(kcal mol!1)

Ion–ion E# q1q2/Dr 14Ion–dipole E# q„!/Dr2 !2 to "2Dipole–dipole E#„1„2!

0/Dr3 !0.5 to "0.5Ion–induced dipole E# q2fi/2Dr2r4 0.06Dispersion E# 3h”fi2/4r6 0 to 10

a Charge q1 interacts with charge q2 at a distance r in medium of dielectric D.b Charge q interacts with dipole „ at a distance r from the dipole in medium of dielectric D. !and !0 are functions of the orientation of the dipoles.

c Dipole „1 interacts with dipole „2 at an angle q relative to the axis of dipole „2 and adistance r from the dipole in medium of dielectric D.

d Charge q interacts with molecule of polarizability at fi distance r from the dipole in mediumof dielectric D.

e Charge fluctuations of frequency ” occur in mutually polarizable molecules of polarizabilityfi separated by a distance r.

The� data� are� from� Table� 1.1� of� van� Holde� (1985).



results from the concurrent breaking of a large number of weakinteractions. In water, these interactions are hydrogen bonds; inproteins, they are the several kinds mentioned above. The meltingof pure water or any other pure solid is a cooperative phenomenon.That is, melting occurs at a single or over a very narrow range oftemperatures, not over a broad range. The same is true of coop-erative protein unfolding or the melting of DNA.

A number of experimental studies have been carried out tomeasure the energy required to break a hydrogen bond at roomtemperature. This is pertinent not only to the unfolding of proteinsbut also to the “melting” of double-stranded DNA, which is heldtogether by hydrogen bonds. Estimates of the bond energy vary, but areasonable and generally agreed rough figure is 1kcal mol!1. Indi-vidual hydrogen bonds are weak; collections can be quite strong.

In terms of Eqn. (2.10), the enthalpy of the folded state of aprotein is H"

F, the enthalpy of the unfolded state is H"U, and the dif-

ference, H"U ! H"

F, is the enthalpy of denaturation or unfolding, 1Hd".

In this case the folded state of the protein is the reference state, as theenthalpy of the unfolded state is measured with respect to it. Whatis this enthalpy difference? As discussed above, the enthalpy changefor a process is equal to the heat absorbed by the system at constantpressure, and the rigid folded state of a protein can be pictured as asolid, and the flexible unfolded state as a liquid. So the enthalpydifference between the unfolded and folded states of a protein is theamount of heat needed to unfold the protein. As we shall see, themagnitude of that heat depends on the temperature.

Table 2.4. Principal features of protein structure

Folded (native) stateUnfolded (denatured)state

Highly ordered polypeptidechain

Highly disordered chain– “random coil”

Intact elements of secondarystructure, held together byhydrogen bonds

No secondary structure

Intact tertiary structure contacts,as in an organic crystal, heldtogether by van der Waalsinteractions

No tertiary structure

Limited rotation of bonds in theprotein core

Free rotation of bondsthroughout polypep-tide chain

Desolvated side chains in proteincore

Solvated side chains

Compact volume Greatly expandedvolume

44 THE FIRST LAW OF THERMODYNAMICS


The temperature at which a protein unfolds (or double-strandedDNA melts) is called the melting temperature, Tm. This temperaturedepends not only on the number and type of non-covalent bonds inthe folded state but also on the pH and other solution conditions. Tmalso depends on the pressure, but most biological science experi-ments are done at 1 atm pressure. In the case of proteins, changingthe pH of solution changes the net charge on the protein surface.This can have a marked impact on Tm and 1H!

d, as shown in Fig. 2.7for the example of hen egg white lysozyme, a well-studied smallglobular protein. The figure also illustrates that the slope of 1H!

against Tm for this protein is more or less constant throughout thepH range shown.

Above we saw how a bomb calorimeter can be used to obtainthermodynamic information. Here we introduce isothermal titra-tion calorimetry (ITC)12 and explain how it can be used to measurethe enthalpy of a biochemical process (Fig. 2.8). By Eqn. (2.10) theheat absorbed at constant pressure measures the enthalpy change.Suppose, for example, we are interested in the energetics of thebinding of the Fc portion of immunoglobulin G (IgG), important inhumoral immunity and biotechnology, to soluble protein A, a bac-terial protein. We need not be concerned at the moment just whichpart of IgG the Fc portion of is: we just need to know that antibodymolecules can be dissected into components and that the Fc portionis one of them. The thermodynamic states of interest here are theunbound state, where protein A is free in solution, and the boundstate, where protein A is physically associated with Fc. The heatexchanged at constant pressure upon injection of protein A into acalorimetric cell containing the antibody can thus be used todetermine 1Hb

!, the enthalpy of binding (under standard state con-ditions). The heat of injection will change as the number of vacantbinding sites decreases.

Fig. 2.7 Enthalpy of unfolding of hen

egg white lysozyme as a function of

transition temperature. Filled

symbols: intact lysozyme. Open

symbols: lysozyme in which one of

the four native disulfide bonds has

been removed. When folded, 3-SS

lysozyme closely resembles the

native state of intact lysozyme.

Change in transition temperature

was induced by a change of pH.

Note that 1H is approximately

linear in Tm. The data are from

Cooper et al. (1991).

12 The isothermal titration calorimeter was first described in 1922 by Theophilede Donder, founder of the Brussels School of thermodynamics.



What if we’re interested in the energetics of an enzyme bindingto its substrate? This can be measured if a suitable substrate analogcan be found or the enzyme can be modified. For instance, ITC hasbeen used to measure the enthalpy of binding of a small compoundcalled 20-cytidine monophoshate (20CMP) to ribonuclease A, whichhydrolyzes RNA to its component nucleotides. 20CMP binds to andinhibits the enzyme. If the enzyme of interest is, say, a proteinphosphatase with a nucleophilic cysteine in the active site, muta-tion of the Cys to Ser or Asn will abolish catalytic activity, as in theN-terminal domain of the cytoskeleton-associated protein tensin,and the energetics of binding can be studied. A deeper under-standing of binding will be sought in Chapters 5 and 7.

If you’ve spent any time in a biochemistry lab, you may haveexperienced the large heat given off by a salt solution as the saltdissolves. There are several contributions to the effect, but the mainone is the enthalpy of hydration. This is the enthalpy change thatoccurs when an ion in vacuum is dropped into a sea of pure water.Water molecules form what is called a hydration shell around theion, the number depending on the radius of the ion and its charge.Calorimetry can be used to measure the hydration enthalpy of bio-logically important ions. Values are given in Table 2.5. Why is thisimportant? In one example, some of the water molecules hydratingan ion must be stripped away before the ion can pass through aselective ion channel in the plasma membrane, and this requires aninput of energy. Complete dehydration of the ion would require avery large input of energy, so it is easy to imagine that a few watermolecules remain associated with an ion as it passes through a pore.Ion channels that are specific for the passage of certain types of ionare part of the molecular machinery underlying the transmission ofnerve impulses.

Fig. 2.8 Isothermal titration

calorimeter. The temperature is

constant. There are two identical

chambers, the sample cell and the

reference cell. In most cases, the

sample cell will contain a

macromolecule, and the syringe/

stirrer is used to inject a ligand into

the sample cell. The syringe is

usually coupled to an injector

system under software control and

rotated at a constant speed. The

reference cell is filled with buffer;

no reaction occurs there. 1Tmeasures the temperature

difference between cells, which are

surrounded by insulation to

minimize heat exchange with the

surroundings. Electronic (power

feedback) circuitry minimizes 1T

on a continuous basis. If injection of

ligand results in binding, there will

ordinarily be a change in the

temperature of the sample. The

sign of the change will depend on

whether the reaction is exothermic

or endothermic. An experiment

consists of equal-volume injections

from the syringe into the sample

cell.


What if we’re interested in the energetics of an enzyme bindingto its substrate? This can be measured if a suitable substrate analogcan be found or the enzyme can be modified. For instance, ITC hasbeen used to measure the enthalpy of binding of a small compoundcalled 20-cytidine monophoshate (20CMP) to ribonuclease A, whichhydrolyzes RNA to its component nucleotides. 20CMP binds to andinhibits the enzyme. If the enzyme of interest is, say, a proteinphosphatase with a nucleophilic cysteine in the active site, muta-tion of the Cys to Ser or Asn will abolish catalytic activity, as in theN-terminal domain of the cytoskeleton-associated protein tensin,and the energetics of binding can be studied. A deeper under-standing of binding will be sought in Chapters 5 and 7.

If you’ve spent any time in a biochemistry lab, you may haveexperienced the large heat given off by a salt solution as the saltdissolves. There are several contributions to the effect, but the mainone is the enthalpy of hydration. This is the enthalpy change thatoccurs when an ion in vacuum is dropped into a sea of pure water.Water molecules form what is called a hydration shell around theion, the number depending on the radius of the ion and its charge.Calorimetry can be used to measure the hydration enthalpy of bio-logically important ions. Values are given in Table 2.5. Why is thisimportant? In one example, some of the water molecules hydratingan ion must be stripped away before the ion can pass through aselective ion channel in the plasma membrane, and this requires aninput of energy. Complete dehydration of the ion would require avery large input of energy, so it is easy to imagine that a few watermolecules remain associated with an ion as it passes through a pore.Ion channels that are specific for the passage of certain types of ionare part of the molecular machinery underlying the transmission ofnerve impulses.

Fig. 2.8 Isothermal titration

calorimeter. The temperature is

constant. There are two identical

chambers, the sample cell and the

reference cell. In most cases, the

sample cell will contain a

macromolecule, and the syringe/

stirrer is used to inject a ligand into

the sample cell. The syringe is

usually coupled to an injector

system under software control and

rotated at a constant speed. The

reference cell is filled with buffer;

no reaction occurs there. 1Tmeasures the temperature

difference between cells, which are

surrounded by insulation to

minimize heat exchange with the

surroundings. Electronic (power

feedback) circuitry minimizes 1T

on a continuous basis. If injection of

ligand results in binding, there will

ordinarily be a change in the

temperature of the sample. The

sign of the change will depend on

whether the reaction is exothermic

or endothermic. An experiment

consists of equal-volume injections

from the syringe into the sample

cell.



Box 2.2. Cont.

micromachined nanocalorimeter which functions as a biosensor. A small number

of living cells are present in a sub-nanoliter chamber. The small size of the

chamber could be useful for rapid screening of small samples. The sensor

comprises a 10-junction gold and nickel thermopile on a silicon chip. A thermopile

is a number of thermocouples, 10 in this case, connected end on end, and a

thermocouple is simply a temperature-measuring device consisting of two wires of

different metals fused at each end. A temperature difference between the metals

results in a difference in an electrical potential, which can be calibrated to a

temperature. The nanocalorimeter of the Glasgow group can detect a mere

13 nW of power generated by the cells on exposure to a chemical stimulus, the

temperature resolution is 0.125mK, the heat capacity is 1.2 nJ mK!1, and the

response time is 12ms. Primary cell lines or tissue biopsies can be analyzed.

Fig. 2.10 Differential scanning

calorimetry. (A) Schematic diagram

of the instrument. In

this case the reference cell contains

buffer only, and the sample cell

contains the macromolecule

dissolved in buffer. Both cells are

heated very slowly (e.g. 1 "C min!1)

in order to maintain equilibrium,

and feedback electronic circuitry is

used to add heat so that 1T # 0

throughout the experiment. Other

types of DSC have been used for

other purposes in biophysics, for

example, to investigate the

physiological limits of the freeze

tolerance and freeze-avoidance

strategies taken by different insect

species to survive subzero

temperatures. (B) Data. The heat

added to keep 1T # 0 can be

plotted as a function of

temperature. The endothermic

peak corresponds to heat absorbed,

for example, on protein

denaturation. The peak maximum

corresponds roughly to the

transition temperature, or melting

temperature. The area below the

peak is 1Hd(Tm). The heat capacity

of the unfolded state of a protein

minus the heat capacity of the

folded state is 1Cp,d. There is more

about DSC in Chapter 5.



H. Heat capacity

Above we noted that the heat taken up or released per unit changein temperature from a material at constant pressure is a property ofthat material. The name of this property is the heat capacity atconstant pressure, Cp.

13 This quantity is readily measured, and it canbe used to calculate changes in the enthalpy. The heat capacity perunit mass of Coke, for example, which is mostly water, differs fromthe heat capacity per unit mass of an egg, which contains a largeamount of protein; the amount of heat energy that must beextracted from 1g of each in order to lower the temperature by1 degree K will not be the same in the two cases. The heat capacitytells us how much energy is in the system for transfer between itselfand the environment per degree.

It is evident from Fig. 2.7 that the enthalpy of a protein rises asits temperature is increased. This is true of substances in general.The numerical relationship between H and T, however, depends onthe conditions. We concern ourselves here with constant pressureonly. The slope of a graph of H versus T at constant pressure is theheat capacity at constant pressure.

We are all familiar with heat capacity, even in the absence of aformal introduction. Returning to our water-in-a-saucepan example,if the water is heated at a high enough rate, it will eventually boil.The amount of heat that must be added to increase the temperatureof 1 g of a substance by 1 degree K is the specific heat capacity. At 1 atmpressure, the heat capacity of liquid water varies only very slightlywith temperature over the range 0–100 !C. This comes from thebonding structure of water (Fig. 2.9). Just as the extent of motionchanges substantially when a quantity of water freezes or vaporizes,the heat capacity of water depends substantially on its state. This istrue of substances in general. But the number of hydrogen bonds

Table 2.5. Standard ion hydration enthalpies

H" #1090 Mg2" #1920Li" #520 Ca2" #1650Na" #405 Ba2" #1360K" #321 Fe2" #1950— — Zn2" #2050NH4" #301 Fe3" #4430

The data refer to X"(g)!X"(aq) at 1 bar and are from Table 2.6c in Atkins (1998). 1 bar$ 105

Pa$ 105 N m#2$ 0.987 atm. 1 Pa$ 1 pascal. Blaise Pascal (1623–1662) was a French scientistand religious philosopher.

13 The heat capacity per unit mass of material, or specific heat, was firstdescribed in detail by Joseph Black.

HEAT CAPACITY 47Hidratação e desidratação iônica ocorre

constantemente nos canais/bombas de íons e na transmissão de impulsos nervosos.


EnergiasEnergias mais relevantes para

sistemas biológicos:1. Energia Química2. Energia Mecânica3. Energia Eletromagnética4. Energia Térmica Fotossíntese

Energias mais relevantes para sistemas biológicos:

1. Energia Química2. Energia Mecânica3. Energia Eletromagnética4. Energia Térmica


EnergiasEnergias mais relevantes para

sistemas biológicos:1. Energia Química2. Energia Mecânica3. Energia Eletromagnética4. Energia Térmica

Forcas no interior da célula

Deterministicas Térmicas

Movimento Browniano

A razão entre a escalas derteminísticas e termicas é:

Edet/kBT


A razão entre a escalas derteminísticas e termicas é:

Edet/kBT

kBT = 4.1 pNnm

= 0.6 kcal/mol

= 2.5 kJ/mol

= 25meV

grees of freedom is to consider collective excitations. Forexample, phonons characterize the vibrations of a crys-talline solid and magnons describe collective excitations ofmagnetic spins.

Indeed, physicists talk of “-ons” of all kinds. The bio-logical setting provides a loose analogy because somebiological structures are characterized with the label “-somes,” which derives from the Greek word for “body.”The term refers to macromolecular assemblies that aremade from multiple molecular components that act in acollective fashion to perform multiple functions. Some ofthe most notable examples include the ribosome, used inprotein synthesis; the nucleosome, which is the individualpacking unit for eukaryotic DNA; the proteasome, an as-sembly that mediates protein degradation; and the tran-scriptisome, which mediates gene transcription. By mech-anisms and principles that are still largely unknown,proteins assemble into -somes, perform a task, and thendisassemble again.

One of the most pleasing examples of biological col-lective action is revealed by the machines of the so-calledcentral dogma. The term refers to the set of processeswhereby DNA is copied (replication), genes are read andturned into messenger RNA (transcription), and finally,messenger RNA is turned into the corresponding proteinby ribosomes (translation). Such processes involve multi-ple layers of orchestration that range from the assemblyof macromolecular complexes to the simultaneous actionof multiple machines to the collective manner in whichcells may undertake the processes. Figure 3 shows the ma-chines of the central dogma in bacteria engaged in theprocesses of transcription and translation simultaneously.

The theme of collective action is also revealed in theflow of information in biological systems. For example, theprecise spatial and temporal orchestration of events that oc-curs as an egg differentiates into an embryo requires thatinformation be managed in processes called signal trans-duction. Biological signal transduction is often broadly pre-sented as a series of cartoons: Various proteins signal by in-teracting with each other via often poorly understoodmeans. That leads to a very simple representation: a net-work of blobs sticking or pointing to other blobs. Despite lim-ited knowledge, it should be possible to develop formal the-ories for understanding such processes. Indeed, the generalanalysis of biological networks—systems biology—is nowgenerating great excitement in the biology community.

Information flow in the central dogma is likewise oftenpresented as a cartoon: a series of directed arrows show-ing that information moves from DNA to RNA to proteins,and from DNA to DNA. But information also flows fromproteins to DNA because proteins regulate the expressionof genes by binding to DNA in various ways. Though all bi-ologists know that interesting feature of information flow,central-dogma cartoons continue to omit the arrow thatcloses the loop. That omission is central to the differencebetween a formal theory and a cartoon. A closed loop in aformal theory would admit the possibility of feedback andcomplicated dynamics, both of which are an essential partof the biological information management implemented bythe collective action of genes, RNA, and proteins.

Understanding collective effects in the cell will requiremerging two philosophical viewpoints. The first is that lifeis like a computer program: An infrastructure of machinescarries out arbitrary instructions that are encoded into DNA

www.physicstoday.org May 2006 Physics Today 41

Electrostatic energyof a spherical shell

Binding energy of anelectron in a box

Bending ofa 20:1 rod

Chemicalbonds

Fracture ofa 20:1 rod

Proton

Nucleus

Thermal energy

10010 310 610 910 1210 15

10 30

10 25

10 20

10 15

10 10

1010

105

10 5

100

LENGTH (meters)

EN

ER

GY

(jou

les)

Figure 2. The confluence of energy scales is illustrated in this graph, which shows how thermal, chemical, mechanical, andelectrostatic energies associated with an object scale with size. As the characteristic object size approaches that at which mo-lecular machines operate (shaded), all the energies converge. The horizontal line shows the thermal energy scale kT which, ofcourse, does not depend on an object’s size. We estimate binding energy (purple) by considering an electron in a box; for com-parison, the graph shows measured binding energies for hydrogen bonds (square), phosphate groups in ATP (triangle), and co-valent bonds (circle), along with characteristic energies for nuclear and subatomic particles. In estimating the bending energy(blue), we took an elastic rod with an aspect ratio of 20:1 bent into a semicircular arc, and to compute the fracture energy(green) we estimated the energy in chemical bonds in a longitudinal cross section of the rod. The electrostatic energy (orange)was obtained for a spherical protein with singly charged amino acids of specified size distributed on the surface.

Maquinaria molecular: Ligação de Hidrogênio (quadrado), grupos de fosfato em ATP (triângulo), ligações covalentes (círculo), energia de torção (azul), energia de fratura (verde), energia eletrostática (laranja). [Rob Phillips and Stephen R. Quake, Physics Today (2006)]


Geração de Energias (Glicolise)

0

-20

-40

-60

-80

P PA

AP P P

!G' (kJ · mol-1)

P PA

AP P P

P PA

AP P P

P PA A

P P P

8

76

5

4

9

1

10

3

2

P PAA

P P P P PAA

P P P

P PAA

P P P

P PA A

P P P

1 32

8 7

4

5

22

22

N AN A

6

1

2

3

4

510

9

7

9

P

P

P

P

P

P

10

P P

6

8

2 H2O

P PA A

P P P

N A N A

P

2

2

2

2

2

!GOI = –35 kJ · mol–1

2 2

P

PP P

O

HO

OH

OH

OH

HH

HH

CH2

H

HO

O

HO

OH

OH

OH

HH

HH

CH2

H

HO

O

HO

OH

OH

OH

HH

HH

CH2

H

OO

CH2O

OH H

CH2OH

OH

HH HO

OCH2O

OH H

CH2

OH

HH HO

O

HC OH

H2C

C

O

O O

HC OH

H2C

CO O

O

HC O

H2C

CO O

OH

HC OH

H2C

C

O

O H

C O

CH2

H2C

O

OH

C O

CH2

CO O

C O

CH3

CO O

C O

CH3

COO

C O

CH3

COO

P

Pyruvate

Steps 1, 3 and 10are bypassed ingluconeogenesis

Glyceraldehyde3-phosphate

1,3-Bisphospho-glycerate

3-Phospho-glycerate

Phospho-enolpyruvate

2-Phospho-glycerate

Glycerone3-phosphate

Fructose6-phosphate

Glucose6-phosphate

Fructose1,6-bisphosphate

2 2 2

2

Hexokinase 2.7.1.1

Glucose 6-phosphateIsomerase 5.3.1.9

6-Phosphofructo-kinase 2.7.1.11

Fructose bisphosphatealdolase 4.1.2.13

Triose-phosphateisomerase 5.3.1.1 Pyruvate kinase

2.7.1.40

Phosphopyruvatehydratase 4.2.1.11

Phosphoglyceratekinase 2.7.2.3

Glucose

Pyruvate2

Glyceraldehyde-3- dehydro-genase 1.2.1.12

Phosphoglyceratemutase 5.4.2.1

Glucose Pyruvate Pyruvate

Glycolysis

A. Glycolysis: balance

C. Energy profile

B. Reactions

2

151Carbohydrate Metabolism

All rights reserved. Usage subject to terms and conditions of license.Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme

0

-20

-40

-60

-80

P PA

AP P P

!G' (kJ · mol-1)

P PA

AP P P

P PA

AP P P

P PA A

P P P

8

76

5

4

9

1

10

3

2

P PAA

P P P P PAA

P P P

P PAA

P P P

P PA A

P P P

1 32

8 7

4

5

22

22

N AN A

6

1

2

3

4

510

9

7

9

P

P

P

P

P

P

10

P P

6

8

2 H2O

P PA A

P P P

N A N A

P

2

2

2

2

2

!GOI = –35 kJ · mol–1

2 2

P

PP P

O

HO

OH

OH

OH

HH

HH

CH2

H

HO

O

HO

OH

OH

OH

HH

HH

CH2

H

HO

O

HO

OH

OH

OH

HH

HH

CH2

H

OO

CH2O

OH H

CH2OH

OH

HH HO

OCH2O

OH H

CH2

OH

HH HO

O

HC OH

H2C

C

O

O O

HC OH

H2C

CO O

O

HC O

H2C

CO O

OH

HC OH

H2C

C

O

O H

C O

CH2

H2C

O

OH

C O

CH2

CO O

C O

CH3

CO O

C O

CH3

COO

C O

CH3

COO

P

Pyruvate

Steps 1, 3 and 10are bypassed ingluconeogenesis

Glyceraldehyde3-phosphate

1,3-Bisphospho-glycerate

3-Phospho-glycerate

Phospho-enolpyruvate

2-Phospho-glycerate

Glycerone3-phosphate

Fructose6-phosphate

Glucose6-phosphate

Fructose1,6-bisphosphate

2 2 2

2

Hexokinase 2.7.1.1

Glucose 6-phosphateIsomerase 5.3.1.9

6-Phosphofructo-kinase 2.7.1.11

Fructose bisphosphatealdolase 4.1.2.13

Triose-phosphateisomerase 5.3.1.1 Pyruvate kinase

2.7.1.40

Phosphopyruvatehydratase 4.2.1.11

Phosphoglyceratekinase 2.7.2.3

Glucose

Pyruvate2

Glyceraldehyde-3- dehydro-genase 1.2.1.12

Phosphoglyceratemutase 5.4.2.1

Glucose Pyruvate Pyruvate

Glycolysis

A. Glycolysis: balance

C. Energy profile

B. Reactions

2

151Carbohydrate Metabolism


Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme

Pyruvate possui grande valor

energético e pode ser utilizado para produzir mais ATP.

Assim, uma molécula de glicose pode gerar até 30

ATPs.


Geração de Energias


Armazenamento de Energias

ATP

ADP

Pi

ATP +H2O ! ADP + Pi

� 30.5 > �Go > �50 kJ/mol

kBT = 4.1 pNnm

= 0.6 kcal/mol

= 2.5 kJ/mol

= 25meV

C � C ! 346 kJ/mol

C = C ! 602

C �H ! 415

H �H ! 436

O = O ! 498


-10

-20

-30

!G OI

kJ · mol-1

" #$Mg

P PA

AP P P

P

ATP

H

P PA

AP P PP

P

P

e

N

CHN

C

CC

NHC

N

NH2

OCH2O

H

OH OH

HH H

P

O

O

OPO

O

O

P

O

O

O

#"$

P

P

P

P

+

4

ATP

P

P

P

Aden

osin

e+

3

AMP

P

P

ATP

+

2

ADP

ATP

P

+

1

321

A

H

OCH2O

H

OH

H

P

O

O

OPO

O

O

#"

A. ATP: structure

C. Types of ATP formation

2. Mg2 -Complex

B. Hydrolysis energies

Phosphorylatedsubstrate

Enzyme

Substrate

1. Phosphate transfer

Electrons

Protons ATPsynthase

ADP

2. Oxidative phosphorylation

Phosphoric acidanhydride bonds

Phosphoric acidester bond

Aden

ine

1. Formula

2. ATP: charge density

ATP

Substratechain phos-phorylation

N-glycosidicbond

Positive

Neutral

Negative

1. Hydrolysis energies

Ared

AdenosinePhosphate residue

Ribose

ADP

123Energy Metabolism


Koolman, Color Atlas of Biochemistry, 2nd edition © 2005


ATP-ADP ~ varias tipos de reações bioquímicasATP-ADP ~ 20 kBT

Ligação covalente típica ~ 150 kBT

NADP+


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