Cell &iology 1

MODULE 1
Upon completion of this module, the learner will be able to:

After going through this unit, you should be able to: Learn about Cell theory and its Modern interpretation Understand the Structure of prokaryotic and eukaryotic Cells. et knowledge about Cellular organelles. !ypes of cell organelles eukaryotic and prokaryotic. Learn about the formation of Cell Membrane"#lasma Membrane. Understand the $luid Mosaic model of #lasma Membrane. Learn the functions of plasma membrane et the knowledge of composition of #lasma Membrane After going through this unit, you should be able to: Understand the cell motility and more about cilia and flagella. Learn more about molecular e%ents and model systems Understand the cellular responses and mechanism of signal transduction.

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2 Cell &iology

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Cell &iology 3

Unit 1: Bioenergetics:

CONTENTS 'ntroduction Learning (b)ecti%es *.*

Summary +eywords ,-ercise $urther .eadings

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4 Cell &iology

Introduction
'n this unit you will be going to study about concept of free energy and standard free energy. /etermination of 0 for a reaction relationship between e1uilibrium constant and standard free energy change, biological standard state 2 standard free energy change in coupled reactions. &ioenergetics is the sub)ect of a field of biochemistry that concerns energy flow through li%ing systems. !his is an acti%e area of biological research that includes the study of thousands of different cellular processes such as cellular respiration and the many other metabolic processes that can lead to production and utili3ation of energy in forms such as A!# molecules.

Le rning O!"ecti#es

After going through this unit, you should be able to: Learn about Cell theory and its Modern interpretation Understand the Structure of prokaryotic and eukaryotic Cells. et knowledge about Cellular organelles. !ypes of cell organelles eukaryotic and prokaryotic .

1$1 Conce%t o& &ree energ'

T(e energ' ssoci ted )it( c(e*ic + re ction t( t c n !e used to do )or,$ T(e &ree energ' o& s'ste* is t(e su* o& its ent( +%' -./ %+us t(e %roduct o& t(e te*%er ture -0e+#in/ nd t(e entro%' -S/ o& t(e s'ste*:

1ree energ' o& re ction

- 2/

!he change in the enthalpy 4 56 of the system minus the product of the temperature 4+el%in6 and the change in the entropy 4 S6 of the system:

St nd rd3st te &ree energ' o& re ction - 2 /

!he free energy of reaction at standard state conditions:

St nd rd3st te conditions
7 !he partial pressures of any gases in%ol%ed in the reaction is 8.* M#a. 7 !he concentrations of all a1ueous solutions are * M.
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Cell &iology 6

!abulated standard9state thermodynamic data are generally for a temperature of :; C 4:<= +6

St nd rd3St te 1ree Energ' o& 1or* tion - 2& /

!he change in free energy that occurs when a compound is formed from its elements in their most thermodynamically stable states at standard9state conditions. 'n other words, it is the difference between the free energy of a substance and the free energies of its elements in their most thermodynamically stable states at standard9state conditions. !he standard9state free energy of reaction can be calculated from the standard9state free energies of formation as well. 't is the sum of the free energies of formation of the products minus the sum of the free energies of formation of the reactants:

S#(>!A>,(US: >(>9S#(>!A>,(US:

is negati%e 4 is positi%e 4

? 8, +e1 @ *6 @ 8, +e1 ? *6

,AU'L'&.'UM:

B 8 4+e1 B *6 5 ? 8 6 and entropy 4 S @ 86 changes, then the reaction

'f a reaction is fa%orable for both enthalpy 4 will be S#(>!A>,(US 4

? 8 6 at any temperature. 5 @ 8 6 and entropy 4 S ? 8 6 changes, then the reaction

'f a reaction is unfa%orable for both enthalpy 4 will be >(>9S#(>!A>,(US 4

@ 8 6 at any temperature.

'f a reaction is fa%orable for only one of either entropy or enthalpy, the standard9state free energy e1uation must be used to determine whether the reaction is spontaneous or not. $or non9standard9state conditions 4# C 8.* M#aD concentrations C * M6, %alues of reaction conditions must be calculated and used to determine and 5 and S for the actual

+e1.

S *%+e &ree energ' c +cu+ tion -st nd rd3st te conditions/:

Co*%ound .& S >5E>(F4s6 9FG;.;G *;*.8= >5EH4aq6 9*F:.;* **F.E 9 >(F 4aq6 9:8;.8 *EG.E

C +cu+ te . 5 S 5 nd 2 &or t(e !o#e re ction to deter*ine )(et(er t(e re ction is s%ont neous or not$
$irst letIs calculate .& . >ote that in the abo%e reaction, one mole of >5E>(F dissociates in water to gi%e one mole each of >5EH and >(F9:

>e-t, letIs calculate

S:
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; Cell &iology

>ow we can plug in these %alues weI%e calculated into the free energy e1uation. 7 NOTE: !he units of .& is ,7 and the units of S is 780. Since 2 is generally reported in ,7, we can di%ide S by *888 to con%ert it to units of ,780 7 NOTE: !he temperature in the free energy e1uation must be in +el%in, so we must con%ert the gi%en temperature in Celsius to +el%in by adding :JF.*;.

C(ec, Your 9rogress 1

Mu+ti%+e C(oice :uestion: Cell is disco%ered by:

a6 c6 .obert 5ook !heodor Schwann

b6 Kakob Schleiden d6 .udolf Lirchow

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Cell &iology ?

*.: Deter*in tion o& &or re ction Re+ tions(i% !et)een St nd rd 1ree energ' c( nge nd E<ui+i!riu* Const nts
!he following e1uation relates the standard9state free energy of reaction with the free energy of reaction at any moment in time during a reaction 4not necessarily at standard9state conditions6:

7 7

B free energy at any moment B standard9state free energy

7 . B ideal gas constant B =.F*E K"mol9+ 7 ! B temperature 4+el%in6

7 lnA B natural log of the re ction <uotient

Re ction <uotient -:c or :%/

9 !he mathematical product of the concentrations 4or partial pressures6 of the products of a reaction di%ided by the mathematical product of the concentrations 4or partial pressures6 reactants of a reaction A! A>M M(M,>! '> !'M,.

Note: Nhen Ac B +c 4or when Ap B +p6, a reaction is at e1uilibrium.

't was stated earlier that when B 8, a reaction is at e1uilibrium. LetIs consider the abo%e reaction at e1uilibrium:

'f we mo%e .!ln+ to the opposite side by subtracting it from both sides, we get the following reaction which relates the free energy of a reaction to the e1uilibrium constant of a reaction:

S9ONT=NEOUS ?8 @8

NON3S9ONT=NEOUS +@* +?*

!he magnitude of measures how far a reaction is from e1uilibrium. !he larger the %alue of , the further the reaction is from e1uilibrium and the further the reaction must shift to reach e1uilibrium. 'n reactions in which enthalpy is fa%orable and entropy is unfa%orable, the reaction becomes less spontaneous 4 not spontaneous 4when @ 86. As the magnitude of increases6 until e%entually the reaction is changes, so does the e1uilibrium constant. +.

!he &ree energ' c( nge - 2/ of a reaction determines its spontaneity. !he free energy change 4 6, and its relation to e1uilibrium constant. A reaction is s%ont neous i& 2 is neg ti#e 4if the free energy of the products is less than the free energy of the reactants6. 2 B change in free energy, 2o> B standard free energy change 4with * M reactants and products, at p5 J6, R B gas constant, T B absolute temperature.
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E Cell &iology

>ote that the standard free energy change 4 oI6 of a reaction may be positi%e, for e-ample, and the actual free energy change 4 6 negati%e, depending on cellular concentrations of reactants and products. Many reactions for which oI is positi%e are spontaneous because other reactions cause depletion of products or maintenance of high substrate concentrations.

At e<ui+i!riu*, 2 e1uals 3ero. Sol%ing for 2o> yields the relationship at left. 0>e<, the ratio OCPO/P"OAPO&P at e1uilibrium, is called the e<ui+i!riu* const nt. =n e<ui+i!riu* const nt gre ter t( n one 4more products than reactants at e1uilibrium6 indicates a s%ont neous re ction 4negati%e I6.

!he %ariation of e1uilibrium constant with 0e< 1@4 1@2 1@@ B 1 1@A2 1@A4 2o> 4kK"mol6 A 23 A 11 @ C 11 C 23

I is shown in the table below. Starting with * M reactants and products, the reaction: proceeds forward 4spontaneous6 proceeds forward 4spontaneous6 is at e<ui+i!riu* proceeds in re%erse proceeds in re%erse

Energ' cou%+ing

A spontaneous reaction may dri%e a non9spontaneous reaction.

Bio+ogic + st nd rd st te D St nd rd 1ree Energ' C( nge in Cou%+ed re ctions$ Cou%+ed Re ctions

!wo reactions are said to be coupled when the product of one of them is the reactant in the other: AQ & &Q C

'f the standard free energy of the first reaction is positi%e but that of the second reaction is sufficiently negati%e, then for the o%erall process will be negati%e and we say that the first reaction is Rdri%enS by the
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Cell &iology F

second one. !his, of course, is )ust another way of describing an effect that you already know as the Le ChTtelier principle: the remo%al of substance & by the second reaction causes the e1uilibrium of the first to Rshift to the rightS. Similarly, the e1uilibrium constant of the o%erall reaction is the product of the e1uilibrium constants of the two steps. 1 Cu:S4s6 Q : Cu4s6 H S4s6 2 S4s6 H (:4g6Q S(:4g6 UGV B H =G.: kK UGV B WF88.* kK UHV B H JG.F kK UHV B H :<G.= kK UHV B W :*J.F kK

3 Cu:S4s6Q : Cu4s6 H S(:4g6 UGV B W:*F.< kK

'n the abo%e e-ample, reaction 1 is the first step in obtaining metallic copper from one of its principal ores. !his reaction is endothermic and it has a positi%e free energy change, so it will not proceed spontaneously at any temperature. 'f Cu:S is heated in the air, howe%er, the sulfur is remo%ed as rapidly as it is formed by o-idation in the highly spontaneous reaction 2, which supplies the free energy re1uired to dri%e 1. !he combined process, known as ro sting, is of considerable industrial importance and is one of a large class of processes employed for winning metals from their ores .

1ree energ' c( nges of coupled reactions are dditi#e.

,-amples of different types of coupling: =$ Some en3yme9cataly3ed reactions are interpretable as t)o cou%+ed ( +&3re ctions, one spontaneous and the other non9 spontaneous. At the en3yme acti%e site, the coupled reaction is kinetically facilitated, while the indi%idual half9reactions are pre%ented. !he free energy changes of the half9reactions may be summed, to yield the free energy of the coupled reaction. $or e-ample, in the reaction cataly3ed by the lycolysis en3yme 5e-okinase, the two half9reactions are:

A!# H 5:( A/# H #i .................. #i H glucose glucose9G9# H 5:( ...

I B F* kKoules"mol I B H*E kKoules"mol

Cou%+ed re ction: A!# H glucose A/# H glucose9G9# .. oI B *J kKoules"mol !he structure of the en3yme acti%e site, from which water is e-cluded, pre%ents the indi%idual hydrolytic reactions, while fa%oring the coupled reaction. B$ !wo separate en3yme9cataly3ed reactions occurring in the same cellular compartment, one spontaneous and the other non9 spontaneous, may be coupled by a co**on inter*edi te 4reactant or product6. 9'ro%(os%( te 4##i6 is often the product of a reaction that needs a dri%ing force. 'ts spontaneous hydrolysis, cataly3ed by #yrophosphatase en3yme, dri%es the reaction for which ## i is a product. $or an e-ample of such a reaction, see the discussion of cAM# formation below. C. Ion tr ns%ort may be cou%+ed to synthesis of A!#. c(e*ic + re ction, e.g., hydrolysis or

'n the diagram at right and below, water is not shown. 't should be recalled that the A!# hydrolysis"synthesis reaction is A!# H 5:( A/# H #i. ,1ui%alent to e1uation, the free energy change 4electrochemical potential difference6
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1@ Cell &iology

associated with transport of an ion S across a membrane from side * to side : is represented below.

R B gas constant, T B temperature, G B charge on the ion, 1 B $araday constant, and B %oltage across the membrane.

Since free energy changes are additi%e, the s%ont neous direction for the coupled reaction will depend on the re+ ti#e * gnitudes of: 2 &or t(e ion &+uH 4 %aries with the ion gradient and %oltage.6 2 &or t(e c(e*ic + re ction 4 oI is negati%e in the direction of A!# hydrolysis. !he magnitude of concentrations of A!#, A/#, and #i .6 depends also on

!wo e-amples of such coupling are: *. =cti#e tr ns%ort$ Spontaneous A!# hydrolysis 4negati%e 6 is coupled to 4dri%es6 ion flu- against a gradient 4positi%e 6. $or an e-ample, see the discussion of S,.CA.

:. =T9 s'nt(esis in mitochondria. Spontaneous 5H flu- across a membrane 4negati%e 6 is coupled to 4dri%es6 A!# synthesis 4positi%e 6. See the discussion of the A!# Synthase.

Kust as commerce is facilitated by the use of a common currency, the commerce of the cellXmetabolism Xis facilitated by the use of a common energy currency, adenosine triphosphate 4A!#6. #art of the free energy deri%ed from the o-idation of foodstuffs and from light is transformed into this highly accessible molecule, which acts as the free9energy donor in most energy9re1uiring processes such as motion, acti%e transport, or biosynthesis. A!# is a nucleotide consisting of an adenine, a ribose, and a triphosphate . !he acti%e form of A!# is usually a comple- of A!# with Mg:H or Mn:H. 'n considering the role of A!# as an energy carrier, we can focus on its triphosphate moiety. ATP is an energy-rich molecule because its triphosphate unit
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Cell &iology 11

contains two phosphoanhydride bonds. A large amount of free energy is liberated when A!# is hydroly3ed to adenosine diphosphate 4A/#6 and orthophosphate 4#i6 or when A!# is hydroly3ed to adenosine monophosphate 4AM#6 and pyrophosphate 4##i6.

Structures of A!#, A/#, and AM#. !hese adenylates consist of adenine 4blue6, a ribose 4black6, and a tri9, di9, or monophosphate unit 4red6. !he innermost phosphorus atom of A!# is designated #Y, the middle one #Z, and the outermost one !he precise UGV[ for these reactions depends on the ionic strength of the medium and on the concentrations of Mg:H and other metal ions. Under typical cellular concentrations, the actual UG for these hydrolyses is appro-imately 9*: kcal mol9* 49;8 kK mol9*6. !he free energy liberated in the hydrolysis of A!# is harnessed to dri%e reactions that re1uire an input of free energy, such as muscle contraction. 'n turn, A!# is formed from A/# and #i when fuel molecules are o-idi3ed in chemotrophs or when light is trapped by phototrophs. This ATPADP cycle is the fundamental mode of energy exchange in biological systems Some biosynthetic reactions are dri%en by hydrolysis of nucleoside triphosphates that are analogous to A!#Xnamely, guanosine triphosphate 4 !#6, uridine triphosphate 4U!#6, and cytidine triphosphate 4C!#6. !he diphosphate forms of these nucleotides are denoted by /#, U/#, and C/#, and the monophosphate forms by M#, UM#, and CM#. ,n3ymes can cataly3e the transfer of the terminal phosphoryl group from one nucleotide to another. !he phosphorylation of nucleoside monophosphates is cataly3ed by a family of nucleoside monophosphate kinases, as discussed in Section <.E.*. !he phosphorylation of nucleoside diphosphates is cataly3ed by nucleoside diphosphate kinase, an en3yme with broad specificity. 't is intriguing to note that, although all of the nucleotide triphosphates are energetically e1ui%alent, A!# is nonetheless the primary cellular energy carrier. 'n addition, two important electron carriers, >A/H and $A/, are deri%ati%es of A!#. The role of ATP in energy metabolism is paramount.
C(ec, Your 9rogress 2

Mu+ti%+e C(oice :uestions T(e ter*s %ro, r'otic nd eu, r'otic )ere suggested !'
a6 c6 5ans .is !heodor Schwann

b6 Kakob Schleiden d6 .obert 5ook

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12 Cell &iology

Le rner =cti#it'
Analyse the +ey functions of all cell organelles.

Su** r'

0e')ords EHercise

=ns)ers to C(ec, Your 9rogress :uestions

CYP 1

.obert 5ook
CYP 2

5ans .is
CYP 3

*. * \m to *8 \m :. ram9negati%e F. #lasmids E. &acterial Cyp 4

a6 c6 !rue !rue *. b6 $alse d6 $alseCYP 2

1urt(er Re dings Ie! Lin,s

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