Basic Physical Chemical Concepts in Biology€¦ · Structure of Atoms, Molecules and Chemical...

Structure of Atoms, Molecules andChemical BondsA chemical element is a pure chemical substance consisting of one type of atomdistinguished by its atomic number, which is the number of protons in its nucleus. Theterm is also used to refer to a pure chemical substance composed of atoms with the samenumber of protons.

In total, 118 elements have been observed so far, of which 94 occur naturally on Earth.80 elements have stable isotopes, namely all elements with atomic numbers 1 to 82,except elements 43 and 61 (technetium and promethium). Elements with atomicnumbers 83 or higher (bismuth and above) are inherently unstable, and undergoradioactive decay. The elements from atomic number 83 to 94 have no stable nuclei, butare nevertheless found in nature. Of the total stable elements in nature, fifteen arepresent in all living things, and a further 8-10 are only found in particular organisms.More than 99% of the atoms in animals’ bodies are accounted for by just fourelements—hydrogen (H), oxygen (O), carbon (C) and nitrogen (N).

Table 1.1 Elemental Composition of Earth’s Crust

Element Per cent by Mass Element Per cent by Mass

Oxygen 46.71 Potassium 2.58

Silicon 27.69 Magnesium 2.08

Aluminium 8.07 Titanium 0.62

Iron 5.05 Hydrogen 0.14

Calcium 3.65 Phosphorus 0.13

Sodium 2.75 Carbon 0.094

Basic PhysicalChemical Conceptsin Biology

and

1

Syllabus

l Structure of Atoms, Moleculesand Chemical Bonds.

l Composition, Structure andFunctions of Biomolecules,Carbohydrates, Lipids, Proteins,Nucleic Acids and Vitamins.

l Biomolecular Weak Interactions(van der Waals, Electrostaticforce, Hydrogen Bonding,Hydrophobic Interaction, etc.).

l Principles of BiophysicalChemistry (pH, Buffer, ReactionKinetics, Thermodynamics,Colligative Properties).

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Table 1.2 Elemental Composition of Earth’sOcean Water

ElementPer cent by

MassElement

Per cent byMass

Oxygen 85.84 Sulphur 0.091

Hydrogen 10.82 Calcium 0.04

Chlorine 1.94 Potassium 0.04

Sodium 1.08 Bromine 0.0067

Magnesium 0.1292 Carbon 0.0028

Table 1.3 Composition of Earth’s Atmosphere

GasPer cent by

VolumeGas

Per cent byVolume

Nitrogen 78.084 Hydrogen 0.000055

Oxygen 20.946 Nitrous oxide 0.00003

Argon 0.9340 Carbon monoxide 0.00001

Carbon

dioxide

0.0390 Xenon 9 × 10−6

Neon 0.001818 Ozone 0-7 × 10−6

Helium 0.000524 Nitrogen dioxide 2 × 10−6

Methane 0.000179 Iodine 1 × 10−6

Krypton 0.000114 Ammonia Trace

Table 1.4 Elemental Composition of the HumanBody

ElementPer cent by

MassElement

Per cent byMass

Oxygen 65 Potassium 0.2

Carbon 18 Sulphur 0.2

Hydrogen 10 Chlorine 0.2

Nitrogen 3 Sodium 0.1

Calcium 1.5 Magnesium 0.05

Phosphorus 1.2

Iron, Cobalt, <0.05 each

Copper, Zinc

and Iodine

Selenium and <0.01 each

Fluorine

Hydrogen and oxygen are the constituents of water, whichalone makes up 60-70% of cell mass. Together with carbonand nitrogen, hydrogen and oxygen are also the majorconstituents of the organic compounds on which mostliving processes depend. Many biomolecules also containsulfur (S) or phosphorus (P). The above macro-elementsare essential for all organisms.

Other biologically important group of elements, which together represent only about 0.5% of the body mass, is present almostexclusively in the form of inorganic ions. This group includes the alkali metals sodium (Na) and potassium (K), and the alkalineearth metals magnesium (Mg) and calcium (Ca). The halogen chlorine (Cl) is also always ionized in the cell. All other elementsimportant for life are present in such small quantities that they are referred to as trace elements. These include transition metalssuch as iron (Fe), zinc (Zn), copper (Cu), cobalt (Co) and manganese (Mn). A few nonmetals, such as iodine (I) and selenium (Se),can also be classed as essential trace elements.

Electromagnetic RadiationElectromagnetic radiation is a form of energy transmission inwhich electric and magnetic fields are propagated as wavesthrough empty space (a vacuum) or through a medium suchas glass. According to a theory proposed by James ClerkMaxwell (1831-1879) in 1865, electromagnetic radiation—apropagation of electric and magnetic fields, is produced by anaccelerating electrically charged particle (particle whosevelocity changes).

The SI unit for frequency, s–1, is the hertz (Hz), and the basicSI wavelength unit is the meter (m). Because many types ofelectromagnetic radiation have very short wavelengths,however, smaller units, including those listed below, are alsoused. The angstrom, named for the Swedish physicistAnders Ångström (1814-1874), is not an SI unit.

1 centimeter (cm) = 1 × 10−2 m

1 micrometer (mm) = 1 × 10−6 m

2 UGC-CSIR NET Tutor Life Sciences

H

Li

Na

K

R

Cs

Be

Mg

Ca

Sr

Ba

Sc

Y

La

Ti

Zr

Hf

V

Nb

Ta

Cr

Mo

W

Mn

Tc

Re

Fe

Ru

Os

Co

Rh

Ir

Ni

Pd

Pt

Cu

Ag

Au

Zn

Cd

Hg

B

Al

Ga

In

Tl

C

Si

Ge

Sn

Pb

N

P

As

S

Bi

O

S

Se

Te

Po

F

Cl

Br

I

At

He

Ne

Ar

Kr

Xe

Rn

Essential to all animalsand plants

Essential to several classesof animals and plants

Believed essential to avariety fo species

Possible essential traceelements for some species

Fig. 1.1 Elements known to be essential to living beings. The 11 elements–C, H, O, N, S, P, Na, K, Mg, Ca and Cl–make up 99.9% of the massof a human being. An additional 13 are known to be essential for higher animals in trace amounts. Boron is essential to higher plantsbut apparently not to animals, microorganisms or algae.

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1 nanometer (nm) = 1 × 10−9 m = 1 × 10−7 cm = 10 Å

1 picometer (pm) = 1 × 10−12 m = 1 × 10−10 cm = 10−2 Å

1 angstrom (Å) = 1 × 10−10 m = 1 × 10−8 cm = 100 pm

A distinctive feature of electromagnetic radiation is itsconstant speed 2.997925 × 108 ms–1 of in a vacuum, oftenreferred to as the speed of light.

When a beam of white light is passed through a transparentmedium, the wavelength components are refracteddifferently. The light is dispersed into a band of colours, aspectrum.

Subatomic ParticlesThe atom is composed of many types of subatomicparticles, but only three types will be important in thiscourse. Protons and neutrons exist in the atom’s nucleus,and electrons exist outside the nucleus.

An uncombined atom is neither positive nor negative butelectrically neutral, and thus the number of protons (p)must equal the number of electrons:

Number of protons = Number of electrons (For a neutralatom)

ElectronA negatively charged subatomic particle of an atom or ionthat is outside of the nucleus. A neutral atom contains thesame number of electrons as there are protons in the nucleus.A negatively charged Beta Particle is an electron that isemitted from the nucleus as a result of a nuclear decayprocess.

ProtonA subatomic particle having a mass of 1.0073 amu and acharge of +1, found in the nuclei of atoms. The nucleus ofnormal hydrogen is made up of a proton; thus the ionizedform of normal hydrogen is often called a proton.

NeutronAn atomic particle found in the nuclei of atoms that is similarto a proton in mass but has no electric charge.

Some Important Termsl The atomic number (Z) is equal to the number of protons

(p) in the atom, and determines its identity Z = p.

l The number of neutrons in the nuclei of atoms of the sameelement can differ.

l Mass number (A) The sum of the numbers of protons andneutrons in an atom.

A = p + n = Z + n

l Atomic mass unit (amu) One-twelfth of a mass of an atomof the carbon-12 (12C) isotope; a unit used for stating atomicand formula weights; also called a dalton.

l Isotope Different forms of a single element that have thesame number of protons but have different numbers ofneutrons in their nuclei. Radioactive isotopes are unstableand break down until they become stable. Carbon-14 is aradioactive isotope of carbon that is used to date fossilizedorganic matter.

Structure of AtomsThe word ‘atom’ has been derived from the Greek word‘a-tomio’ which means ‘uncutable’ or ‘non-divisible’. Theatomic theory of matter was first proposed on a firm scientificbasis by John Dalton, a British school teacher in 1808.Dalton’s atomic theory—Atom as the ultimate particle ofmatter. The experimental observations made by scientiststowards the end of nineteenth and beginning of twentiethcentury have established that atoms can be further divided into

Basic Physical and Chemical Concepts in Biology 3

1024

1022

1020

1018

1016

1014

1012

1010

108

106

104

10–16

10–14

10–12

10–10

10–8

10–6

10–4

10–2

100

102

104

γ-rays

X-rays

Ultra-violet Infra-red

Micro-wave

Radio Wave

Frequency, s–1

Wavelength, m

Visible

l = 390 450 500 550 600 650 700 760 nm

Fig. 1.2 The electromagnetic spectrum

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subatomic particles, i.e., electrons, protons and neutrons—concept very different from that of Dalton.

Dalton’s Atomic TheoryIn 1803, John Dalton (1766-1844) proposed his atomictheory, including the following postulates, to explain thelaws of chemical combination:

(i) Matter is made up of very tiny, indivisible particlescalled atoms.

(ii) The atoms of each element all have the same mass, butthe mass of the atoms of one element is different fromthe mass of the atoms of every other element.

(iii) Atoms combine to form molecules. When they do so,they combine in small, whole-number ratios.

(iv) Atoms of some pairs of elements can combine with eachother in different small, whole-number ratios to formdifferent compounds.

(v) If atoms of two elements can combine to form morethan one compound, the most stable compound has theatoms in a 1:1 ratio (this postulate was quickly shownto be incorrect).

The first three postulates have had to be amended, and thefifth was quickly abandoned altogether. But the postulatesexplained the laws of chemical combination known at thetime, and they caused great activity among chemists, whichled to more generalizations and further advances inchemistry.

Thomson’s Plum Pudding Modelof the AtomIn 1904 Sir JJ Thomson proposed the first definite theoryas to the internal structure of the atom. According to thistheory the atom was assumed to consist of a sphere ofuniform distribution of about 10 10− m positive charge withelectrons embedded in it such that the number of electronsequal to the number of positive charges and the atom as awhole is electrically neutral. This model of atom couldaccount the electrical neutrality of atom, but it could notexplain the results of gold foil scattering experiment carriedout by Rutherford.

Rutherford’s Scattering ExperimentRutherford conducted a scattering experiment in 1911 to findout the arrangement of electrons and protons. He bombardeda thin gold foil with a stream of fast moving positivelycharged a-particles emanating from radium.

(i) He designs experiment to use alpha particles as atomicbullets The alpha particle was heavy and positivelycharged, it is a helium nuclei (2 protons and2 neutrons). The beta particle was light and negativelycharged, the electron. Rutherford designed anexperiment to use the alpha particles emitted by aradioactive element as probes to the unseen world ofatomic structure.

(ii) Rutherford beamed alpha particles through gold foiland detected them as flashes of light or scintillations ona screen. The gold foil was only 0.00004 centimeterthick, meaning on a few hundreds of atoms thick.

(iii) If the Thomson model of atoms was correct, then thealpha particles should pass through with relativelylittle deflection.

Rutherford’s Nuclear Modelof an AtomThis model resulted from conclusion drawn fromexperiments on the scattering of alpha particles from aradioactive source when the particles were passed throughthin sheets of metal foil. According to him

(i) Most of the space in the atom is empty as most of thea-particles passed through the foil.

(ii) A few positively charged α-particles are deflected. Thedeflection must be due to enormous repulsive forceshowing that the positive charge of the atom is notspread throughout the atom as Thomson had thought.The positive charge has to be concentrated in a verysmall volume that repelled and deflected the positivelycharged α-particles. This very small portion of the atomwas called nucleus by Rutherford.

(iii) Calculations by Rutherford showed that the volumeoccupied by the nucleus is negligibly small as comparedto the total volume of the atom. The diameter of theatom is about 10 10− m, while that of nucleus is 10 15− m.


Non-deflectedparticlesFluorescent

screen

Gold foil

Deflected particles

Radioactive source

Fig. 1.3 Rutherford’s scattering experiment

Where the mass of theelectron is 1/2000 themass of the proton andthe mass of the protonequals the mass of theneutron

Electron orbits

Helium atom

Elementary Particles

Electron (–)

Proton (+)

Neutron (0)

Nucleus

Fig. 1.4 Rutherford’s nuclear model of a atom model

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On the basis of above observations and conclusions,Rutherford proposed the nuclear model of atom. According tothis model:

(a) An atom consists of a tiny positively charged nucleus atits centre.

(b) The positive charge of the nucleus is due to protons.The mass of the nucleus, on the other hand, is due toprotons and some neutral particles each having massnearly equal to the mass of proton. This neutralparticle, called neutron, was discovered later on byChadwick in 1932. Protons and neutrons present in thenucleus are collectively also known as nucleons. Thetotal number of nucleons is termed as mass number(A) of the atom.

(c) The nucleus is surrounded by electrons that movearound the nucleus with very high speed in circularpaths called orbits. Thus, Rutherford’s model of atomresembles the solar system in which the sun plays therole of the nucleus and the planets that of revolvingelectrons.

(d) The number of electrons in an atom is equal to thenumber of protons in it. Thus, the total positive chargeof the nucleus exactly balances the total negativecharge in the atom making it electrically neutral. Thenumber of protons in an atom is called its atomicnumber (Z).

(e) Electrons and the nucleus are held together byelectrostatic forces of attraction.

Defects of Rutherford’s Model(a) According to Rutherford’s model, an atom consists of a

positive nucleus with the electrons moving a round it incircular orbits. However JC Maxwell shown thatwhenever an electron is subjected to acceleration, itemits radiation and loses energy. As a result of this, itsorbit should become smaller and smaller and finally itshould drop into the nucleus by following a spiral path.This means that atom would collapse and thusRutherford’s model failed to explain stability of atoms.

(b) Another drawback is that Rutherford’s model saidnothing about the electronic structure of the atoms, i.e.,how the electrons are distributed around the nucleusand what are the energies of these electrons. Therefore,this model failed to explain the existence of certaindefinite lines in the hydrogen spectrum.

Bohr’s Model of an AtomTo overcome the above defects of Rutherford’s model, NielsBohr in 1913 gave a modification based on quantum theory ofradiation. The important postulates are:

(i) The electrons revolve round the nucleus only in certainselected circular paths called orbits. These orbits areassociated with definite energies and are called energyshells or energy levels or quantum levels. These arenumbered as 1, 2, 3, 4 ….., etc. (starting from thenucleus) or designated as K, L, M, N, …., etc.

(ii) As long as an electron remains in a particular orbit, itdoes not lose or gain energy. This means that energy ofan electron in a particular path remains constant.Therefore, these orbits are also called stationary states.

(iii) Only those orbits are permitted in which angularmomentum of the electron is a whole number multipleof h/2π, where ‘h’ is Planck’s constant. An electronmoving in a circular orbit has an angular momentumequal to mvr where m is the mass of the electron and v,the angular momentum, the angular momentum, mvr

is a whole number multiple of h/2π, i.e.,

mvr = nh/2 where, n = 1, 2, 3, …In other words, angular velocity of electrons in an atomis quantised.

(iv) If an electron jumps from one stationary state toanother, it will absorb or emit radiation of a definitefrequency giving a spectral line of that frequency whichdepends upon the initial and final levels. When anelectron jumps back to the lower energy level, itradiates same amount of energy in the form ofradiation.

Limitations of Bohr’s Theory(i) According to Bohr, the radiation results when an

electron jumps from one energy orbit to another energyorbit, but how this radiation occurs is not explained byBohr.

(ii) Bohr’ theory had explained the existence of variouslines in H spectrum, but it predicted that only a seriesof lines exist. At that time this was exactly what hadbeen observed. However, as better instruments andtechniques were developed, it was realized that thespectral line that had been thought to be a single linewas actually a collection of several lines very closetogether (known as fine spectrum).


Electrons

Nucleus

–+

Fig. 1.5 Failure of Rutherford’s atom model

4 or N

3 or M

2 or L

1 or K

+ Nucleus

Fig. 1.6 Bohr’s orbits

5

(iii) Thus, the appearance of the several lines implies thatthere are several energy levels, which are close togetherfor each quantum number n. This would require theexistence of new quantum numbers.

(iv) Bohr’s theory has successfully explained the observedspectra for hydrogen atom and hydrogen like ions(e.g., He+ , Li2+ , Be3+ , etc.), it can not explain thespectral series for the atoms having a large number ofelectrons.

(v) There was no satisfactory justification for theassumption that the electron can rotate only in thoseorbits in which the angular momentum of the electron(mvr) is a whole number multiple of h/2π, i.e., he couldnot give any explanation for using the principle ofquantisation of angular momentum and it wasintroduced by him arbitrarily.

(vi) Bohr assumes that an electron in an atom is located at adefinite distance from the nucleus and is revolvinground it with definite velocity, i.e., it is associated with afixed value of momentum. This is against theHeisenberg’s Uncertainty Principle according to whichit is impossible to determine simultaneously withcertainty the position and the momentum of a particle.

(vii) No explanation for Zeeman effect If a substancewhich gives a line emission spectrum, is placed in amagnetic field, the lines of the spectrum get split upinto a number of closely spaced lines. This phenomenonis known as Zeeman effect. Bohr’s theory has noexplanation for this effect.

(viii)No explanation of the Stark effect If a substancewhich gives a line emission spectrum is placed in anexternal electric field, its lines get spilt into a number ofclosely spaced lines. This phenomenon is known asStark effect. Bohr’s theory is not able to explain thisobservation as well.

Quantum NumbersThe quantum numbers are nothing but the details that arerequired to locate an electron in an atom. These orbitals aredesignated by a set of numbers known as quantum numbers.In order to specify energy, size, shape and orientation of theelectron orbital, three quantum numbers are required theseare discussed below.

The Principal Quantum Number (n)The electrons inside an atom are arranged in different energylevels called electron shells or orbits. Each shell ischaracterized by a quantum number called principalquantum number. This is represented by the letter ‘n’ andhave values, 1, 2, 3, 4, etc. The first level is also known as K,

L, M and N respectively.

The Subsidiary or Azimuthal QuantumNumber (lq )According to Sommerfeld, the electron in any particularenergy level could have circular path or a variety of ellipticalpaths about the nucleus resulting in slight differences in

orbital shapes with slightly differing energies due to thedifferences in the attraction exerted by the nucleus on theelectron. This concept gave rise to the idea of the existence ofsub energy levels in each of the principal energy levels of theatom. This is denoted by the letter ‘l’ and have values from0 to n –1.

Thus, if

n = 1, l=0 only one value (one level only) s level.

n = 2, l=0 and 1 (2 values or 2 sub-levels) s and p level.

n = 3, l=0, 1 and 2 (3 values or 3 sub-levels) s, p and d level.

n = 4, l=0, 1, 2 and 3 (4 values or 4 sub-levels) s, p, d and flevel.

Magnetic Quantum Number (Ml)In a strong magnetic field a subshell is resolved into differentorientations in space. These orientations called orbitals haveslight differences in energy. This explains the appearance ofadditional lines in atomic spectra produced when atoms emitlight in magnetic field. Each orbital is designated by amagnetic quantum number m and its values depend on thevalue of ‘l’. The values are –‘l’ through zero to +‘l’ and thusthere are (2l+1) values. Thus, when

l = 0, m = 0 (only one value or one orbital)

l = 1, m = –1, 0, +1 (3 values or 3 orbitals)

l = 2, m = –2, –1, 0, +1, +2 (5 values or 5 orbitals)

l = 3, m = –3, –2, –1, 0, +1, +2, +3 (7 values or 7 orbitals).

The three quantum numbers labeling an atomic orbital canbe used equally well to label electron in the orbital. However,fourth quanta number, the spin quantum number, (s) isnecessary to describe an electron completely.

Spin Quantum Number (MS )The electron in the atom rotates not only around the nucleusbut also around its own axis and two opposite directions ofrotation are possible (clockwise and anti clockwise).Therefore, the spin quantum number can have only twovalues +1/2 or –1/2. For each values of m including zero,there will be two values for s.

Summarized information of the four quantum numbers:

(a) n identifies the shell, determines the size of the orbitaland also to a large extent the energy of the orbit.

(b) There are n subshells in the nth shell. l identifies thesubshell and determines the shape of the orbital. Thereare (2l + 1) orbitals of each type in a subshell, i.e., ones-orbital (l = 0), three p-orbitals (l = 1), and fived-orbitals (l = 2) per subshell. To some extent l alsodetermines the energy of the orbital in a multi-electronatom.

(c) ml designates the orientation of the orbital. For a given

value of l, ml has (2l + 1) values, the same as thenumber of orbital’s per sub shell. It means that thenumber of orbitals is equal to the number of ways inwhich they are oriented.

(d) ms refer to orientation of the spin of the electron.


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Shapes or Boundary Surfacesof Orbitals

s-orbitalsFor s-orbital l = 0 and hence, m can have only one value,i.e., m = 0 This means that the probability of finding them = 0 electron in s-orbital is the same in all directions at aparticular distance. In other words s-orbitals are sphericallysymmetrical.

The electron cloud picture of 1s-orbital is spherical. Thes-orbitals are more diffused and have spherical shells withinthem where probability of finding the electron is zero. Theseare called nodes. In 2s-orbital there is one spherical node. Inthe s-orbital, numbers of nodes are (n – 1).

p-orbitalsFor p-orbitals l = 1 and hence ‘m’ can have three possiblevalues +1, 0, –1. This means that there are three possibleorientations of electron cloud in a p-subshell. The threeorbitals of a p-subshell are designated as p px y, and pz

respectively along x-axis, y-axis and z-axis respectively. Eachp-orbital is thus dumpbell-shaped.In the absence of magnetic field these three p-orbitals areequivalent in energy and are, therefore, said to be three-folddegenerate or triply degenerate. In the presence of anexternal magnetic field, the relative energies of the threep-orbitals vary and depend on their orientation or magneticquantum number. This probably accounts for the splitting ofa single spectral line into a number of closely spaced lines inpresence of a magnetic field (fine structure).

d-orbitalsFor d-orbitals l = 2, m = 0, ±1, ±2 indicating that d-orbitalshave five orientations, i.e., there are five d-orbitals which arenamed as d d dxy yz zx, , and d y

x22− . The three orbitals namely

d dxy yz, and dzx have their lobes lying symmetrically between

the coordinate axes indicated in the subscript to d, e.g., thelobes of dxy orbital are lying between the x-and y-axes. This

set of three orbitals is known as T2g set. d yx2

2− and dz 2

orbitals have their lobes along the axes (i.e., along the axialdirections), e.g., the lobes of d-orbital lie along the x andy-axes, while those of d

z 2 orbital lie along the z-axis. This set

is known as Eg set.

Chemical BondingThe atoms do not remain individually but form bonds amongthemselves.

In the period from 1916-1919, two Americans, GN Lewis andIrving Langmuir, and a German, Walther Kossel, advancedan important proposal about chemical bonding. Somefundamental ideas associated with Lewis’s theory are

(i) Electrons, especially those of the outermost (valence)electronic shell, play a fundamental role in chemicalbonding.

(ii) In some cases, electrons are transferred from oneatom to another. Positive and negative ions are formedand attract each other through electrostatic forcescalled ionic bonds.

(iii) In other cases, one or more pairs of electrons areshared between atoms. A bond formed by the sharingof electrons between atoms is called a covalent bond.

(iv) Electrons are transferred or shared in such a way thateach atom acquires an especially stable electronconfiguration. Usually this is a noble gas configuration,one with eight outer-shell electrons or an octet.

Ionic BondsIn chemical bonds, atoms can either transfer or share theirvalence electrons. In the extreme case where one or moreatoms lose electrons and other atoms gain them in order toproduce a noble gas electron configuration, the bond is calledan ionic bond. Typical of ionic bonds are those in the alkalihalides such as sodium chloride, NaCl.

Ionization energy, electron affinity and lattice energyinfluencing the fermation of ionic bonds. Lattice energy isdefined as amount of energy released when cations andanions are brought from infinity to their respectiveequilibrium sites in crystal lattice.

Covalent BondsCovalent chemical bonds involve the sharing of a pair ofvalence electrons by two atoms, in contrast to the transfer ofelectrons in ionic bonds. Such bonds lead to stablemolecules if they share electrons in such a way as to create anoble gas configuration for each atom. Hydrogen gas formsthe simplest covalent bond in the diatomic hydrogenmolecule. The halogens such as chlorine also exist as diatomicgases by forming covalent bonds. The nitrogen and oxygenwhich makes up the bulk of the atmosphere also exhibitscovalent bonding in forming diatomic molecules.


Na Cl Na+

Cl

Forming ionicbond

Sodium contributeselectron, leaving itwith a closed shell

Chlorine gainselectron, leaving itwith a closed shell

–

Forming ionicbond

+

Mg O+

Ca Cl Cl+ +

+

Mg2+

O2–

+

Ca2+

Cl Cl+ +– –

Fig. 1.7 Ionic bonding

7

Valence Bond Theory(i) The electron-pair bond forms through the interaction

of an unpaired electron on each of two atoms.(ii) The spins of the electrons have to be opposed.

(iii) Once paired, the two electrons cannot take part inadditional bonds.

(iv) The electron-exchange terms for the bond involves onlyone wave function from each atom.

(v) The available electrons in the lowest energy level formthe strongest bonds.

(vi) Of two orbitals in an atom, the one that can overlap themost with an orbital from another atom will form thestrongest bond, and this bond will tend to lie in thedirection of the concentrated orbital.

HybridizationThe ‘mixing’ or ‘blending’ of atomic orbitals to accommodatethe spatial requirements in a molecule is known as

hybridization. Hybridization occurs to minimize electronpair repulsions when atoms are brought together to formmolecules. Each of these hybridization schemes correspondsto one of the five fundamental VSEPR geometries.

Sigma (σ) bonds arise from the ‘end-on’ overlap betweenadjacent orbitals. This leads to a region of high electrondensity along the inter-nuclear axis (cylindricallysymmetrical).

Pi (π) bonds arise from the ‘side-on’ overlap betweenadjacent orbitals. This leads to two regions of high electrondensity on opposite sides of the inter-nuclear axis (notcylindrically symmetrical).

Table 1.5 Shape and Examples of MoleculesPredicted from VSEPR Theory

Number ofElectron Pair

MolecularFormula

MolecularGeometry

Example

3 AX2E V-shaped

molecule

SO3 and SnCl2

AX3 Trigonal planar BF3 and SO3

4 AX4 Tetrahedral CH4 and SiCl4

AX3E Trigonal

pyramidal

NH3 and PF3

AX2E2 V-shaped

molecule

H2O and H2S

5 AX5 Trigonal

bipyramidal

PCl5 and

Fe(CO)5

AX4E Irregular

tetrahedral

SF4 and SCl4

AX3E2 T-shaped BrF3 and IBr3

AX2E3 Linear XeF2 and ICl2−

6 AX6 Octahedral SF6 and FeF63−

AX5E Square pyramidal BrF3 and IF5

AX4E2 Square planar XeF4


Table 1.6 Five Fundamental VSEPE Geometries

Number of Effective Pair Arrangement of Pair Hybridization (symbolic) Hybridization (figure)

2 → Linear bipyramidal sp

3 → Trigonal planar sp2

4 → Tetrahedral sp3

180°

120°

109.5º

Cl Cl+

H H+

ClH or H— Cl

Cl Cl Cl Cl—or

H Cl+

H H or H—H

Constituent atomsshare a pair of electrons,closing the shell for each

Bondingpair

Lonepair

Forming covalent bond

Fig. 1.8 Covalent bonding

8

WaterWater is the most abundant substance in living systems,making up 70% or more of the weight of most organisms. Thefirst living organisms doubtless arose in an aqueousenvironment.

A water molecule is tetrahedron with oxygen at its center.The two hydrogens and the unshared electrons of theremaining two sp3-hybridized orbitals. The 105-degree anglebetween the hydrogens differs slightly from the idealtetrahedral angle, 109.5 degrees.

The water molecule and its ionization products, H+ and OH−,influence the structure, self-assembly, and properties of allcellular components, including proteins, nucleic acids, andlipids. The noncovalent interactions responsible for thestrength and specificity of ‘recognition’ among biomoleculesare decisively influenced by the solvent properties of water,including its ability to form hydrogen bonds with itself andwith solutes.

Water has a higher melting point, boiling point, andheat of vaporization than most other common solvents.These unusual properties are a consequence of attractionsbetween adjacent water molecules that give liquid watergreat internal cohesion which is the cause of intermolecularattractions.

Water is a dipole, a molecule with electrical chargedistributed asymmetrically about its structure. The stronglyelectronegative oxygen atom and a partial positive chargedhydrogen atom. Water, a strong dipole, has a high dielectricconstant. The dielectric constant for hexane is 1.9; forethanol is 24.3; and for water is 78.5. Water, therefore greatlydecreases the force of attraction between charged and polarspecies relative to water-free environments with lowerdielectric constants. Its strong dipole and high dielectricconstant enable water to dissolve large quantities of chargedcompounds such as salts.

Polar biomolecules dissolve readily in water because they canreplace water-water interactions with more energeticallyfavorable water-solute interactions. In contrast, non-polarbiomolecules interfere with water-water interactions but areunable to form water-solute interactions—consequently,nonpolar molecules are poorly soluble in water. In aqueoussolutions, nonpolar molecules tend to cluster together.

Hydrogen bonds are relatively weak. Those in liquid waterhave a bond dissociation energy (the energy required tobreak a bond) of about 23 kJ/mol, compared with 470 kJ/molfor the covalent OOH bond in water or 348 kJ/mol for acovalent COC bond. The hydrogen bond is about 10%covalent, due to overlaps in the bonding orbitals, and about90% electrostatic.

Each hydrogen atom of a water molecule shares an electronpair with the central oxygen atom. The oxygen nucleusattracts electrons more strongly than does the hydrogennucleus (a proton); that is, oxygen is more electronegative.The sharing of electrons between H and O is therefore,unequal; each hydrogen bears a partial positive charge (2δ+)and the oxygen atom bears a partial negative charge equal tothe sum of the two partial positives (2δ−). As a result, there isan electrostatic attraction between the oxygen atom of onewater molecule and the hydrogen of another, called ahydrogen bond.

When water is heated, the increase in temperature reflectsthe faster motion of individual water molecules. At any giventime, most of the molecules in liquid water are engaged inhydrogen bonding, but the lifetime of each hydrogenbond is just 1 to 20 picoseconds; upon breakage of onehydrogen bond, another hydrogen bond forms, with the samepartner or a new one, within 0.1 ps.


90º

120º

90º

90º

Number of Effective Pair Arrangement of Pair Hybridization (symbolic) Hybridization (figure)

5 → Trigonal bipyramidal dsp3

6 → Octahedral d2sp3

9

Water Influences the Structure ofBiomoleculesWater forms about 60-70% of biomass. It directly or indirectlyinfluences the biomolecular structures.

Stabilizes Biological MoleculesThe covalent bond is the strongest force that holds moleculestogether. Non-covalent forces, while of lesser magnitude,make significant contributions to the structure, stability, andfunctional competence of macromolecules in living cells.These forces, which can be either attractive or repulsive,involve interactions both within the biomolecule andbetween it and the water that forms the principal componentof the surrounding environment.

Folding of BiomoleculesMost biomolecules are amphipathic that is, they possessregions rich in charged or polar functional groups as well asregions with hydrophobic character. Proteins tend to foldwith the R-groups of amino acids with hydrophobic sidechains in the interior. Amino acids with charged or polaramino acid side chains (e.g., arginine, glutamate, serine)generally are present on the surface in contact with water. Asimilar pattern prevails in a phospholipid bilayer, where thecharged head groups of phosphatidyl serine or phosphatidylethanolamine contact water while their hydrophobic fattyacyl side chains cluster together, excluding water. Thispattern maximizes the opportunities for the formation ofenergetically favorable charge-dipole, dipole-dipole, andhydrogen bonding interactions between polar groups on thebiomolecule and water. It also minimizes energeticallyunfavorable contact between water and hydrophobic groups.

Note that water can serve simultaneously both as a hydrogendonor and as a hydrogen acceptor.

Table 1.7 Bond Energies for Atoms of BiologicSignificance

Bond TypeEnergy

(kcal/mol)Bond Type

Energy(kcal/mol)

O—O 34 O==O 96

S—S 51 C—H 99

C—N 70 C==S 108

S—H 81 O—H 110

C—C 82 C==C 147

C—O 84 C==N 147

N—H 94 C==O 164

While the hydrogens of non-polar groups such as themethylene groups of hydrocarbons do not form hydrogenbonds, they do affect the structure of the water thatsurrounds them. Water molecules adjacent to a hydrophobicgroup are restricted in the number of orientations (degrees offreedom) that permit them to participate in the maximumnumber of energetically favorable hydrogen bonds. Maximalformation of multiple hydrogen bonds can be maintainedonly by increasing the order of the adjacent water molecules,with a corresponding decrease in entropy.

It follows from the second law of thermodynamics that theoptimal free energy of a hydrocarbon-water mixture is afunction of both maximal enthalpy (from hydrogen bonding)and minimum entropy (maximum degrees of freedom). Thus,nonpolar molecules tend to form droplets with minimalexposed surface area, reducing the number of water moleculesaffected. For the same reason, in the aqueous environment ofthe living cell the hydrophobic portions of biopolymers tend tobe buried inside the structure of the molecule, or within a lipidbilayer, minimizing contact with water.


H H

HH

H

H

O

H H

H

H

O

OO

O

HO

H

HH

O

Fig. 1.9 Left Association of two dipolar water moleculesby a hydrogen bond (dotted line).

Right Hydrogen-bonded cluster of four water

CH3 CH2 O H OH

H

R

O HCR′

N

R′′

R′′′

CH3 CH2 O H O

H

CH2 CH3

Fig. 1.10 Additional polar groups participate in hydrogen bonding.Shown are hydrogen bonds formed between an alcoholand water, between two molecules of ethanol, andbetween the peptide carbonyl oxygen and the peptidenitrogen hydrogen of an adjacent amino acid.

10

Composition, Structure and Functions of Biomolecules

Biomolecules form the base of cellular organization. Theyinclude carbohydrates, lipids, proteins, nucleic acids andvitamins.

CarbohydratesCarbohydrates are the most abundant class of organiccompounds found in living organisms.

General formula of carbohydrates is Cn(H2O)n.Carbohydrates are a major source of metabolic energy, forboth plants and animals.

Single units of sugar, such as glucose, are calledmonosaccharide. Sugars can be readily linked together toform disaccharides (contains two monosaccharides), oligo-saccharides (contains several monosaccharides) andpolysaccharides (contains many monosaccharides).

1. MonosaccharidesThe simple sugars, or monosaccharide arepolyhydroxyaldehydes (aldoses) or polyhydroxyketones(ketoses). All have the composition (CH2O)n, hence, the

family name carbohydrate. A typical sugar, and the one withthe widest distribution in nature, is glucose.

The six-membered ring formed in this way (pyranose rings)are especially stable, but five membered furanose ring alsoexist in many carbohydrates.

The two configurations about this carbon atom aredesignated a and b as indicated above. In an equilibriummixture, ring forms of most sugars predominate over openchains. Although polysaccharides are composed almostexclusively of sugar residues in ring forms, the open chainforms are sometimes metabolic intermediates.

Because of their many polar hydroxyl groups, most sugars arevery soluble in water. However, hydrogen bonds betweenmolecules stabilize sugar crystals making them insoluble innon-polar solvents. Intermolecular hydrogen bonds betweenchains of sugar rings in cellulose account for much of thestrength and insolubility of these polysaccharides.


H H

C C

O O

C C

C C

C C

C C

OH H

H OH

OH H

OH H

H HO

HO H

H HO

H HO

2

3

4

5

CH OH2CH OH26

D-Mannose (Man)has the oppositeconfiguration at C-2

D-Galactose (Gal)has the oppositeconfiguration at C-4

D-Glucose (Glc)showing

numberingof atoms

Sugars are named as D or Laccording to the configurationabout this carbon atom, oneremoved from the terminalposition

1

L-Glucose

Fig. 1.11 Structures of D and L-glucose

H

C

O

HCOH

HOCH

HCOH

HCOH

CH OH2

D-Glucose (Glc)(free aldehyde form)

HO

HO

CH OH2

CH OH2

O

O

HO

HO

OH

HO

H

HO

β

α

OH

H

Fig. 1.12 Pyranose ring forms (hemiacetal forms)

D-Fructose (Fru), a ketose that isa close structural and metabolicrelative of D-glucose.It occurs in honey and fruit juicesin free form, in the disaccharidesucrose (table sugar) as a5-membered furanose ring, andin other oligosaccharides andpolysaccharides.

CH OH2

C

C

C

C

O

H

O

O

H

H

H

OH

H

H

CH OH2

Fig. 1.13 D-fructose

11


C

CHO

OHH

CH OH2

Glyceraldehyde

C

CHO

C

C

C

OH

OH

OH

OH

H

H

H

H

CH OH2

Altrose (Alt)

C

CHO

C

C

C

H

OH

OH

OH

HO

H

H

H

CH OH2

Allose (All)

C

CHO

C

C

C

OH

H

OH

OH

H

HO

H

H

CH OH2

Glucose (Glc)

C

CHO

C

C

C

H

H

OH

OH

HO

HO

H

H

CH OH2

Mannose (Man)

C

CHO

C

C

C

OH

OH

H

OH

H

H

HO

H

CH OH2

Gulose (Gul)

C

CHO

C

C

C

H

OH

H

OH

HO

H

HO

H

CH OH2

Idose (Ido)

C

CHO

C

C

C

OH

H

H

OH

H

HO

HO

H

CH OH2

Galactose (Gal)

C

CHO

C

C

C

H

H

H

OH

HO

HO

HO

H

CH OH2

Talose (Tal)

C

CHO

C

OH

OHH

H

CH OH2

Erythrose

C

CHO

C

H

OHH

HO

CH OH2

Threose

CHO CHO

H

H

H

C

C

C

OH

OH

OH

H

OH

OH

C

C

C

HO

H

H

CH OH2

Ribose (Rib)CH OH2

Arabinose (Ara)

CHO CHO

H

HO

H

C

C

C

OH

H

OH

H

H

OH

C

C

C

HO

HO

H

CH OH2

Xylose (Xyl)CH OH2

Lyxose (Lyx)

Fig. 1.14 Formulas for the D-aldoses. Prefixes derived from the names of these aldoses are used in describing various other sugarsincluding ketoses

C

CH OH2

C

C

C

O

OH

OH

OH

H

H

H

CH OH2Psicose

C

CH OH2

C

C

C

C

OH

H

OH

OH

OH

HO

H

H

H

CH OH2Sedoheptulose

C

CH OH2

C

C

C

O

H

OH

OH

HO

H

H

CH OH2Fructose

C

CH OH2

C

C

C

O

OH

H

OH

H

HO

H

CH OH2

Sorbose

C

CH OH2

C

C

C

O

H

H

OH

HO

HO

H

CH OH2Tagatose

C

CH OH2

O

CH OH2Dihydroxyacetone

(not chiral)

C

CH OH2

C

C

O

OH

OH

H

H

CH OH2Ribulose

C

CH OH2

C

C

O

H

OH

HO

CH OH2Xylulose

C

CH OH2

O

CH OH2

Erythrulose

C OHH

Fig. 1.15 Formulae for the open forms of the D-ketoses

12

Natural Derivatives of SugarsThe aldehyde group of an aldose can be oxidized readily to acarboxyl group to form an aldonic acid. Among the severalaldonic acids that occur naturally is 6-phosphogluconic acid.

Sugar chains with —COOH at both ends are called aldaricacids, e.g., glucaric acid. The—OH group in the 2 position ofglucose may be replaced by —NH2 to form 2-amino-2-deoxyglucose, commonly called glucosamine (GlcN) or by—NH—CO—CH3 to form N-acetylglucosamine (GlcNAc).Similar derivatives of other sugars exist in nature. In manypolysaccharides, sulfate groups are attached in ester linkageto the sugar units. The sulfo (—SO3—) sugar 6-sulfo-a-D-quinovose is found in lipids of photosynthetic membranes.

The sugar alcohols, in which the carbonyl group has beenreduced to —OH, also occur in nature. For example,D-Glucitol (D-Sorbitol), the sugar alcohol obtained byreducing either D-Glucose or L-Sorbose, is a major product ofphotosynthesis and widely distributed in bacteria andthroughout the eukaryotic kingdom. It is present in largeamounts in berries of the mountain ash and in many otherfruits. It exists in a high concentration in human semen andaccumulates in lenses of diabetics. D-Glucitol and other sugaralcohols arise in some fungi during metabolism of thecorresponding sugars. Mannitol, another product ofphotosynthesis, is also present in many organisms.

Two common 6-deoxy sugars which lack the hydroxyl groupat C-6 are rhamnose and fucose. Both are of the ‘unnatural’L-configuration but are derived metabolically from D-glucoseand D-mannose, respectively.

Vitamin-C (ascorbic acid) is another important sugarderivative. Neuraminic acid is a 9-carbon sugar made bytransferring a 3-carbon piece onto a hexosamine. Its N-acetyland N-glycolyl derivatives are called sialic acids.

2. Disaccharides/OligosaccharidesTwo molecules of α-D-glucopyranose can be joined, in anindirect synthesis, to form maltose. Maltose is formed by thehydrolysis of starch and is otherwise not found in nature.There are only three abundant naturally occurringdisaccharides which are important to the metabolism ofplants and animals.

Lactose (milk), Sucrose (green plants) and Trehalose(fungi and insects).

Disaccharides are linked by glycosidic (acetal) linkages. Thesymbol α-1, 4 used above, refers to the fact that in maltose theglycosidic linkage connects carbon atom 1 (the anomericcarbon atom) of one ring with C-4 of the other and that theconfiguration about the anomeric carbon atom is a. While theα and β ring forms of free sugars can usually undergo readyinterconversion, the configuration at the anomeric carbonatom is ‘frozen’ when a glycosidic linkage is formed.

Lactose, whose structure follows, can be described as adisaccharide containing one galactose unit in a β-pyranosering form and whose anomeric carbon atom (C-1) is joined tothe 4 position of glucose, giving a β-1, 4 linkage:

The systematic name for α-lactose, O-β-D-galactopyranosyl(1→4)-α-D-glucopyranose, provides a complete description ofthe stereochemistry, ring sizes, and mode of linkage(β-D-Galp-(1→4)-α-D-Glcp).

In sucrose and in α′, α-trehalose the reducing groups of tworings are joined. Each of these sugars exists in single form.Sucrose serves as the major transport sugar in green plants,while Trehalose plays a similar role in insects, similarto D-glucose in our blood.

Trehalose or ‘mushroom sugar,’ is found not only in fungi butalso in many other organisms. It serves as the primarytransport sugar in the haemolymph of insects and also acts as‘antifreeze’ in many species.

Disaccharides, as well as higher oligosaccharides andpolysaccharides, are thermodynamically unstable with respectto hydrolysis, for example, for lactose in aqueous solution:

Lactose + H2O → D-Glucose + D-Galactose;∆G° ≈ – 8.7 ± 0.2 kJ mol−1 at 25°C


α-D-Glucopyranose (2 molecules)

HOH C2

HO

HO OH

O

H O

OH H HO

HOH C2 O

OHOH

H

HOH C2O

OHHO

HOαH

O

HOH C24

HO

O

OH OH

H

α-1, 4-Glycosidic linkage

H C2

1

Fig. 1.16 Maltose, a disaccharide

Note aconfiguration

at this reducingend of the

molecule of-lactoseα

OHCH OH2 O

HOOH

β

1

D-Galactose

O4

HOOH

OH

OCH OH2

D-Glucose

Fig. 1.17 α-Lactose

O

O

OHOH C2

HO

CH OH2

2

HOCH2

HOHO

OH

Sucrose: Glcp 1 2Fruα →β f

HOCH2

HOHO OH

O

O

O

HO

CH OH2

OH

OH

OH

1

Fig. 1.18 α′, α-Trehalose: Glcapα1→α1Glcf

13

The joining of additional sugar rings through glycosidiclinkages to a disaccharide leads to the formation ofoligosaccharides, which contain a few residues, and topolysaccharides, which contain many residues. Among thewell-known oligosaccharides are the substituted sucrosesraffinose, Galp(1→6) Glcp(1→2) Fruf, and stachyose,Galp(1→6) Galp(1→6) Glcp(1→2) Fruf. Both sugars are foundin many legumes and other green plants in which they areformed by attachment of the galactose rings to sucrose.Oligosaccharides have many functions. For example, Gramnegative bacteria often synthesize oligosaccharides of 6-12glucose units in β-1, 2 linkage joined to sn-1-phosphoglycerylgroups. They are found in the periplasmic space between theinner and outer cell membranes and may serve to controlosmotic pressure. Oligosaccharides of 10-14 α-1, 4-linkedD-galacturonic acid residues serve as signals of cell walldamage to plants and trigger defensive reactions againstbacteria in plants.

Just as alcohols can be linked to sugars by glycosideformation, amines can react similarly to giveglycosylamines (N-glycosides).

Lactose and Maltose are reducing sugars, while sucrosenon-reducing.

3. Polysaccharides (Glycans)The simple sugars commonly used in the assembly ofpolysaccharides include D-glucose, D-mannose, D-galactose,D-fructose, D-xylose, L-arabinose, related uronic acids, andamino sugars. These monomer units can be put together inmany ways, either as homopolysaccharides containing asingle kind of monomer or as heteropolysaccharidescontaining two or more different monomers.

HomopolysaccharidesCell walls of yeasts contain mannans in which the main α-1,6-linked chain carries short branches of one to three

mannose units joined in α-1, 2, α-1, 3 and sometimes α-1, 6linkages.

The cell walls of some seaweeds contain a β-1, 3-linked xylaninstead of cellulose.

Fructose, a 6-carbon sugar, is present as five-memberedfuranose rings in inulin, the storage polysaccharide of theJerusalem artichoke and other Compositae, and also in sweetpotatoes.

The major structural polysaccharide in the exoskeletons

of arthropods and of other lower animal forms is chitin, alinear β-1, 4-linked polymer of N-acetylglucosamine whosestructure resembles that of cellulose.

HeteropolysaccharidesMany polysaccharides contain repeating units consisting ofmore than one different kind of monomer. Some of these arecomposed of two sugars in a simple alternating sequence.Examples are hyaluronan (hyaluronic acid) and thechondroitin, dermatan, keratan, and heparansulphates. They are important components of the ‘groundsubstance’ or intracellular cement of connective tissue inanimals.

Fibres of cellulose, which run like rods through theamorphous matrix of plant cell walls, appear to be coatedwith a monolayer of hemicelluloses. Predominant amongthe latter is a xyloglucan, which has the basic cellulosestructure but with α-1, 6-linked xylose units attached tothree-fourths of the glucose residues. L-Fucose may also bepresent in trisaccharide side chains: L-Fucα1 → 2Galα1 →2Xylα1 →. Pectins of higher plants contain β-1, 4-linkedpolygalacturonates interrupted by occasional 1, 2-linkedL-rhamnose residues. Some of the carboxyl groups of theserhamnogalacturonan chains are methylated. Arabinans andgalactans are also present in pectin. A possible arrangementof cellulose fibres, hemicelluloses and pectic materials in acell wall has been proposed.


Table 1.8 Some of the Many Polysaccharides Found in Nature

Name Source Monomer Main Linkage Branch Linkage

Starch Green plants

Amylose D-Glucose α-1, 4

Amylopectin D-Glucose α-1, 4 α-1, 6

Glycogen Animals and bacteria D-Glucose α-1, 4 α-1, 6

Cellulose Green plants and some

bacteria

D-Glucose β-1, 4

Dextrans Some bacteria D-Glucose α-1, 6 α-1, 3

Pullulan Yeast D-Glucose α-1, 6 + α-1, 4

Callose Green plants D-Glucose β-1, 3

Yeast glucan Yeast D-Glucose β-1, 3

Schizophyllan, curdlan and paramylon D-Glucose β-1, 3 β-1, 6 on every third

residue

Mannans Algae D-Mannose α-1, 4

Yeast D-Mannose α-1, 6

14

Glucans From glucose alone various organisms synthesize awhole series of polymeric glucans with quite differentproperties. Of these, cellulose, an unbranched β-1, 4-linkedpolyglucose, is probably the most abundant. It is the primarystructural polysaccharide of the cell walls of most greenplants. For the whole Earth, plants produce ~1014 kg ofcellulose per year.

Starch, another of the most abundant polymers of glucose, isstored by most green plants in a semicrystalline form innumerous small granules. These granules, which are usuallyformed within colourless.

Membrane-bounded plastids, have characteristic shapes andappearances that vary from plant to plant. One component ofstarch, amylose, is a linear polymer of manyα-D-glucopyranose units in 1, 4 linkage as in maltose. Starchgranules always contain a second kind of molecule known asamylopectin. Both amylopectin and glycogen (animalstarch) consist of highly branched bushlike molecules.Branches are attached to α-1, 4-linked chains through α-1, 6linkages

Beta-1, 3-linked glucans occur widely in nature. When anew green plant cell is formed the first polysaccharide to besynthesized is not cellulose but the β-1, 3-linked glucosepolymer callose. Cellulose appears later. Callose is alsoproduced in some specialized plant tissues, such as pollentubes, and is formed in massive amounts at the site of woundsor of attack by pathogens. The major structural component ofthe yeast cell wall is a β-1, 3-linked glucan with some β-1, 6branches.

Agarose, an alternating carbohydrate polymer consisting of~120-kDa chains, is the principal component of agar and thecompound that accounts for most of the gelling properties ofthat remarkable substance.

A similar structure has been established for the gelformingcarrageenans from red seaweed.

Alginates, found in cell walls of some marine algae and alsoformed by certain bacteria, consist in part of a linear β-1,4-linked polymer of D-mannuronate with a cellulose-likestructure.

Bacteria form and secrete a variety of heteropolysaccharides,several of which are of commercial value because of theiruseful gelling properties. Xanthan gum (formed byXanthomonas campestris) has the basic cellulose structurebut every second glucose residue carries an α-1, 3-linkedtrisaccharide consisting of 6-O-acetylmannose, glucuronicacid, and mannose in the following repeating unit:

(4Glcβ1-4Glcβn1-)n

↑6-O-acetyl-Man-α-1

2

↑Man-β-1-4-GlcAβ1

Acetan of Acetobacter xylinum has pentasaccharide sidechains that contain L-rhamnose. A helical structure for thestrands has been observed by atomic force microscopy.

Polysaccharides of BacterialSurfacesThe innermost layer of bacterial cell walls is a porousnetwork of a highly crosslinked material known aspeptidoglycan or murein. The backbone of thepeptidoglycan is a β-1, 4-linked alternating polymer ofN-acetyl-D-glucosamine and N-acetyl D-muramic acid.Alternate units of the resulting chitin-like molecule carry


Name Source Monomer Main Linkage Branch Linkage

Xylans Green plants D-Xylose β-1, 3

Brown seaweed

Inulin Dahlia plant tubers D-Fructose β-2, 6

Chitin Fungi and arthropods N-Acetyl-D-Glucosamine β-1, 4

Alternating polysaccharides

Hyaluronan Animal connective tissue Glucuronic acid +

N-Acetylglucosamine β-1, 4

Chondroitin sulphate D-Glucosamine

N-Acetyl-D-Galactosamine β-1, 3 + β-1, 4

Dermatan sulphate α-L-Iduronate +

N-Acetyl-D-Galactosamine β-1, 3 + β-1, 4

Pectin Higher plants D-galactunonate + others β-1, 4 + others

Alginate Seaweed D-Mannuronate +

L-Guluronate β-1, 4 + α-1, 4

Agar-agar Red seaweed Galactose β-1, 4 and α-1,

3

Carageenan Red seaweed Galactose-4-sulphate + β-1, 4 + α-1, 3

3, 6-anhydro-

D-Galactose-2-sulphate

Murein Bacterial cell wall N-acetyl D-Glucosamine +

N-acetyl D-Muramic acid

β-1, 4

15

unusual peptides that are attached to the lactyl groups of theN-acetylmuramic acid units and crosslink the polysaccharidechains. In E. coli and other Gram negative bacteria thepeptidoglycan forms a thin (2 nm) continuous networkaround the cell. This ‘baglike molecule’ protects the organismfrom osmotic stress. In addition, Gram negative bacteriahave an outer membrane and on its outer surface a complexlipopolysaccharide.

LipidsLipids are organic compounds, found in living organisms thatare soluble in non-polar organic solvents. The solubility oflipids in nonpolar organic solvents results from theirsignificant hydrocarbon component. The hydrocarbonportion of the compound is responsible for its ‘oiliness’ or‘fattiness’. The word lipid comes from the Greek lipos, whichmeans ‘fat’.

Biological Importance of Lipids(i) Fat under skin serve as thermal insulator against cold.

(ii) Lipids present in myelinated nerves act as insulatorsfor propagation of depolarization wave.

(iii) Fat serves as a source of energy for man likecarbohydrates.

(iv) Fat is an ideal form for storing energy in the humanbody compared to carbohydrates and proteins because:(a) Energy content of fat is higher. (b) Only fat can bestored in a concentrated water free form which is notpossible with carbohydrates and proteins.

(v) Lipids are structural components of cell membrane andnervous tissue.

(vi) Some lipids serve as precursors for the synthesis ofcomplex molecules. For example, acetyl Co-A is used forthe synthesis of cholesterol.

(vii) Lipoproteins, which are complexes of lipids andproteins are involved in the transport of lipids in theblood and components of cell membrane.

(viii)Some lipids serve as hormones and fat soluble vitaminsare lipids.

(ix) Fats are essential for the absorption of fat solublevitamins.

(x) Fats serve as surfactants by reducing surface tension.

Unlike proteins, polysaccharides, and nucleic acids, mostlipids are not polymers. However, they are made by linkingtogether smaller molecules. Among the ‘building blocks’ oflipids are fatty acids, glycerol, phosphoric acid andsugars. Many lipids have both polar and non-polar regions.

This gives them an amphipathic character, i.e., a tendencytoward both hydrophobic and hydrophilic behavior, andaccounts for their tendency to aggregate into membranousstructures.

1. Fatty AcidsFatty acids are carboxylic acids with long hydrocarbonchains. Fatty acids can be saturated with hydrogen (andtherefore have no carbon–carbon double bonds) orunsaturated (have carbon–carbon double bonds). Fatty acidswith more than one double bond are calledpolyunsaturated fatty acids. Double bonds in naturallyoccurring unsaturated fatty acids are never conjugated—theyare always separated by one methylene group.

The double bonds in unsaturated fatty acids generally havethe cis configuration. This configuration produces a bend inthe molecules, which prevents them from packing together astightly as fully saturated fatty acids. As a result, unsaturatedfatty acids have fewer intermolecular interactions and,therefore, lower melting points than saturated fatty acidswith comparable molecular weights. The melting points ofthe unsaturated fatty acids decrease as the number of doublebonds increases. For example, an 18-carbon fatty acid meltsat 69°C if it is saturated, at 13°C if it has one double bond, at–5°C if it has two double bonds, and at –11°C if it has threedouble bonds.

Most naturally occurring fatty acids are esterified orcombined via amide linkages in complex lipids. For example,ordinary fats are largely the fatty acid esters of glycerol calledtriacylglycerols (triglycerides).

Most fatty acid chains contain an even number of carbonatoms. In higher plants the C-16 palmitic acid and the C-18unsaturated oleic and linoleic acids predominate. The C-18saturated stearic acid is almost absent in plants and C-20 toC-24 acids are rarely present except in the outer cuticle ofleaves. Certain plants contain unusual fatty acids which maybe characteristic of a taxonomic group. For example, theComposite (daisy family) contain acetylene fatty acids andthe castor bean contains the hydroxy fatty acid ricinoleicacid.

Phospholipids of photoreceptor membranes of the retinacontain fatty acid chains as long as C-36. The variety of fattyacids found in animals is greater than in a given plantspecies.

Bacteria usually lack polyunsaturated fatty acids but oftencontain branched fatty acids, cyclopropane containing acids,hydroxy fatty acids, and unesterified fatty acids.Mycobacterium, including the human pathogenMycobacterium tuberculosis, contains mycolic acids.


16

`

2. WaxesWaxes are esters formed from long-chain carboxylic acids andlong-chain alcohols. For example, beeswax, the structuralmaterial of beehives, has a 16-carbon carboxylic acidcomponent and a 30-carbon alcohol component. Both fattyalcohols and free fatty acids occur in waxes together withesterified forms. These mixtures are found on exteriorsurfaces of plants and animals.

Carnauba wax is a particularly hard wax because of itsrelatively high molecular weight, arising from a 32-carboncarboxylic acid component and a 34-carbon alcoholcomponent. Carnauba wax is widely used as a car wax and infloor polishes.

Insects make unsaturated as well as saturated hydrocarbons.The former as well as long-chain alcohols and their estersoften form the volatile pheromones with which insectscommunicate.

Triacylglycerols that are solids or semisolids at roomtemperature are called fats. Fats are usually obtained fromanimals and are composed largely of triacylglycerols witheither saturated fatty acids or fatty acids with only onedouble bond. The saturated fatty acid tails pack closelytogether, giving the triacylglycerols relatively high meltingpoints, causing them to be solids at room temperature.

Liquid triacylglycerols are called oils. Oils typically comefrom plant products such as corn, soybeans, olives, andpeanuts. They are composed primarily of triacylglycerolswith unsaturated fatty acids that cannot pack tightlytogether. Consequently, they have relatively low meltingpoints, causing them to be liquids at room temperature.


A wax

O

C

O

Fig. 1.19 An ester of a fatty acid and a fatty alcohol

CH2 OH

CH

CH2

Glycerol

OH

OH

C

C

C

O

O

O

OH

Fatty acids

OH

OH

R1

R2

R3

C

C

O

R1

R2

OCH2

OCH

C

A triacylglycerola fat or an oil

R3

OCH2

O

O

Fig. 1.20 Structure of glycerol and fatty acid

COOH

COOH

COOH

COOH

COOH

COOH

COOH

COOH

COOH

COOH

Table 1.9 Common and Naturally Occurring Fatty Acids

Number ofCarbon

Common Name Systematic Name StructureMeltingPoint °C

Saturated

12 Lauric acid Dodecanoic acid 44

14 Myristic acid Tetradecanoic acid 58

16 Palmitic acid Hexadecanoic acid 63

18 Stearic acid Octadecanoic acid 69

20 Arachidic acid Eicosanoic acid 77

Unsaturated

16 Palmitoleic acid (9Z)-hexadecenoic acid 0

18 Oleic acid (9Z)-octadecenoic acid 13

18 Linoleic acid (9Z, 12Z)-octadecadienoic acid –5

18 Linolenic acid (9Z, 12Z, 15Z)-octadecatrienoic

acid

–11

20 Arachidonic acid (5Z, 8Z, 11Z,

14Z)-eicosatetraenoic acid

–50

20 EPA (5Z, 8Z, 11Z, 14Z,

17Z)-eicosapentaenoic acid

–50

17

Organisms store energy in the form of triacylglycerols. A fatprovides about six times as much metabolic energy as anequal weight of hydrated glycogen because fats are lessoxidized than carbohydrates and, since fats are nonpolar,they do not bind water. In contrast, two-thirds of the weightof stored glycogen is water.

Important LipidsThe major three kinds of membrane lipids arephospholipids, glycolipids and steroids, while otherpresent in cells.

1. PhospholipidsThese are abundant in all biological membranes. Aphospholipid molecule is constructed from four components:fatty acids, a platform to which the fatty acids are attached, aphosphate, and an alcohol attached to the phosphate. Thetwo principal groups of phospholipids are theglycerophospholipids which contain the alcohol glyceroland the sphingophospholipids which contain the alcoholsphingosine.

The platform on which phospholipids are built may beglycerol, a 3-carbon alcohol, or sphingosine, a morecomplex alcohol. Phospholipids derived from glycerol arecalled phosphoglycerides. A phosphoglyceride consists of aglycerol backbone to which two fatty acid chains and aphosphorylated alcohol are attached. The majorphosphoglycerides are derived from phosphatidate by theformation of an ester bond between the phosphate group ofphosphatidate and the hydroxyl group of one of severalalcohols. The common alcohol moieties of phosphoglyceridesare the amino acid serine, ethanolamine, choline, glycerol,and the inositol.

Choline, serine or ethanolamine yields a glycerophos-pholipid. The resulting three groups of phospholipids arecalled phosphatidylcholine (lecithin), phosphatidylserineand phosphatidylethanolamine respectively.

The alkenyl ether analogs of phosphatidylcholine are calledplasmalogens. Another group of phosphatides contain thehexahydroxycyclohexane known as inositol.

Phosphatidylinositol, as well as smaller amounts ofphosphatides derived from phosphate esters of inositol arepresent in membranes of all eukaryotes. Plays important rolein regulating responses of cells to hormones and otherexternal agents.

Phosphoacylglycerols form membranes by arrangingthemselves in a lipid bilayer. The polar heads of thephosphoacylglycerols are on the outside of the bilayer, andthe fatty acid chains form the interior of the bilayer.Cholesterol—a membrane lipid is also found in the interior ofthe bilayer.

The fluidity of a membrane is controlled by the fatty acidcomponents of the phosphoacylglycerols. Saturated fattyacids decrease membrane fluidity because their hydrocarbonchains can pack closely together. Unsaturated fatty acidsincrease fluidity because they pack less closely together.Cholesterol also decreases fluidity. Only animal membranescontain cholesterol, so they are more rigid than plantmembranes.


Fatty acid

Fatty acidGlycerol

Phosphate Alcohol

O

O

O

C

C

P

R1

R2

OH

O

O

O

CH2

CH2

CH2

O–

A phosphatidic acid

R configuration

Fig. 1.21 Schematic structure of a phospholipid

O

O

O

C

C

P

R1

R2

OCH CH NH2 2 3

O

O

O

CH2

CH

CH2

O–

A phosphatidylethanolamine(a cephalin)

+

O

O

O

C

C

P

R1

R2

OCH CH NCH2 2 3

O

O

O

CH2

CH

CH2

O–

A phosphatidylcholine(a lecithin)

CH3

CH3

+

O

O

O

C

C

P

R1

R2

OCH CHCOO2–

O

O

O

CH2

CH

CH2

O–

A phosphatidylserine

NH3+

Fig. 1.22 Various phospholipids

18

A Membrane lipid is an amphipathic molecule containinghydrophilic and hydrophobic moieties. The twohydrophobic fatty acid chains are approximately parallel toeach other, whereas the hydrophilic moieties points in theopposite direction. Sphingomyelin has a similarconformation, as of the archaeal lipid.

The unsaturated fatty acid chains of phosphoacylglycerolsare susceptible to reaction with O2. Oxidation ofphosphoa-cylglycerols can lead to the degradation ofmembranes.

Vitamin-E is an important antioxidant that protects

fatty acid chains from degradation via oxidation. Becausevitamin-E reacts more rapidly with oxygen thantriacylglycerols do, the vitamin prevents biologicalmembranes from reacting with oxygen.

2. SphingolipidsSphingomyelin is a phospholipid found in membranes thatis not derived from glycerol. Instead, the backbone insphingomyelin is sphingosine, an amino alcohol thatcontains a long, unsaturated hydrocarbon chain. Insphingomyelin, the amino group of the sphingosine backboneis linked to a fatty acid by an amide bond. In addition, theprimary hydroxyl group of sphingosine is esterified tophosphoryl choline. Two of the most common kinds ofsphingolipids are sphingomyelins and cerebrosides(Cerebrosides are not phospholipids).

The simplest glycolipid, called a cerebroside, contains asingle sugar residue, either glucose or galactose. Morecomplex glycolipids, such as gangliosides, contain abranched chain of as many as seven sugar residues.

3. GlycolipidsThe polar heads of the glycoglycerolipids lack phosphogroups but contain sugars in glycosidic linkage. Chloroplastsalso contain the following sulfolipid, an anionic sulfonate.Marine algae as well as aquatic higher plants accumulatearsenophospholipids.

4. ProstaglandinsThese are found in all body tissues and are responsible forregulating a variety of physiological responses, such asinflammation, blood pressure, blood clotting, fever, pain, theinduction of labor, and the sleep–wake cycle. Allprostaglandins have a five-membered ring with aseven-carbon carboxylic acid substituent and an eightcarbonhydrocarbon substituent. The two substituents are trans toeach other.

5. TerpenesThese are a diverse class of lipids. They can be hydrocarbons,or they can contain oxygen and be alcohols, ketones, oraldehydes. Oxygen-containing terpenes are sometimes calledterpenoids. Certain terpenes and terpenoids have been usedas spices, perfumes, and medicines for many thousands ofyears.

Isoprene is the common name for 2-methyl 1, 3-butadiene, acompound containing five carbon atoms. That isoprene unitsare linked in a head-to-tail fashion to form terpenes is knownas the isoprene rule.


CH CH(CH ) CH2 12 3

CH OH

CH

CH2

NH R

O

C

P

O

O

O

OCH CH NCH2 2 3

CH3

CH3

+

–

A sphingomyelin

CH CH(CH ) CH2 12 3

CH OH

CH

CH2

NH RC

O

O

OH

HO

CH OH2

HH

H

HO

H

O

H

A glucocerebroside

Fig. 1.23 The sphingolipids

H

H

COOH

Fig. 1.24 Prostaglandin skeleton

OH

HO

Menthol(peppermint oil)

Geraniol(geranium oil)

Zingiberene(oil of ginger)

b-selinene(ril of celery)

Fig. 1.25 Various terpenes

19

Terpenes are classified according to the number of carbonsthey contain. Monoterpenes are composed of two isopreneunits, so they have 10 carbons. Sesquiterpenes, with 15carbons, are composed of three isoprene units. Manyfragrances and flavorings found in plants are monoterpenesand sesquiterpenes. These compounds are known asessential oils.

Triterpenes (six isoprene units) and tetraterpenes(eight isoprene units) have important biological roles. Forexample, squalene, a triterpene, is a precursor of steroidmolecules.

Carotenoids are tetraterpenes. Lycopene, the compoundresponsible for the red colouring of tomatoes andwatermelon, and β-carotene, the compound that causescarrots and apricots to be orange, are examples ofcarotenoids. β-carotene is also the coloring agent used inmargarine. The many conjugated double bonds in lycopeneand β-carotene cause the compounds to be coloured.

Vitamin-A Vitamin-A, D, E and K are lipid soluble.

SteroidsMany hormones are steroids. Because steroids are non-polar compounds, they are lipids. Their non-polar character allows themto cross cell membranes, so they can leave the cells in which they are synthesized and enter their target cells. All steroidscontain a tetracyclic ring system. The four rings are A, B and C are six-membered rings and D is a five-membered ring. Therings can be trans fused or cis fused and that trans fused rings are more stable. In steroids, the B, C and D rings are all transfused. In most naturally occurring steroids, the A and B rings are also trans fused.

The steroid hormones can be divided into five classes:glucocorticoids, mineralocorticoids, androgens, estrogens,and progestins. Glucocorticoids and mineralocorticoids are

synthesized in the adrenal cortex and are collectively knownas adrenal cortical steroids. All adrenal cortical steroidshave an oxygen at C-11.


Head Head

Tail Tail

Fig. 1.26 α-farnesene a sesquiterpene found inthe waxy coating on apple skins

O

Tail

Head

O

Fig. 1.27 Carvone spearmint oil a monoterpene

Fig. 1.28 Squalene

β-carotene

Lycopene

Fig. 1.29 The carotenoid-lycopene and β-carotene

1

4

210

35

9

A B

C D

8

7

6

1415

16

1713

12

11

H C3

H

H C3

RH

HHCH and Hare

3trans

HH C3

H

H C3

RH

HHC and Hare

H3cis

H

Angular methylgroups

Fig. 1.30 The steroid ring system

20

Mineralocorticoids cause increased reabsorption of Na+ , Cl–

and by HCO3– the kidneys, leading to an increase in blood

pressure. Aldosterone is an example of a mineralocorticoid.

The male sex hormones, known as androgens, are secretedby the testes. They are responsible for the development ofmale secondary sex characteristics during puberty. Theyalso promote muscle growth. Testosterone and5α-dihydrotestosterone are androgens.

Estradiol and estrone are female sex hormones known asoestrogens. They are secreted by the ovaries and areresponsible for the development of female secondary sexcharacteristics. They also regulate the menstrual cycle.

In addition to being the precursor of all the steroid hormonesin animals, cholesterol is the precursor of the bile acids. Infact, the word cholesterol is derived from the Greek wordschole meaning ‘bile’ and stereos meaning ‘solid’. The bileacids— cholic acid and chenodeoxycholic acid—aresynthesized in the liver, stored in the gall bladder andsecreted into the small intestine, where they act asemulsifying agents so that fats and oils can be digested bywater-soluble digestive enzymes. Cholesterol is also theprecursor of vitamin-D.

ProteinsThe amino acid units that make up a protein molecule arejoined together in a precise sequence. The chain is thenfolded, often into a very compact form. Sometimes the chainis then cut in specific places. Pieces may be discarded andparts may be added. A metal ion, a coenzyme derived from avitamin, or even a single methyl group may be attached toform the biologically active protein. The biologicalfunctioning of a protein is determined both by the propertiesof the chemical groups in the amino acids that are joined toform the protein chain and by the way the chain is folded.The ways in which the different parts of the protein interactwith each other and with other molecules are equallyimportant. These interactions play a major role indetermining the folding pattern and also provide much of thebasis for the biological functioning of proteins.

Proteins and peptides serve many functions in biologicalsystems. Some protect organisms from their environment orimpart strength to certain biological structures. Hair, horns,hooves, feathers, fur, and the tough outer layer of skin are allcomposed largely of a structural protein, e.g., keratin,collagen, etc.

Some proteins have other protective functions. Snakevenoms and plant toxins, for example, protect their ownersfrom other species, blood-clotting proteins protect the


H C3

H C3

HH

H

HO

Cholesterol

Cortisone

H C3

HH

H

O

O OHCH3

C O

CH OH2

Aldosterone

H C3

HH

H

O

HO

C

CH OH2

HC

O

O

Fig. 1.31 The cortical steroids

5 -dihydrotestosteroneα

H C3

HH

H

O

OHH C3

Testosterone

H C3

HH

H

O

OHH C3

H

Fig. 1.32 The androgens

Estrone

HH

H

HO

CH3

O

Estradiol

HH

H

HO

CH3

OH

Progesterone

HH

H

O

CH3

C=O

H C3

CH3

Fig. 1.33 The estrogens

21

vascular system when it is injured, and antibodies andprotein antibiotics protect us from disease.

A group of proteins called enzymes catalyzes the chemicalreactions that occur in living systems, and some of thehormones that regulate these reactions are peptides.Proteins are also responsible for many physiologicalfunctions, such as the transport and storage of oxygen in thebody and the contraction of muscles.

Biological Importance of Proteins(a) Proteins are involved in the transport of substances in

the body.(b) Enzymes which catalyze chemical reactions in the body

are proteins.(c) Proteins are involved in defence function,

e.g., Immunoglobulins.(d) Hormones are proteins. They control many biochemical

events, e.g., Insulin.(e) Some proteins have role in contraction of muscles.(f) Proteins are involved in the gene expression. They

control gene expression and translation, e.g., Histones.(g) Proteins function as anti-vitamins, e.g., Avidin of egg.(h) Proteins are infective agents, e.g., Prions which cause

mad cow disease are proteins.(i) Some toxins are proteins, e.g., Enterotoxin of cholera

microorganism.(j) Some proteins provide structural strength and elasticity

to the organs and vascular system, e.g., Collagen.

(k) Some proteins are components of structures of tissues,e.g., α-keratin.

Amino AcidsThese are molecules containing an amine group, a carboxylicacid group and a side chain that varies between differentamino acids. Alpha amino acids are the most common formfound in nature. In the alpha amino acids, the a-carbon is achiral carbon atom, with the exception of glycine. In aminoacids that have a carbon chain attached to the carbon (such aslysine) the carbons are labeled in order as α β γ δ, , , and so on.In some amino acids, the amine group is attached to the β orγ-carbon, and these are therefore, referred to as beta orgamma amino acids.

Amino acids are usually classified by the properties of their side chain into four groups. The side chain can make an amino acida weak acid or a weak base, and a hydrophile if the side chain is polar or a hydrophobe if it is non-polar.


NH3+

CH2

CH2

C2

CH2

CH2

H N3 H

C OO1 –

α

β

γ

δ

ε 6

5

4

3

+

H N3R

C

O

O–

L-amino acid

+

Fig. 1.34 Lysine with the carbon atoms

COO–

+H3N C

CH3

H

COO–

+H3N C

CH

H

H C3 CH3

COO–

+H3N C

C

H

CH3

CH2

H

CH3

COO–

+H3N C

CH2

H

CH

H C3 CH3

Valine(Val or V)

Isoleucine(lie or l)

Leucine(Lue or L)

Alanine(Ala or A)

COO–

+H3N C

CH2

H

CH2

CH3

S

Methionine(Met or M)

COO–

+H3N C

CH2

H

Phenylalanine(Phe or F)

COO–

+H3N C

CH2

H

H

Tyrosine(Tyr or Y)

COO–

+H3N C

C=CH

H

NH

CH2

Tryptophan(Trp or W)

Fig. 1.35 Hydrophobic amino acids

22

Every amino acid has a carboxyl group and an amino group, and each group can exist in an acidic form or a basic form,depending on the pH of the solution in which the amino acid is dissolved. The carboxyl groups of the amino acids have values ofpKa approximately 2, and the protonated amino groups have pKa values near 9. Both groups, therefore, will be in their acidicforms in a very acidic solution. At pH = 7, the pH of the solution is greater than the of the carboxyl group, but less than the ofthe protonated amino group. The carboxyl group, therefore, will be in its basic form and the amino group will be in its acidicform. In a strongly basic solution both groups will be in their basic forms.

An amino acid can never exist as an uncharged compound, regardless of the pH of the solution. To be uncharged, an amino acidwould have to lose a proton from an + NH3 group with a pKa of about 9 before it would lose a proton from a COOH group with apKa of about 2. This clearly is impossible: A weak acid cannot be more acidic than a strong acid. Therefore, at physiological pH(7.3) an amino acid exists as a dipolar ion, called a Zwitter ion. A Zwitter ion is a compound that has a negative charge on oneatom and a positive charge on an adjacent atom.


R R RCH CH CHC C COH O–

O–

+NH3

+NH3

+NH2

O O O

+ +H+

H+

pH = 0 a Zwitter ionpH = 7

pH = 11

CH CHCO2–

NH2

O

NHN

pH = 12

CH CHCO2–

+NH3

O

NHN

pH = 8

Histidine

HN+

CH CHCOH2

+NH3

O

pH = 0

HN+

CH CHCO2–

+NH3

O

NH

pH = 4

NH

Fig. 1.37 The Zwitter ion form

COO–

H N3

+C

CH2

H

CH2

CH2

CH2

NH3+

COO–

+H N3 C

CH2

H

CH2

CH2

NH

NH2

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)

NH2+C

COO–

+H N3 C

CH2

H

C

CH

NHCH

N+

H

COO–

COO–

+H N3 C

CH2

H

Aspartate(Asp or D)

COO–

OH

+H N3 C

CH2

H

Serine(Ser or S)

COO–

CH3

+H N3

H

C

C

H

OH

Threonine(Thr or T)

Glutamate(Glu or E)

COO–

COO–

+H N3 C

CH2

H

CH2

Asparagine(Asn or N)

COO–

+H N3 C

CH2

H

C

OH N2

Glutamine(Gln or Q)

COO–

+H N3 C

CH2

H

C

OH N2

CH2

Basic amino acid Acidic amino acids Polar amino acids with uncharged groupsR

Fig. 1.36 Hydrophilic amino acids

23

Table 1.10 The pKa Values of Amino Acids

Amino AcidpK

a

α-COOH

pKa

α-NH3+

pKa

Side Chain

Alanine 2.34 9.69 —

Arginine 2.17 9.04 12.48

Asparagine 2.02 8.84 —

Aspartic acid 2.09 9.82 3.86

Cysteine 1.92 10.46 8.35

Glutamic acid 2.19 9.67 4.25

Glutamine 2.17 9.13 —

Glycine 2.34 9.60 —

Histidine 1.82 9.17 6.04

Isoleucine 2.36 9.68 —

Leucine 2.36 9.60 —

Lysine 2.18 8.95 10.79

Methionine 2.28 9.21 —

Phenylalanine 2.16 9.18 —

Proline 1.99 10.60 —

Serine 2.21 9.15 —

Threonine 2.63 9.10 —

Tryptophan 2.38 9.39 —

Tyrosine 2.20 9.11 10.07

Valine 2.32 9.62 —

The Isoelectric PointThe isoelectric point (pI) of an amino acid is the pH at whichit has no net charge. In other words, it is the pH at which theamount of positive charge on an amino acid exactly balancesthe amount of negative charge:

pI = pH at which there is no net charge.

An amino acid will be positively charged if the pH of thesolution is less than the pI of the amino acid and will benegatively charged if the pH of the solution is greater thanthe pI of the amino acid. At the average of the two pK a values,the number of negatively charged groups equals the numberof positively charged groups.

pI = + = =2 34 9 692

12 032

6 02. . .

.

pI = + = =8 95 10792

19742

9 87. . .

.

pI = + = =219 4252

6 442

322. . .

.

Absorption SpectraPhenylalanine is purely hydrophobic, whereas tyrosine andtryptophan are less so because of their hydroxyl and NHgroups. The aromatic rings of tryptophan and tyrosinecontain delocalized p electrons that strongly absorbultraviolet light.

Peptide Bonds and Disulphide BondsPeptide bonds and disulphide bonds are the only covalent bondsthat hold amino acid residues together in a peptide or a protein.

Peptide BondsThe amide bonds that link amino acid residues are calledpeptide bonds. By convention, peptides and proteins arewritten with the free amino group (the N-terminal aminoacid) on the left and the free carboxyl group (theC-terminal amino acid) on the right.


O

CH CHCOH3

+NH3 p =9.69Ka

p =2.34Ka

Alanine

H NCH CH CH CH CHCOH3 2 2 2 2

+NH3 p =8.95Ka

Op =2.18Ka

p =10.79Ka

Lysine

*

HOCCH CH CHCOH2 2

+NH3 p =9.67Ka

OO

p =2.19Ka

p =4.25Ka

Glutamic acid

10,000

8,000

6,000

4,000

2,000

220 240 260 280 300 3200

Tyr

Trp

Extin

ctio

nco

effic

ien

t(M

cm

)–

1–

1

Fig. 1.38 Absorption spectra of the aromatic amino acids tryptophan andtyrosine. Only these amino acids absorb strongly near 280 nm

O O O

H NCHCO3–

H NCHCO3–

H NCHCO3–+ + +

R R′ R′′

+ +

O O O

H NCHC3 NHCHC NHCHCO–+ + +

R R′ R′′Peptide bonds

The C-terminal amino acidThe N-terminalamino acid

+ 2H O2

Fig. 1.39 A tripeptide

24

The Peptide Bond has Partial Double Bond CharacterAlthough peptides are written as if a single bond linked the a-carboxyl and a-nitrogen atoms, this bond in fact exhibits partialdouble-bond character:

Disulphide bonds When thiols are oxidized under mild conditions, they form disulphides. A disulphide is a compound with anS—S bond.

2 — SH S — SA thiol

Mild oxidation

AdisulphideR R R→

Two cysteine residues in a protein can be oxidized to a disulphide. This is known as a disulphide bridge. Disulphide bridgesare the only covalent bonds that can form between non-adjacent amino acids.

Insulin, a hormone secreted by the pancreas, controls the level of glucose in the blood by regulating glucose metabolism. Insulin is apolypeptide with two peptide chains. The short chain (the A-chain) contains 21 amino acids and the long chain (the B-chain) contains30 amino acids. The two chains are held together by two disulphide bridges. These are interchain disulphide bridges (betweenthe A and B-chains). Insulin also has an intrachain disulphide bridge (within the A-chain).

Some Important Peptidesl Enkephalins are pentapeptides that are synthesized

by the body to control pain. They decrease the body’ssensitivity to pain by binding to receptors in certainbrain cells.

l Bradykinin, vasopressin and oxytocin are peptidehormones. They are all nonapeptides. Bradykinin

inhibits the inflammation of tissues. Vasopressincontrols blood pressure by regulating the contraction ofsmooth muscle. It is also an antidiuretic. Oxytocininduces labor in pregnant women and stimulates milkproduction in nursing mothers.

l Gramicidin S is an antibiotic produced by a strain ofbacteria. It is a cyclic decapeptide.


O O–

C C

N N

H H

+

Oxidation

reduction

Disulphide bridgescross-linking portionsof a polypeptide

.

S S

SS

SS

SH

SH

SH

HS

SH

Polypeptide

Fig. 1.40 Disulphide bridges cross-linking portions of a peptide

S

Gly ile Val Glu Gln Cys Cys Thr Ser ile Cys Ser Leu Tyr Gln Leu Glu Asn Tyr Cys Asn

Phe Val Asn Gln His Leu Cys Gly Ser His Leu Val Glu Ala Leu Tyr Leu Val Cys Glu Glu Arg Gly Phe Phe Tyr Thr Pro Lys Ala

An intrachain disulphide bridge

S S

SInterchain disulphide bridges

Insulin

B-chain

A-chain

S S

Fig. 1.41 The interchain disulphide bridges in insulin

25

Structure of ProteinProtein molecules are described by several levels of structure:

1. Primary structure of a protein is the sequence of amino acids in the chain and the location of all the disulphide bridges.2. Secondary structure describes the regular conformation assumed by segments of the protein’s backbone. In other words,

the secondary structure describes how local regions of the backbone fold.3. Tertiary structure describes the three-dimensional structure of the entire polypeptide. If a protein has more than one

polypeptide chain, it has quaternary structure.4. Quaternary structure of a protein is the way the individual protein chains are arranged with respect to each other.

1. Primary Structure of a ProteinThe first step in determining the sequence of amino acids in a peptide or a protein is to reduce any disulphide bridges in thepeptide or protein. A commonly used reducing agent is 2-mercaptoethanol, which is oxidized to a disulphide.

There are several ways to identify the N-terminal amino acid of a peptide or protein. One of the most widely used methods is totreat the protein with phenyl isothiocyanate (PITC), more commonly known as Edman’s reagent. This reagent reacts withthe N-terminal amino group.

The C-terminal amino acid of the peptide or protein can be identified by treatingthe protein with carboxypeptidase A. Carboxypeptidase A cleaves off theC-terminal amino acid as long as it is not arginine or lysine. On the other hand,carboxypeptidase B cleaves off the C-terminal amino acid only if it is arginine orlysine. Carboxypeptidases are exopeptidases. An exopeptidase is an enzymethat catalyzes the hydrolysis of a peptide bond at the end of a peptide chain.


NHCHC NHCHC NHCHC–O

O O O

R R′ R′′

Site where carboxypeptidase cleaves

Tyr-Gly-Gly-Phe-Leuleucine enkephalin

Bradykinin Agr-Pro-Pro-Gly-Phe-Ser-Pro-Pho-Arg

Vasoperssin

Oxytocin

Tyr-Gly-Gly-Phe-Leumethionine enkephalin

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2

S S

Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2

S SL-Vall

L-Pro

D-Phe

L-Leu

O-OrnL-Val

L-Pro

L-Phe

L-Leu

D-Orn

Gramicidin S

Fig. 1.42 The peptide hormones

NHCH C

CH2

S

S

CH2

NHCH

O

O

C

NHCH C

CH2

SH

SH

CH2

NHCH

O

O

C

NHCH C

CH2

SCH COH2

O

O

+ 2HI

ICH COH2iodoacetic acid

O

NHCH

SCH COH2

CH2

O

O

C

Cleaving disulphide bridges

+ 2 HSCH CH OH2 22-mercaptoethanol

SCH CH OH2 2

SCH CH OH2 2

+

Fig. 1.43 Amino acid sequence determination

26

Table 1.11 Specificity of Peptide or ProteinCleavage

Reagent Specificity

Chemical reagents

Edman’s reagent Removes the N-terminal amino acid

Cyanogen bromide hydrolyzes on the C-side of Met

Exopeptidases*

Carboxypeptidase A Removes the C-terminal amino acid

(not Arg or Lys)

Carboxypeptidase B Removes the C-terminal amino acid

(only Arg or Lys)

Endopeptidases*

Trypsin Hydrolyzes on the C-side of Arg and Lys

Chymotrypsin hydrolyzes on the C-side of amino acids

that contain aromatic six-membered

rings (Phe, Tyr and Trp)

Elastase Hydrolyzes on the C-side of small

amino acids (Gly and Ala)

*Cleavage will not occur if Pro is on either side of the bond tobe hydrolyzed.

2. Secondary Structure of ProteinsSecondary structure describes the conformation of segmentsof the backbone chain of a peptide or protein. To minimizeenergy, a polypeptide chain tends to fold in a repeatinggeometric structure such as an α-helix or a β-pleated sheet.Three factors determine the choice of secondary structure:

(i) The regional planarity about each peptide bond (as aresult of the partial double bond character of the amidebond), which limits the possible conformations of thepeptide chain.

(ii) Maximization of the number of peptide groups thatengage in hydrogen bonding (i.e., hydrogen bonding

between the carbonyl oxygen of one amino acid residueand the amide hydrogen of another).

(iii) Adequate separation between nearby R groups to avoidsteric hindrance and repulsion of like charges.

In 1951, Linus Pauling and Robert Corey proposed twoperiodic structures called the α-helix (alpha helix) and the βpleated sheet (beta pleated sheet). Subsequently, otherstructures such as the α turn and omega (Ω) loop wereidentified. Although not periodic, these common turn or loopstructures are well defined and contribute with α helices andβ sheets to form the final protein structure.

Alpha HelixIn the α-helix, the polypeptide backbone is folded in such away that the —C==O group of each amino acid residue ishydrogen-bonded to the —N—H group of the fourth residuealong the chain, i.e., the —C==O group of the first residuebinds to the —N—H group of the fifth residue, and so on. Thebackbone of the helix winds around the long axis, as shown inFig. 1.44. The hydrogen bonds are all aligned approximatelyparallel to this axis, and side chains protrude outward. Eachresidue is spaced 0.15 nm from the next one along the axis, and3.6 residues are required to make a complete turn of the helix.

The α-helix is a right-handed helix; that is, it rotates in aclockwise direction as it spirals down. Each turn of the helixcontains 3.6 amino acid residues, and the repeat distance ofthe helix is 5.4 Å. A proline residue, for example, forces abend in a helix because the bond between the prolinenitrogen and the α-carbon cannot rotate to enable it to fitreadily into a helix. Similarly, two adjacent amino acids thathave more than one substituent on a β-carbon (valine,isoleucine or threonine) cannot fit into a helix because ofsteric crowding between the R groups. Finally, two adjacentamino acids with like-charged substituents cannot fit into ahelix because of electrostatic repulsion between the R groups.


CN C

CC

NC

CN

N CC

0.54 nm pitch(3.6 residues)

0.15 nm

CN

CN

CC

NC

CN

C

CCN

C

N

NC

CC

3.6 residues/turn

O

HR

R

R

R

R

R

CR

R

N

N

N

N

N

N

NC

C N

C

H

H

H

H

H

HH

C

C N

O

O

O

O

R

O

O

O

O

H

C

C

C

H

Fig. 1.44 Right-handed α-helix

27

Basic Physical Chemical Concepts in Biology€¦ · Structure of Atoms, Molecules and Chemical...

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