10.1.13

FORCES GOVERNING BIOLOGICAL SYSTEMS

Electronic structure of atomsNegatively charged electrons revolve

around positively charged nucleus. Atom is neutral

Shells: The electrons move around the atomic nuclei in discrete, concentric volumes, the shells. The electrons of each shell possess a definite energy with reference energy numbers n = 1, 2, 3 ….. designated K, L, M, N ……. . The maximum number of electrons which each shell accommodates is 2n2..Due to Coulomb interaction between electrons and nucleus the electrons tend to occupy the shells as close to the nucleus as possible

Orbitals: Angular momentum quantum number

Orbitals: Electrons behave both as particles and as waves. It is not possible to accurately determine the position of the electron because of its wave nature. The regions within each shell in which the electrons are most likely to be found are known as orbital

Based on the shape of the orbital and the angular momentum electrons exhibit when located within the orbital, an angular momentum quantum number l is assigned

Orbitals

‘l’ can have values l=0, 1…..n-1 designated as s, p, d, f…

s-orbital is spherical in shape, d-orbital is dumbbell shaped with constriction in the region of the nucleus, d-orbital is double dumbbell shaped

Orientations of Orbitals

Another quantum number called “magnetic quantum number, m” is assigned to electrons depending on the orientation of orbital in space

m can have values from –l,…..-1,0,1…..+l

For l=0, m=0. s-orbital can have only one orientation. So there is only one s-orbital per shell

For l=1, m=-1,0,1. p-orbital can have three orientations designated as px, py, pz

d-orbitals (l=2) can have five orientations so there are five d-orbitals per shell. Similarly a shell can have seven f-orbitals

Electron SpinA fourth quantum number “s”

denotes the spin of electron. ‘s’ can have +1/2 value (spin up ) or -1/2 (spin down )

According to Pauli’s exclusion principle “No two electrons of a given atom are allowed to possess the same four quantum numbers at a time”

Each orbital can therefore have a maximum of two electrons one with spin up and other with spin down

When there are many orbitals, orbitals of each type are first filled singly. Only after all these orbitals contain one electron each, a second electron is added to the orbitals to complete a pair and thereby fill the orbital

The elements that life is primarily made up of are: Hydrogen (H), Carbon (C), nitrogen (N), oxygen (O) and phosphorus (P)

H: 1s1

C: 1s2, 2s2, 2p2

O: 1s2,2s2,2p4

N: 1s2, 2s2, 2p3

P: 1s2, 2s2, 2p6,3s2,3p3

Intramolecular and intermolecular forcesIntramolecular ForcesIonic bonds which is the attraction

between positive and negative ions in a crystal of an ionic compound

Covalent bondsMetallic bondsIntermolecular ForcesHydrogen bondingVan der Waals forces

Ionic bondAn electropositive atom loses an electron

forming a cation. This electron is gained by an electronegative atom forming an anion. These ions being oppositely charged will be attracted towards each other by Coulombic attraction

e.g. NaClNa Na+ + 1e- Cl + 1e- Cl-

Covalent bonds

Bond formed when atoms achieve the octet configuration by sharing their electrons. The orbitals of atoms sharing their electrons overlap and their electrons move into a new orbital called “Molecular orbital” where the pair of electrons are attracted towards both the nuclei

Polar & Nonpolar Covalent Bonds

Non polar covalent bond: with equal sharing of the bond electrons, arise when the electronegativities of the two atoms are equal.

Polar covalent bondA bond between 2 atoms

that have different electronegativities and therefore have unequal sharing of the bonding electron pair

Coordinate covalent bondA coordinate covalent bond is a covalent

bond in which both electrons are furnished by one atom

These bonds involve unequal sharing of electron pair by two atoms. The electron pair donor is the ligand or Lewis base while the acceptor is Lewis acid

These bonds are formed between transition metals (central atoms) and organic ligands

e.g. Fe2+ in hemoglobin and the cytochromes

Coordinate Covalent Bonds in HemoglobinHemoglobin is a very large

molecule (a macromolecule), but of all the atoms in this molecule, the only ones that concern us here are four iron atoms. Each of these four atoms is embedded in a portion of the hemoglobin called heme.

An iron atom in the center is held in place by covalent bonds to two nitrogen atoms and by coordinate covalent bonds to two other nitrogen atoms.

The protein called hemoglobin carry oxygen, O2 to the cells of the body. The O2 attaches itself to the hemoglobin by a coordinate covalent bond

When hemoglobin picks up oxygen in the lungs, each O2 molecule bonds to one of the Fe atoms by a coordinate covalent bond, with both electrons supplied by the oxygen, because the Fe atom, though bonded to four N atoms, still has room for additional electrons

Coordinate Covalent Bonds in Hemoglobin

Carbon monoxide poisoning

The coordinate covalent bonding ability of the Fe in hemoglobin is not restricted to O2. There are many other species that are also able to use an electron pair to form such a bond with the Fe in hemoglobin. Among these is the poison carbon monoxide, CO.

Carbon monoxide is poisonous because the bond it forms with the Fe in hemoglobin is stronger than the O2-Fe bond. When a person breathes in CO the hemoglobin combines with this molecule rather than with O2. The cells, deprived of O2, can no longer function, and the person dies.

Hydrogen Bonding

Hydrogen bonding can be both “intramolecular” as well as “intermolecular”

When a hydrogen atom is covalently linked with a strongly electronegative atom such as oxygen or nitrogen, it carries a partial positive charge

Hydrogen bonding is the interaction occurring between the partial positively charged H atom of a proton donor group A-H and a region of high electron density (e.g. a lone pair) of a proton acceptor group B (A is an electronegative atom)

Intramolecular Hydrogen Bonding

Intramolecular H-bonding occurs in molecules where the proton donor group and the proton acceptor group belongs to the same molecule

Here the proton donor and the proton acceptor sites on the same molecule is in a favorable spatial configuration to form a H-bond

This positively charged hydrogen atom gets attracted towards the negative end of another molecule and this attraction weakly binds the two molecules

A number of molecules attracted to each other by these electrostatic forces may associate together to form large clusters of molecules with hydrogen acting as bridge between the electronegative atoms

Intermolecular Hydrogen Bonding

Intermolecular hydrogen bonding is the attractive force between covalently bonded hydrogen atom of one molecule with the lone pair of an electronegative atom of another molecule

H- bonding in Proteins

H- bonding in Proteins

Hydrogen Bonding in Nucleic Acids

Vander Waals Forces (Intermolecular)Ion-dipole interactionDipole-dipole interaction (Keesom forces)Dipole induced dipole Interaction (Debye

forces)Instantaneous dipole-induced dipole

forces (London dispersion forces)

Ion-dipole interaction

Force between two permanent dipoles (Keesom force)

+–

+ –

+

–

+ –

Force between a permanent dipole and a corresponding induced dipole (Debye force)

London ForcesNon-polar molecules do not have dipoles like polar

moleculesThough the electron density in an atom or a molecule is

constant, there occurs a rapid but continuous oscillation of electrons (fluctuation of electron density) with respect to the nucleus

As a result, at a given instant, positive charges may be concentrated at one end & negative charges to another region of molecule. Thus a nonpolar molecule may become momentarily polarized-an instantaneous dipole and this dipole may attract other molecules by a dipole induced dipole mechanism

London Forces

Hydrophobic InteractionsThese interactions cause non-polar side

chains (aromatic rings and hydrocarbon groups) to cling together in polar solvents especially water

Non-polar groups try to arrange themselves in such a way that they are not in contact with water molecules i.e. water has a tendency to exclude non-polar groups