Stabilizing interactions converted

How stabilizing interaction play role in biology

1. BY Dr. EKHLAQUE [email protected] S tabiliz ing interactions

2. Covalent bonds Non-covalent bonds Nature of bonding depends largely on electronegativity differences between individual atoms involved in the interaction. Thus , small differences between atoms involved in interactions lead to covalent bonding and large electronegativity differences lead to electrostatic ionic interactions. Bonding is based on the interactions of the outer shell electrons.

3. chemical interactions that stabilize polypeptides Interaction Distance dependence Typical dist a nce Free energy (bond dissociation enthalpies for the covalent bonds) Covalent - 1.5 Å 356 kJ/mol (610 kJ/mol for C=C bond) Disulfide - 2.2 Å 167 kJ/mol Salt bridge Donor and acceptor < 3.5 Å 2.8 Å 12.5-17 kJ/mol; may be as high as 30 kJ/mol for fully or partially buried salt bridges; less if the salt bridge is external Hydrogen bond Donor and acceptor < 3.5 Å 3.0 Å 2-6 kJ/mol in water; 12.5-21 kJ/mol if either donor or acceptor is charged Long-range elec t r o sta ti c Depends on dielectric constant of medium. Screened by water. 1/r dependence Variable Depends on distance and environment. Can be very strong in nonpolar region but very weak in water Van der Waals Short range. Falls off rapidly beyond 4 separation. 1/r 6 dependence. 3.5 Å 4 kJ/mol (4-17 in protein interior) depending on the size of the group (for comparison, the average thermal energy of molecules at RT is 2.5 kJ/mol General relative strength of each of these is typically much less than covalent bond Electrostatic > Hydrophobic interactions > Hydrogen bonds > van der Waals

4. Electrostatic or ionic Hydrogen bonds Van der Waals Hydrophobic interactions Non-covalent i nteractions in macromolecules

5. L a r ger struc t u r e s asse m ble sp ont a neous l y due to su f fi c i e nt nu m ber of weak bonds formation . A consequence: weak forces restrict organisms to a narrow range of environmental conditions (temperature, ionic strength, relative acidity). Weak interactions can break and reform under normal, physiological conditions. This allows conformational or shape changes in large molecules . These changes drive biochemical reactions, motility, etc . and are essential for many proteins to function. Biomolecular recognition is performed via interplay of complementary molecules. So , biological function is achieved through mechanisms based on structural complementarity and weak chemical interactions. Why non-covalent interactions ?

6. Electrostatic Interactions Ionic bonds are forces of attraction between ions of opposite charge (+and -). Any kind of biological molecule that can form ions. An example of a functional group that can enter into ionic bonds is shown below. The carboxyl group is shown . Under the right conditions of pH the carboxyl group will ionize and form the negatively charged COO ion and a positively charged H ion (or proton).

7. F unction of ionic bonds in biology? D etermin e the shapes ( tertiary and quaternary structures) of proteins. I nvolved in the process of enzymatic catalysis. I n determining the shapes of chromosomes . R ole in muscle contraction and cell shape . I n establishing polarized membranes for neuron function and muscle contraction. These interactions do not majorly play role in protein stability.

8. Electrostatic interaction depends on the distance of the two charges and the medium between them i.e. q 1 , q 2 : charges; r: distance; D: dielectric constant (vacuum: 1, water: 80) In the case of molecules where q 1 , q 2 and D are constants: where c: constant (=q 1 ∗q 2 /D). For example: two groups which are 2Å and 3Å apart, the interaction force between them is distance dependent i.e. & The optimal distance for electrostatic interaction is 2.8 Å. q 1 q 2 Dr 2 F 1 r 2 c F F q 1 q 2 4D F q 1 q 2 9D

9. Hydrogen Bond Hydrogen bonds are formed when a charged part of a molecule having polar covalent bonds forms an electrostatic interaction with a substance of opposite charge. Under the right environmental conditions, any compound that has polar covalent bonds can form hydrogen bonds. Hydrogen bonds are classified as weak bonds because they are easily and rapidly formed and broken under normal biological conditions. The strength of a H-bond is 3-7 kcal/mol.

10. Hydrogen donor - holds H more tightly, has partial positive charge Hydrogen acceptor - has partial negative charge that attracts H atom For creating a H-bond a "lone pair" of electrons in the acceptor atom is necessary. N has one lone pair of electrons, so it can be acceptor in one H-bond. O has 2 lone pairs of electrons and can therefore accept 2 H-bonds.

11. Vander Waals force It is the su m of the a t t r acti v e or r epulsi v e forces between molecule These were named after -: Johannes Diderik van der Waals

12. C haracteristics Features :- W eaker than normal covalent ionic bonds . Van der Waals forces are additive and cannot be saturated. They are all short - range forces and hence only interactions between nearest need to be considered instead of all the particles. The greater is the attraction if the molecules are closer due to Van der Waals forces. Van der Waals forces are independent of temperature except dipole - dipole interactions.

13. In Protein folding www.intechopen.com H elps in stabilizing the protein structure . In the coiled-coil protein , there is interaction between side chain in alpha helix . If these repeating residues are hydrophobic, such as leucine, van der waals interaction will be formed to stabilize this protein structure .

14. Graphenes Bonding Forces in Graphite Weak forces between graphenes suggest that they are the van der Waals Forces.

15. In P olymer F ormation Many polymeric chain are cross linked by vander waals force and get stable. www.m2polymer.com

16. Used by some animal Gecko lizard use these forces to climb on the walls. Some other animal use to walk on water . en.wikipedia.org dieffi.deviantart.com

17. www.wired.com In May 2014, DARPA demonstrated the latest iteration of its Geckskin Tests are ongoing, but DARPA hopes one day to make the technology available for military use, giving soldiers Spider Man-like abilities in urban combat In modern technology

18. D esc r i bes the re l ation between water and hydrophobes. Hydrophobes are non polar molecule and usually have a long chain of carbons that do not interact with water molecule. The mixing of fat and water is a good example of this interaction. Hydrophobic interactions

19. The hydrophobic effect is the observed tendency of non polar substances to aggregate in an aqueous solution and exclude water molecules . A droplet of water forms a spherical shape, minimizing contact with hydrophobic leaf.

20. a polar solvent (usually water) to interact with one another is called The tendency of non-polar molecule in hydrophobic effect. The interaction between the non- polar molecule are called hydrophobic interaction .

21. The non-polar substance like fat molecules tend to clump up together rather than distributing itself in a water medium , because this allow the fat molecules to have minimal contact with water.