BIOPHYSICS II. By Prof. Xiang Yang Liu Department of Physics,

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1 BIOPHYSICS II By Prof. Xiang Yang Liu Department of Physics, NUS 1

2 Hydrogen bond and the stability of macromolecular structure Membrane Model Amphiphilic molecule self-assembly at the surface and din the bulk Packing parameter 2

3 Molecular l Interactions ti in Bio molecular l Structures water and hydrogen bond Weak interaction Formed between a hydrogen bond donor and acceptor pair. Linus Pauling was the first to emphasize the significance of hydrogen bonds in the folding of macromolecules. 3

4 Molecular Interactions in Bio molecular Structures water and hydrogen bond The implications of hydrogen bond in the stabilization of bimolecular structure: Hydrogen bonding is a stabilizing or destabilizing interaction in macromolecules depending on the solvent environment. In water, intramolecular hydrogen bonding is unfavorable. The donor acceptor pairs are sequestered from competing interactions with water. In the interior of a globular protein or in the stacked bases of nucleic acids, the formation of intramolecular hydrogen bonding is favored. (Forming the 2 nd or tertiary structure.) Hydrogen bonding potential will often overestimate the Hydrogen bonding potential will often overestimate the effect of intramolecular hydrogen bonds. 4

5 Molecular Interactions in Bio molecular Structures water and hydrogen bond Hydrogen bonding interactions stabilize the structures of macromolecules in aqueous solution. Example: NMA dimerizes in solution by forming hydrogen bonds between the amino N H group and the carboxyl oxygen. The competing interactions are between NMA and the solvent, and between two NMA molecules l to form a dimer. The higher concentration of water favors the fully solvated monomers. 5

6 Molecular Interactions in Bio molecular Structures water and hydrogen bond Energies for Dimerization of NMA 6

7 Molecular l Interactions in Bio molecular l Structures water and hydrogen bond In water: Dimer formation is unfavorable. Water competes for the hydrogen bonding potential of donors and acceptor group of NMA. There is a net loss of one hydrogen bond to water. ΔH o i f th d f it d f th ΔH o is of the same order of magnitude for the interaction of NMA to NMA and NMA to water, the higher concentration of bulk solvent greatly favors hydrogen bonding to water. 7

8 Molecular l Interactions in Bio molecular l Structures water and hydrogen bond For CCl 4 : Dimer formation is favored. The loss in entropy from bringing two NMA molecules together to form hydrogen bonds is nearly identical to that in water. In water this negative ΔS o makes ΔG o positive. The enthalpy hl in CCl 4 is negative ( 17 kj/mol). The negative ΔH o makes ΔG o negative, indicating that a hydrogen bond is inherently stable. 8

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10 Cll Cell and biomenbraneb The four essential parts of cell: Nucleus, Cytoplasm (gelatinous, semi-transparent fluid that fills most cells), Organelles, Membrane In order to keep cells alive and function properly, the intracellular condition is different from extra cellular conditions. How about biomembrane? 10

11 Cll Cell and biomenbraneb The plasma membrane is common to all cells Separates: Internal living cytoplasmic from External environment of cell Phospholipid bilayer: External surface lined with hydrophilic polar heads Cytoplasmic surface lined with hydrophilic polar heads Nonpolar, hydrophobic, fatty acid tails sandwiched in between 11

12 Phospholipid h d& Cholesterol lmolecules l Charged, polar groups Hydrophilic head: O, S, N, Hydrophobic tails: H, C, Non- polar/ weak polar groups 12

13 Structure and Function: Phospholipid Bilayer Semi-ordered Liquid! Biomembrane: Lipid Bilayer 13

14 Membrane Models: Unit Membrane vs. Fluid Mosaic Model Fluid Mosaic Model Three components: Basic membrane referred to as phospholipid bilayer Protein molecules l Float around like icebergs on a sea Membrane proteins may be peripheral or integral Peripheral proteins are found on the inner membrane surface Integral proteins are partially or wholly embedded (transmembrane) in the membrane Some have carbohydrate chains attached Cholesterol 14

15 Membrane Models: Unit Membrane vs. Fluid Mosaic Model 15

16 Membrane Models: Membrane Models: Unit Membrane vs. Fluid Mosaic Model 16

17 Membrane Protein Diversity 17

18 Self Assembly in Cells Questions: How can amphiphilic p molecules satisfy their hydrophobic tails in a pure water environment? How do the amphiphilic molecules assemble in an aqueous solution? How do amphiphilic molecules are packed into different shapes of aggregates 18

19 Amphiphilicmolecules hili l l Hydrophobic vs hydrophilic hili force Amphipathic (Amphiphilic) Molecules Both hydrophilic hili and hydrophobic hbi A hydrophobic part A hydrophilic part 19

20 Amphiphilicmolecules hili l l Two classes of amphiphiles. (a) Structure of sodium dodecyl sulfate (SDS), a strong detergent. A nonpolar, hydrophobic, tail (left) is chemically linked to a polar, hydrophilic head (right). In solution, the Na+ ion dissociates. Molecules from this class form micelles. (b) Structure of a generic phosphatidylcholine, o e,a class cassof phospholipid molecule. Two hydrophobic tails (left) are chemically linked to a hydrophilic head (right). g Molecules from this class form bilayers. 20

21 Slf Self assembly Self assembly: appropriate molecules gather together spontaneously to assemble into some entities of certain structures. What is the driving ii force behind it? 21

22 Drivingforce for amphiphilicmolecular molecular self assembly Optimal interaction/packing for amphiphilic molecules: Hydrophobic region in contact with hydrophobic region hydrophilic region in contact with hydrophilic region hydrophilic region avoiding hydrophilic region 22

23 Amphiphilic molecule self-assembly at the interface Hydrophobic-hydrophobic Hydrophilic-hydrophilic 23

24 Amphiphilic molecule self assembly at the interface Lower surface (interfacial) tension High surface (interfacial) tension air water oil water 24

25 Surface tensiometer to measure the Surface tensiometer to measure the surface tension 25

26 Amphiphilic molecule self assembly at the interface Lower the surface tension Micelles self-assemble suddenly at a critical concentration (Critical Micellization Concentration-CMC) CMC 26

27 Amphiphilic molecule self assembly at the interface Amphipathic (Amphiphilic) Molecules 27

28 Slf Self assembly of amphiphilies hili Assembly of amphiphilic molecules at the interface will reduce the interracial tension At the water surface reduce the surface tension. What happens after CMC? Assembly into different shapes of micelles 28

29 Amphiphilic molecule self assembly in the bulk At C > CMC Self-assembly Micelle Micelle solution 29

30 Amphiphilic molecule self assembly in the bulk How can these How can these aggregates be built into different shapes? 30

31 Amphiphilic molecule self assembly in the bulk Hydrophobic forces: Hydrophilic forces: Van der Waals Electrostatic Steric Polar-polar Configurational Hydrogen bond U(r) 0 Virtual Diameter r s tail s head s tail > s head s tail = s head s tail < s head 31

32 Amphiphilic p molecule self assembly in the bulk The optimal intermolecular interactions correspond to optimal packing of these molecules, which leads to the self assembly of molecules into different shapes. 32

33 Amphiphilic molecule self assembly in the bulk l v P = s tail /s head s tail = v/l s Packing parameter P: Due to different physical forces, amphiphilic molecules will self assemble into aggregates with different shapes P < 1 3 Spherical 1 3 P Rod-like 1 2 P~1 Disk-like Bilayer Perfect balance of fhydrophobic h and hydrophilic forces 33

34 Emulsion form when amphiphlic molecules reduce the oil water interfacial tension (a) An oil water interface stabilized by the addition of a small amount of (a) An oil water interface stabilized by the addition of a small amount of surfactant. Some surfactant molecules are dissolved in the bulk oil or water regions, but most migrate to the boundary as shown in the inset. (b) An oil water emulsion stabilized by surfactant: The situation is the same as (a), but for a finite droplet of oil. 34

35 Micellization A special type of phase transition N monomers One aggregate (N mer) C N /C 1N = K eq 35

36 Key Message Hydrogen bond key inter molecules determining the higher levels of structure of molecules Water or salts interrupt both intra/inter molecular hydrogen bonds, therefore will destabilize the hierarchical structure t of bio macromolecules. 36

37 Key Message Amphiphilc molecules Self assembly at the Surface Self assembly in the Bulk Lowering of surface free energy CMC Different shapes of aggregates, P 37

38 References Chapter 8 in Biological physics Chapter 1, D. Fennell Evans, Hakan Wennerstrom, The Colloidal l Domain where physics, chemistry, biology, and Technology Meet, VCH,