Pre-Med Lecture 6 - Molecular Interactions PDF

MOLECULAR INTERACTIONS Dr. Alya A. Arabi Department of Biochemistry College of Medicine and Health Sciences https://slideplayer.com/slide/8733835/ Bonds Intra-molecular (within the molecule) Covalent bonds Ionic bonds Inter-molecular (between two molecules) 1. Hydrogen bonds 2. Van der Waal’s...

MOLECULAR INTERACTIONS Dr. Alya A. Arabi Department of Biochemistry College of Medicine and Health Sciences https://slideplayer.com/slide/8733835/ Bonds Intra-molecular (within the molecule) Covalent bonds Ionic bonds Inter-molecular (between two molecules) 1. Hydrogen bonds 2. Van der Waal’s forces 3. Hydrophobic interactions http://bionano.physics.illinois.edu/node/212 Summary of Intra-molecular Forces https://chem.fsu.edu/chemlab/chm1046course/interforces.html https://slidetodoc.com/intermolecular-forces-intra-vs-interu-intra-inward-u/ https://socratic.org/questions/which-of-the-forces-of-molecularattraction-is-the-weakest-hydrogen-bond-dipole- Hydrogen bonds (characteristics) ➢ They are stronger than most other intermolecular forces and much weaker than both the ionic bond and the covalent bond. ➢ When many of them are formed, they can exert considerable effects on the structure and interactions of molecules. ➢ They stabilize the a-helical structures of proteins and hold together the two strands of the DNA. 1- Hydrogen bonds The attraction of the partially positive end (H) of one highly polar molecule for the partially negative end of another highly polar molecule is called a hydrogen bond. (or and H between two electronegative atoms) Examples: N H …. N C O H …. N C N H …. O C O H …. O C d + d - d + d - Hydrogen bonding between water molecules https://socratic.org/questions/what-are-someexamples-of-hydrogen-bonds https://www.guyhowto.com/hydrogen-bondingdefinition-properties-examples-and-applications/ https://www.chemistrylearner.com/chemical-bonds/hydrogen-bond Hydrogen bonds (characteristics) ➢ They are highly directional and they are strong when the atoms involved are collinear (aligned straight). O O H …O Strong hydrogen bond O H Weak hydrogen bond Hydrogen bonds (characteristics) ➢ They are stronger than most other intermolecular forces and much weaker than both the ionic bond and the covalent bond. https://socratic.org/questions/which-of-the-forces-of-molecularattraction-is-the-weakest-hydrogen-bond-dipole- Hydrogen bonds (characteristics) ➢When many of them are formed, they can exert considerable effects on the structure and interactions of molecules. https://teacherhead.com/2014/04/28/pedagogy-postcard-20-the-abstract-concrete-connection/ Hydrogen bonds Hydrogen bonds in snowflakes https://teacherhead.com/2014/04/28/pedagogy-postcard-20-the-abstract-concrete-connection/ Hydrogen bonds (characteristics) ➢They stabilize the a-helical structures of proteins and hold together the two strands of the DNA. https://www.obo7.xyz/products.aspx?cname=alfa+helix 2- Van der Waal’s forces Van der Waal’s forces are also called London Dispersion Forces. Van der Waal’s forces are temporary weak attractive forces that hold non-polar molecules together. Examples of non-polar molecules: H2 CO2 N2 noble gases Van der Waal’s forces electron motion Then Original temporary dipole Induced dipole Van der Waal’s forces Graphite: sheets of strong covalent bonded atoms held together by weak Van der Waals forces Van der Waal’s forces (1) Characteristics: ➢ They are much more important as the pressure increases (molecules get closer) and/or the temperature decrease (molecules slow down). ➢ They are stronger as the size of the molecule increases. Van der Waal’s forces (2) Characteristics: ➢They contribute to the stability of a folded protein molecule where the uncharged non-polar groups are packed tightly together. ➢ They help to stabilize the bilayer or micelle structure adopted by lipids. Noble gases on surfaces http://www.sci-news.com/physics/van-der-waalsforces-individual-atoms-03890.html https://medium.com/sci-five-university-ofbasel/van-der-waals-interactions-measured-for-thefirst-time-at-the-university-of-basel-ccd76f6ef9b8 3- Hydrophobic interactions Hydrophobic interaction: attractions between nonpolar molecules (or parts of molecules). For example: non-polar molecules such as oil combine when placed into a polar environment such as water. Due to the repulsion between the non-polar and polar molecules, the non-polar molecules aggregate in hydrophobic interactions spontaneously. Two regions containing hydrophobic substances (oil) The two hydrophobic molecules combine and form one larger hydrophobic region. Hydrophobic interactions ➢ Another example: hydrophobic interactions between different non-polar regions within molecules. ➢ They are not bonding interactions but provide a significant factor in the overall stabilization of molecules, for example in biological systems https://www.sciencedirect.com/topics/chemistry/hydrophobic-effect https://sites.google.com/site/vmhstr opicalaroma/chemistry-of-soap Functions of non-covalent bonds in biological systems ➢ Hold together the subunits of multimeric proteins and the two strands of the DNA molecule. ➢ Hold together membranes. the lipid molecules in cell Determine the 3D structures and hence the function of macromolecules such as proteins and nucleic acids. ➢ Reversible interactions between: substrates and enzymes, hormones and receptors, drugs and receptors, antigens and antibodies. Example in Medicine 25