1. Lecture 14 Dr. Souradyuti Ghosh souradyuti.ghosh@bennett.edu.in

2. Reading Hydrophobicity and hydrophilicity https://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Physical_Properti es_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_I nteractions https://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Physical_Properti es_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_I nteractions http://web.chem.ucla.edu/~harding/IGOC/H/hydrophilic.html http://web.chem.ucla.edu/~harding/IGOC/H/hydrophobic.html Sugars https://en.wikibooks.org/wiki/Structural_Biochemistry/Organic_Chemistry/Carbohydrates Amino acids and their properties http://wbiomed.curtin.edu.au/biochem/tutorials/AAs/AA.html http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid- reference-chart.html http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid- reference-chart.html

3. Reading Hydrophobicity and hydrophilicity in amino acids Page 4 and 5 http://www3.uah.es/farmamol/New_Science_Press/nsp-protein-1.pdf Cell wall from phospholipid https://www.ncbi.nlm.nih.gov/books/NBK9928/

4. Biomolecules We will primarily discuss the chemical and biological properties + functions of Amino acids and their biopolymer = peptides / proteins Sugars (in not so detail) Nucleic acids (DNA/RNA)

5. Importance of biomolecules into engineering Molecular docking of a small molecule into a protein http://bit.ly/2iUcY1a Docking: Simulation and optimization of drug binding with protein molecules Heavily used in computer science Hydrophobicity of biomaterials = used in mechanical / textile engineering

6. Cell Diameter = 20 micron Nuclear Diameter = 10 micron Water content of cell = 60 – 70%

7. Cellular structure Bacteria Fungus Human cell How much protein and where? Everywhere in the cell Including membranes, cytoplasm Density (concentration) of protein in cell= 0.19 g/ml Water’s density = 1 g/mL Gasoline’s density = 0.7 g/mL How much DNA and where? In nucleus (approx. 50% of cell volume) and in mitochondria Water content of cell = 60 – 70% http://kirschner.med.harvard.edu/files/bionumbers/fundament alBioNumbersHandout.pdf http://book.bionumbers.org/how-many-proteins-are-in-a-cell/

8. Proteins are not just another sitting structure Not just another static sitting structures Proteins can function as dynamic molecular machines, doing jobs like organic chemistry, signal processing, screening Proteins on a cell surface, that can act as signalling molecules Also determines how virus and bacteria attacks our native cells Scanning electron microscopy photo of a B lymphosite (type of white blood cells) http://www.su.se/mbw/research/research-groups/infection-and-immunobiology/emeritus- severinson

9. What are proteins made of? Amino acids R = various groupsR = H glycine Peptide Protein (3D structure) = poly-peptide

10. All biologically relevant amino acids have  -amino (NH 2 ) groups and have a common structure (R group)     R = H     R R R = CH 2 -SH R Amine Carboxylic acid

11. Same is true for all 20 essential amino acids                      

12. Quiz time Match if the structures described in LMS could be biologically relevant amino acids

13. How proteins function and form 3D structure: Hydrophilicity and hydrophobicity Phile = attract Phobe = repel  = contact angle Hydro philic = attracts water Hydro phobic = repels water  << 90   < 90   > 90   >> 90  Super-hydrophilic surface Hydrophilic surface Hydrophobic surface Super hydrophobic surface liq Solid surface liq Solid surface liq Solid surface liq Solid surface Why we want to study them? Explains why biomolecules have their 3D shape How cellular structures are formed Contact of liquid with surface decreases as hydrophobicity of surface increases Less hydrophobic More hydrophobic

14. Hydrophilicity and hydrophobicity: what is the chemistry?  < 90   > 90  Hydrophilic surface Hydrophobic surface liq Solid surface liq Solid surface Polar groups: that has a large partial charge separation due to electronegativity difference  hydrophilicity Non-polar groups: with zero or low charge separation  hydrophobicity O – H O = C COO  NH 2 NH 3 + CH 3 CH 2 CH 3 alkyl groups aromatic groups Show how water molecules orient themselves around these molecules These groups needs to be present in the surface

15. Real life example of hydrophilicity and hydrophobic surfaces Glass surface: hydrophilic because of silica structure, contact angle 45 deg Composition: silica Lotus Leaf surface: super hydrophobic, contact angle = 147 deg Material: epicuticular wax composed of aliphatic groups https://en.wikipedia.org/wiki/Epicuticular_wax

16. Why knowing the hydrophobicity is important Lotus leaf self- cleans itself due to hydrophobicity Cleaning of surface becomes easier if coated with hydrophobic material

17. In bio: part of same molecule can be hydrophilic and hydrophobic (amphiphilic) hydrophilic hydrophobic Hydrophilics like each other and water Hydrophobic liking each other Hydrophilics liking each other and water Phospholipid water 2 sets of molecules forming a bilayer Cavity containing water (for cellular organelles) Phospholipid bilayer hydrophobic hydrophilic water Discuss energy

18. Quiz time See the electronegativity table and match the groups in LMS as hydrophobic or hydrophilic

19. Hydrophobic amino acids

20. Hydrophili c amino acids These groups can get protonated (show formal charge calculation) These groups can loss H + (show formal charge calculation)