Lecture 14 Dr. Souradyuti Ghosh

Reading Hydrophobicity and hydrophilicity es_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_I nteractions es_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_I nteractions Sugars Amino acids and their properties reference-chart.html reference-chart.html

Reading Hydrophobicity and hydrophilicity in amino acids Page 4 and 5 Cell wall from phospholipid

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)

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

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

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% alBioNumbersHandout.pdf

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) severinson

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

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

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

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

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

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

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

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

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

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

Hydrophobic amino acids

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