Chemical Properties & Interactions of C, B, N, Si, P, & H2O, Slides of Biochemistry

Download Chemical Properties & Interactions of C, B, N, Si, P, & H2O and more Slides Biochemistry in PDF only on Docsity! Molecules and Water January 22 2003 Docsity.com Molecules in life processes C, H, O, N, P, and S all readily form covalent bonds. Only 35 naturally occurring elements are found in life processes. Earth’s Crust 47% O2, 28% Si, 7.9% Al, 4.5% Fe, and 3.5% Ca. B, C, N, Si and P can form three or more bonds and can link together. Docsity.com Nitrogen • Symbol: N •Atomic number: 7 •Atomic weight: 14.0067 (2) g r •Nitrogen has five valence electrons •repulsion between the lone pair and the other orbital electrons make the N-N bond less stable (171 kJ/mole) than the C-C bond (348 kJ/mole). • However, N triple bond is so stable 946 kJ/mole it can not break easily. Docsity.com Silicon and Phosphate • Silicon has a large radius preventing good orbital overlap thus Si-Si bonds are relatively weaker at 177 kJ/mole • This makes longer Si-Si chains are unstable • Si-O bonds are very stable 369 kJ/mole • Si cannot have higher oxidation states other than SiO2 which is sand • Poly phosphates are even less stable Docsity.com Carbon heteronuclear bonds • Heteronuclear are stable and form in living matter • These bonds are less stable than C-C bonds • Often C-O-C and C-N bonds are places where cleavage sites are found. Docsity.com Chemical Evolution. From HCN, NH3, H2O give rise to adenine or carbohydrates. By sparking CH4, NH3, H2O and H2 these are formed: Glycine glycolic acid Sarcosine Alanine Lactic acid N-Methalanine a-Amino-n-butyric acid a - Aminoisobutyric acid b- Alanine Succinic Acid Glutamic acid and more Docsity.com Valence orbitals: outermost orbital that is filled or partially filled with electrons. These can overlap and form covalent bonds. Each orbital can have two electrons. Orbitals are designated by quantum numbers which define shells, orbital types spin etc. electron or Val Max # 0f own val Bond Lone Element proton # orbital # electrons electrons # pairs H 1 1 2 1 1 0 C 6 4 8 4 4 0 N 7 4 8 5 3 1 O 8 4 8 6 2 2 Atoms of these elements can form stable covalent bonds. Docsity.com Covalent bond: the force holding two atoms together by the sharing of a pair of electrons. H + H  H:H or H-H The force: Attraction between two positively charged nuclei and a pair of negatively charged electrons. Orbital: a space where electrons move around. Electron can act as a wave, with a frequency, and putting a standing wave around a sphere yields only discrete areas by which the wave will be in phase all around. i.e different orbitals. Docsity.com Measurement of polarity Dipole moment directionality: Vector from - to + X + - m = qx Docsity.com Polarity of Bonds H | d+ d- CH3OH H—C—OH C O | H or even stronger polarity H d+ d- d+ d- C O C O H O> N> C, H electronegativity d- d+ d+ d- d+ d- O H C N C O Docsity.com Geometry also determines polarity • d+ d- • while C Cl is polar carbon tetrachloride is not. The sum of the vectors equals zero and it is therefore a nonpolar molecule mCCl4 = m1+m2+m3+m4 = 0 C Cl Cl Cl Cl m1 m2 m3 m4 C Cl Cl Cl m2 m3 m4 H CHCl3 is polar Docsity.com Hydrogen bonds O-H N N-H O 2.88 Å 3.04 Å H bond donor or an H bond acceptor N H O C 3-7 kcal/mole or 12-28 kJ/mole very strong angle dependence Docsity.com A hydrogen bond between two water molecules Docsity.com The structure of ice Docsity.com Dielectric effect D hexane 1.9 benzene 2.3 diethyl ether 4.3 CHCl3 5.1 acetone 21.4 Ethanol 24 methanol 33 H2O 80 HCN 116 H2O is an excellent solvent and dissolves a large array of polar molecules. However, it also weakens ionic and hydrogen bonds Therefore, biological systems sometimes exclude H2O to form maximal strength bonds!! Docsity.com •Heat of sublimation of ice is 46.9 kJ/mol •Only 6 kJ/mol can be attributed to Kinetic energy of the gaseous water vapor molecules. 41 kJ/mol must come from hydrogen bonds. Only 15% of the hydrogen bonds are disrupted by melting Short term interactions are tetrahydral in nature Water reorients once in 10-12 sec that is a pico second Liquid water therefore consists of a rapidly fluctuating, -space filling network of hydrogen-bonded H2O molecules that, over short distances, resembles that of ice. Docsity.com Water of Hydration • Hydration - to be surrounded by H2O • A polar molecule is hydrated by the partial charge interaction of the water molecule • Multiple H bonds increase solubility Docsity.com . van der Waals attraction Non-specific attractions 3-4 Å in distance (dipole-dipole attractions) Contact Distance Å H 1.2 1.0 kcal/mol C 2.0 4.1 kJ/mol N 1.5 weak interactions O 1.4 important when many atoms S 1.85 come in contact P 1.9 Can only happen if shapes of molecules match Docsity.com Steric complementarity •Occurs when large numbers of atoms are in contact Specificity When there is a large affinity for a unique molecule to bind to another a) antibodies b) enzyme substrate c) restriction enzymes Docsity.com Hydrophobic interactions Non-polar groups cluster together DG = DH - TDS The most important parameter for determining a biomolecule’s shape!!! Entropy order-disorder. Nature prefers to maximize entropy “maximum disorder”. How can structures form if they are unstable? Are they unstable? Structures are driven by the molecular interactions of the water! Docsity.com STRUCTURED WATER A cage of water molecules surrounding the non-polar molecule This cage has more structure than the surrounding bulk media. DG = DH -TDS Entropy decreases!! Not favorable! Nature needs to be more disorganized. A driving force. SO To minimize the structure of water the hydrophobic molecules cluster together minimizing the surface area. Thus water is more disordered but as a consequence the hydrophobic molecules become ordered!!! Docsity.com Free energy of transfer for hydrocarbons form water to organic solvent CH4 in H2O  CH4 in C6H6 11.7 -22.6 -10.9 CH4 in H2O  CH4 in CCl4 10.5 -22.6 -12.1 C2H6 in H2O  C2H6 in C6H6 9.2 -25.1 -15.9 Process DH -TDS DG Docsity.com Amphiphiles • Most biological molecules contain both polar and non-polar segments • They are at the same time hydrophobic and hydrophilic Docsity.com Osmosis and diffusion • Osmosis is the movement of solvent from aregion of high concentration to low concentration • Osmotis pressure depends on solute concentration • 1 M solution osmotic pressure is 22.4 atm Docsity.com Dialysis (a) At start of (b) — At equilibrium dialysis Dialysis membrane Solvent Concentrated solution Copyright 1999 John Wiley and Sons, Ine, All rights reserved, Docsity.com Proton and hydroxide mobility is large compared to other ions • H3O+ : 362.4 x 10 -5 cm2•V-1•s-1 • Na+: 51.9 x 10-5 • Hydronium ion migration; hops by switching partners at 1012 per second. Docsity.com