PowerPoint PresentationSIBS programMolecules and Water January 22 2003Slide 4CarbonSlide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Molecules have a definite shapeTetrahedron is a common shapeSlide 17Slide 18Geometry also determines polaritySlide 20Slide 21Slide 22A hydrogen bond between two water moleculesThe structure of iceThe structure of water is irregularSlide 26Slide 27Slide 28Water of HydrationSlide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Free energy of transfer for hydrocarbons form water to organic solventAmphiphilesAmphipiles: both polar and non-polarAmphiphiles form micelles, membrane bilayes and vesiclesOsmosis and diffusionDialysisProton and hydroxide mobility is large compared to other ionsBCHS 3304: General Biochemistry I, Section 07553Spring 2003 1:00-2:30 PM Mon./Wed. AH 101http://www.uh.edu/sibs/faculty/gleggeInstructor: Glen B. Legge, Ph.D., Cambridge UKPhone: 713-743-8380Fax: 713-743-2636E-mail: [email protected] hours: Mon. and Wed. (2:30-4:00 PM) or by appointment353 SR2 (Science and Research Building 2)1SIBS program•Monday Chat room on Webct: 8:00-10:00 PM Tuesday Workshop: 5:00-7:00 PM in 101 AH Wednesday Office Hours: 3:00-4:45 PM in 114 S Wednesday Workshop: 5:00-7:00 PM in 116 SR1•Students must activate their webct accounts. •SIBS will not print out exam reviews •Jerry Johnson (BCHS 3304 workshops) contact email: [email protected] and WaterJanuary 22 2003Molecules in life processesC, 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.Carbon•Carbon forms the basis of life•Carbon has a tremendous chemical diversity•can make 4 covalent bonds•can link together in C-C bonds in all sorts of flavors•Readily forms stable hetronuclear bondsBoron •Symbol: B•Atomic number: 5•Atomic weight: 10.811 (7) g m r•Boron has only three valence electrons-this limits the stability and types of compounds it can make.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.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 stableCarbon 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.Life developed from “carbon-based” Self Replicating RNA molecules “RNA World” Catalytic RNA. Chemical EvolutionChemical Evolution.From HCN, NH3, H2O give rise to adenine or carbohydrates. By sparking CH4, NH3, H2O and H2 these are formed:Glycineglycolic acidSarcosineAlanineLactic acidN-Methalanine-Amino-n-butyric acid - Aminoisobutyric acid- AlanineSuccinic AcidGlutamic acidand moreValence 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 LoneElement 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 2Atoms of these elements can form stable covalent bonds.Covalent bond: the force holding two atoms together by the sharing of a pair of electrons.H + H  H:H or H-HThe 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.Molecules have a definite shapeCOBAOHHOHHOHOHOHHHOH•A, B, C, and O all lie in the same plane.•As the molecule becomes larger the shape becomes more complicated•And may have many different conformationsCCH4NNH3H2OOTetrahedron is a common shapeMeasurement of polarityDipole moment directionality: Vector from - to +X + - = qxPolarity of Bonds H | + -CH3OH H—C—OH C O | Hor even stronger polarity H + - + - C O C O HO> N> C, H electronegativity - + + - + -O H C N C OGeometry also determines polarity• + - •while C Cl is polar carbon tetrachloride is not. The sum of the vectors equals zero and it is therefore a nonpolar moleculeCCl4 = 1+2+3+4 = 0CClClClCl1234CClClCl234HCHCl3 is polarProperties of WaterBent geometry, O-H bond length of 0.958Å Can form Hydrogen bondsHydrogen bondsPhysical properties of ice and water are a result of intermolecular hydrogen bondingHeat of sublimation at 0 oC is 46 kJ/mol yet only 6 kJ/mol is gaseous kinetic energy and the heat of fusion of ice is 6 kJ/mol which is only 15% of the energy needed to melt ice. Liquid water is only 15% less hydrogen bonded than ice CH4 boils at -164 oC but water is much higher.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 C3-7 kcal/mole or 12-28 kJ/molevery strong angle dependenceA hydrogen bond between two water moleculesThe structure of iceThe structure of water is irregularElectrostatic interactions by coulombs law F= kq1q2 q are charges