1、BCHS 3304: General Biochemistry I, Section 07553 Spring 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: gleggeuh.eduOffice hours: Mon. and Wed. (2:30-4:00 PM) or by appointment353 SR2 (Sci
2、ence and Research Building 2),1,SIBS 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 J
3、erry Johnson (BCHS 3304 workshops) contact email: MYSTIK,Molecules and Water January 22 2003,Molecules in life processesC, H, O, N, P, and S all readily form covalent bonds. Only 35 naturally occurring elements are found in life processes.Earths Crust 47% O2, 28% Si, 7.9% Al, 4.5% Fe, and 3.5% Ca. B
4、, 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 bonds,Boron Symbol: B Atomic number
5、: 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.,NitrogenSymbol: 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 electro
6、ns 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 PhosphateSilicon has a large radius preventing good orbital overlap thus Si-Si bonds are relatively weaker at 177 kJ/moleThis makes lon
7、ger 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,Carbon heteronuclear bondsHeteronuclear are stable and form in living matter These bonds are less stable than C-C bonds Often
8、 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 Evolution,Chemical Evolution. From HCN, NH3, H2O give rise to adenine or carbohydrates. By sparking CH4, NH3, H2O and H2 these are for
9、med: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,Valence orbitals: outermost orbital that is filled or partially filled with electrons. These can overlap and form covalent bonds.Each
10、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 # pairsH 1 1 2 1 1 0C 6 4 8 4 4 0N 7 4 8 5 3 1O 8 4 8 6 2 2Atoms of these elements can form
11、 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
12、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 shape,A, B, C, and O all lie in the same plane. As the molecule becomes larger the shape becomes more compli
13、cated And may have many different conformations,Tetrahedron is a common shape,Measurement of polarityDipole moment directionality: Vector from - to +X + -m = qx,Polarity of BondsH| d+ d- CH3OH HCOH C O |H or even stronger polarityH d+ d- d+ d-C O C OH O N C, H electronegativityd- d+ d+ d- d+ d- O H
14、C N C O,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,Properties of WaterBent geometry, O-H bond length of 0.958 Can form Hydrogen bonds,Hydrogen bondsPhysica
15、l 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 bonde
16、d than ice CH4 boils at -164 oC but water is much higher.,Hydrogen bondsO-H N N-H O2.88 3.04 H bond donor or an H bond acceptorN H O C3-7 kcal/mole or 12-28 kJ/mole very strong angle dependence,A hydrogen bond between two water molecules,The structure of ice,The structure of water is irregular,Elect
17、rostatic interactionsby coulombs law F= kq1q2 q are chargesr2D r is radius D = dielectric of the media, a shielding of charge. And k =8.99 x109Jm/C2 D = 1 in a vacuum D = 2-3 in grease D = 80 in waterResponsible for ionic bonds, salt linkages or ion pairs, optimal electrostatic attraction is 2.8,Die
18、lectric 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 116H2O 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 fo
19、rm maximal strength bonds!,Heat of sublimation of ice is 46.9 kJ/molOnly 6 kJ/mol can be attributed to Kinetic energy of the gaseouswater vapor molecules.41 kJ/mol must come from hydrogen bonds.Only 15% of the hydrogen bonds are disrupted by meltingShort term interactions are tetrahydral in natureWa
20、ter 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.,Water of Hydration,Hydration - to be surrounded by H2OA polar molecule is hydrate
21、d by the partial charge interaction of the water moleculeMultiple H bonds increase solubility,Solvation of ions,Forms Hydrogen bonds with Functional Groups,. van der Waals attractionNon-specific attractions 3-4 in distance (dipole-dipole attractions)Contact Distance H 1.2 1.0 kcal/mol C 2.0 4.1 kJ/m
22、ol 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,Steric complementarityOccurs when large numbers of atoms are in contactSpecificityWhen there is a large affinity for a unique molecule to bind to anothera) antibodies
23、b) enzyme substrate c) restriction enzymes,Hydrophobic interactionsNon-polar groups cluster togetherDG = DH - TDSThe most important parameter for determining a biomolecules shape!Entropy order-disorder. Nature prefers to maximize entropy “maximum disorder”.How can structures form if they are unstabl
24、e?Are they unstable? Structures are driven by the molecular interactions of the water!,Non-polar molecules are not soluble in H2OTendency to associate with each other and to be excluded from water.HYDROPHOBIC INTERACTIONSGrease or gasoline does not mix with water.However, small non-polar molecules l
25、ike CH4 (methane) have a small solubility. But when the water is evaporated, a solid remains . A calatherate is formed! H2O surrounds the CH4 and forms a caged molecule. .,STRUCTURED WATER,STRUCTURED WATERA cage of water molecules surrounding the non-polar molecule This cage has more structure than
26、the surrounding bulk media. DG = DH -TDSEntropy decreases! Not favorable! Nature needs to be more disorganized. A driving force.SOTo minimize the structure of water the hydrophobic molecules cluster together minimizing the surface area. Thus water is more disordered but as a consequence the hydropho
27、bic molecules become ordered!,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,Amphiphiles,Most biological molecules contain both polar an
28、d non-polar segments They are at the same time hydrophobic and hydrophilic,Amphipiles: both polar and non-polar,Detergents, Fatty acids, lipid molecules polar head; non-polar tail. Water is more concentrated than the molecules it surrounds so the shear numbers of ordered molecules is much greater. T
29、he greatest entropy is a function of both the dissolved molecule and the solvent. Proteins are also amphipathic and hydrophobic interactions are the greatest contributor the the three dimensional shape of proteins.,Amphiphiles form micelles, membrane bilayes and vesicles,A single amphiphile is surro
30、unded by water, which forms structured “cage” water. To minimize the highly ordered state of water the amphiphile is forced into a structure to maximize entropy DG = DH -TDS driven by TDS,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,Dialysis,Proton and hydroxide mobility is large compared to other ions,H3O+ : 362.4 x 10-5 cm2V-1s-1 Na+: 51.9 x 10-5 Hydronium ion migration; hops by switching partners at 1012 per second.,
