Biomolecules: The Molecules of Life. 1.2 Biomolecules: The Molecules of Life. Covalent bonding alternatives
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1 Biomolecules: The Molecules of Life What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life? Answer: Their ability to form covalent bonds by electron-pair sharing. 1.2 Biomolecules: The Molecules of Life What property unites H, O, C and N and renders these atoms so appropriate to the chemistry of life? Answer: Their ability to form covalent bonds by electron-pair sharing. Bond strength: the more you have the harder they are to break. Covalent bonding alternatives Resonance structures STABILIZE bonds and make the Molecule Stable (makes the bonds harder to break) 1
2 Arrow pushing shows the way electrons flow During chemical Reactions! Each arrow represents an electron pair: they Constitute the birth of a new chemical bond. The strength of an IONIC BOND is determined By Coulomb s law E=kq 1 q 2 /Dr 2 q1 & q2 are charges on the atoms k= 332 (a constant) D=dielectric constant (environment) r= distance between the atoms in angstroms A problem to ponder E=kq 1 q 2 /Dr 2 Two Monovalent atoms separated in Water (D=80) VS. Two Monovalent atoms separated in a vacuum (D=1) How is the electrostatic interaction between atoms affected by their environment? 2
3 Hydrogen Bonds are Big Players in Biological Molecules Van der Waals Bonds only contribute At certain atomic distances Each atom has a certain Van der Waals radius Where bonding is best! 3
4 The Biochemistry of a Geico.er.a Gecko! September 2, 2002 Volume 80, Number 35 Chemical and Engineering News Biochemistry in the News OFF THE WALL... HOLDING FAST Van der Waals bonding, not capillary adhesion, attaches geckos to ceilings 4
5 5
6 Attention: Gecko foot update! Popular Mechanics October 2007 issue 6
7 Hydrophobic Effect Stabilizing force between nonpolar surfaces! Oily things stick to oily things Entropic driven event Coelescing frees water molecules Significant force in the correct folding of biological molecules, since they evolved to work best in an aqueous environment. Properties of Water High b.p., m.p., heat of vaporization, surface tension Bent structure makes it polar Non-tetrahedral bond angles H-bond donor and acceptor Potential to form four H-bonds per water Amazing Water! Often overlooked and under-appreciated! Life as we know it could not have existed without water. All life (even terrestrial life) is dependent on the water molecule. Land animals brought water along with us during evolution specialized organisms in arid environments developed ways to conserve water. 7
8 Amazing Water... Water s amazing properties comes from its molecular shape and composition Its colligative properties comes from its ability to be both an efficient hydrogen bond donor and acceptor. Def. of colligative properties - a set of properties related to a common characteristic Amazing molecular Properties come from Water s atomic Structure Electronegativity revisited. Def- ability of an atom to pull electrons toward itself. electron greedy atoms have large electronegativities Those atoms pull electrons towards them What is the induced electrical charge of electronegative atoms? Electronegativity and Bonding Polar covalent bonding is what? Polar covalent bonding involving atoms of unequal electronegativities & results in an electron tug of war electronegative atom wins. Sets up a dipole moment a polarity across the bond in water, bond angle also is slightly squished by oxygen s electronegativity Bond length shortened 8
9 Colligative Properties of Water High boiling point for such a small molecule Water s M.W still a liquid at ambient temp. Carbon dioxide (CO 2 ) M.W a gas at ambient temp (CO2 has a much lower b.p.) What would happen if water was a gas at ambient temp? Comparison of Ice and Water Issues: H-bonds and Motion Ice: 4 H-bonds per water molecule slowed down so it can make more bonds Water: 2.3 H-bonds per water molecule Ice: H-bond lifetime - about 10 microsec Water: H-bond lifetime - about 10 psec (10 psec = sec) Thats "one times ten to the minus eleven second"! 9
10 The formation and breaking of hydrogen bonds is very rapid. It is a dynamic process Hydrogen Bonding in ICE Notice the shape that crystallized water takes Hydrogen Bonding in Ice Ice looks solid, but actually there is molecular movements going on hydrogen bonds are constantly breaking and reforming A more rigid molecular structure in ice means less water molecules per unit of volume compared to liquid water. 10
11 Consequence... Ice is actually less dense as a solid than in its liquid state. Not typical for matter (solid is usually more dense than liquid) Water is most dense around 4 degree C, it freezes at 0 degrees What is the consequence with regards to the evolution of life on earth? Where did life originate according to science? Heat Capacity Water also has a large heat capacity a measure of how much energy has to be added to a system to change the temp. Compared to other solvents (like in organic), it takes a lot of heating to get water to go through a phase change A watched pot never boils Much energy has to be absorbed by the water molecule to break free of its hydrogen bonded neighbors. Consequence of Heat Capacity of Water Helps maintain a fairly constant body temp. you don t freeze solid in winter you don t boil in the summer. Both would be bad! Can be used in regulation of body temp evaporative cooling extra body heat is absorbed by water molecule and released at water evaporates from your skin surface. 11
12 Surface tension Water sticks to its neighbor feel when you do a belly smack some organism rely on this phenomenon for their existence water striders contributes to capillary action in plants it helps move water to the highest branches,defying gravity! Solvent Properties of Water The Universal Solvent Ions are always hydrated in water and carry around a "hydration shell Water has a high dielectric constant def - ability to cause ions to dissociate from ionic compound and associate with water. Dissolve NaCl in water vs. oil Water forms H-bonds with polar solutes carbohydrates Hydrophobic interactions - a "secret of life" 12
13 Hydration Shell of water around ionic compounds Notice placement of water around the ions Hydrogen Bonding (Competition) Allows non ionic (but POLAR)Molecules (like carbos and proteins) to be soluble in water. 13
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