Lecture 3

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Transcript Lecture 3

BCHS 3304: General Biochemistry I, Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101 http://www.uh.edu/sibs/faculty/glegge Instructor:

Glen B. Legge, Ph.D., Cambridge UK Phone: 713-743-8380 Fax: 713-743-2636 E-mail: [email protected]

Office hours:

Mon. and Wed. (2:30-4:00 PM) or by appointment 353 SR2 (Science 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 • Jerry Johnson (BCHS 3304 workshops) contact email: [email protected]

Molecules and Water January 22 2003

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.


• 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


•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.


• 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 SiO 2 which is sand • Poly phosphates are even less stable

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.

Chemical Evolution Life developed from “carbon-based” Self Replicating RNA molecules “RNA World” Catalytic RNA.

Chemical Evolution .

From HCN, NH 3 , H 2 O give rise to adenine or carbohydrates. By sparking CH 4 , NH 3 , H 2 O and H 2 these are formed: Glycine glycolic acid Sarcosine Alanine Lactic acid N-Methalanine a -Amino-


-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 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.

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.

Molecules have a definite shape

A B C O HO HO H OH H H H O OH OH H • 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 conformations

Tetrahedron is a common shape

C CH 4 N NH 3 O H 2 O

Measurement of polarity

Dipole moment directionality: Vector from to + X + m = qx

Polarity of Bonds

H | d + d CH 3 OH H—C—OH C O | H H d + d or even stronger polarity d + d C O C O H O> N> C, H electronegativity d d + d + d d + d O H 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 m CCl4 = m 1 + m 2 + m 3 + m 4 = 0 Cl Cl m 3 m 4 C m 2 Cl m 1 Cl Cl m 4 H Cl m 3 C m 2 Cl CHCl 3 is polar

Properties of Water

Bent geometry, O-H bond length of 0.958Å Can form Hydrogen bonds

Hydrogen bonds

Physical properties of ice and water are a result of intermolecular hydrogen bonding Heat of sublimation at 0 o C 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 CH 4 boils at -164 o C 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 C

3-7 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

Electrostatic interactions

by coulombs law F= kq 1 q 2 r 2 D q are charges r is radius D = dielectric of the media, a shielding of charge. And k =8.99 x10 9 Jm/C 2 D = 1 in a vacuum D = 2-3 in grease D = 80 in water Responsible for ionic bonds, salt linkages or ion pairs, optimal electrostatic attraction is 2.8Å

Dielectric effect hexane benzene diethyl ether CHCl 3 acetone Ethanol methanol H 2 O HCN D 1.9





24 33 80 116 H 2 O 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 H 2 O to form maximal strength bonds!!

•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 H 2 O molecules that, over short distances, resembles that of ice.

Water of Hydration

• Hydration - to be surrounded by H 2 O • A polar molecule is hydrated by the partial charge interaction of the water molecule • Multiple H bonds increase solubility

Solvation of ions

Forms Hydrogen bonds with Functional Groups


van der Waals attraction

Non-specific attractions 3-4 Å in distance (dipole-dipole attractions) H C N O S P Contact Distance Å 1.2 1.0 kcal/mol 2.0 4.1 kJ/mol 1.5

weak interactions 1.4

important when many atoms 1.85 come in contact 1.9

Can only happen if shapes of molecules match

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

Hydrophobic interactions

Non-polar groups cluster together D G = D H - T D S 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!

Non-polar molecules are not soluble in H 2 O Tendency to associate with each other and to be excluded from water.

HYDROPHOBIC INTERACTIONS Grease or gasoline does not mix with water.

However, small non-polar molecules like CH 4 (methane) have a small solubility. But when the water is evaporated, a solid remains .

A calatherate is formed!!

H 2 O surrounds the CH 4 and forms a caged molecule . .



A cage of water molecules surrounding the non-polar molecule This cage has more structure than the surrounding bulk media. D G = D H -T D S Entropy decreases!! Not favorable! Nature needs to be more disorganized. A driving force.


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!!!

Free energy of transfer for hydrocarbons form water to organic solvent

Process D H -T D S D G CH 4 in H 2 O  CH 4 in H 2 O  C 2 H 6 in H 2 O  CH CH 4 4 in C 6 H in CCl 6 4 C 2 H 6 in C 6 H 6 11.7 -22.6 -10.9 10.5 -22.6 -12.1

9.2 -25.1 -15.9


• Most biological molecules contain both polar and 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. The 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 surrounded 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 D G = D H -T D S driven by T D S

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


Proton and hydroxide mobility is large compared to other ions • H 3 O+ : 362.4 x 10 -5 • Na + : 51.9 x 10 -5 cm 2 •V -1 •s -1 • Hydronium ion migration; hops by switching partners at 10 12 per second.