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: glegge@uh.edu
Office hours:
Mon. and Wed. (2:30-4:00 PM) or by appointment
353 SR2 (Science and Research Building 2)

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: MYSTIK1775@aol.com

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.

Earths 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
bonds

Boron
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 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, 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
-Amino-n-butyric acid
- Aminoisobutyric acid
- 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
Element proton # orbital # electrons
H
C
N
O

1
6
7
8

1
4
4
4

2
8
8
8

own val Bond Lone

electrons #
pairs
1
4
5
6

1
4
3
2

0
0
1
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
O

H OH
H

HO
H

HO

H
H

OH
OH

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

CH4

NH3

H2O

Measurement of polarity

Dipole moment directionality: Vector from -

to

= qx

Polarity of Bonds
H

+ -

CH3OH

+
C

HCOH
|
H
O

C O

or even stronger polarity

+ C O

H
O> N> C, H electronegativity
-

+ -

O H

C O

Geometry 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 = 0

Cl

Cl

Cl

Cl

Cl
3

Cl

C
2

Cl

CHCl3 is polar

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

Hydrogen bonds
Physical properties of ice and water are a result of
intermolecular hydrogen bonding
Heat 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
2.88

N-H
O
3.04

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= kq1q2
r 2D

q are charges
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 water
Responsible for ionic bonds, salt linkages or ion
pairs, optimal electrostatic attraction is 2.8

Dielectric effect
hexane
benzene
diethyl ether
CHCl3
acetone
Ethanol
methanol
H2O
HCN

D
1.9
2.3
4.3
5.1
21.4
24
33
80
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!!

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.

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

Solvation of ions

Forms Hydrogen bonds with Functional Groups

van der Waals attraction

Non-specific attractions 3-4 in distance (dipole-dipole attractions)
Contact Distance
H
C
N
O
S
P

1.2
2.0
1.5
1.4
1.85
1.9

1.0 kcal/mol
4.1 kJ/mol
weak interactions
important when many atoms
come in contact

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

G = H - TS
The 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 unstable?

Are they unstable?

Structures are driven by the molecular interactions of
the water!

Non-polar molecules are not soluble in H 2O

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 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 WATER
A cage of water molecules surrounding the non-polar molecule
This cage has more structure than the surrounding bulk media.
G = H -TS
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!!!

Free energy of transfer for hydrocarbons

form water to organic solvent
Process

-TS

CH4 in H2O

CH4 in C6H6

11.7

-22.6

-10.9

CH4 in H2O

CH4 in CCl4

10.5

-22.6

-12.1

9.2

-25.1

C2H6 in H2O C2H6 in C6H6

-15.9

Amphiphiles
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
G = H -TS driven by TS

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.