Molecules and Water 2.28 MB
BCHS 3304: General Biochemistry I, Section 07553
Spring 2003 1:00-2:30 PM Mon./Wed. AH 101
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
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
Chemical Evolution
Life developed from “carbon-based” Self Replicating RNA molecules “RNA World” Catalytic RNA.
Chemical Evolution.
From HCN, NH 3, H 2O give rise to adenine or carbohydrates.
By sparking CH 4, NH 3, H 2O and H 2 these are formed:
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 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
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
CH 4 boils at -164 oC but water is much higher.
Electrostatic interactions
by coulombs law F= kq 1q 2 q are charges
r 2D r is radius
D = dielectric of the media, a shielding of charge.
And k =8.99 x10 9Jm/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
.
van der Waals attraction
Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)
Contact Distance
Å
H 1.2 1.0 kcal/mol
C 2.0 4.1 kJ/mol
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 complementarity
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
DG = DH - TDS
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 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 CH 4 (methane) have a small solubility. But when the water is evaporated, a solid remains
.
A calatherate is formed!!
H 2O surrounds the CH 4 and forms a caged molecule.
.
STRUCTURED WATER
A cage of water molecules surrounding the non-polar molecule
This cage has more structure than the surrounding bulk media.
DG = DH -TDS
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!!!
Amphiphiles
Detergents, Fatty acids, lipid molecules
Osmosis and diffusion
Proton and hydroxide mobility is large compared to other ions
BCHS 3304: General Biochemistry I, Section 07553
Spring 2003 1:00-2:30 PM Mon./Wed. AH 101
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
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
- 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 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
- 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
Chemical Evolution
Life developed from “carbon-based” Self Replicating RNA molecules “RNA World” Catalytic RNA.
Chemical Evolution.
From HCN, NH 3, H 2O give rise to adenine or carbohydrates.
By sparking CH 4, NH 3, H 2O and H 2 these are formed:
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 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, and O all lie in the same plane.
- As the molecule becomes larger the shape becomes more complicated
- And may have many different conformations
- 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
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
CH 4 boils at -164 oC but water is much higher.
Electrostatic interactions
by coulombs law F= kq 1q 2 q are charges
r 2D r is radius
D = dielectric of the media, a shielding of charge.
And k =8.99 x10 9Jm/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
.
van der Waals attraction
Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)
Contact Distance
Å
H 1.2 1.0 kcal/mol
C 2.0 4.1 kJ/mol
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 complementarity
- Occurs when large numbers of atoms are in contact
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
DG = DH - TDS
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 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 CH 4 (methane) have a small solubility. But when the water is evaporated, a solid remains
.
A calatherate is formed!!
H 2O surrounds the CH 4 and forms a caged molecule.
.
STRUCTURED WATER
A cage of water molecules surrounding the non-polar molecule
This cage has more structure than the surrounding bulk media.
DG = DH -TDS
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!!!
Amphiphiles
- Most biological molecules contain both polar and non-polar segments
- They are at the same time hydrophobic and hydrophilic
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.
- 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
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 3O+ : 362.4 x 10 -5 cm 2•V -1•s -1
- Na +: 51.9 x 10 -5
- Hydronium ion migration; hops by switching partners at 10 12 per second.
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