BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah
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)
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: 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.
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
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
C
B
H OH
H
O
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
O
N
NH3
H2O
Measurement of polarity
Dipole moment directionality: Vector from
- to
+
X
+
-
= qx
Polarity of Bonds
H
|
CH3OH
+ -
H—C—OH
|
H
C O
or even stronger polarity
H
+
C
O
+ C O
H
O> N> C, H electronegativity
-
+
+
-
+ -
O H
C
N
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
4
C
3
Cl
1
Cl
2
Cl
3
Cl
H
4
C
2
Cl
CHCl3 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 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 Å
N-H
O
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= 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 2.8Å
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 Å in distance (dipole-dipole attractions)
Contact Distance
H
C
N
O
S
P
Å
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 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 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
H
-TS
G
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 cm2•V-1•s-1
• Na+:
51.9 x 10-5
• Hydronium ion migration; hops by switching
partners at 1012 per second.
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)
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: 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.
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
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
C
B
H OH
H
O
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
O
N
NH3
H2O
Measurement of polarity
Dipole moment directionality: Vector from
- to
+
X
+
-
= qx
Polarity of Bonds
H
|
CH3OH
+ -
H—C—OH
|
H
C O
or even stronger polarity
H
+
C
O
+ C O
H
O> N> C, H electronegativity
-
+
+
-
+ -
O H
C
N
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
4
C
3
Cl
1
Cl
2
Cl
3
Cl
H
4
C
2
Cl
CHCl3 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 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 Å
N-H
O
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= 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 2.8Å
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 Å in distance (dipole-dipole attractions)
Contact Distance
H
C
N
O
S
P
Å
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 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 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
H
-TS
G
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 cm2•V-1•s-1
• Na+:
51.9 x 10-5
• Hydronium ion migration; hops by switching
partners at 1012 per second.