BCHS 3304: General Biochemistry I, Section 07553

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BCHS 3304 General Biochemistry I, Section
07553 Spring 2003 100-230 PM Mon./Wed. AH
101 http//www.uh.edu/sibs/faculty/glegge Instr
uctor Glen B. Legge, Ph.D., Cambridge
UK Phone [phone] Fax [phone] E-mail
glegge_at_uh.edu Office hours Mon. and Wed.
(230-400 PM) or by appointment 353 SR2 
(Science and Research Building 2)
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SIBS program

• Monday Chat room on Webct 800-1000 PM Tuesday
  Workshop 500-700 PM in 101 AH Wednesday Office
  Hours 300-445 PM in 114 S Wednesday Workshop
  500-700 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_at_aol.com

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Molecules and WaterJanuary 22 2003
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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.
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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

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• 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.

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• 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.

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• 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

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• 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.

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Chemical Evolution
Life developed from carbon-based Self
Replicating RNA molecules RNA World Catalytic
RNA.
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Chemical Evolution. From HCN, NH3, H2O give rise
to adenine or carbohydrates. By sparking CH4,
NH3, H2O and H2 these are formed Glycine glycoli
c acid Sarcosine Alanine Lactic
acid N-Methalanine a-Amino-n-butyric acid a -
Aminoisobutyric acid b- Alanine Succinic
Acid Glutamic acid and more
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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.
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Covalent bond the force holding two atoms
together by the sharing of a pair of
electrons. H H ? HH 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.
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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

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Tetrahedron is a common shape
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Measurement of polarity Dipole moment
directionality Vector from - to X

- m qx
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Polarity of Bonds H

d d- CH3OH HCOH
C O
H or even stronger polarity H d
d- d d- C
O C O H Ogt Ngt C, H
electronegativity d- d
d d-
d d- O H C N
C O
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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
• mCCl4 m1m2m3m4 0

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Properties of Water Bent geometry, O-H bond
length of 0.958Å Can form Hydrogen bonds
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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.
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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
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A hydrogen bond between two water molecules
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The structure of ice
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The structure of water is irregular
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Electrostatic interactions by coulombs law F
kq1q2 q are charges
r2D 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
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Dielectric effect D hexane 1.9 benze
ne 2.3 diethyl ether 4.3 CHCl3 5.1 acet
one 21.4 Ethanol 24 methanol 33 H2O 8
0 HCN 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!!
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• 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.

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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

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Solvation of ions
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Forms Hydrogen bonds with Functional Groups
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. 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
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• 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

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Hydrophobic interactions Non-polar groups
cluster together DG DH - TDS 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!
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Non-polar molecules are not soluble in
H2O 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. .
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STRUCTURED WATER
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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!!!
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Free energy of transfer for hydrocarbons form
water to organic solvent
Process DH
-TDS DG
CH4 in H2O ? CH4 in C6H6 11.7
-22.6 -10.9 CH4 in H2O ?
CH4 in CCl4 10.5 -22.6
-12.1 C2H6 in H2O ? C2H6 in C6H6
9.2 -25.1 -15.9
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Amphiphiles

• Most biological molecules contain both polar and
  non-polar segments
• They are at the same time hydrophobic and
  hydrophilic

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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.

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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
• DG DH -TDS driven by TDS

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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

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Dialysis
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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.