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Lecture 2: The Chemical Basis of Life


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Sense of scale
A. Organism organs tissues cells molecules atoms
B. Scale:
1.millimeter (mm) 10 -3 m
2.micrometer (m) also called a micron 10 -6 m
3.nanometer (nm) 10 -9 m
4.Angstrom = 0.1 nm = 10-10 m (used to measure the distance of atoms in molecules)
C. Eukaryotic cells range from 5 - 100 m in length
D. Prokaryotic cells are ~1 m in length.
The chemistry of life is dominated by the chemistry of H, C, O, P and N and their ability to form
covalent bonds to make larger molecules.
A. Primarily because of the strength of bonds formed by small molecules and the diversity of
molecules that can be formed with C, H, N and O.
B. Ca, Mg, Na, K and Cl primarily exist as mono-atomic ions (Ca++, Mg++, Na+, K+ and Cl-)
C. Most of the phosphorus (P) is present as phosphate (PO 4) in larger molecules (nucleotides, RNA,
DNA)
D. Phosphorus and sulfur form intermediate strength covalent bonds that are very useful in energy
transfer reactions.
E. Life evolved in water, and water is the most abundant molecule in living creatures (~70% of the
weight).
Arrangement of electrons in a few common atoms
A. Fundamental Principle: An atom is most stable when its outermost electron shell is full. So, the
number of bonds that can be formed is dictated by number of electrons required to fill the shell (also
called the valency of the atom).
B. Carbon has 4 unpaired electrons in its outer shell and will form 4 covalent bonds with other atoms
C. Nitrogen has 3 unpaired electrons in its outer shell
D. Oxygen has 2 unpaired electrons
E. Hydrogen has 1 unpaired electron
F. Na has a strong tendency to lose its lone outer shell electron to become a Na+ ion
G. Cl has a strong tendency to gain an electron to fill its outer shell to become a Cl- ion
Bonds
A. Covalent and noncovalent chemical bonds contribute to the structure of biomolecules
B. Covalent bonds (50-110 kcal/mol)
C. Noncovalent bonds (<5 kcal/mol)
Covalent bonds (50-110 kcal/mol)
A. Covalent bonds are formed when atoms share pairs of electrons
B. The energy required to cleave is great, making covalent bonds stable under most cellular conditions
C. -C-C- bonds ~85 kcal/mol
1.Free rotation
D. Double bonds are formed when atoms share two pairs of electrons. -C=C- ~150 kcal/mol.
1.Constrains bond geometry to a plane
E. Carbon compounds can be linear, branched or cyclic.
F. Energy is released when bonds form. Breaking bonds require an input of energy.
1.The Bond Energy is a measure of the strength of a chemical bond, and is described as the
amount of heat required to break the bonds in a mole of molecules.
2.Thermal energy at body temperature is ~0.6 kcal/mol
3.The kcal/mol unit is the same Calorie (capital C) used to describe the amount of energy stored
in our food
4.One kcal is the amount of energy required to raise the temperature of one Kg of water 1C (from
14.5 to 15.5C).
5.One mole (mol) is 6.02 x 1023 items - in this case bonds between two molecules.

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6.The covalent bond energies here (50 110 kcal/mol) are for the atoms of biological relevance
and typical types of bonds (single, double) (C-C, C-H, C-N, N-O, N-H) etc.
7.The First Law of Thermodynamics states that the total energy of an isolated system is constant.
Energy can be transformed from one form to another, but cannot be created or destroyed. In the
context of the first bullet point, this means that the unbonded atoms with unpaired electrons are
at a higher energy state than the bonded atoms with shared electrons. As the bonds form, energy
must be released to the environment.
G. Bond configurations for key biological elements
1.carbon, nitrogen, oxygen, and hydrogen form strong covalent bonds
a. Carbon: tetrahedral
Notice the tetrahedral shape of the carbon bonds.
b. Nitrogen: trigonal pyramidal
c. Oxygen: bent
The presence of two electron pairs in O (for example) constrain the position of the
shared electrons - thus characteristic bond angles are formed.
The bond angles for H2O gives rise to the polar nature of the water molecule
2.The number of bonds formed depends on the number of unshared electrons (also called the
valence of an atom)
3.Covalent bonding is the sharing of electrons between atoms to fill the outer shell
4.Each line represents an electron pair and so each bonded configuration will have 8 electrons in
the outer shell.