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Lecture 3

BIOL 3113 Lecture Notes - Lecture 3: Non-Covalent Interactions, Cytosine, Monosaccharide


Department
BIOL
Course Code
BIOL 3113
Professor
Barbara S
Lecture
3

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*notes
*!!! important
Composition of the cell
92 naturally occurring elements
Living organisms made of only small selection of elements
Carbon, Hydrogen, Nitrogen and Oxygen - make up 96.5% of an organisms weight
Chemical Components of the Cell
Properties of materials from which living cells are made depend on which atoms they
contain and the way these atoms are linked together to form molecules
Atoms are held together in molecules by chemical bonds
Two types:
Covalent
*involve sharing of electrons between atoms
*strong bonds
Non-covalent
*attractions between atoms that do not involve sharing of electrons
*weak bonds
Covalent Bonds
Two atoms share a pair of electrons
*When one atom forms covalent bonds with several others - multiple bonds have definite
orientations in space relative to one another
*Specific bond angles, lengths and energies depend on atoms involved in molecule formation
Single and double covalent bonds
Single - sharing of 2 electrons (1 from each atom)
-allows the rotation of one part of molecule relative to another around the bond
axis
Double - sharing of more than 2 electrons
-shorter and stronger than single
-no rotation, more rigid than single - it influences the 3-D shape of molecules
The pair of electrons is often shared unequally

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One atom attracts the shared electrons more than other polar covalent bond
positive charge concentrated toward one end of the molecule (positive pole) and
negative toward the other end (negative pole)
Polar bonds - allow molecules to interact through electrical forces extremely important
in cell biology
-Large molecules with multiple polar groups have a pattern of partial (+) and (-) charges
on their surface attraction of molecule with a complementary set of charges
surfaces will stick to each other
Types of Noncovalent bonds
Ionic Bond
caused by attraction between positively and negatively charged atoms (ions) formed by
giving electrons to - or accepting electrons from - another atom
cation = positively charged atom or molecule
anion = negatively charged atom or molecule
Hydrogen Bond
caused typically by attraction between a positively charged hydrogen atom held in one
molecule by a polar covalent bond and another atom (typically N or O) that is partially
negatively charged in another polar molecule
Water - each molecule forms hydrogen bonds with 2 other water molecules network
responsible for surface tension
Can also occur between different parts of a single large molecule special shapes
(molecule folding)
van der Waals Attraction
attraction between atoms caused by fluctuating electrical charges
Hydrophobic Interaction
attraction between non-polar atoms and molecules in aqueous solution caused by their
inability to form hydrogen bonds with water molecules
Hydrophobic molecules are insoluble in water and tend to self-associate to minimize the
disruption of hydrogen bonds among water molecules (minimum energy state: weak)
Ex: cholesterol
Bond strength
Table
Covalent: 0.15 nm, strength 90 kcal/mole; in water. => short thus strong strength
Ionice: 0,25nm, 3
Hydrogen: 0.30 nm, 1
Van der waals: 0.35nm, 0.1

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*measured by the amount of energy needed to break a bond
Average thermal motion of atoms = 0.8 kcal/mole
Single non-covalent bond is not strong enough to hold two atoms together for very long -
but they are important in situations where molecules have to associate and dissociate
readily to carry out their functions in the cell
Because non-covalent bonds are weak, it takes a large number of bonds to achieve a
stable molecular association
Because non-covalent bonds act over short distances, the number of bonds formed
depends on the degree to which two molecules or different parts of the same molecule fit
together ("goodness of fit")
*weak bond=won’t stay bonded together
Water and Solubility
Life evolved in an aqueous environment and cells are made up predominately of water.
Therefore, the properties of water are very important in determining the chemistry of
cells
*life still depends on water
*Over 80% of mass of liing organisms is water
*Almost all chemical rxn of life take place in aq solution
Properties of Water
*Water molecules are polar
-Electrons spend more time associated with the oxygen atom, making it slightly negative
and less time associated with the hydrogen atoms, making them relatively positive
*Water molecules are transiently attracted to one another by hydrogen bonds water
molecules are very cohesive
*Cohesiveness of water responsible for:
-high surface tension
-solubility properties of other molecules
Solubility in Aqueous Solution
*The ability of other molecules to dissolve in aqueous solution is determined by how they
interact with water molecules.
*Molecules that attract water molecules through electrical charge effects are soluble in
water
*Molecules that disrupt hydrogen bonding between water molecules are insoluble
Soluble molecules = hydrophilic ("water-loving")
*Ionic substances
attract the polar end of water molecules with the opposite charge and surround
themselves with a shell of water molecules
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