BIO130H1 Chapter Notes -Molecular Motor, Guanine, Ribulose

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12 Apr 2012
Pgs. 51-54.
*An atom often behaves as if it has a fixed radius.
For more clarity atoms are represented schematically as line structures or ball stick models,
however the Space-filing model gives us a more accurate representation
Of molecular structure. In these models, a solid envelope represents
The radius of the electron cloud at which strong repulsive forces prevent a closer
Approach of any second, non-bonded atom-the so-called van der Waals radius
For an atom.
At slightly greater distances any two atoms will experience a weak attractive force AKA Van
der Waals attraction.
*fig 2-11, 2-12
As a result of these two forces , there is a distance at which repulsive and attractive
Forces precisely balance to produce an energy minimum in each atom's interaction
with an atom of a second, non-bonded element.
*Water is the most Abundant substance in cells
Water accounts for about 70% of the cells body weight, and most intracellular
Hydrophilic: Water loving, dissolve in water and are polar ions (carry a + or - charge). Ex,
Alcohols, DNA RNA & most Proteins.
When positively charged hydrogen atoms bond with the negatively charged oxygen atoms,
they form a weak bond called a hydrogen bond.
These bonds are weak and can be broken easily by thermal motion.
Each of the hydrogen's on the water molecule can produce hydrogen forces with two other
water molecules; producing a network of hydrogen bonds that are continually being broken
and formed.
It’s because of these hydrogen bonds that gives water its properties at different temperatures.(
liquid at room temp. solid at freezing point and gas at boiling point)
Hydrophobic: water hating, are uncharged and form few or no hydrogen
bonds, and so do not dissolve in water. Hydrocarbons are an important example
(See Panel 2-I, pp. 106-107).
In these molecules the H atoms are covalently
linked to C atoms by a largely non-polar bond. Because the H atoms have almost
no net positive charge, they cannot form effective hydrogen bonds to other
*Some polar molecules are both acids and bases: water
Proton: H+
Hydronium ion: H30+
Acids: Substances that release protons to form H3O+ when they dissolve in water.
In other words, it donates protons to a water molecule so as to raise the concentration of
H3O+ ions.
The higher the concentration of H3O+, the more acidic the
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