*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
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
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
The higher the concentration of H3O+ , the more acidic the solution.
As H3O+ rises, the concentration oOH- falls, according to the equilibrium
equation for water: [H3O+] [OH-] = 1.0 x 10^(-14).
The concentration of H+ is expressed using a logarithmic scale called the
pH scale, as illustrated in Panel 2-2 (pp.108-109).
H2O has a ph of 7; Neutral.
Base: it accepts protons so as to lower
the concentration of H3O+ ions, and thereby raise the concentration of hydroxyl
A base can either combine with protons directly or form hydroxyl
ions that immediately combine with protons to produce H2O.
Thus, sodium hydroxide (NaOH) is basic (or alkaline) because it dissociates in aqueous
to form Na+ ions and OH- ions.
Other bases, especially important in living
cells, contain NH2 groups. These groups directly take up a proton from water:
NH2 + H2O -+ -(NH3+) + OH
*Four types of non-covalent bonds bring atoms closer together which are: Hydrogen
bonds, Electrostatic Attractions( ionic bonds ), an der Waals Attractions and
* pg 54- in depth definitions.
A cell is formed from a Carbon Compounds
Amino acids are the basic units of proteins.
amino acids have one defining property, they all possess a carboxylic acid group and an
amino group, both linked to a single carbon
atom called the (sigma bonded)carbon (Figure 2-23) .
The function of amino acids is to make protein; which are polymers of amino acids joined
from head to tail in long chains that fold into three dimensional shapes that are unique to
each type of protein.
The covalent linkage between two adjacent amino acids in a protein chain forms an amide
which is called a peptide bond.
Regardless of the specific amino acids from which it
is made, the polypeptide has an amino (NH2) group at one end (its N-terminus)
and a carboxyl (COOH) group at its other end (its C-terminus).This gives it a definite
Directionality; a structural polarity.
Each of the 20 amino acids found commonly in proteins has a different side
chain attached to the o-carbon atom (see Panel 3-1, pp. 128-129).
All organisms have the same 20 amino acids, how these specific amino acids came to be is
however, unknown but serve a highly important role.
Like sugars all amino acids exist as optical isomers in D and L forms, except for glycine.