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Atoms, Molecules, and Chemistry
What are atoms?
1. Atoms are the fundamental units of matter.
2. They are composed of smaller parts:
a. Nucleus
i. Protons (positively charged)
ii. Neutrons (have no charge)
b. Electrons
The different components of atoms
determine the type and “behavior” of
the elements…
Atoms, Molecules, and Chemistry
Atoms, Molecules, and Chemistry
Atoms, Molecules, and Chemistry
What are molecules?
The smallest unit of a substance made up of two or more atoms bound to
each other.
Molecules can form by both ionic as well as covalent bonds…
Atoms, Molecules, and Chemistry
Ionic Bonds:
In case of ionic bonds, atoms first either
loose or gain an electron, and become
either positively or negatively charged.
Note that only certain types of atoms can do
this. The ability of an atom to become
positively or negatively charged (i.e. become
an ion), as well as the level of the charge,
depends on the characteristics of the atoms,
particularly the number of electrons on their
outer shells…
Once ions are formed, positive and negative
charges attract, creating individual molecules.
In case of molecules formed by ionic bonds,
many of these molecules can also come
together to form more organized crystal
structures / salts…
Atoms, Molecules, and Chemistry
Covalent Bonds:
In case of covalent bonds, atoms share electrons
on their outermost shells/orbits. This creates a
physically more stable condition.
Again, the ability to form covalent bonds, the number
of the bonds, etc., depends on various characteristics
of the atoms.
Remember that covalent bonds are very strong…
Atoms, Molecules, and Chemistry
Water is a very special molecule, important to all biological systems.
Water is a polar molecule (part of the
molecule is slightly positively charged
and the other side is slightly negatively
This polarity allows for formation
of weak bonds between water (and
other charged) molecules… these
bonds are referred to as hydrogen bonds.
The polarity and ability to form
hydrogen bonds gives water some
very special characteristics, many
of which are essential for maintaining
life on earth as we know it…
Atoms, Molecules, and Chemistry
Water can be a great solvent for both salts and certain biological molecules…
How do you think this works?
Water as solvent of salts
Water as solvent for organic molecules
Atoms, Molecules, and Chemistry
The hydrogen bonds formed by water molecules also give water a
certain “stickiness” (very scientific eh?)… we therefore say that water has high cohesion.
Cohesion on the surface of the water creates surface tension (resistance to being broken).
These characteristics allow water to be carried to the top of trees, or for some organisms
to float, swim, or “walk” on water.
Atoms, Molecules, and Chemistry
The hydrogen bonding also allows for water to remain liquid on earth…
Without hydrogen bonding, water (molecular weight 18), would freeze at
-100 degrees C, and would boil at –80 degrees C (instead of 0 and 100 degrees).
A similar molecule (methane, molecular weight 16) freezes at –183 degrees C,
Boils at –162 degrees C.
This simple characteristic allows for life on earth as we know it!!
A lot more to water… take marine bio and we’ll talk more about it there!!!
Biological Molecules
Typically, we think of biological molecules as carbon based, organic molecules.
Carbon is very important, as it can form single, double, or triple covalent bonds
with a number of other atoms, creating large, complex, yet stable structures.
In Biology 3, we will discuss four major groups of biological molecules:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Biological Molecules
Carbohydrates – small, water-soluble sugars, capable of making chains of
sugar molecules.
Can form monosaccharides, disaccharides, or polysaccharides.
Generally take on the approximate molecular formula: (CH2O)n
Note however that there are exceptions to this…
1. Energy source / storage
(remember that biological bonds have energy
that organisms can break down and use)
2. Structural
(this is particularly the case in plants)
Biological Molecules
Two sugar molecules can bond to each other by a dehydration process, thus
creating a disaccharide… glucose and fructose for example can join each other
And form sucrose…
Biological Molecules
Larger number of sugar molecules can join each other to form large
polysaccharides such as starch….
Biological Molecules
Carbohydrates can be very important at the structural level… particularly in case of plants.
Biological Molecules
2 major characteristics of lipids:
1. Lipids have large region of just hydrogen and carbon (no oxygen)
2. They are very hydrophobic and insoluble in water (because of 1)
Major functions of lipids:
1. Energy storage
2. Water-proofing
3. Cellular membranes
4. hormones
Biological Molecules
Different types of Lipids:
1. Oils, fats, and waxes
Just contain C, H, O and are very hydrophobic
2. Phospholipids
*like oils, but also contain
phosphorous and nitrogen…
*very important in forming
cellular membranes…
*have hydrophilic and
hydrophobic parts…
3. Steroids
form fused rings…
many work as hormones,
some are
involved in regulating
fluidity of cellular
Biological Molecules
Proteins are made up of chains of amino acids. There are 20 common amino acids,
each with their own characteristics… the total number of amino acids, as well as
the type of amino acids determine the protein form and function.
Some examples of amino acids:
Biological Molecules
All amino acids have a carboxyl group and an amino group. Amino acids join each
Other by a dehydration process involving these two groups.
Chains of amino acids form peptides. Some of the larger peptides may function
as proteins. (i.e. all proteins are peptides, but not all peptides are proteins…)
Biological Molecules
Protein Functions:
Function is however dependent on structure!
Biological Molecules
Proteins – relationship between structure and function
Primary structure –
The sequence of the amino acids
Secondary structure Formation of helixes and sheets
by the chain of amino acids
Tertiary structure –
Folding of the molecule based
on hydrophobic, hydrophilic,
and other interactions.
Quaternary structure –
Binding and interacting of
different peptide/protein units
to form one functional unit
All these combine to determine the form and function
of the protein… these same characteristics may also be
involved in regulating the protein function
Biological Molecules
Nucleic Acids
Nucleic acids are made up of individual or chains of nucleotides.
Nucleotides are typically made up of
1. A five carbon sugar group (ribose or deoxyribose)
2. A phosphate group
3. A nitrogen containing base
Biological Molecules
Nucleic Acids
Nucleic acids include: DNA and RNA, as well as
intracellular messengers, energy carriers, and coenzymes
Biological Molecules
Table 3-2 from text.
Page 40.