Download basic chemistry of atoms and molecules

BASIC CHEMISTRY OF ATOMS AND MOLECULES
Vocabulary Terms – PLEASE DEFINE EACH TERM AFTER YOU COMPLETE THE TUTORIAL
acid
amino acid
atom
atomic nucleus
base
C
Ca
carbohydrate
Cl
dehydration synthesis
DNA
electrolyte
electrons
element
fat
fatty acid
glucose
glycerol
glycogen
H
hydrophillic
hydration sphere
hydrogen bond
hydrophobic
ion
ionic bond
K
lipid
micelles
molecule
monomer
N
Na
neutrons
non-polar covalent bond
non-polar molecules and atoms
nucleic acid
nucleotide
O
oil
peptide bond
periodic table of elements
pH scale
phosphate-nitrogen group
phospholipid bilayer
phospholipid
polar covalent bond
polar molecules and atoms
polymer
polypeptide
primary structure
protein
protons
quaternary structure
R-group
RNA
secondary structure
starch
tertiary structure
Introduction
Most of the substances you interact with in every day life are compounds of different elements. The
chemical properties of an element do not change, even if you divide the element down to a single
atom. Wood is a compound made mostly from the elements carbon, nitrogen, and hydrogen. The
air you breathe is a mixture of nitrogen, oxygen, and carbon dioxide. Even carbon dioxide is a
compound, built from the elements carbon and oxygen. The smallest piece of an element you can
have, that still has the chemical properties of the element, is an atom.
The periodic table of elements is a list of all the elements scientists have found. The smallest atoms
in the periodic table are at the upper left of the table. As you move to the right and down the
periodic table, the atoms become larger and larger. You do not have to memorize the entire periodic
table in this course, but you will become familiar with a number of the elements important to
biologic systems. Carbon, nitrogen, oxygen, and hydrogen are the most common elements in living
organisms. Sodium, potassium, calcium, and chloride are salts that will be important to many of the
processes we study this semester. You should memorize the chemical abbreviations for these
elements.
C = carbon
Ca = calcium
Cl = chlorine
H = hydrogen
K = potassium
N = nitrogen
Na = sodium
O = oxygen
Use the periodic table of elements to organize the eight elements listed above from the smallest atom
to the largest atom. COMPLETE THIS ACTIVITY
____ ____ ____ ____ ____ ____ ____ ____
In order to understand how an organism works, you will need to understand interactions at the level
of atoms, interactions at the level of molecules and cells, and interactions at the level of organs and
organ systems. In the next part of the tutorial, you will explore some of levels of complexity we have
discussed in more detail. Once you understand the structure of atoms, molecules, and cells, we can
begin discussing the physiology of an organism.
Atoms
Atoms are made of three types of subatomic
particles, protons, neutrons, and electrons. Each of
these particles is actually made up of even smaller
particles, called quarks, but that is beyond the
scope of this course. Protons and neutrons form
the nucleus of an atom (atomic nucleus), and the
electrons form a cloud as they move around the
nucleus. Keep in mind that the atoms pictured here
are not drawn to scale. Most of an atom is empty
space between the nucleus and the outer
electrons.
Protons have a positive electric charge. The number of protons in the nucleus of an atom determines
the identity of that element. An atom of carbon always has six protons. If there is any different
number of protons in the nucleus, then the atom is not carbon. An atom of nitrogen has seven
protons in its nucleus, an atom of oxygen has eight protons in its nucleus, and an atom of hydrogen
just has one proton in its nucleus. The elements of the periodic table are listed in the order of
protons found in the nucleus of each atom. Hydrogen is the first element listed with just one proton,
helium (He) is the second with two protons, lithium (Li) is the third with three protons, etc.
Neutrons have no electric charge (they are neutral). The numbers of neutrons in the nucleus do not
change the identity of an atom, but they do change the mass. Atoms of carbon usually have six
protons and six neutrons in the nucleus, but sometimes there are six protons and eight
neutrons. This second element is still carbon (there are six protons), but it is an isotope of carbon
called carbon-14. Isotopes are just versions of an element with a different number of
neutrons. Some isotopes are unstable and emit radiation.
Electrons have a negative electric charge equal in magnitude to the positive electric charge carried
by protons. However, electrons are tiny compared to protons and neutrons, so electrons do not have
an important effect on the mass of an atom.
If an atom has an equal number of protons and electrons, then the atom has no overall charge – it is
electrically neutral.
If you add electrons to an atom, so that there are more electrons than protons, then the atom has a
negative electric charge.
If you remove electrons from an atom, so that there are fewer electrons than protons, then the atom
has a positive electric charge.
If an atom has any sort of charge (positive or negative), then the atom is called an ion. Sodium,
potassium, calcium, and hydrogen are some ions that play an important role in physiology. (Note:
molecules can be ions too.)
FILL IN THE BLANKS
If an atom has 11 protons and 10 electrons, then it has an electric charge of +1.
So...
If an atom has 17 protons and 16 electrons, then it has an electric charge of _______.
If an atom has 20 protons and 18 electrons, then it has an electric charge of _______.
If an atom has 6 protons and 6 electrons, then it has an electric charge of _______.
The atoms of helium used to fill balloons each have two protons, two neutrons, and two
electrons. Draw a simple picture of a helium atom. Be sure to label the protons, neutrons, electrons,
and nucleus. On your drawing, make a note of the charge associated with the protons, the charge
associated with the electrons, and the charge associated with the neutrons.
What is the overall charge of a helium atom?
If it was possible to remove one proton from a helium atom, what atom would you have then?
Molecules
Atoms can be bound together to form molecules.
Two hydrogen atoms bonded to an oxygen atom forms a water molecule.
A sodium atom bonded to a chloride atom forms the salt molecule, sodium chloride.
Six carbon atoms, twelve hydrogen atoms, and six oxygen atoms bonded together form a
carbohydrate molecule like the simple sugar; glucose.
There are three different types of chemical bonds which hold atoms together to form molecules.
Covalent bonds
In a covalent bond, pairs of electrons are shared
between neighboring atoms. If only one pair of
electrons is shared, then it is a single covalent
bond. Double and triple covalent bonds are
possible when two or three pairs of electrons are
shared between neighboring atoms.
In a covalent bond, the electrons may or may not be shared equally between two atoms. If the
electrons are shared unequally, then the atom they spend the most time near develops a negative
charge, and the atom the atom they spend the least time near develops a positive charge. This is
called a polar covalent bond. The word “polar”, means that two things are opposite. In this case,
one atom of the molecule has a negative charge and another atom of the molecule has a positive
charge. Water molecules contain polar covalent bonds. The oxygen atom contains more protons
than the hydrogen atoms, so the oxygen atom attracts electrons more strongly than the single proton
in a hydrogen atom. A negative charge develops around the oxygen atom, and positive charges
develop around the hydrogen atoms. Water molecules are charged and are examples of polar
molecules. The charges on a water molecule help give water its chemical properties.
If the electrons in a covalent bond are shared equally between two atoms, then neither atom is more
positively charged or more negatively charged than the other. This is called a non-polar covalent
bond.
Ionic bonds
In an ionic bond, no electrons are shared between atoms. One atom has a positive charge because it
has one fewer electrons than protons (such as sodium), and the other atom has a negative charge
because it has one more electrons than protons (such as chlorine). The two atoms are bonded
together because their opposite electric charges create an attraction between the atoms. When
discussing electric charges, opposites really do attract. Something with a positive charge is always
attracted to something with a negative charge. Conversely, two positive charges will repel each
other, as will two negative charges. The sodium chloride crystals you sprinkle on your food from a
salt shaker are held together by ionic bonds. Ionic bonds are not as strong as covalent bonds.
Hydrogen Bonds
Hydrogen bonds do not create molecules, but rather, weakly bond
neighboring molecules. As noted above, hydrogen atoms can form
polar covalent bonds, and have a positive charge. A hydrogen bond
exists when the positively charged hydrogen on one molecule is
attracted to a negatively charged atom (such as an oxygen or
nitrogen atom) on a different molecule. Water molecules form
hydrogen bonds with one another because the oxygen atoms forms
polar covalent bonds with its hydrogen atoms. In the figure at the
right, the negatively charged oxygen atoms are noted by a and
the positively charged hydrogen atoms are noted by a . Notice
that the hydrogen bonds form between the positive hydrogen atom
on one water molecule and the negatively charged oxygen atom on
a different water molecule. Hydrogen bonds are the reason that it
takes a lot of energy to boil water.
FILL IN THE BLANKS
Electrons are shared between atoms in a ____________________ bond.
A weak bond between neighboring molecules is a ____________________ bond.
The attraction between oppositely charged atoms to form a single molecule is an example of a
____________________ bond.
If a molecule has an electric charge, then it is a ___________________ molecule.
Chemistry of Water
Before we begin discussing even larger molecules, you should take some time to consider the
chemistry of water. The preceding sections of this tutorial introduced the following concepts.



Any atom that has an electric charge is called an ion.
Water molecules are polar, which means water molecules have both a negatively
charged portion (the oxygen atom) and a positively charged portion (the hydrogen
atoms).
Things with opposite electric charges are attracted to one another.
Any molecule that becomes an ion when mixed with water is an electrolyte. Table salt (sodium
chloride) is an electrolyte because the ionic bond between the individual sodium and chlorine atoms
breaks in water, releasing sodium ions and chloride ions (the ion form of chlorine is called
“chloride”). Other common ions released by electrolytes include hydrogen, potassium and calcium.
When an ion enters water, water molecules
surround the ion. If it is a positively charged ion,
then the water molecules will turn so that their
negatively charged oxygen atoms are oriented
toward the positive ion (remember, opposite
electric charges attract) as seen on the left. If a
negatively charged ion is mixed in water, then the
water molecules will turn so that their positively
charged hydrogen atoms are oriented toward the
negative ion as seen on the right. The water
molecules actually form a shell around the
ion. This water shell around an ion (which may be
an atom or molecule) is called a hydration
sphere.
Substances that dissolve in water become surrounded by hydration spheres. Any substance that
dissolves in water has some type of charge. If an atom or molecule does not have a charge, then no
hydration spheres can form, and that substance will not dissolve in water. Non-polar substances, like
oils, do not dissolve in water because their atoms and molecules do not carry any charge.
FILL IN THE BLANKS
A positive charge is associated with the __________________ of a water molecule, and a negative
charge is associated with the __________________ a water molecule.
If an ion is dissolved in water, and the hydrogen atoms of the water molecules are oriented toward
the ion, then the ion must have a __________________ charge.
If an ion is dissolved in water, and the oxygen atoms of the water molecules are oriented toward the
ion, then the ion must have a __________________ charge.
Why does oil float on top of water?
Acids, Bases, and pH
Acids and bases are important electrolytes. An electrolyte that releases a
hydrogen ion (H+) in water is an acid. An electrolyte that binds a hydrogen
ion in water is a base. The pH scale is a measure of how much acid or base
is in a solution. The pH scale goes from 0 to 14. pH values below 7 are
acidic, while pH values above 7 are basic (also called alkaline). If a liquid has
a pH equal to 7, it is neutral. The pH of pure water equals 7.
The pH scale shown at the right lists the pH values of a variety of
substances. Blood is slightly alkaline with a pH of 7.40. Other body fluids
have more acidic or more alkaline pH values.
FILL IN THE BLANKS
The pH of pure water is ________.
Acids have a pH value ___________________ 7.
Bases (or alkali) have a pH value ___________________ 7.
What body fluid is closes to neutral?
What is the pH of this fluid?
What body fluid is the most acidic?
What is the pH of this fluid?
What body fluid is the most alkaline?
What is the pH of this fluid?
MONOMERS AND POLYMERS
96% of the matter in living organisms is carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). The
other 4% is calcium (Ca), phosphorous (P), and other trace elements such as sodium (Na), potassium
(K), chloride (Cl), iron (Fe), and iodine (I).
These atoms can be bonded together to form molecules important to the body
called monomers. Monomers are the basic building blocks used to create even
larger molecules called polymers. Some common monomers are glucose,
glycerol and fatty acids, amino acids, and nucleotides. These monomers can
be used to build the four biologically important polymers, which are
carbohydrates, lipids, proteins, and nucleic acids.
List the four most common atoms in a living organism.
Carbohydrates
Carbohydrate polymers are built from monomers of simple sugars such as glucose. Plants use
glucose molecules to build the polymer starch. The figure below illustrates the long spiral chain of
glucose molecules that form starch (each green hexagon is an individual glucose molecule). Only
plants produce starch molecules. Humans and other animals can bond glucose molecules in a
different pattern to form the polymer glycogen. Glycogen is produced in the liver, and stored in your
body cells. The primary function of carbohydrates in your body is to provide your cells with
fuel. Your cells can break down carbohydrate molecules to produce energy that can be used for
growth, reproduction, movement, or any of the hundreds of other things cells do.
ANSWER THE FOLLOWING QUESTIONS
What monomer is used to build the polymer glucagon?
What is the primary function of carbohydrate molecules in your body?
Lipids
There are two types of lipid molecules used by your body: fats and phospholipids. Both lipid
polymers are made by attaching long chains of fatty acid molecules (long chains of carbon atoms
covalently bonded together) to a glycerol molecule (a short chain of 3 carbon atoms covalently
bonded together).
Fats and oils
Fat and oil molecules are made by attaching three fatty acid chains to a glycerol
molecule. Different kinds of fats and oils (animal fat, fish oil, corn oil, olive oil,
palm oil, etc.) contain different kinds of fatty acid molecules. Notice that there
are no “+” signs or “-” signs associated with these molecules. This is because
glycerol and fatty acids are non-polar molecules. Since there are no polar
molecules within fat or oil molecules, these molecules do not dissolve in water
(no hydration sphere can form around the molecule). Fats and oils
are hydrophobic molecules (literally, “water-fearing”) because they do not
dissolve in water.
Phospholipids
Phospholipids are also lipid molecules. Phospholipids begin with a glycerol
molecule backbone with two (instead of three) fatty acids attached. Instead of
a third fatty acid, phospholipids have aphosphate and nitrogen group attached
to the third carbon in the glycerol molecule. Notice that this
phosphate/nitrogen group is a polar molecule (the phosphate carries a negative
charge and the nitrogen carries a positive charge). Remember that polar
molecules can create hydration spheres and dissolve in water (because they
carry a charge, just like water molecules). Substances that can create hydration
spheres are called hydrophilic (water-loving).
The polar phosphate/nitrogen group is called the “head” of the phospholipid
molecule, and the two non-polar fatty acid chains are called the “tails”. The
head of the phospholipid molecule is hydrophilic and the tails are
hydrophobic. When a group of these molecules are tossed into water, they will
form spheres called micelles, where the hydrophobic tails are hidden in the
center of the sphere away from water molecules. Phospholipid molecules will
also form membranes, called a phospholipid bilayer, with the hydrophobic tails
hidden away from water molecules in the center of the bilayer, and the
hydrophilic heads oriented outward and interacting with water molecules.
An easy-to-draw sketch of a
Micelle: a sphere of phospholipid molecules
phospholipid molecule.
surrounded by polar water molecules (notice how the
Phospholipid Bilayer:
phospholipid molecules
hydrophobic tails are toward the inside).
organized into a double layer
(notice how the hydrophobic
tails are toward the inside).
ANSWER THE FOLLOWING QUESTIONS
How are fat and oil molecules the same as phospholipid molecules?
How are fat and oil molecules different than phospholipid molecules?
What portion of a phospholipid molecule is hydrophobic?
What portion of a phospholipid molecule is hydrophilic?
Why can phospholipids interact with water molecules, but fats and oils cannot?
In a lipid bilayer, why do you find the fatty acid chains of the of the phospholipid molecule on the
inside of the bilayer.
Proteins
Proteins are the machinery that make all of life’s processes possible. Every time you move a finger,
think a thought, or blink your eyes, proteins are involved. Every time you your heart beats, you take
a breath, digest a meal, or become aroused, proteins are involved. The function of a protein depends
on its three dimensional shape, and the three dimensional shape of a protein is mostly determined
by the order that the amino acid monomers used to build proteins are strung together.
Proteins are polymers built from amino acids. There are twenty amino
acids that can be used to build proteins. Most proteins do not contain all
twenty amino acids, and some proteins are richer in some amino acids
than others. All twenty amino acids share the same chemical backbone
(shown at the right) of a central carbon bonded to a carboxyl group on one
end and an amino group on the other end. Extending from this central
carbon is an atom or molecule called the R group. The R groups are what
make each of the twenty amino acids distinct from one another. The
twenty different amino acids all have different R groups.
Simple sturcture of an amino acid
The different R groups (pictured in the yellow boxes) have
different chemical properties. For instance, valine and tyrosine
have non-polar R-groups, while arginine, cysteine, and aspartic
acid have polar R groups. Some R groups are acidic, some are
basic, and others are especially useful for creating covalent,
ionic, or hydrogen bonds with other R groups. The final
function of the protein will depend on what amino acids were
used to build the protein and how the R groups of the amino
acids interact.
ANSWER THE FOLLOWING QUESTIONS
The monomers used to build a protein polymer are called ______________________.
Draw a sketch of a simple amino acid.
There are _________ different R groups.
Identify two amino acids that could dissolve easily in water.
If you were building a protein to function in the cell membrane, identify one amino acid you might use
in the fatty acid region of the lipid bilayer.
The amino acids in a protein are connected to one another,
end to end, through a reaction called dehydration
synthesis. During dehydration synthesis, the OH (hydroxyl
molecule) of the carboxyl group on one amino acid is
removed, and a hydrogen atom from the amino group of a
second amino acid is removed. Two things happen as a
result: first, a water molecule is created (OH + H = H2O);
and second, a covalent bond is created between the
carboxyl group of the first amino acid, and the amino group
of the second amino acid. This covalent bond between
amino acids is called apeptide bond. Two amino acids
bonded together are called a “dipeptide” (three amino
acids bonded together are a “tripeptide”, many amino
acids bonded together are called a “polypeptide” –
proteins and polypeptides are the same thing). By bonding
amino acids together, one after the other, you create a
string, or sequence of amino acids. Each amino acid is like
an individual pearl; strung together, they form a protein.
ANSWER THE FOLLOWING QUESTIONS
If a cell bonds four amino acids together, how many water molecules are formed?
Why are proteins sometimes called polypeptides?
Levels of Protein Structure
Before a protein can start functioning in a cell, it must be folded into its final three dimensional
shape. Inside the cell, there are organelles containing proteins that help fold a new protein into its
final shape. There are four levels of organization associated with creating a functional protein. The
four levels of protein structure are primary structure, secondary structure, tertiary structure, and
quaternary structure.
Primary Structure
The primary structure of a protein is simply the linear order
of the individual amino acids used to create the
protein. Remember that there are 20 different amino acid
building blocks that can be used to create a protein. These
can be used in almost any order and number. At this point,
the structure of a protein is no more complicated than the
order of individual beads on a string.
Secondary Structure
The linear chain of amino acids described above can now be
woven into more complex shapes. Hydrogen bonds can
from between the carboxyl groups and amino groups of
different amino acids. These hydrogen bonds can twist and
stabilize the amino acid chain so that it is woven together
into a series of sheets, called a pleated sheet, or so that it is
woven together into a series of spirals, called an alpha helix
(sort of like a slinky). A single chain of amino acids can be
woven into pleated sheets in one area, and alpha helixes in
a different area.
Tertiary Structure
If secondary structure is like a sheet of paper or a slinky,
then tertiary structure is folding that sheet of paper or tying
the slinky into a more complex shape. The tertiary
structure of a protein is stabilized by interactions between
different R groups.
Quaternary Structure
Two or more proteins are associated with one another is
quaternary structure. The protein hemoglobin is a good
example of quaternary structure because it is made from
four separate protein chains.
Proteins serve different functions in a cell. Proteins that have the correct shape to make chemical
reactions happen are called enzymes. Other proteins have a shape that allows them to help a cell
maintain its shape, or help one cell form strong connections with neighboring cells; these proteins
are called structural proteins.
Remember, the function of a protein is determined by its structure. For a protein to work properly, it
must have the correct three dimensional structure. The final structure of a protein depends on the
linear sequence of amino acids (the primary structure).
ANSWER THE FOLLOWING QUESTIONS
When a cell is building a protein, how does the cell know which amino acids belong in which order?
At what level of protein structure could you first see some sort of three dimensional shape (think
about this a little).
What is the difference between tertiary structure and the quaternary structure of a protein?
The following amino acids are strung together…
alanine-valine-serine-glycine
This is an example of _________________________ structure.
Nucleic Acids
Nucleic acids include DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid). DNA and RNA store and transmit the
instructions to build proteins. DNA and RNA are polymers that are
built from monomers called nucleotides. A nucleotide is a
phosphate and sugar molecule connected to a base such as
adenine, guanine, thymine, cytosine, or uracil. A DNA molecule is
a linear sequence of nucleotides. A nucleotide sequence that
serves as the instructions to build one protein is called a
gene. One DNA molecule may have thousands of genes. When
your cells need to build a protein, a copy of the instructions is
copied from DNA to a short strand of RNA (messenger RNA). The
short strand of messenger RNA instructions is then used by other
RNA molecules (ribosomes) to create the primary structure of a
protein.
Nucleotides forming the double
strands of a DNA molecule
When you expose yourself to things that can damage your DNA, such as
chemicals in cigarette smoke, or ultra violet light and other forms of radiation,
you are potentially damaging the instructions to create the primary structure
of your proteins. If a protein has the wrong primary structure, then the
secondary, tertiary, and quaternary structure may be wrong. Since a
protein’s function is dependent on its shape, the protein may no longer be
able to do its job.
You learned earlier that proteins are the machinery which make all of life’s
processes possible. For example, proteins tell your cells when to divide and
produce more cells. If the DNA instructions for a protein controlling cell
division are damaged, then a cell may divide over and over, producing more
and more cells, and become a tumor. Cancer is simply uncontrolled division
of your own body cells caused by damaged DNA.
A three dimensional model of
the double stranded DNA
molecule.
ANSWER THE FOLLOWING QUESTIONS
What polymers contain the coded instructions to make all of the proteins in your body?
What is a gene?
What may happen if the primary structure of a protein is changed?