BASIC CHEMISTRY OF ATOMS AND MOLECULES

Vocabulary Terms

 
acid 
amino acid 
atom 
atomic nucleus 
base 

Ca 
carbohydrate 
Cl 
dehydration synthesis 
DNA 
electrolyte 
electrons 
element 
fat 
fatty acid 
glucose 
glycerol 
glycogen 

hydrophillic 
hydration sphere 
hydrogen bond 
hydrophobic 
ion 
ionic bond 

lipid 
micelles 
molecule
monomer 

Na 
neutrons 
non-polar covalent bond 
non-polar molecules and atoms 
nucleic acid 
nucleotide 

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.

____    ____    ____    ____    ____    ____    ____    ____





 

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.)

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.

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.

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.


 


 

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.

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 a phosphate 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 phospholipid molecule. Micelle: a sphere of phospholipid molecules surrounded by polar water molecules (notice how the hydrophobic tails are toward the inside). Phospholipid Bilayer: phospholipid molecules organized into a double layer (notice how the hydrophobic tails are toward the inside).

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.

 

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 a peptide 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.

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).  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

 
A three dimensional model of the double stranded 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.

 


 

 

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?