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Biological Molecules
All living things are composed of organic compounds. Generally, organic compounds are distinguished
from inorganic compounds by the presence of both carbon and hydrogen. We are referred to as carbonbased life forms, as is all life on earth. This means that carbon is a component of most of the chemical
molecules that make up living organisms on this planet.
Why is carbon so ubiquitous in nature? Carbon's participation in organic chemistry is probably due to its
relatively unique chemical bonding properties. These properties allow carbon to participate in the formation
of an incredibly wide variety of chemical compounds and electron configurations. Carbon is also a
relatively small, non-bulky atom so it can share electrons easily with other atoms.
Carbon, atomic number six, has six electrons. Two are in the first electron shell and four are in the second
electron shell. Carbon must share four electrons with other atoms to fill its outermost electron shell and
attain a stable configuration. Carbon atoms can share electrons with a wide variety of elements also
commonly found in organic compounds, the most notable being other carbon atoms, hydrogen atoms and
oxygen atoms. As a matter of fact, the simplest organic molecules are defined as being comprised of only
carbon and hydrogen, and are therefore referred to as hydrocarbons.
Hydrocarbons are non-polar, hydrophobic compounds. The term hydrophobic comes from the Latin roots
"hydro" (water) and "phobia" (fear). Literally speaking, a hydrophobic compound is afraid of water. The
term non-polar is often used in conjunction with the term hydrophobic, because those compounds that have
no charges on them will not mix with polar water. A non-polar compound repels a polar solvent and
collects together in a film on top of the solvent, or forms a layer on the bottom of the container. Most oils,
waxes, and fat compounds are hydrocarbons, as are the fossil fuels gasoline, kerosene, and similar
compounds. Just think of how well these compounds mix with water and you'll easily grasp the concept of
hydrophobicity.
Since we have introduced the concept of hydrophobicity we should discuss its complement, hydrophilicity.
Hydrophilic comes from the Latin roots "hydro" (water) and "philia" (love). Hydrophilic compounds love
water, and mix with it easily. These compounds are polar, and so dissolve easily in the polar solvent water.
Figure 1. Structural formulas of some simple hydrocarbons.
Methane CH4
Ethane C2H6
Propane C3H8
Ethylene C2H4
Now that you have seen the structures associated with the bonds around carbon, let's discuss how carbon
can form so many different compounds. Carbon always needs to share four electrons to fill its outermost
electron shell. Each straight line extending from the carbon in the diagrams represents one electron carbon
is sharing with another atom. In turn, that atom shares one of its electrons with carbon, forming a covalent
bond. Each atom involved in the covalent bond has essentially gained an electron. When carbon shares two
electrons with another carbon or another atom a double covalent bond is formed. Two straight lines
extending from the carbon to its electron-sharing partner represent a double bond. All structural formulas
use the same characters to represent bonds. One line equals one shared electron from carbon, two lines
equals two shared electrons, and three lines equals three shared electrons. These are called single bonds,
double bonds, and triple bonds, respectively. Single and double bonds are the most common and single
bonds are the most stable (least likely to react with other molecules). Carbon is not the only element that
can form double bonds, as you will see when you review the structural formulas of other compounds.
Now that you have some information about carbon and simple organic compounds, we must consider some
of the other elements essential to more complex organic compounds. While the simplest organic
compounds consist of carbon and hydrogen, many organic compounds also include one or more of the
following elements:
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phosphorus
sulfur
oxygen
nitrogen
Not all complex organic compounds contain every one of these elements. For example, sulfur is a
component of protein but is never a component of nucleic acid. Scientists have capitalized on this fact to
differentiate between these two major biological molecules. Historically, the presence of phosphorus was
used to determine that nucleic acid, and not protein, was the biological molecule of heredity!
The Major Classes of Biological Molecules
Now that we have introduced two groups of biological molecules, let us discuss all four major groups of
biological molecules:
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Proteins
Nucleic Acids
Carbohydrates
Lipids
These four types of biological molecules compose all life on earth.
Proteins have an incredible variety of functions in living organisms. The functions of proteins include but
are not limited to:
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acting as biological catalysts
forming structural parts of organisms
participating in cell signal and recognition factors
acting as molecules of immunity
Nucleic Acids consist of two distinct, but closely related chemical forms: deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA). The main functions of these biomolecules include the storage of all heritable
information of all organisms on earth and the conversion of this information into proteins.
Carbohydrates are the major source of food and the major form of energy for most living organisms.
When carbohydrates combine together to form polymers they can function as long term food storage
molecules, as protective coverings for cells and organisms, as the main structural support for land plants
and constituents of many cells and their contents.
Lipids are the major constituents of all membranes in all cells. They also serve as food storage molecules.
This class of biological molecules includes the hydrophobic fats, oils and waxes.
Often times students have difficulty remembering the four major classes of biological molecules, so I have
a way to help. To recall the four major classes of biological molecules I want you to think of lunch at a
hamburger joint. No endorsements intended! Take a hamburger, fries, and a milkshake and you have all the
components of the four major classes of biological molecules.
Of all four classes which do you think is most abundant in this meal?
If you guessed LIPIDS you would be right! The hamburger is full of fat, and processors add fat to the
hamburger bun. Mayonnaise is oil and egg yolk, which is mostly fat. Milk contains fat (if your shake has
any milk product in it), and fat is added to nondairy shakes. As for the fries, we all know why they are
called fries!
Okay - we know there are plenty of lipids, but where do the rest of the biological molecules come in?
The hamburger bun is made from wheat flour, which is full of starch, a carbohydrate. The sugar in your
shake is the disaccharide sucrose, which is also a carbohydrate. As a matter of fact, the lettuce, onion and
tomato on that burger all contain carbohydrates.
Meat is composed of muscle tissue, and muscle tissue is a structural form of protein. Also most of the
formerly living things that we eat have some form of protein in them: wheat, milk, potatoes, and so on.
All cells contain DNA and RNA, except mature mammalian red blood cells, so DNA and RNA can be
found in all organic matter. The lettuce, onion, and tomato contain nucleic acid, and the hamburger meat
contains cow DNA.
Biological molecules: Structure and Function
Figure 2 shows the structural formula of a particular type of lipid (a phospholipid) which is the major
component of cell membranes. Please notice the long hydrocarbon chains at one end of the molecule. This,
as you should now realize, is a non-polar, hydrophobic, hydrocarbon structure. This part of the molecule is
often referred to as the hydrophobic tail.
At the opposite end of the molecule you will see carbons attached to oxygen, nitrogen and phosphorus.
These components make this end of the phospholipid hydrophilic and therefore water-soluble. This end of
the phospholipid is called the hydrophilic head. The dual hydrophobic and hydrophilic nature of this
phospholipid is essential to the structure of all cell membranes.
Figure 2, below. The
Structural Formula of a
Phospholipids will spontaneously form membranes in water because of their hydrophobic
and hydrophilic ends. As hydrophobic elements try to avoid the polar water molecules they
attract other hydrophobic molecules to them, excluding the water molecules. Hydrophobic
forces are very important to both membrane and protein structure, and therefore are very
important to the functions of these biomolecules. The force that comes from the
hydrophobic attraction for other hydrophobic molecules and the repulsion of water is as
essential to the processes of life as chemical bonds.
Imagine millions of these lipid molecules dumped into aqueous surroundings. Their
hydrophobic nature causes them to aggregate with all the hydrophobic tails clustered
together and all the hydrophilic heads oriented toward the water-based medium. If this
phospholipid cluster occurs in a single layer as seen in Figure 3, then a structure called a
micelle is formed. If this occurs in a double layer as is seen in Figure 4, a bilipid layer
membrane is formed. The bilipid layer membrane is the primary structure of all cells.
Because the function of membranes is to either exclude or retain components solubilized in
aqueous solutions, you can see that lipids are structurally well suited for this role.
Figure 3. A micelle and bilipid layer.
Phospholipid Molecule.
Carbohydrates are a class of biomolecules composed of carbon, hydrogen and oxygen. They can be referred
to as hydrated skeletons of carbon. Basically, carbohydrates are carbons covalently bonded to each other
and covalently bonded to oxygens and hydrogens. The best way to understand carbohydrate structure is to
examine the linear and cyclic structures of glucose. Glucose (C6H12O6) is the major food source for most
cells.
Figure 4. The linear and cyclic structural formulas of glucose.
Not only is the glucose monomer the major source of energy for organisms, but it also has many polymeric
forms. These include starch, the long-term glucose food storage molecule; and cellulose, the major
structural support molecule in plants and chitin and a major component of animal exoskeletons. Monomer
actually means "single unit," from the Latin "mono" (one) and "mer" (unit). Many chemical molecules exist
as single units and may also chemically combine in a long string of repeating monomeric units called
polymers. You've certainly heard of polyester - this is the polymer made of repeating ester units.
Just as artificial polymers are formed through the bonding of monomers, glucose monomers can covalently
bond together to form naturally occurring biological polymers. Glucose can actually form several different
polymers, as mentioned previously, which are quite different in their characteristics. For example, starch
and cellulose, both polymers of glucose, have quite different properties. Starch is easily broken down by
organisms into the single glucose monomer and then taken up by cells for use as an energy source.
Cellulose, however, resists digestion and breakdown by all organisms except a few unusual microbes. That
is why the cellulose in plants is known as fiber, or the indigestible portion of plants. Fiber is still healthful
to eat in moderate quantities because it facilitates the passage of materials through the digestive system.
Polymerization is an essential aspect of three of the four major biological molecules, so it is very important
to understand this concept. Before we continue, lets review how monomers of biological molecules bond
together to form polymers.
In the cases of carbohydrate, protein, and nucleic acid, polymers are formed through the chemical reaction
called a dehydration reaction. A dehydration reaction can take place when the oxygen and hydrogen on one
end of a molecule combine with a hydrogen on another molecule. When these monomers come together
under the appropriate conditions, an oxygen and two hydrogens are lost from the two molecules and a
covalent bond is formed between the two monomers. The byproduct of this reaction is water, formed by the
oxygen and two hydrogens that were removed from the monomeric units. In a sense, the monomers are
now dehydrated, because they have lost water. As the bond formation is continued between several more
monomers, a polymer or multiunit structure is formed.
The dehydration reaction is a very common reaction inside cells. The companion reaction to the
dehydration reaction is the hydrolysis reaction. This is exactly opposite of what occurs in dehydration. In
the hydrolysis reaction a molecule of water is added across the covalent bond, breaking the bond and
adding the oxygen and hydrogens back on the ends of the molecules. Remember, what is built up in the cell
must be able to be broken down eventually. In this self-instructional you will be able to see examples of
dehydration reactions between monomers of carbohydrates, proteins, and nucleic acids.
Figure 5. The dehydration reaction between glucose monomers to form amylose, a simple form of starch.
Proteins
Proteins are composed of repeating monomeric units called amino acids. These monomers are named for
the presence of the functional groups common to all amino acids, the amine group at one end of the
molecule and the carboxylic acid group at the other. The amine functional group is NH2 and the carboxylic
acid functional group is COOH. Although there are 20 different amino acids that compose all proteins, all
amino acids have the amine and carboxylic acid ends. The ends of the amino acid monomer are essential in
the formation of bonds between amino acids. The bond that links amino acids together is called the peptide
bond, as seen below in Figure 6. Because of the peptide bond formation between all amino acids, the
polymeric form of amino acids is called a polypeptide. Most people use the terms polypeptide and protein
interchangeably; however, the term protein implies a functional, three-dimensional molecule while a
polypeptide is simply a string of amino acids bonded together.
The 20 essential amino acids are quite different from each other. Biochemists usually categorize groups of
amino acids together according to the types of functional characteristics they exhibit. These groups include
the charged, or ionizable, amino acids; the non-polar amino acids; the polar, uncharged, amino acids; and
those with unique structural properties. The amino acids can be categorized in many different ways but the
grouping itself is insignificant. The real significance in the structure of amino acids resides in the ability of
the chemical groups on different amino acids to impart very important structural and functional information
into the protein that they form.
All of the proteins in living systems perform essential functions for organisms, and the functions of proteins
are defined by the characteristics of the amino acids that compose them. In particular, the sequence of
amino acids in a protein determines the function of that protein. This explains how there can be seemingly
limitless types of proteins from a mere 20 different amino acids.
Compare two polypeptides: one composed of a string of 99 glycine amino acids and a final asparagine
amino acid on the end. The other composed of a string of 98 glycine amino acids, with one asparagine
amino acid in the next position, and then a final glycine on the end. Are these two polypeptides different?
Absolutely! One might make a functional protein and the other may not. Change the amino acid sequence
of any polypeptide or protein and the polypeptide or protein structure changes.
For example, consider the genetic condition called sickle cell anemia. People who have this condition make
a hemoglobin protein (the oxygen carrying protein molecule of red blood cells) that has one different amino
acid from normal hemoglobin. One charged aspartic acid amino acid is replaced with an uncharged glycine
amino acid. This amino acid replacement results in a drastic alteration in the structure and function of the
hemoglobin protein. The sickle cell hemoglobin protein actually precipitates out of solution under low
oxygen conditions and causes the red blood cell to become sickle shaped. This, as you may imagine, has
devastating effects upon individuals who have only this type of hemoglobin and usually results in a greatly
shortened life span. Never underestimate the power of the sequence of amino acids, for it determines the
structure and function of all proteins.
Figure 6. Two glycine amino acids combining through the formation of a peptide bond to form a dipeptide.
Nucleic Acids
Nucleic Acids are truly the biomolecules that define life. You may think that this is a rather startling
statement when one considers the power of proteins; however, the information for the manufacture of all
proteins - indeed for all biological molecules - resides in the nucleic acid molecule.
Nucleic acids are polymers as are proteins and carbohydrates. The monomeric units of nucleic acids are
called nucleotides. Nucleotides are made up of three parts covalently bonded together:
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a ribose, which is a five carbon sugar
a phosphate functional group comprised of one phosphorus and four oxygens
one of four possible nitrogenous bases, which may be either a purine or pyrimidine
Each nucleotide is identical except for the specific nitrogenous base that is covalently bonded to the #1
carbon of ribose.
There are two main types of nucleic acid: deoxyribonucleic acid (DNA), and ribonucleic acid (RNA).
These two types differ from each other in that the ribose of DNA lacks an oxygen on the #2 carbon, and the
nitrogenous base thymine is replaced by uracil in RNA. DNA is normally double-stranded, or consists of
two polymers wound up together, while RNA is normally single-stranded. RNA's function in the cell is to
carry small pieces of information to various regions of the cell, while DNA functions as a storage for all
genetic information.
Figure 7. Structural formula of one complete nucleotide found in DNA and one complete nucleotide found
in RNA for comparison.
When the nucleotide monomers of nucleic acids covalently bond together through a dehydration reaction, a
special kind of bond, called a phosphodiester bond, is formed.
Figure 8. Three nucleotides covalently bonded together through their phosphodiester bonds.
The four different bases of DNA are shown below in Figure 10.
Figure 9. The purines, Adenine and Guanine and the pyrimidines Cytosine and Thymine, as well as uracil.
The double-stranded structure of DNA is due to hydrogen bonds that form between the bases on one strand
of DNA and the bases on a different strand.
The hydrogen bond, although one of the weakest chemical bonds, is absolutely essential to the structure
and function of nucleic acids and proteins. The potential for hydrogen bond formation arises when two
atoms are bonded together that have very different electronegativities. In the case of the hydrogen bond,
hydrogen is the electropositive element developing a partial positive charge. Oxygen or nitrogen are both
electronegative elements, and develop a partial negative charge. In nucleic acids, a hydrogen on one
nitrogenous base will form a hydrogen bond with either an oxygen or nitrogen on another nitrogenous base.
Hydrogen bonding occurs between bases on opposite strands. Adenine and Thymine (or Uracil) hydrogen
bond together, as do Cytosine and Guanine. Hydrogen bonding cannot occur properly in any other
combination of bases. The A and T bases share two hydrogen bonds, while C and G share three hydrogen
bonds.
Figure 10. Hydrogen bonds formed between A and T or C and G.
The ability of the bases on one molecule of DNA to hydrogen bond to another molecule of DNA or RNA is
called complementarity. This ability is the single most important feature of nucleic acid. Complementarity
allows DNA to replicate or duplicate itself, and to be transcribed, or rewritten, in the RNA format. RNA
travels through the cell to the organelles that translate its sequence of bases into the sequence of amino
acids making up proteins. Complementarity also allows certain types of RNA molecules to fold up into 3dimensional structures necessary for protein translation and a variety of cellular and regulatory processes.
Base Pairing Rules:
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Adenine pairs with thymine: A-T.
Guanine pairs with cytosine: G-C.
In RNA, where thymine has been replaced by the nitrogenous base uracil, the base-pairing rules
do not change. Uracil also pairs with adenine.
The sequence of the amino acids in a protein is critically important to the structure and thus the function of
a protein, and protein sequence is ultimately determined by DNA sequence. Therefore the linear sequence
of bases in DNA determines the linear sequence of the amino acids in a protein. Change the base sequence
of a DNA molecule and you will alter the amino acid sequence in the protein molecule obtained from that
DNA sequence. The two critical features of nucleic acid function are the importance of the sequence of
nucleotides, and complementarity, or the base pairing rules.