Molecules of Life
Most of the molecules of life are carbon based. Carbon based molecules are
termed organic compounds and are unique to living systems with the exception of
CO2 and carbides. Carbon is necessary for life. Carbon atoms never lose nor gain
electrons. They always shares electrons to form covalent bonds. Carbon is able to
form 4 covalent bonds with other elements or with itself since it has 4 electrons in
its outermost shell. This makes each carbon atom a connecting point from which
another molecule can branch in four directions. Since carbon can bind to itself it
has the capacity to construct endless numbers of carbon skeletons varying in size
and branching patterns.
The simplest organic compounds are hydrocarbons. These organic molecules are
comprised of a C skeleton bounded by 4 H atoms. The simplest hydrocarbon is
CH4 or methane. It is one of the most abundant hydrocarbons; it is found in natural
gas made by bacteria and in the digestive tract of cows. Larger hydrocarbons are
found in gasoline. Hydrocarbons are important body fuels. They make up fat
molecules. They are non-polar due to the nonpolar C-H bond.
The chain of carbons in an organic molecule is called a carbon skeleton. The
skeleton can be branched or unbranched. It may include double or single bonds
and may be straight or arranged in a ring form. Each organic molecule has a unique
3-D shape.Properties of organic molecules depend on both the carbon skeleton and
on the atoms attached to that skeleton. Groups of atoms participating in chemical
reactions are called functional groups.
Five functional groups are especially important in the body. OH- (hydroxyl), NH2
(amino), COOH (carboxyl), OPO3-2 (phosphate) and C=O (carbonyl). Any one
compound may have 2 or more of these. These functional groups are found on the
four main classes of molecules: carbohydrates, proteins, lipids and nucleic acids.
COOH & NH2 are functional groups found on amino acids which form proteins.
Hydroxyl groups are found on alcohols. Carboxyl groups can be found on
carboxylic acids such as acetic acid. Sugars contain both a carbonyl group and
several hydroxyl groups and phosphate groups are found on nucleic acids.
Macromolecules
The 4 main classes of molecules are carbohydrates, lipids, proteins and nucleic
acids. These are macromolecules and are comprised of many identical or similar
molecular units called monomers strung together. Cells link monomers in anabolic
reactions by dehydration synthesis, a chemical reaction which removes water.
Macromolecules are broken down into their constituent monomers by adding
water; catabolic reactions involving hydrolysis.
Carbohydrates
Carbohydrates are made with C, H, and O in a 1:2:1 ratio and may contain
nitrogen, phosphate and/or sulfur. Carbohydrates include substances from small
sugar molecules to large polysaccharides such as starches. Monomers for
carbohydrates are monosaccharides. 2-10 monosaccharides form an
oligosaccharide. Hundreds of monosaccharides combine to form a polysaccharide.
All carbohydrates are hydrophilic or water loving. Larger molecules are however
less soluble in water.
Monosaccharides are simple sugars. They consist of a single chain or ring of 3-7
carbons. Since the ratio is 1:2:1 The formula: (CH2O)n should yield any
carbohydrate. Monosaccharides are named for the number of carbons they contain.
5 carbon compounds are called pentoses and six are hexoses. Glucose contains 6
carbons and therefore it is a hexose. Its formula is C6H1206 and is the most
important metabolic fuel in the body. Glucose is broken downATP + CO2.
Fructose is another 6 carbon monosaccharide which can form a straight chain or a
ring. Notice that is has the same formula as glucose or C6H1206. Fructose and
glucose are isomers-chemical compounds with the same molecular formula but
with elements arranged in different configurations. Galactose is also an isomer of
glucose & fructose. Separate enzymes and reaction sequences control the
breakdown and synthesis of each.
Disaccharides are double sugars. A covalent bond is found between the hydroxyl
groups of two simple sugars. Physiologically important disaccharides include
sucrose, lactose and maltose. Sucrose is found in sugar cane and sugar beets.
Glucose + fructosesucrose + H20. Lactose is found exclusively in the milk of
mammals. It is a disaccharide of galactose & glucose. Maltose is the major
degradation product of starch. It is composed of 2 glucose monomers.
Disaccharides are too large to pass through cell membranes. They must be broken
down into their constituent parts by hydrolysis. Sucrose + H20 glucose +
fructose. Polysaccharides are complex carbohydrates. Dehydration synthesis
reactions add more monosaccharides polysaccharides. Most carbohydrates in
nature are in this form. Polysaccharides are fairly insoluble and make perfect
storage molecules. Only 2 are of major importance to the body: starch and
glycogen. Both are polymers of glucose. They differ in the amount of branching.
Glycogen is the major form of stored carbohydrate in animal liver and muscle
cells. It is highly branched at about every 8-10 residues. Starch is the major form
of stored carbohydrate in plants. Its structure is identical to glycogen but has much
less branching at every 20-30 residues. Cellulose is another polysaccharide found
in plants. It is the most abundant compound on earth but cannot be digested by
humans.
Lipids
Lipids also known as fat contain mostly C & H in a 1:2 ratio. They also contain
oxygen but less than carbohydrates. Lipids often have N, S and phosphorous.
Lipids are hydrophobic and therefore do not dissolve in water. They are soluble in
organic solvents. Lipids include neutral fats, phospholipids and steroids.
Physiologically important lipids have 4 major functions: they serve as structural
components of biological membranes. Cholesterol, phospholipids and glycolipids
also help form and maintain intracellular structures. Lipids are important energy
reserves-providing 2X as much energy as carbohydrates. Hormones and vitamins
are a type of lipid called steroids. Various steroid hormones regulate tissue
metabolism and mineral balance and are responsible for secondary sex
characteristics. Finally lipophilic bile acids are lipids important for lipid
solubilization. Lipids are composed of fatty acids and glycerol (an alcohol). Fatty
acids are long-chain hydrocarbon molecules. These hydrocarbon chains make
lipids nonpolar and therefore insoluble in water. Fat synthesis involves attaching 3
fatty acid chains to one glycerol by dehydration synthesis producing triglycerides.
Glycerol is always the same; fatty acid composition varies. The length of a neutral
fat’s fatty acid chains and its degree of saturation determine how solid a fat is at
room temperature. Fatty acids with no carbon to carbon double bonds allow less H
to be attached to the carbon skeleton. They are called saturated. Those with double
bonds are termed unsaturated. Monounsaturated fats have one unsaturated bond;
polyunsaturated fats have multiple unsaturated bonds. Double bonds make for
lower melting points. Short chains or the presence of unsaturated fatty acids
makes a fat liquid at room temperature.
Saturated fatty acids with less than 8 carbons are also liquid at physiological
temperature; those containing more than 10 are solid. Longer chains and saturated
fatty acids are more common in animal fat and are solid at room temperature. Fatty
acids can be acquired in the diet or made by the body. 2 highly unsaturated fatty
acids linoleic and linolenic acid cannot be synthesized in body. These fatty acids
are termed essential and must be provided by the diet.Hydrolysis breaks
triglycerides fatty acid + glycerol. Lipids are the primary energy source in times
of need. When supply > than demands for energystored as fat in adipose cells.
Triglycerides are important for insulation comprising a layer of fat under the skin
which insulates and prevents heat loss to the environment and fat deposits around
organs cushions them from injury. Steroids are large lipid molecules with their
carbon skeleton bent into 4 rings. The most important steroid is cholesterol.
Cholesterol is obtained from animal products in the diet. It can also be made by the
body. It is absolutely essential for life. It is a component of cell membranes. It is
the raw material for Vitamin D, steroid hormones and bile salt synthesis. Without
cholesterol there would be no steroid hormones such as estrogen and testosterone
and therefore no reproduction, without corticosteroids we would die.
Proteins
Proteins are the most abundant organic compounds in the human body and may be
the most important. Proteins serve several major functions. They provide support
for cells, tissues and organs and create a 3-D framework for the body. Contractile
proteins allow for movement via muscle contractions. Transport proteins carry
insoluble lipids, respiratory gases & minerals in the blood. Proteins serve as
buffers; helping to prevent dangerous pH changes. Enzymes are proteins important
in metabolic regulation; needed to speed the rate of chemical reactions. Protein
hormones coordinate, control and influence metabolic activities of nearly every
cell and finally proteins are important for defense. Skin, hair, & nails protect
underlying tissues from the environment, antibodies protect us from disease and
clotting proteins protect from us bleeding out.
Proteins are composed of C, H, O, N, and small amounts of S and sometimes
phosphorous. The monomer for proteins is amino acids. 1-7 amino acids form a
peptide; up to 100 form a polypeptide & more than 100 comprise a protein.
20 amino acids are relevant to mammalian proteins. Amino acids (excluding
proline) contain a carboxylic acid-COOH and an amino-NH2 or amine group.
These functional groups are attached to the same carbon atom. Distinct R-groups,
distinguish one amino acid from another. The R group also attaches to the same
carbon (except glycine whose R-group is hydrogen). Each amino acid is
distinguished by its particular R-group. 2 broad classes of amino acids are based
upon whether the R-group is hydrophobic or hydrophilic. Hydrophobic repel
aqueous environments and thus reside predominantly in the interior of proteins.
Hydrophilic amino acids which interact with aqueous environments and often form
H-bonds are found predominantly on the exterior of proteins. Dehydration
synthesis combines amino acids creating covalent bonds between the COOH of
one amino acid and the amino group of another. This covalent bond is termed a
peptide bond. 2 amino acids combined is a dipeptide and three is a tripeptide.
Each protein contains a unique sequence of amino acids. This long polypeptide
chain interacts with itself and sometimes with one or more polypeptide chains to
form a functional protein with a 3-D shape. The shape is essential for a protein to
accomplish its job in the body. Shape determines function. Proteins whose job is to
fill in a space (active site) on another molecule are globular in shape; whereas
those that make up something like muscles or tendons are fibrous or long and thin
in shape.
There are four levels of protein structure. The primary structure is the unique
sequence of amino acids which it contains. This sequence is determined by genes.
The secondary structure of a protein refers to the bonds that form between
different parts of a polypeptide chain. H bonding within the chain produces either
coiling of the protein into a spiral form called an alpha helix or folding the protein
into a flat pleated sheet. Which shape develops depends on the sequence of amino
acids and where H bonding occurs.Tertiary structure is the overall 3-D shape of a
polypeptide. This is the result of the polypeptide chain interacting with
surrounding water molecules and to a lesser degree between R groups in different
parts of the molecule. Most tertiary structures are either fibrous or globular.
Quaternary structure is found in proteins that are comprised of two or more
polypeptide chains. This structure is due to the interaction between the individual
polypeptide chains that form the protein. Structure determines function. The shape
of a protein allows it to carry out its specific duties. The primary and secondary
structures form spontaneously once the protein is made. 3o and 4o shapes depend on
environmental characteristics such as ionic composition, pH and temperature. A
non homeostatic change in any one of these will denature a protein. Denaturation
causes a protein to lose shape and with the loss of shape comes the inability to
function properly.
Nucleic Acids
Nucleic acids are one of most important metabolites. They provide directions for
building proteins. There are 2 main types: RNA and DNA. DNA or
deoxyribonucleic acid contains genetic information that is inherited from our
parents. DNA is unique to each of us and is found in the nucleus of every one of
our cells. DNA consists of long stretches of nucleotides (the monomer for nucleic
acids) in which specific stretches code for amino acid sequences of proteins. This
code is translated by RNA or ribonucleic acid.
Nucleotides are the largest, organic molecules in the body. They are made of C, H,
O, N, and phosphorous. Nucleic acids have 3 parts: a nitrogen containing base, a
pentose sugar (ribose for RNA and deoxyribose for DNA) and a phosphate group.
There are 5 major nitrogen containing bases. DNA contains adenine, guanine,
thymine, cytosine and RNA has uracil instead of thymine. These bases are referred
to by their first initial or: A, G, T, C and U. Genetic information is written in a
code using these bases.
Polymers of nucleotides are linked by dehydration synthesis. In this process the
phosphate group of one nucleotide bonds to the sugar of the next monomer. The
end result is a repeating sugar-phosphate backbone.
DNA takes a double helix form made from two polynucleotide chains wrapped
around one another. The nitrogenous bases from the two chains are found in the
center of the helix. Nitrogenous bases pair up in a precise way. A with T and C
with G. therefore if you know the sequence of one strand you should be able to
figure out the sequence of the other. The 2 strands separate to regenerate a
complementary or new strand. Individual chains are held together by hydrogen
bonds between base pairs. Each sequence of three bases codes for a specific amino
acid.
Nucleic acids exist in mono-, di-, & tri-phosphorylated forms. An example of a
monophosphorylated nucleic acid is adenosine or adenosine-5'-monophosphate
which is often abbreviated to AMP. Di- and tri-phosphorylated forms of adenosine
are abbreviated ADP and ATP. Di- and tri-phosphates are linked by acid anhydride
bonds is a process called phosphorylation in which a PO4 group is attached. These
bonds are high energy bonds meaning they have a high potential to transfer
phosphates to other molecules. It is this property that results in their involvement
in group transfer reactions. ADP + PO4-3 + energy ATP + H2O. ATP is the
energy currency of all cells and runs all of our functions.
RNA is a single polynucleotide chain made of the same nitrogen containing bases
as DNA except it contains uracil instead of thymine so A pairs with U in RNA
molecules. RNA contains the pentose sugar ribose while DNA is comprised of 2'deoxy form of ribose. There are 3 types of RNA: Messenger mRNA, transfer tRNA
and ribosomal rRNA.