Organic Chemistry, Biochemistry

Introduction

Organic molecules are molecules that contain carbon and hydrogen.

All living things contain these organic molecules: carbohydrates, lipids, proteins,
and nucleic acids. These molecules are often called macromolecules because they
may be very large, containing thousands of carbon and hydrogen atoms and because
they are typically composed of many smaller molecules bonded together. These four
macromolecules will be discussed in the second half of this chapter..

Carbon

Carbon has four electrons in its outer shell.

Hydrogen has one electron and one proton.

Carbon can bond by covalent bonds with as many as 4 other atoms.

The diagram above shows a molecule of methane. Lines can be used to represent
bonds in the shorthand formula seen in the upper right side of the diagram.

Carbon can also form double covalent (shares 2 pairs of electrons) or triple covalent
bonds (shares 3 pairs).

Carbon can form 4 covalent bonds because it has 4 electrons in its outer shell. It can
form the following number of bonds. Notice that in each case below, there is a total of
four bonds.

 4 single bonds
 two double bonds
 one double bond and two single bonds
 one triple and one single bond

Long chains of carbon atoms are common. The chains may be branched or form
rings.
Hydrophilic and Hydrophobic

Polar and ionic molecules have positive and negative charges and are therefore
attracted to water molecules because water molecules are also polar. They are said to
be hydrophilic because they interact with (dissolve in) water by forming hydrogen
bonds.

Nonpolar molecules are hydrophobic (means "water fearing"). They do not dissolve
in water.

Nonpolar molecules are hydrophobic.

Polar and ionic molecules are hydrophilic.

Portions of large molecules may be hydrophobic and other portions of the same
molecule may be hydrophilic.
Functional Groups

Organic molecules may have functional groups attached. A functional group is a

group of atoms of a particular arrangement that gives the entire molecule certain
characteristics. Functional groups are named according to the composition of the
group. For example, COOH is a carboxyl group.

Organic chemists use the letter "R" to indicate an organic molecule. For example, the
diagram below can represent a carboxylic acid. The "R" can be any organic molecule.

Some functional groups are polar and others can ionize. For example, if the hydrogen
ion is removed from the COOH group, the oxygen will retain both of the electrons it
shared with the hydrogen and will have a negative charge. The hydrogen that is
removed leaves behind its electron and is now a hydrogen ion (proton).

If polar or ionizing functional groups are attached to hydrophobic molecules, the

molecule may become hydrophilic due to the functional group. Some ionizing
functional groups are: -COOH, -OH, -CO, and -NH2.

Some important functional groups are shown below.

Structure
Name
Non-ionized Ionized
Hydroxyl

Carboxyl
Amino

Phosphate

Sulfhydry
l

Aldehyde

Ketone

Isomers

Different molecules that are composed of the same number and kinds of atoms are
called isomers. Glucose and fructose (shown below) are both C6H12O6 but the atoms
are are arranged differently in each molecule. Three kinds of isomers are described
below.

Structural isomers differ in their overall construction as shown above for glucose and
fructose.
Geometric isomers maintain the same carbon skeleton but a double bond occurs
between carbon atoms. The location of atoms bonded to a double-bonded carbon atom
differs. The two molecules below are geometric isomers because the double bond
cannot rotate. If the bond between the two carbon atoms below were a single bond,
they would not be isomers because atoms attached by single bonds can rotate. The
carbon atoms would be able to rotate from one orientation to another if the bond were
a single bond.

Enantiomers are molecules that are mirror images of each other. The molecules shown
below are enantiomers.

Condensation

In order to bond the two molecules shown below together, you must first remove a
hydrogen from each one. This is necessary because carbon has a maximum of 4 bonds
and hydrogen can have only one.

In biological systems, macromolecules are often formed by removing H from one

atom and OH from the other (see the diagram below). The H and the OH combine to
form water. Small molecules (monomers) are therefore joined to build
macromolecules by the removal of water. The diagram below shows that sucrose (a
sugar) can be produced by a condensation reaction of glucose and fructose.
Sucrose:

This is called a condensation or dehydration reaction.

Energy is required to form the bond.

Hydrolysis

This is a type of reaction in which a macromolecule is broken down into smaller

molecules.

It is the reverse of condensation (above).

Macromolecules and Monomers

Many of the common large biological molecules (macromolecules) are synthesized

from simpler building blocks (monomers). Each of the types of molecules listed in the
table are discussed below.

Example of a Macromolecule Monomer

polysaccharide (complex carbohydrate) monosaccharide (simple sugar)
fat (a lipid) glycerol, fatty acid
Protein amino acid
nucleic acid Nucleotide

Proteins

Importance of proteins

Some important functions of proteins are listed below.

enzymes (chemical reactions)

hormones
storage (egg whites of birds, reptiles; seeds)
transport (hemoglobin)
contractile (muscle)
protective (antibodies)
membrane proteins (receptors, membrane transport, antigens)
structural
toxins (botulism, diphtheria)

Enzymes

Enzymes are proteins that speed up the rate of chemical reactions.

Example:

The presence of an enzyme in the chemical reaction diagrammed below causes

hypothetical chemicals A and B to react, producing C.

Proteins are able to function as enzymes due to their shape. For example, enzyme
molecules are shaped like the reactants, allowing the reactants to bind closely with the
enzyme. The diagrams below show that the enzyme matches the shape of the substrate
molecules. The enzyme is therefore able to hold the substrate molecules in the correct
orientation needed for the chemical reaction to proceed. The enzyme does not
participate in the reaction and is not changed by the reaction.
Amino Acids

Amino acids are the building blocks of proteins.

Twenty of the amino acids are used to make protein. Each has a carboxyl
group (COOH) and an amino group (NH2) attached to the same carbon atom, called
the alpha carbon.

Each amino acid is different and therefore has its own unique properties.

Some amino acids are hydrophobic, others hydrophilic. The carboxyl or amino group
may ionize (forming NH3+ or COO-). The "R" group of some amino acids is nonpolar
and the "R" group of some others is polar or it ionizes.

Amino acids are joined together by a peptide bond. It is formed as a result of

a condensation reaction between the amino group of one amino acid and the carboxyl
group of another.

Click here to view a web page which shows an animation of the formation of a
peptide bond.

Polypeptides

A short chain of amino acids bonded together is called a peptide. A longer chain of
many amino acids, typically 50 or more, is referred to as a polypeptide. The complete
product, consisting of one or more polypeptides, is called a protein.

There is unequal sharing of electrons in a peptide bond. The O and the N are negative
and the H is positive.
Levels of structure

The large number of charged atoms in a polypeptide chain facilitates hydrogen

bonding within the molecule, causing it to fold into a specific 3-dimensional shape.

The 3-dimensional shape is important in the activity of a protein.

Primary Structure

Primary structure refers to the sequence of amino acids found in a protein. The
following is the primary structure of one of the polypeptide chains of hemoglobin.

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gluvalglyglyglualaleuglyargleuleuvalvaltyr pro try thrglnargphephegluserphegly asp
leuserthr pro asp alaval met glyasn pro lysvallysala his glylyslysvalleuglyalapheser
asp glyleuala his leu asp aspleulysglythrphealathrleuserglnleu his cys asp lysleu his
val asp pro gluasnpheargleuleuglyasnvalleuvalcysvalleuala his hispheglylysgluphethr
pro provalglnalaalatyrglnlysvalvalalaglyvalala asp alaleuala his lystyr his

Secondary structure

The amino and carboxyl groups of the polypeptide backbone are capable of hydrogen-
bonding with each other. This bonding produces two common kinds of shapes seen in
protein molecules- coils , called alpha helices, and beta sheets. A single polypeptide
may contain many of these helices and sheets. Hydrogen bonding between amino and
carboxyl groups that produces alpha helices and beta sheets is referred to as secondary
structure.

Tertiary structure

Tertiary structure refers to the overall 3-dimensional shape of the polypeptide chain.

Hydrophobic interactions with water molecules are important in creating and

stabilizing the structure of proteins. Hydrophobic (nonpolar) amino acids aggregate to
produce areas of the protein that are out of contact with water molecules.

Hydrophilic (polar and ionized) amino acids form hydrogen bonds with water
molecules due to the polar nature of the water molecule.

Hydrogen bonds and ionic bonds form between R groups to help shape the
polypeptide chain.
Disulfide bonds are covalent bonds between sulfur atoms in the R groups of two
different amino acids. These bonds are very important in maintaining the tertiary
structure of some proteins.

The shape of a protein is typically described as being globular or fibrous. Globular

proteins contain both coils and sheets.

Quaternary structure

Some proteins contain two or more polypeptide chains that associate to form a single
protein. These proteins have quaternary structure. For example, hemoglobin
contains four polypeptide chains.

Other Kinds of Proteins

Simple proteins contain only amino acids. Conjugated proteins contain other kinds of
molecules. For example, glycoproteins contain carbohydrates, nucleoproteins contain
nucleic acids, and lipoproteinscontain lipids.

Denaturation

Denaturation occurs when the normal bonding patterns are disturbed causing the
shape of the protein to change. This can be caused by changes in temperature, pH, or
salt concentration. For example, acid causes milk to curdle and heat (cooking) causes
egg whites to coagulate because the proteins within them denature.

If the protein is not severely denatured, it may regain its normal structure.

Nucleic Acids

DNA

DNA (deoxyribonucleic acid) is the genetic material. An important function of DNA

is top store information regarding the sequence of amino acids in each of the body’s
proteins. This "list" of amino acid sequences is needed when proteins are synthesized.
Before protein can be synthesized, the instructions in DNA must first be copied to
another type of nucleic acid called messenger RNA.
Structure of DNA

Nucleic acids are composed of units called nucleotides, which are linked together to
form a larger molecule. Each nucleotide contains a base, a sugar, and a phosphate
group. The sugar is deoxyribose (DNA) or ribose (RNA). The bases of DNA are
adenine, guanine, cytosine, and thymine. Notice that the carbon atoms in one of the
nucleotides diagrammed below have been numbered.

The diagram below shows how nucleotides are joined together to form a "chain" of
nucleotides.

DNA is composed of two strands in which the bases of one strand are hydrogen-
bonded to the bases of the other. The sugar-phosphate groups form the outer part of
the molecule while the bases are oriented to the center.
The strands are twisted forming a configuration that is often referred to as a double
helix. The photograph below is of a model of DNA.
Complimentary base pairing

The adenine of one strand is always hydrogen-bonded to a thymine on the other.

Similarly, Guanine is always paired with Cytosine.

A-T
G-C

Antiparallel

The end of a single strand that has the phosphate group is called the 5’ end. The other
end is the 3’ end.

The two strands of a DNA molecule run in opposite directions. Note the 5’ and 3’
ends of each strand in the diagram.
RNA

RNA (ribonucleic acid) is similar to DNA and is involved in the synthesis of

polypeptides and proteins as discussed above.

RNA is single-stranded as shown below.

RNA contains the base Uracil instead of Thymine.

The table below lists differences between DNA and RNA.

DNA RNA
# Strands 2 1 (see diagram below)
Sugar deoxyribose ribose
Bases A, T, G, C A, U, G, C

Codons

One strand of DNA (the anti-sense strand) is used as a template to produce a single
strand of mRNA. The bases in the mRNA strand are opposite (complimentary) to the
bases in the DNA template strand; it resembles the sense strand of DNA except that
the base thymine is replaced by uracil. The mRNA contains three-letter (three-base)
codes used to determine the sequence of amino acids in the polypeptide that it codes
for. For example, in the diagram below, GUG is the code for valine. The sequence of
codes in DNA therefore determines the sequence of amino acids in the protein.
Each three-letter code in mRNA is a codon. It is the code for one amino acid.

Click here for details on how information is stored in DNA.

ATP

ATP (adenosine triphosphate) is a nucleotide that is used in energetic reactions for

temporary energy storage.

Energy is stored in the phosphate bonds of ATP. When ATP breaks down to form
ADP and Pi, energy is released. Normally, cells use the energy stored in ATP by
breaking one of the phosphate bonds, producing ADP. Energy is required to convert
ADP + Pi back to ATP.

ATP is continually produced and consumed as illustrated below.

Carbohydrates

The general formula for carbohydrates is (CH2O)n.

Monosaccharides

Monosaccharides are simple sugars, having 3 to 7 carbon atoms. They can be bonded
together to form polysaccharides.

The names of most sugars end with the letters ose.

Example: Glucose, fructose, and galactose are monosaccharides; their structural

formula is C6H12O6.

Glucose and other kinds of sugars may be linear molecules as shown below but in
aqueous solution they become a ring form.

There are two isomers of the ring form of glucose. They differ in the location of the
OH group on the number 1 carbon atom (in red below).
The number 1 carbon atom (numbered in red above) of the linear form of glucose is
attached to the oxygen on the number 5 carbon atom.

Simple sugars store energy for cells. Details concerning energy storage and release by
glucose are in the chapter on cellular respiration.

Cells also use simple sugars to construct other kinds of organic molecules.

Disaccharides

Disaccharides are composed of 2 monosaccharides joined together by a condensation

reaction.

Examples:

Sucrose (table sugar) is composed of glucose and fructose.

Like glucose, sucrose stores energy. Plants synthesize sucrose to transport to

nonphotosynthetic parts of the plant.

Lactose is found in milk. It is formed when glucose bonds to galactose.

The digestion of complex carbohydrates (polysaccharides) typically

involves hydrolysis reactions in which the molecules are broken down to maltose, a
disaccharide. Maltose is then further broken down to produce two glucose molecules.

Polysaccharides

Monosaccharides may be bonded together to form long chains called polysaccharides.

Ten or more monosaccharides may be bonded together to form long chains called
polysaccharides. The chains are typically composed of hundreds of
monosaccharaides.
Starch and Glycogen

Starch and glycogen are polysaccharides that function to store energy. They are
composed of glucose monomers bonded together producing long chains.

Animals and some bacteria store extra carbohydrates as glycogen.

In animals, glycogen is stored in the liver and muscle cells. Between meals, the liver
breaks down glycogen to glucose in order to keep the concentration of glucoses in the
blood stable. After meals, as glucose levels in the blood rise, it is removed from and
stored as glycogen.

Plants and some algae produce starch to store carbohydrates.

Amylopectin is a form of starch that is very similar to glycogen. It is branched but

glycogen has more branches. Amylose is a form of starch that is unbranched.

Below: Glycogen or Starch

Cellulose and Chitin

Cellulose and Chitin are polysaccharides that function to support and protect the
organism. The cell walls of plants are composed of cellulose. The cell walls
of fungi and the exoskeleton of arthropods are composed of chitin.

Cellulose is composed of beta-glucose monomers; starch and glycogen are composed

of alpha-glucose. The bond orientation between the glucose subunits of starch and
glycogen allows the polymers to form compact spirals. The monomers of cellulose
and chitin are bonded together in such a way that the molecule is straight and
unbranched. The molecule remains straight because every other glucose is twisted to
an upside-down position compared to the two monomers on each side. Cellulose
fibers are composed of long parallel chains of these molecules. The chains are
attached to each other by hydrogen bonds between the hydroxyl groups of adjacent
molecules.
Below: Cellulose

The glucose monomers of chitin (N-acetyl glucosamine) have a side chain containing
nitrogen.

Cellulose is the most abundant carbohydrate on earth. Cotton and wood are composed
mostly of cellulose. They are the remains of plant cell walls.

Digestibility of Cellulose and Chitin

Humans and most animals do not have the necessary enzymes needed to break the
linkages of cellulose or chitin.

Some bacteria and some fungi produce enzymes that digest cellulose. Some animals
have microorganisms in their gut that digest cellulose for them.

Fiber is cellulose, an important component of the human diet.

Lipids

Lipids are compounds that are insoluble in water but soluble in nonpolar solvents.

Lipids are also an important component of cell membranes.

Some lipids function in long-term energy storage. One gram of fat stores more than
twice as much energy as one gram of carbohydrate.

Fats and Oils (Triglycerides)

Fats and oils are composed of fatty acids and glycerol.

Fatty acids have a long hydrocarbon (carbon and hydrogen) chain with
a carboxyl (acid) group. The chains usually contain 16 to 18 carbons.

Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts with 3 fatty acids to form
a triglyceride or fat molecule.
Fats are nonpolar and therefore they do not dissolve in water.

Saturated and Unsaturated Fat

Saturated fatty acids have no double bonds between carbons. Unsaturated fatty acids
have at least one double bond. Each double bonds produces a "bend" in the molecule.

Double bonds produce a bend in the fatty acid molecule (see diagram above).
Molecules with many of these bends cannot be packed as closely together as straight
molecules, so these fats are less dense. As a result, triglycerides composed of
unsaturated fatty acids melt at lower temperatures than those with saturated fatty
acids. For example, butter contains more saturated fat than corn oil, and is a solid at
room temperature while corn oil is a liquid.
Phospholipids

Phospholipids have a structure like a triglyceride (see diagram above), but contain a
phosphate group in place of the third fatty acid. The phosphate group is polar and
therefore capable of interacting with water molecules.

Phospholipids spontaneously form a bilayer in a watery environment. They arrange

themselves so that the polar heads are oriented toward the water and the fatty acid
tails are oriented toward the inside of the bilayer (see the diagram below).

In general, nonpolar molecules do not interact with polar molecules. This can be seen
when oil (nonpolar) is mixed with water (polar). Polar molecules interact with other
polar molecules and ions. For example table salt (ionic) dissolves in water (polar).

The bilayer arrangement shown below enables the nonpolar fatty acid tails to remain
together, avoiding the water. The polar phosphate groups are oriented toward the
water.

Membranes that surround cells and surround many of the structures within cells are
primarily phospholipid bilayers.
Steroids

Steroids have a backbone of 4 carbon rings.

Cholesterol (see diagram above) is the precursor of several other steroids, including
several hormones. It is also an important component of cell membranes.

Saturated fats and cholesterol in the diet can lead to deposits of fatty materials on the
linings of the blood vessels.

Waxes

Waxes are composed of a long-chain fatty acid bonded to a long-chain alcohol

They form protective coverings for plants and animals (plant surface, animal ears).

Review

Use the symbols below to draw a disaccharide, polysaccharide, triglyceride,

phospholipid, polypeptide, and DNA. Use short, straight lines to represent covalent
bonds.