PassGAMSAT Science eClass 5

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Organic Chemistry Reactions
and Processes

Learning Objectives
After studying this lesson, students should be able to write organic reactions, identify the type of
reaction and reaction mechanism of a given reaction. They should know the basic structure and
function of important biomolecules.
1. Conventions unique to organic chemistry
notation
classification of reagents reaction
mechanisms
2. Addition, substitution, and elimination reactions
addition
substitution
elimination
3. Biological molecules
carbohydrates
lipids proteins
nucleic acids
enzymes

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 CONVENTIONS UNIQUE TO ORGANIC CHEMISTRY
Notation
Most organic chemistry reactions are variations on acid-base reactions, therefore it is important to
be able to identify which compounds are acidic, which are basic, and the relative strengths of
each. That clarifies where the electrons are moving as they form bonds. Organic reactions chiefly
use the Lewis definition for acids and bases, with compounds donating or accepting electrons.

Organic chemists use somewhat different terminology than inorganic chemists when discussing
reactions. Inorganic chemists call the compounds on the left-hand side of the equation reactants,
while organic chemists call them substrates if they contain carbon, and reagents if they don't. On
the right-hand side of the equation, what inorganic chemists lump together as products are
distinguished by organic chemists as the product of interest (the one created from the substrate)
and by-products.

Organic chemists also usually don't write a full, balanced equation; they merely write a
transformation. A transformation is a depiction of the reaction which shows only the substrate(s),
reagent(s), and product(s) of interest. By-products and balancing coefficients are omitted. This can
be a source of confusion to students just beginning organic chemistry after a year of having
balanced equations and the Law of Conservation of Mass drilled into their brains. The fact that the
coefficients and by-products aren't written doesn't mean they're not present; it just means that
they are unimportant (even irrelevant) to the reaction being studied. A transformation can show
the sequence of the reaction if multiple steps are involved or if the reagents must be added in a
certain order. As with inorganic reactions, any specific reaction conditions such as temperature are
written above the reaction arrow. A generic example which shows conditions and a sequence of
steps is given below.

first reagent catalyst reagent second reagent

substrate product
→ → →

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Here's an example of an actual reaction. If the balanced reaction is CH3COCl + H2O → CH3COOH +
HCl, first identify the substrate and product; they will be the ones that contain carbon.

CH3COCl + H2O → CH3COOH + HCl

substrate reagent product by-product

Then, write the transformation:

H2O
CH3COCl → CH3COOH

Classification Of Reagents
As noted above, most organic reactions are Lewis acid-base reactions. Therefore the substrates
and reagents are either acid or base. Reagents can be classified as electrophiles or nucleophiles.
Electrophiles are positively charged while nucleophiles are negatively charged. An electrophilic
reagent is a Lewis acid that reacts with an electron-rich substrate (which is a Lewis base) and
accepts an electron pair from it. A nucleophilic reagent is the opposite. It is a Lewis base that
reacts with an electron-poor Lewis acid substrate and donates an electron pair. (Recall that acids
in inorganic chemistry yield protons, H+, and bases give hydroxyl ions, OH-, in solution).

Electrophiles Nucleophiles
Lewis status acid base
substrate match electron-rich Lewis base electron-poor Lewis acid
action accepts electrons donates electrons
charge positive negative
examples H+, Cl+, Br+, +CH3, BF3, +NO2 -OH, CH3O- CH3CH2O-,

-SH, CH3S-, CH3CH2S-,

-CN, I-, Br-, NH3, -CH3, CH3NH2

Reaction Mechanisms
Reaction mechanisms are descriptions of the steps of the process. They detail the movement of
electrons and the sequence of movement from the base to the acid. Reaction mechanisms differ
from reaction types in that reaction types only describe the end result of what is often a multi-
step process. An analogy from cooking might help you understand it better: A reaction type is
like a menu item, perhaps a steak cooked medium-

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rare accompanied by mushrooms and onions. But how were they cooked? Was the steak grilled,
broiled, or pan-fried? Were the mushrooms and onions sautéed, grilled with the steak (if it was
grilled), roasted, or raw? Was there any kind of sauce? The cooking methods and conditions are
like the reaction mechanisms.

The steps of a reaction may convert one functional group to another, or rearrange the carbon
skeleton of a molecule. The mechanisms show how the electrons flow. Understanding the
mechanisms of a reaction allows you to visualize the structural changes that occur, and ultimately
to be able to predict the outcome of new reactions. There are five general electron- flow
operations (reaction mechanisms).

A heterolytic bond cleavage operation is the breaking of a bond between two atoms. One atom
takes the electron pair and becomes negatively charged, while the other loses the electrons and
becomes positively charged. It is generically represented as:

In a heterogenic bond forming operation, an atom with a pair of nonbonding electrons reacts
with an atom that has an empty orbital. The atom with the pair of electrons donates them to the
bond and becomes more positively charged, while the other becomes more negative. It is
essentially the opposite of the bond cleavage above, and is represented as:

The 1,3-electron pair displacement operation involves a flow of electrons across three atoms.
The first atom, a Lewis-base nucleophile which has a pair of nonbonding electrons, initiates the
process by forming a bond with the second atom. That action displaces a pair of bonding electrons
from the second atom to the third, which is a Lewis-acid electrophile. The generic form of the
process is:

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 One bond is broken as another is formed. This operation also describes the addition of a
nucleophile to a double bond.

To initiate a 1,3-electron pair abstraction operation, and electron-deficient Lewis-acid

electrophile draws an electron pair from a Lewis-base, breaking a bond, forming a new one and
causing the displaced atom to become electron-deficient. This also describes the addition of an
electrophile to a double bond. The operation takes this general form:

A 1,5-electron pair displacement operation causes electrons to flow across five atoms. It is
initiated by an electron-donor Lewis-base nucleophile; the electrons pass across three central atoms
and finally arrive at a Lewis-acid electron-acceptor electrophile. Multiple bonds are broken and re-
formed. Generically it is written as:

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An electrophile can be added to a double bond by this mechanism as well.

ADDITION, SUBSTITUTION, AND ELIMINATION REACTIONS

There are three main types of reactions in organic chemistry: addition, substitution, and
elimination. If a reaction rearranges the carbon skeleton of the substrate molecule, some
chemists call that a fourth type. All types use one or more of the five reaction mechanisms
discussed above.

Addition
Addition reactions (also called electrophilic addition reactions) primarily occur in alkenes and
alkynes--compounds which contain double or triple (π) bonds. An atom or alkyl group is added to
a carbon that is part of the π-bond, and the π-bond is converted to a single (σ) bond. The
substrate does not lose any atoms or electrons in the process. These reactions occur readily
because σ-bonds are more stable than π-bonds.

The electrophilic addition reaction is a bimolecular two-step process. The two molecules involved
are the substrate and a polar reagent. When the π-bond is broken, the carbon atom becomes a
cation (called a carbocation) intermediate and the electrophilic component of the reagent forms a
σ-bond at that location by means of a 1,3-electron pair abstraction operation. The second step
adds the nucleophilic portion of the reagent to the carbocation bringing the net charge back to
neutral.

For example, when the substrate ethene reacts with the reagent hydrogen bromide, the HBr
dissociates and the electrophilic hydrogen bonds to one of the carbons, creating a fourth σ- bond
for that carbon and creating the carbocation. In the second step the nucleophilic Br- bonds to the
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carbocation. In more highly substituted alkenes, the electrophile will bond to the less-substituted
carbon, and the nucleophile bonds to the more highly substituted carbon.

It is possible to have a trimolecular electrophilic addition, requiring two reagents--one

electrophilic, the other nucleophilic--to act upon the substrate. This is a rare occurrence
because of the improbability of three reactive substances colliding. When it does occur, it
uses the 1,5-electron pair displacement operation as its first step.

Substitution
In a substitution reaction (or nucleophilic substitution reaction), an alkyl group (referred to as the

leaving group) that is more electronegative than the SP3-hybridized carbon to which it is bonded
breaks that bond, leaving an electrophilic carbocation. A nucleophilic atom or group of atoms from
the reagent then bonds to the carbocation. There are two possible pathways for a substitution
reaction. Which one is used depends upon the nature of the substrate.
In an SN1 (unimolecular nucleophilic substitution) reaction, the first step is the heterolytic bond
cleavage of the leaving group from its carbon, making it an electron-deficient carbocation. The
second step is a heterolytic bond forming operation between the nucleophile reagent and the
carbocation. The progress of the reaction depends only on the substrate.

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An SN2 (bimolecular nucleophilic substitution reaction) is a single-step 1,3-electron pair
displacement operation in which the leaving group departs at the same time the nucleophile bonds to
the carbon.

Elimination
An elimination reaction removes at least two atoms or functional groups from a molecule, then a
multiple (π) bond forms between the two carbons that lost their substituents. There are two
pathways by which this can occur.

The E1 reaction is unimolecular and has two steps. Step 1 is an ionization reaction, then step 2 is
a 1,3-electron pair abstraction operation. In some cases, the substrate molecule may become
cyclic rather than forming a π-bond.

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The E2 reaction is a bimolecular 1,5-electron pair displacement operation. Its progress depends
on the concentrations of both the substrate and the reagent.

There are many similarities between substitution and elimination reactions. They are summarized
below, with the conditions that are needed for each type.

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 Factor SN1 E1 SN2 E2
Nucleophile poor nucleophile very poor nucleophile is hard base
(base) nucleophile or soft base
very low
concentration

leaving weaker base than the nucleophile base

group
solvent polar-protic polar-protic polar-aprotic polar-aprotic
solvent solvent, lower solvent solvent, lower
polarity than polarity than for
for S1 SN2
reaction raising the temperature favors the elimination reaction
temperature

BIOLOGICAL MOLECULES
All of the preceding reaction mechanisms we've discussed have led up to the grand finale-- how
they're used. As previously noted, organic chemistry is the chemistry of life. The human body
runs on organic chemical reactions. It's how we get oxygen from the air we breathe, energy from
the food we eat, and how our brains tell our bodies what to do. There are many types of highly
specialized molecules that allow our bodies to function. An overview is given below:

Carbohydrates
Carbohydrates are more commonly known as sugars and starches. The word carbohydrate
originated when early chemists believed that sugars and starches were hydrated carbon atoms.
Most of them are, and the name stuck, even though we now know that it's not completely
accurate.

Most carbohydrates have the general formula CX(H2O)X. Carbohydrates are divided into
categories of saccharides: monosaccharides, such as glucose and fructose; disaccharides, such
as sucrose and lactose; and polysaccharides, such as starch and glycogen. Glucose provides
energy to fuel life functions while polysaccharides are storehouses of energy. Other
polysaccharides such as cellulose and chitin provide structural support wherever they are

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 present. You may have heard of ribose, a monosaccharide present in vital biomolecules such
as ATP, NAD and RNA; the sugar deoxyribose is a component of DNA.

Lipids

Lipids are composed of building blocks of fatty acids and

glycerol. They include triacylglycerol, fats, prostaglandins,
waxes, and steroids. Fatty acids are carboxylic acids, with the
general formula RCOOH, where R is usually a long, straight-
chain hydrocarbon with few, if any, branches, and the carbon
has a double bond with one of the oxygen molecules. Fatty
acids can be saturated, meaning the hydrocarbon chain
contains only single bonds, or unsaturated, with one or more
π-bonds.

Lipids serve important physiological functions. Cell membranes

are composed of phospholipids which are present in the form of
a bilayer. (You may like to read up on micelles, liposomes and
their use in drug targeting). Many of the hormones that regulate our body functions are steroid
lipids. Steroid medications such as cortisone combat inflammatory processes. They also act as
solvents for fat-soluble vitamins (A, D, E and K).

Any excess food we ingest is converted by our bodies into lipids, mainly triglycerides, which are
stored to be used later when more energy may be needed. For our ancient ancestors and most
animals, it was/still is a survival mechanism when food supplies were unpredictable. In the 21st
century it contributes to an obesity epidemic

Proteins
After water, which makes up 70% of a human's body weight, protein is the next most abundant
component at 15%. All proteins are long-chain polyamide polymers which contain the elements
carbon, hydrogen, oxygen, nitrogen and, usually, sulfur.

Proteins are polymers made of amino acid monomers. Amino acids are carboxylic acids; the amine
group NH2 and carboxyl group COOH bond to a central carbon to which an R (radical) side chain
also bonds. Thus the general formula is NH2CHRCOOH. There are twenty common R groups,
hence twenty common amino acids. Most amino acids are chiral and optically active.

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 When amino acids join together, they form a peptide linkage which gives off water as a by-
product. The polypeptide chains that are formed are named with three-letter abbreviations for
each amino acid in the chain. A protein is a polypeptide with at least forty amino acids; they can
have thousands. Two examples of human proteins are insulin and hemoglobin. Insulin is relatively
small, with only 51 amino acids and a molecular weight of 5733. Hemoglobin has 574 amino acids
and a molecular weight of 65,000. The human body contains approximately 100,000 different
types of protein.

Proteins which are fibrous in nature act as structural proteins. Examples include collagen in cartilage
and keratin in hair and nails. (This is the reason you do not feel any pain when you cut your hair
and nails). Actin and myosin are proteins which make your muscles move. Proteins present in
membranes are involved in receiving signals from the environment and passing the message to the
cell nucleus. Antibodies protect our body from diseases. However, the most important function of
proteins is as enzymes. Enzymes catalyze up to 4000 reactions in the human body.

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Nucleic Acids
If proteins are the "words" describing an organism, nucleic acids are the alphabet. They are
polymers whose monomer units are called nucleotides. A nucleotide has three components:
phosphoric acid, a sugar, and a nitrogen base. The nitrogen base is a derivative of either purine or
pyrimidine. They are the building blocks of DNA and RNA, which Dr. Francis Collins of the Human
Genome Project calls "the language of God."

There are five different nitrogen bases that occur in living things. Two of them, adenine
(abbreviated as A) and guanine (G), are categorized as purines and occur in both DNA and RNA.
The other three are pyrimidines. Of these, cytosine (C) occurs in both DNA and RNA; thymine (T)
occurs only in DNA; and uracil (U) occurs only in RNA. Two different sugars occur in nucleic acids:
ribose and deoxyribose. The type of sugar determines the type of nucleic acid. Deoxyribose is
present in deoxyribonucleic acid (DNA); ribose in ribonucleic acid (RNA).

C
A T G
U

The existence of DNA was known long before James Watson and Francis Crick deduced its unique
double-helix structure in 1953, for which they won the Nobel Prize for medicine and physiology in
1962. A DNA molecule is a double strand made up of nucleotide bases; the two strands are joined
to each other by hydrogen bonds, and are complementary. Each strand is a polypeptide composed
of the nucleotides A, G, C, and T. Each A on the original strand bonds to a T on the complementary
strand; each C bonds to a G. Thus the whole molecule sort of resembles a twisted ladder. In RNA,
U replaces T. By a very complex process, RNA strands form from specific regions of a DNA strand
called genes and encode the instructions for synthesizing proteins.

Protein synthesis occurs not only during an organism's growth and development, but is vital to
healing from injuries and regulating most biological functions.

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Enzymes
Enzymes are highly specialized proteins that regulate many biological processes and serve as
catalysts. Metabolism is the general name for the category of biological reactions. It is divided into
two subgroups: catabolism and anabolism. Catabolism is the breaking down of large molecules into
simpler ones, usually with the release of energy. Anabolism uses energy to build large molecules
from simpler ones. Catabolism and anabolism function as a cycle. When the body takes in food,
say, glucose, the glucose reacts with oxygen in a catabolic process to form water, carbon dioxide,
and adenosine triphosphate (ATP), a high-energy molecule. ATP, in turn, is broken down and the
energy released in its breakdown is used to fuel such anabolic processes as protein synthesis.

There are six main classes of enzymes, each with several subclasses. Each class of enzyme
regulates a particular type of biochemical reaction. Oxidoreductases mediate redox reactions.
Transferases transfer functional groups from one molecule to another. Hydrolases break down
bonds.

There are hundreds of different chemical reactions needed to make a living thing live; although the
specifics vary widely, all of them use the same basic mechanisms that have been discussed in this
lesson

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.

Exercises
1. Label the components of this reaction, then write it as a transformation.

2. Identify the mechanism occurring in each of these reactions.

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3. Show the carbocation intermediate and the end product for this reaction. Be sure to
indicate the electron transfers.

4. Show the carbocation intermediate and the end product for this reaction. Be sure to indicate
the electron transfers

5. Show the intermediate and product of this reaction.

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6. Show the intermediate and product of this reaction.

7. Show the intermediate and product of this reaction.

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 8. Identify each type of biological molecule.

Molecule Type
C6H14N2O2

C6(H2O) 6
CH3(CH2) 2 OOH
C6C6(H2O)6

9. If an original strand of DNA is ACGTCGATG, what is its complementary strand?

Questions to Think About

1. How are organic chemical reactions similar to inorganic ones? How are they different?

2. How does the structure of a molecule affect its behaviour in a reaction?

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