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Gen Chem Recording Powerpoint

Organic Compounds
An organic compound is a compound that
contains carbon and is found in living things
Schematic of a Carbon Atom
Carbon atoms
Carbon atoms can form four covalent bonds, with bonds
between carbon atoms being particularly stable
These properties allows carbon to form a wide variety of
organic compounds that are chemically stable
Carbon atoms
Carbon is the fourth most abundant element in the universe and is the building
block of life on earth. On earth, carbon circulates through the land, ocean, and
atmosphere, creating what is known as the Carbon Cycle. This global carbon
cycle can be divided further into two separate cycles: the geological carbon
cycles takes place over millions of years, whereas the biological or physical
carbon cycle takes place from days to thousands of years. In a nonliving
environment, carbon can exist as carbon dioxide (CO2), carbonate rocks, coal,
petroleum, natural gas, and dead organic matter. Plants and algae convert
carbon dioxide to organic matter through the process of photosynthesis, the
energy of light.
Carbon atoms
Cells are made of many complex molecules called macromolecules, which
include proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The
macromolecules are a subset of organic molecules (any carbon-containing
liquid, solid, or gas) that are especially important for life. The fundamental
component for all of these macromolecules is carbon. The carbon atom has
unique properties that allow it to form covalent bonds to as many as four
different atoms, making this versatile element ideal to serve as the basic
structural component, or “backbone,” of the macromolecules.
Main Classes of
Carbon Compounds
There are four principle groups of organic
compounds that contribute to much of the structure
and function of a cell:
Most abundant organic compound found in nature,
composed primarily of C,H and O atoms in a
common ratio – (CH2O)n
Principally function as a source of energy (and as a
short-term energy storage option)
Also important as a recognition molecule (e.g.
glycoproteins) and as a structural component (part of
Non-polar, hydrophobic molecules which may come
in a variety of forms (simple, complex or derived)
Lipids serve as a major component of cell
membranes (phospholipids and cholesterol)
They may be utilized as a long-term energy storage
molecule (fats and oils)
Also may function as a signaling molecule (steroids)
Nucleic Acids
Genetic material of all cells and determines the
inherited features of an organism
DNA functions as a master code for protein
assembly, while RNA plays an active role in the
manufacturing of proteins
Make over 50% of the dry weight of cells; are
composed of C, H, O and N atoms (some may
include S)
Major regulatory molecules involved in catalysis (all
enzymes are proteins)
May also function as structural molecules or play a
role in cellular signaling (transduction pathways)
Main Classes of Organic Compounds in Cells
“ Life is based on carbon
compounds including
carbohydrates, lipids,
proteins and nucleic acids”
Bonding pattern of Hydrocarbons
Hydrocarbon, any of a class of organic
chemical compounds composed only of the
elements carbon (C) and hydrogen (H).
Hydrocarbons are organic molecules consisting entirely of carbon and
hydrogen, such as methane (CH4). Hydrocarbons are often used as fuels: the
propane in a gas grill or the butane in a lighter. many covalent bonds between
the atoms in hydrocarbons store a great amount of energy, which is released
when these molecules are burned (oxidized). Methane, an excellent fuel, is
the simplest hydrocarbon molecule, with a central carbon atom bonded to four
different hydrogen atoms. The geometry of the methane molecule, where the
atoms reside in three dimensions, is determined by the shape of its electron
orbital's. The carbon and the four hydrogen atoms form a shape known as a
tetrahedron, with four triangular faces; for this reason, methane is described
as having tetrahedral geometry.
As the backbone of the large molecules of living things, hydrocarbons
may exist as linear carbon chains, carbon rings, or combinations of
both. Furthermore, individual carbon-to-carbon bonds may be single,
double, or triple covalent bonds; each type of bond affects the
geometry of the molecule in a specific way. This three-dimensional
shape or conformation of the large molecules of life
(macromolecules) is critical to how they function.
Methane: Methane has a tetrahedral geometry, with each of the four hydrogen
atoms spaced 109.5° apart.
Hydrocarbons Chains
Hydrocarbon chains are formed by successive bonds between carbon atoms and
may be branched or unbranched. The overall geometry of the molecule is altered
by the different geometries of single, double, and triple covalent bonds. The
hydrocarbons ethane, ethene, and ethyne serve as examples of how different
carbon-to-carbon bonds affect the geometry of the molecule. The names of all
three molecules start with the prefix “eth-,” which is the prefix for two carbon
hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of
single, double, or triple carbon-carbon bonds, respectively. Thus, propane,
propene, and propyne follow the same pattern with three carbon molecules,
butane, butene, and butyne for four carbon molecules, and so on..
Hydrocarbons Chains
Double and triple bonds change the geometry of the molecule: single
bonds allow rotation along the axis of the bond, whereas double bonds
lead to a planar configuration and triple bonds to a linear one. These
geometries have a significant impact on the shape a particular molecule
can assume
Hydrocarbons Chains
Hydrocarbon Chains: When carbon forms single bonds with other atoms, the
shape is tetrahedral. When two carbon atoms form a double bond, the shape is
planar, or flat. Single bonds, like those found in ethane, are able to rotate. Double
bonds, like those found in ethane cannot rotate, so the atoms on either side are
locked in place.
Hydrocarbons Rings
The hydrocarbons discussed so far have been aliphatic hydrocarbons, which
consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic
hydrocarbons, consists of closed rings of carbon atoms. Ring structures are found
in hydrocarbons, sometimes with the presence of double bonds, which can be seen
by comparing the structure of cyclohexane to benzene. The benzene ring is
present in many biological molecules including some amino acids and most
steroids, which includes cholesterol and the hormones estrogen and testosterone.
The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural
component of crude oil and has been classified as a carcinogen. Some
hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an
example of such a hydrocarbon.
Hydrocarbons Rings
Hydrocarbon Rings: Carbon can form five-and six membered rings. Single or
double bonds may connect the carbons in the ring, and nitrogen may be substituted
for carbon.
Properties and reactivity of
common functional groups
Functional group: A specific grouping of elements
that is characteristic of a class of compounds, and
determines some properties and reactions of that
Functional Groups
In organic chemistry, a functional group is a specific group of atoms or bonds within
a compound that is responsible for the characteristic chemical reactions of that
compound. The same functional group will behave in a similar fashion, by
undergoing similar reactions, regardless of the compound of which it is a part.
Functional groups also play an important part in organic compound nomenclature;
combining the names of the functional groups with the names of the parent alkenes
provides a way to distinguish compounds.
The atoms of a functional group are linked together and to the rest of the
compound by covalent bonds. The first carbon atom that attaches to the functional
group is referred to as the alpha carbon; the second, the beta carbon; the third, the
gamma carbon, etc. Similarly, a functional group can be referred to as primary,
secondary, or tertiary, depending on if it is attached to one, two, or three carbon
Functional Groups
Functional groups play a significant role in directing and controlling organic
reactions. Alkyl chains are often nonreactive, and the direction of site-specific
reactions is difficult; unsaturated alkyl chains with the presence of functional groups
allow for higher reactivity and specificity. Often, compounds are functionalized with
specific groups for a specific chemical reaction. Functionalization refers to the
addition of functional groups to a compound by chemical synthesis. Through
routine synthesis methods, any kind of organic compound can be attached to the
surface. In materials science, functionalization is employed to achieve desired
surface properties; functional groups can also be used to covalently link functional
molecules to the surfaces of chemical devices.
In organic chemistry, the most common functional groups are carbonyls (C=O),
alcohols (-OH), carboxylic acids (CO2H), esters (CO2R), and amines (NH2). It is
important to be able to recognize the functional groups and the physical and
chemical properties that they afford compounds.
Functional Groups
Carboxylic Acid
Alcohols are functional groups characterized by the presence of an -OH group.
The structure of an alcohol is similar to that of water, as it has a bent shape. This
geometrical arrangement reflects the effect of electron repulsion and the increasing
steric bulk of the substituent on the central oxygen atom. Like water, alcohols are
polar, containing an unsymmetrical distribution of charge between the oxygen and
hydrogen atoms. The high electronegativity of the oxygen compared to carbon
leads to the shortening and strengthening of the -OH bond. The presence of the OH groups allows for hydrogen bonding with other -OH groups, hydrogen atoms,
and other molecules. Since alcohols are able to hydrogen bond, their boiling points
are higher than those of their parent molecules.
Alcohols are able to participate in many chemical reactions. They often undergo
deprotonation in the presence of a strong base. This weak acid behavior results in
the formation in an alkoxide salt and a water molecule. Hydroxyl groups alone are
not considered good leaving groups. Often, their participation in nucleophilic
substitution reactions is instigated by the protonation of the oxygen atom, leading to
the formation a water moiety—a better leaving group. Alcohols can react with
carboxylic acids to form an ester, and they can be oxidized to aldehydes or
carboxylic acids.
Alcohols have many uses in our everyday world. They are found in beverages,
antifreeze, antiseptics, and fuels. They can be used as preservatives for specimens
in science, and they can be used in industry as reagents and solvents because
they display an ability to dissolve both polar and non-polar substances.
Alcohols are able to participate in many chemical reactions. They often undergo
deprotonation in the presence of a strong base. This weak acid behavior results in
the formation in an alkoxide salt and a water molecule. Hydroxyl groups alone are
not considered good leaving groups. Often, their participation in nucleophilic
substitution reactions is instigated by the protonation of the oxygen atom, leading to
the formation a water moiety—a better leaving group. Alcohols can react with
carboxylic acids to form an ester, and they can be oxidized to aldehydes or
carboxylic acids.
Alcohols have many uses in our everyday world. They are found in beverages,
antifreeze, antiseptics, and fuels. They can be used as preservatives for specimens
in science, and they can be used in industry as reagents and solvents because
they display an ability to dissolve both polar and non-polar substances.
Ethers are a class of organic compounds characterized by an oxygen atom
connected to two alkyl or aryl groups.
Ethers are rather nonpolar due to the presence of an alkyl group on either side of
the central oxygen. The presence of the bulky alkyl groups that are adjacent to it
means that the oxygen atom is largely unable to participate in hydrogen bonding.
Ethers, therefore, have lower boiling points compared to alcohols of similar
molecular weight. However, as the alkyl chain of the ethers becomes longer, the
difference in boiling points becomes smaller. This is due to the effect of increased
Van der Waals interactions as the number of carbons increases, and therefore the
number of electrons increases as well. The two lone pairs of electrons present on
the oxygen atoms make it possible for ethers to form hydrogen bonds with water.
Ethers are more polar than alkenes, but not as polar as esters, alcohols or amides
of comparable structures.
Ethers have relatively low chemical reactivity, but they are still more reactive than
alkanes. Although they resist undergoing hydrolysis, they are often cleaved by
acids, which results in the formation of an alkyl halide and an alcohol. Ethers tend
to form peroxides in the presence of oxygen or air. The general formula is R-O-OR’. Ethers can serve as Lewis and Bronsted bases, serving to donate electrons in
reactions, or accept protons. Ethers can be formed in the laboratory through the
dehydration of alcohols (2R-OH → R-O-R + H2O at high temperature), nucleophilic
displacement of alkyl halides by alkoxides (R-ONa + R’-X → R-O-R’ + NaX), or
electrophilic addition of alcohols to alkenes (R2C=CR2 + R-OH → R2CH-C(-O-R)R2).
Ethers: The general structure of an ether. An ether is characterized by an oxygen
bonded to two alkyl or aryl groups, represented here by R and R’. The substituents
can be, but do not need to be, the same.
Amines are compounds characterized by the presence of a nitrogen atom, a lone
pair of electrons, and three substituent.
Amines are able to hydrogen bond. As a result, the boiling points of these
compounds are higher than those of the corresponding phosphines, but lower than
those of the corresponding alcohols, which hydrogen bond to a stronger extent.
Amines also display some solubility in water. However, the solubility decreases with
an increase in carbon atoms, due to the increased hydrophobicity of the compound
as the chain length increases. Aliphatic amines, which are amines connected to an
alkyl chain, display solubility in organic polar solvents. Aromatic amines, which are
amines that participate in a conjugated ring, donate their lone pair of electrons into
the benzene ring, and thus their ability to engage in hydrogen bonding decreases.
This results in a decrease in their solubility in water and high boiling points.
Industrially, amines are prepared from ammonia by alkylation with alcohols. They
can also be prepared via reduction of nitriles to amines using hydrogen in the
presence of a nickel catalyst. Amines are quite reactive due to their basicity as well
as their nucleophilicity. Most primary amines are good ligands and react with metal
ions to yield coordination complexes. One of the most important reactions for
amines is their formation of imines, or organic compounds where nitrogen
participates in a double bond, upon reacting with ketones or aldehydes.
Tertiary amine: The central carbon is attached to an amine group and three other
carbon atoms.
Esters are functional groups produced from the condensation of an alcohol with a
carboxylic acid, and are named based on these components.
Esters are more polar than ethers, but less so than alcohols. They participate in
hydrogen bonds as hydrogen bond acceptors, but cannot act as hydrogen bond
donors, unlike their parent alcohols and carboxylic acids. This ability to participate
in hydrogen bonding confers some water-solubility, depending on the length of the
alkyl chains attached. Since they have no hydrogens bonded to oxygens, as
alcohols and carboxylic acids do, esters do not self-associate. Consequently,
esters are more volatile than carboxylic acids of similar molecular weight.
Esters react with nucleophiles at the carbonyl carbon. The carbonyl is weakly
electrophilic, but is attacked by strong nucleophiles such as amines, alkoxides,
hydride sources, and organolithium compounds. The carbonyl’s electrophilicity can
increase if it is protonated; in acidic media, an ester can be hydrolyzed by water to
form a carboxylic acid and an alcohol.
The C-H bonds adjacent to the carbonyl are weakly acidic, but undergo
deprotonation with strong bases. This process is the one that usually initiates
condensation reactions. The carbonyl oxygen is weakly basic (less so than in
amides), but can form adducts with Lewis acids.
Esters: An ester is characterized by the orientation and
bonding of the atoms shown, where R and R’ are both
carbon-initiated chains of varying length, also known as
alkyl groups.
Carboxylic Acids
Carboxylic acids are organic acids that contain a carbon atom that participates in
both a hydroxyl and a carbonyl functional group.
Carboxylic acids act as both hydrogen bond acceptors, due to the carbonyl group,
and hydrogen bond donors, due to the hydroxyl group. As a result, they often
participate in hydrogen bonding. Carboxylic acids usually exist as dimeric pairs in
nonpolar media because of their tendency to “self-associate.” This tendency to
hydrogen bond gives them increased stability as well as higher boiling points
relative to the acid in aqueous solution. Carboxylic acids are polar molecules; they
tend to be soluble in water, but as the alkyl chain gets longer, their solubility
decreases due to the increasing hydrophobic nature of the carbon chain.
Carboxylic acids are characterized as weak acids, meaning that they do not fully
dissociate to produce H+ cations in a neutral aqueous solution.
Carboxylic Acids
Carboxylic acids are used in the production of polymers, pharmaceuticals, solvents,
and food additives. As such, they are often produced industrially on a large scale.
Carboxylic acids are generally produced from oxidation of aldehydes and
hydrocarbons, and base catalyzed dehydrogenation of alcohols. They can be
produced in the laboratory for small scale reactions via the oxidation of primary
alcohols or aldehydes, oxidative cleavage of olefins, and through the hydrolysis of
nitriles, esters, or amides.
Carboxylic acids are widely used as precursors to produce other compounds. Upon
exposure to a base, the carboxylic acid is deprotonated and forms a carboxylate
salt. They also react with alcohols to produce esters and can undergo reduction
reactions by hydrogenation or the use of reducing agents. There are also various
specialized reactions that carboxylic acids participate in that lead to the formation of
amines, aldehydes, and ketones.
Carboxylic Acids
A carboxylic acid: Carboxylic acids are organic oxoacids characterized by the
presence of at least one carboxyl group, which has the formula -C(=O)OH, usually
written as -COOH or -CO2H.
Polymers touch almost every aspect of
modern life.
Polymers are materials made of long, repeating chains of molecules. The materials
have unique properties, depending on the type of molecules being bonded and how
they are bonded. Some polymers bend and stretch, like rubber and polyester.
Others are hard and tough, like epoxies and glass.
Polymers touch almost every aspect of modern life. Chances are most people have
been in contact with at least one polymer-containing product — from water bottles
to gadgets to tires — in the last five minutes.
The term polymer is often used to describe plastics, which are synthetic polymers.
However, natural polymers also exist; rubber and wood, for example, are natural
polymers that consist of a simple hydrocarbon, isoprene, according to Encyclopedia
Britannica. Proteins are natural polymers made up of amino acids, and nucleic
acids (DNA and RNA) are polymers of nucleotides — complex molecules
composed of nitrogen-containing bases, sugars and phosphoric acid, for example.
Polymerization is the method of creating synthetic polymers by combining smaller
molecules, called monomers, into a chain held together by covalent bonds,
according to ThoughtCo., an online educational resource. Various chemical
reactions — those caused by heat and pressure, for example — alter the chemical
bonds that hold monomers together, according to Scientific American. The process
causes the molecules to bond in a linear, branched or network structure, resulting
in polymers.
These chains of monomers are also called macromolecules. Most polymer chains
have a string of carbon atoms as a backbone. A single macromolecule can consist
of hundreds of thousands of monomers, according to the Polymer Science
Learning Center.
Polymers are used in almost every area of modern living. Grocery bags, soda and
water bottles, textile fibers, phones, computers, food packaging, auto parts, and
toys all contain polymers.
Even more-sophisticated technology uses polymers. For example, "the membranes
for water desalination, carriers used in controlled drug release and biopolymers for
tissue engineering all use polymers," according to the ACS.
Popular polymers for manufacturing include polyethylene and polypropylene. Their
molecules can consist of 10,000 to 200,000 monomers.
Each biomolecule is essential for body
functions and manufactured within the body.
Biomolecules are defined as any organic molecule present in a living cell which
includes carbohydrates, proteins, fats etc. Each biomolecule is essential for body
functions and manufactured within the body. They can vary in nature, type, and
structure where some may be straight chains, some may be cyclic rings or both.
Also, they can vary in physical properties such as water solubility, melting points.
Polysaccharides, commonly known as carbohydrates are macromolecules. They
are made up of monosaccharides (sugar molecules). Majority of living cells are rich
in carbohydrates and they are the final products of many metabolisms. For
example, Glucose is the final product of photosynthesis. Saccharides can be
monosaccharide, disaccharide, polysaccharide etc. based on the number of sugar
molecules they are made up of.
Proteins are dietary compounds made of monomers called amino acids. Protein is
a long chain of amino acid bonded by polypeptide bonds. Hence proteins are also
called polypeptides. Amino acids are carbon-containing compounds where a
carboxylic acid group and the amino group are present at the two ends. Each
amino acid consists of one central carbon surrounded by four substituents. These
four substituents include an amino group, carboxylic acid group, hydrogen and a
variable group represented by R. The variable group, R decides the nature and
type of amino acid.
Lipids are a group of water-insoluble compounds which include fats, glycerol,
phospholipids, steroids, oils etc. Types of lipids vary according to their constituents.
Fatty acids are simple lipids made up of carboxyl group and a variable group, R.
They may be saturated or unsaturated fatty acids. Glycerol is trihydroxy propane
which combines with fatty acids to give triglycerides. Some lipids consist of
phosphorus group along with the organic chain. Such lipids are called
phospholipids, the constituent of the plasma membrane.
Nucleic acids
Nucleic acids are the genetic materials present in an organism which includes DNA
and RNA. Nucleic acids are the combination materials of nitrogenous bases, sugar
molecules and phosphate group linked by different bonds in a series of steps. Our
body consists of heterocyclic compounds like pyrimidines and purines. These are
nitrogenous compounds like adenine, guanine, cytosine, thymine, and uracil. When
these bases bond with sugar chains, nucleosides are formed. Nucleosides in turn
bond with a phosphate group to give nucleotides like DNA and RNA.
The human body consists of trillions of cells which are made up of carbohydrates,
proteins like biomolecules. Majority of cell activities depend on them.
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