Session Plan
• Introduction to Organic Compounds
• Functional Groups
• Different classes of organic compounds and
Nomenclature
Organic Compounds
Organic compounds:
• All compounds or molecules containing the elements carbon and hydrogen– A compound that contains carbon is a organic compound
• Organic compounds found in living organisms are needed for life’s processes– Carbohydrates, lipids, proteins, and nucleic acids, fats, plastics, and fuels
• Many common organic compounds contain:– Oxygen (O), nitrogen (N), or sulphur (S) atoms
• Hydrocarbons:
Organic compounds containing only carbon and hydrogen atoms– Sources of organic compounds:
• Nature
• Laboratory synthesis
Diversity of Organic Compounds
• What is the basis for the huge
diversity of organic compounds?
– The ability of carbon to form covalent
bonds with other elements (e.g. H, O, N
and S) and itself
– Each carbon has 4 unpaired electrons in
it’s valence shell >>> each can be
involved in one covalent bond
• Total covalent bonds formed by a carbon
atom = 4
C
R
R
RR
R represents a bond to any other group of atoms
Structural Representation of Organic Compounds
• How are the structures of organic compounds represented?
– The structure of organic compounds can be represented by:
• Molecular Formula
– Indicate the number and types of atoms present in a molecule but contain no information about their arrangement
• Structural Formula
– Complete
– Condensed
C3H8
CH3CH2CH3
Hydrocarbons:
Organic compounds that contain only H & C atoms
Saturated
Hydrocarbons
– Have only single
covalent bonds
between C atoms
• Are saturated with
Hydrogen atoms
– Alkane: Propane
– Chemical formula:
C3H8 >>> CH3CH2CH3
Unsaturated Hydrocarbons– Have 1 or more double or triple covalent
bonds between C atoms
– Alkene: Propene
– Chemical formula: C3H6 >>> CH2CHCH3
– Extra carbon-carbon = two less hydrogens in
structure
Common Functional Groups in Organic
Chemistry
• What are functional groups?
– Carbon combines with other elements to form functional groups
• Sites of chemical reactions/key structural components that define how organic molecules react
– Particular functional groups undergo similar chemical reactions
– E.g. Alcohols (contain OH functional group) have certain chemical properties
• Functional groups are used to classify and name organic compounds
Alcohol: Propanol
Common Functional GroupsFamily Functional group Example IUPAC Name
Alkane Carbon- carbon single
bond CH3CH3
(Alkane)
Ethane
Alkene
Carbon-carbon double
bond
CH2 = CH2
(Alkene)
Ethene
Alkyne – C C –
Carbon-carbon triple
bondHC CH
(Alkyne)
Ethyne
Aromatic
Phenyl group
Benzene
Common Functional GroupFamily Functional group Example IUPAC Name
Alcohol OH
hydroxyl group CH3OH(Alkanol)Methanol
Thiol SH CH3SH Methane thiol
Ether O
ether group CH3 O CH3
(Alkoxy alkane)Methoxy Methane
Aldehyde
Aldehyde group
(Alkanal)Methanal
Ketone
carbonyl group
(Alkanone)Propanone
Common Functional GroupsFamily Functional group Example IUPAC Name
Carboxylic acid
Carboxyl group
(Alkanoic acid)Ethanoic acid
Amine
Amine group
CH3NH2
(Alkanamine)
Methylamine
Amide
Amide group
(Alkanamide)
Ethanamide
Ester
Ester group
(Alkyl Alkanoate)Methyl methanoate
Functional groups in macromolecules
Stoker 2014, p650
Stoker 2014, p695
Carbohydrate
Alcohol
Carboxylicacid
Alcohol
EsterLipid
Protein
Glucose Triacylglycerol (TAG)
Amino Acid
Amine
Carboxylic acid
Nucleic acids: DNA/RNA
Nucleotide
Alcohol
Amine
Ether
Amide
Ether
ALKANES
• Aliphatic / Acyclic Saturated Hydrocarbons– C atoms arranged in an open chain (straight or branched)
– Contain single Carbon-Carbon bonds (CH3CH3)
– Alkanes are saturated hydrocarbons
• General molecular formula: CnH2n+2
Cycloalkanes
• Cyloalkanes are cyclic saturated hydrocarbons– C atoms arranged into a closed ring structure
• Prefix Cyclo-– Rings found in nature size from 3–30 C atoms
• Cyclopentane & Cyclohexane rings are the most abundant
• Non-polar compounds– Insoluble in water (do not dissolve in water)
– Soluble in non-polar solvents (chloroform, benzene)
• Density lower than water– Oil stays on top of water (e.g. oil spills)
Chemical Properties of Alkanes
• Combustion– Exothermic reaction with O2 (air), producing CO2, H2O & heat
• CH4 + O2 → CO2 + H2O + Energy
• Halogenation– Direct reaction with halogens (F, Cl, Br, I)
– Substitution of one or more H-atoms of hydrocarbons by halogen atoms, producing haloalkanes or halocycloalkanes
Stoker 2014, p368-70
ALKENES
• Acyclic unsaturated hydrocarbons containing 1 or more DOUBLE BONDS.
• Functional Group:
Ethene
• General molecular formula: CnH2nStoker 2014, p392
H2C = CH2
Hydrogenation of Alkenes • Addition of a H2 molecule via hydrogenation:
– The hydrogen atoms are added to each carbon that forms
the multiple bond (C=C or C≡C)
Stoker 2014, p398
Polymerization of Alkenes
• Many alkenes form polymer chains– Reaction between monomer units removes double bonds
>>> creates a continuous chain• Poly = many
• Meros (G) = part
– Catalyst used to initiate polymerisation of alkenes
• n CH2 = CH2 → ( CH2 – CH2 )n
• Ethene (= ethylene) → Polyethylene (PET)
• Monomer → Polymer
ALKYNES• Alkynes are unsaturated hydrocarbons
containing 1 or more TRIPLE BONDS
– Functional group:
– C ≡ C –
– General molecular formula: Cn H2n-2
Ethyne – The Simplest Alkyne
Many Arenes are Aromatic
• Many compounds containing the benzene ring are fragrant & are responsible for the aroma of plants
• Thymol– Found in thyme Thymus vulgaris
• Vanillin– Found in vanilla Vanilla plantifolia
https://honeyandspice.wordpress.com/nitty-gritty/vanillin/
http://www.lookfordiagnosis.com/mesh_info.php?term=Thymol&lang=1
Thymol
Vanillin
ALCOHOLS
• Functional group: Hydroxyl group
– OH
• General formula:
R – OH
• IUPAC Name: ALKANOL
– An alcohol contains a hydroxyl group (–OH) attached to a carbon chain
• Naming compounds: Replace –ane with –anol at the end of the name
– E.g. methane becomes methanol
Example Name
CH3OH Methanol
CH3CH2OH Ethanol
POLYOLS• Polyols:
– Polyhydroxy-alcohols
– Alcohols with more than 1 –OH group
• DIOLS = alcohols with 2 –OH groups
• TRIOLS = alcohols with 3 –OH groups
Stoker 2014, p424
Many OH groups present in simple monosaccharides (carbohydrates) such as glucose and fructose
Oxidation of 10 Alcohols
Ethanol Ethanal Ethanoic acid
Stoker 2014, p440
Alcohol breakdown in the body:
PHENOLS• Aromatic Alcohols
– –OH group is attached to a benzene ring
• Phenol = is the simplest phenol
– A phenol contains a hydroxyl group (–OH)
attached to a benzene ring
• Other phenols contain same basic structure
as phenol with additional substituted groups
in order to attach to different atoms
Uses of Phenols• Strong anti-septics
– Some phenols are used as:
• Hospital disinfectant (Lysol)
• Dentistry (Eugenol)
• Mouthwashes (Thymol)
• Throat lozenges
Mouthwashes, Throat lozenges Mouthwashes Dentistry
Stoker 2014, p445-7
ETHERS
• Functional group: Oxygen within a carbon chain
– O –
• General formula:
R – O – R
IUPAC Name: ALKOXY ALKANE
– Ethers consist of an oxygen atom that is connected by single
bonds to two carbon groups (alkyl or aromatic)
– CH3CH2-O-CH2CH3 (Ethoxy ethane, diethyl ether)
Ethers• Ethers are more water soluble than alkanes of similar molar
mass– Ethers are polar compounds
– Ethers form hydrogen bonds with H2O• But not ether-ether H-bonds
• Flammable! – Ethoxyethane – BP= 35oC
• a flash-fire hazard
• Generally un-reactive & good solvents– Unreactive towards acids, bases and oxidizing agents
– Medium for organic reactions to reduce formation of by-products
• Ethoxyethane was used as the 1st inhalant anesthetic with strong side effects
– Halogenated ether derivatives are used as anesthetics today• Less side effects
Stoker 2014, Figure 14-20 p457
THIOL
• Functional group: sulphydryl group
– SH
• General formula:
R – SH
• IUPAC Name: Alkane thiol
– A THIOL contains a sulphydryl group (–SH) attached to a carbon
chain
• Naming compounds: Add thiol after -ane
– E.g. methane becomes methanethiol
Thiols• Thiols:
– Similar to alcohols (-SH instead of –OH)
• Commonly known as Mercaptans
– Thiols have strong disagreeable odours
• Mixture of thiols is added to natural gas to detect leaks
– Garlic & onion contain thiols that are activated upon
cutting
• Methanethiol
– Smell of rotten cabbage, “bad breath”,
flatulence & a by-product of asparagus
metabolism
• Ethanethiol
– strong green onion smell
Stoker 2013, p455
1-Propanethiol
(Onions)
CH3 – CH2 – CH2 – SH
ALDEHYDE• Functional group:
O
II
– C – H or – CHO
• General formula:
O
II
R – C – H or R – CHO
• IUPAC Name: Alkanal– An aldehyde contains a carbonyl group whose carbon is linked to at least
one hydrogen atom and is also usually attached to a carbon chain
• Naming compounds: Replace –ane with -anal– E.g. ethane becomes ethanal
Propanal
O
II
CH3 – C – H
Ethanal
Common Aldehydes
• METHANAL– Commonly known as Formaldehyde
– Colorless, pungent smelling gas
– Formalin = 40% aqueous solution, used as germicide & preservative of biological specimens
– Potential carcinogen & teratogen (causes birth defects)
– Present in tobacco smoke
– Used in manufacturing of paper, insulation materials, cosmetics (shampoo) & as a preservative in vaccinations
– Exposure triggers watery & burning eyes, burning throat, nausea, difficulty breathing & asthma attacks in asthmatics
KETONES• Functional group:
O
II
– C – or – CO –
• General formula:
O
II
R – C – R’ or R – CO – R’
• IUPAC Name: ALKANONE– In a KETONE the Carbon of carbonyl group is bonded to two other carbon
atoms
• Naming compounds: Replace –ane with -anone– E.g. propane becomes propanone
•An aldehyde is attached to at least one H atom•A ketone is attached to two carbon groups
2-Pentanone
3-Pentanone
12 3 4 5
Common Ketones
• PROPANONE– Commonly known as Acetone
– Excellent organic solvent
– In paint & nail polish removers
– Hepatotoxic upon ingestion >>> toxic to the liver
– One of the Ketone bodies produced in greater amounts in the human body when large amounts of fats are metabolized for energy production
• Uncontrolled diabetes mellitus, fasting & ketogenic diets
– The “sweet” odor of acetone can be detected on the person’s breath
• Fruity breath
Chemical Properties of Aldehydes & Ketones
• OXIDATION
– Aldehydes readily oxidize to Carboxylic acids
• Utilised in the breakdown of alcohol breakdown
– Ketones resist oxidation
• Unreactive
Stoker 2014, p482
Benedict’s Test• Selective test for the presence of Aldehydes in a
solution– Based on the ease with which aldehydes are oxidized
• Addition to an Aldehyde solution:– Cu2+ ion is reduced to Cu+ ion, and aldehyde oxidised
• The metal ion (Cu2+) is the oxidizing agent
• Cu2+ ion is reduced to Cu+ ion– Precipitates from solution as brick-red colored solid Cu2O
• Benedict’s test can be used to determine the
presence of glucose (an aldehyde) in blood or urine
Stoker 2014, Figure 15-9 p483
2Cu+
CARBOXYLIC ACIDS
• Functional group: CARBOXYL GROUP
O
II
– C – OH or – COOH
• General formula:
O
II
R – C – OH or R – COOH
• IUPAC Name: ALKANOIC ACID– A carboxyl group contains a carbonyl with a hydroxyl group (–OH) attached and is
also bonded to a carbon chain
• Naming compounds: Replace –ane with –anoic acid at the end of the name– E.g. ethane becomes ethanoic acid
– CH3COOH (Ethanoic acid)
AMINES
• Functional group: Amino group
– NH2
• General formula:
R – NH2
• IUPAC Name: ALKANAMINE– An amine contains an amino group (–NH2) attached to a carbon chain
• Naming compounds: Replace –ane with –anamine at the end of the name
– E.g. methane becomes methanamine
Reactions of Amines with Acids• Many amines have biological activity & are used as drugs
• High molecular mass amines are insoluble in
water & body fluids (blood plasma & CSF)– For drugs to be effective on targeted cells, they have to be soluble in body fluids
• Amine containing drugs are therefore treated with an acid to form
water-soluble ammonium salts
• Amines are susceptible to oxidation & decomposition by O2
>>> lose their biological activity– Water-soluble ammonium salts are far less susceptible to oxidation & have a longer shelf life
• Amines in fish (strong odour) interact with acids (vinegar or lemon juice), forming odourless salts, making a fish dish more palatable
https://genevievemorton.wordpress.com
Heterocyclic Amines
• The 2 most widely used central nervous system stimulants
in the world are hetrocyclic amine derivatives:
– Caffeine
– Nicotine
Stoker 2014, p552-555
Biological important amines
Amine Structure Biological role
Acetyl Choline Produced from acetate and choline, released into neuromuscular junction, excitatory neurotransmitter
Adrenalin Adrenalin is synthesized from Phenyl alanine in the adrenal glands acts as a hormone during the “fight-or-flight” response
Serotonin Synthesized from the amino acid Tryptophan,Involved in relaxation, sleep, rational thinking, feeling of wellbeing & calmness
Histamine Produced from the amino acid Histidine a potent pro-inflammatory mediator, involved with allergic reactions
Alkaloids• Alkaloids are a physiologically active
N-containing organic compounds produced by plants– “Alkaloid” refers to the alkaline nature of these amines
• Caffeine – coffee & cacao beans, tea leaves
• Quinine – cinchona tree bark, used to treat malaria
• Nicotine – tobacco plant, addictive stimulant,
high doses cause depression, nausea & vomiting
• Atropine – deadly nightshade plant, used as a preoperative
muscle relaxant & in ophthalmology (causes mydriasis)
• Morphine – opium poppy plant, strong hallucinogen, depresses the
respiratory centre in the CNS & large doses cause respiratory failure
• Codeine & Heroin are derivatives of Morphine
• Cocaine – Coca plantStoker 2014, p561
AMIDES• Functional group: Amino group + Carbonyl group
O
II
– C – NH2
• General formula:
O
II
R – C – NH2
• IUPAC Name: ALKANAMIDE– An amide contains an amino group (–NH2) attached to a carbonyl group (C=O), attached to a
carbon chain
• Naming compounds: Replace –ane with –anamide at the end of the name– E.g. methane becomes methanamide
Useful Amides• UREA
– Simplest one-C atom diamide, produced during the metabolism of proteins
• Used in the removal of N atoms from the body
• Excreted in the urine
• MELATONIN
– Hormone of the pineal gland, that regulates the sleep-wake cycle in humans
• ACETAMINPHEN / PARACETAMOL
– N-acetyl-p-aminophenol
• Top-selling over the counter pain relieverStoker 2014, p568
ESTERS• Functional group:
O
II
– C – O – or – COO –
• General formula:
O
II
R – C – O – R’ or R – COO – R’
• IUPAC Name: ALKYL ALKANOATE– An ester contains a carbonyl group (C=O), attached to an oxygen that is bonded to
another carbon chain (carbonyl group also bonded to another carbon chain)
Ester Functional Group
Preparation of Esters
• ESTERIFICATION– In a reversible chemical reaction one carboxylic acid and one alcohol combine
together to produce one ester
Stoker 2014, p695Alcohol
EsterLipid
Triacylglycerol (TAG)
Carboxylicacid
Methyl salicylate (Wintergreen)
Functional groups in macromolecules
Stoker 2014, p650
Stoker 2014, p695
Carbohydrate
Alcohol
Carboxylicacid
Alcohol
EsterLipid
Protein
Glucose Triacylglycerol (TAG)
Amino Acid
Amine
Carboxylic acid
Nucleic acids: DNA/RNA
Nucleotide
Alcohol
Amine
Ether
Amide
Ether
What must compounds contain to be
classified as organic compounds?
What macromolecule groups that are essential
to life are classed as organic compounds?
What makes them organic compounds?
A carbon atom contains four electrons in it’s valence shell.
How many covalent bonds does the carbon atom form? Why?
Key concept: Organic compounds, macromolecules, covalent bonding
Concept connections
Organic compounds are wide spread in nature. In fact important compounds for our health
like carbohydrate, lipid and protein are all classed as organic compounds. Which of the
following is correct for organic compounds?
a) Organic compounds can only be derived in the laboratory
b) An organic compound will always contain at least one carbon atom
c) Organic compounds can only be derived in nature
d) An organic compound may or may not contain carbon atoms
The outer shell of a carbon atom contains four unpaired valence electrons. The number
of unpaired valence electrons an atom contains is equal to the number of covalent bonds
the atom is capable of forming. Which of the following accurately describes the covalent
bonding of a carbon atom?
a) Each of the four unpaired valence electrons must form a covalent bond with
another carbon atom to become more stable
b) Each of the four unpaired valence electrons within the carbon atom can
covalent bond to each other to become more stable
c) Each of the four unpaired valence electrons of a carbon atom can form a
covalent bond via electron sharing with other atoms such as hydrogen
and carbon
d) Each of the four unpaired valence electrons of a carbon atom can covalent
bond to more than one different atom simultaneously
What is a functional group?
If a compound contains a particular functional group,
what does this allow us to predict about the compound?
Is it possible for a compound to have multiple
functional groups?
Key concept: Functional groups
Concept connections
A functional group is a characteristic set of atoms used to distinguish one functional group
from another. For example, the thiol functional group is R-SH (R = connection to other
atoms). There are a variety of functional groups that compounds may contain such as the
ester, amide and aldehyde. Once you’ve identified that a compound contains a certain
functional group, what do you now know about the compound?
a) The compound will only react with other compounds that contain the same functional
group
b) The compound is stable and unreactive, so it won’t participate in chemical reactions
c) The compound will react similarly to other compounds with the same functional group
d) The compound will have a specific function that is the same as all other compounds
that contain the same functional group
Compounds can be divided into different groups based on the functional groups that they
contain. For example, each amino acid (many of which connect to make proteins) contains
a carboxylic acid and amine functional group. Which of the following is true about the
number of functional groups a compound can contain?
a) Each compound only contains one functional group
b) A compound may either contain many or very few functional groups
c) Each compound only contains two functional groups
d) Compounds may either contain one or two functional groups
Readings & ResourcesStoker, H.S. (2014). General, Organic and Biological Chemistry
(7th ed.). Belmont, CA: Brooks/Cole, Cengage Learning.
Timberlake, K.C. (2016). General, organic, and biological chemistry: structures of life( 5th ed.). Boston, MA: Pearson.
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter P.( 2014). Molecular biology of the cell (6th ed.). New York, NY: Garland Science.
Berg, J.M., Tymoczko, J.L., & Stryer, L. (2012). Biochemistry (7th ed.). New York, NY: W.H. Freeman.
Dominiczak, M.H. (2007). Flesh and bones of metabolism.Edinburgh, UK: Elsevier Mosby.
Tortora, G.J., & Derrickson, B. (2014). Principles of Anatomy and Physiology (14th ed.). Hoboken, NJ: John Wiley & Sons.
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