Introduction to

Organic Chemistry

BIOO211

BIOCHEMISTRY FOR COMPLEMENTARY THERAPISTS

Session 5

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

AROMATIC HYDROCARBONS

• Also known as ARENES

– Benzene & its derivatives

• Functional group:

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.