Biochemistry for Complementary Therapists Session 5 Introduction to Organic Chemistry ... · · 2016-08-11Biochemistry for Complementary Therapists Session 5 ... Introduction to

BIOO211Biochemistry for Complementary Therapists

Session 5

Introduction to Organic Chemistry

Department of Bioscience

endeavour.edu.au

© Endeavour College of Natural Health endeavour.edu.au 2

Biochemistry for Complementary

Therapists

Session 5 Introduction

to Organic Chemistry

© Endeavour College of Natural Health www.endeavour.edu.au 3


Chemistry & Biochemistry –

Introduction To Organic Chemistry

This session includes:

1. Introduction to organic chemistry

and biochemistry

2. Organic compounds and

biochemistry

3. Formulas

4. Naming of organic compounds

5. Carbon and its functional groups

(overview)

6. Isomers


Organic Chemistry And

Biochemistry

o Organic chemistry is the chemistry of organic

compounds

o Biochemistry is the study of the chemical processes in

living organisms: structure and function of cellular

components such as proteins, carbohydrates, lipids,

nucleic acids and other biomolecules

o Organic compounds include proteins, carbohydrates,

lipids, nucleic acids etc

o Metabolism is all the chemical reactions in living cells

that carry out molecular and energy transformation using

organic molecules


Organic Compounds

o Always contain carbon and

hydrogen

o Mostly contain covalent bonds

o Usually large, unique

molecules with complex

functions

o Make up 40% of body mass


Comparing Organic And Inorganic

Compounds

See Table 12.1, Some typical properties of organic and inorganic compounds (Timberlake, (2016, p. 477)


Properties Of Organic Compounds

Typical organic compounds

o Have low boiling

points/evaporate easily.

o Are inflammable.

o Are soluble in non-polar

solvents.

o Are not soluble in water, see

Section 12.1 Organic

Compounds Figure

(Timberlake, 2016, p. 477))

Oil (organic) and

water (inorganic)

© 2016 Pearson Education, Inc.


Bonding with Carbon

o Carbon has 4 valence electrons; hydrogen has 1.

•

• C • H ••

o To achieve an octet, carbon forms four bonds.


Organic Molecules

o In organic molecules, valence electrons form covalent bonds between carbon atoms.

H H H H

• • • • | |H C C H H—C—C—H

• • • • | |H H H H

Ethane, CH3—CH3


Learning Check, C, 4 Covalent Bonds, O,

2 Covalent Bonds To Complete Octets

Complete the structure of the organic molecule

by adding the correct number of hydrogen

atoms.

C—C—C—O


Solution, C, 4 Covalent Bonds, O, 2

Covalent Bonds To Complete Octets

Complete the structure of the organic molecule by

adding the correct number of hydrogen atoms.

H H H| | |

H—C—C—C—O—H| | |

H H H


Types of Organic Compounds

o Organic compounds are divided into different types based on their functional groups


Functional Groupso Carbon combines with other elements to form functional groups.

o Site of chemical reactions

o Particular functional groups undergo similar chemical reactions

o Used to classify and name organic compounds.


Formulas For Organic Compounds

o How are the structures of organic

compounds represented?

• The structure of organic

compounds can be

represented by:

o Molecular formula

• Indicate the number and

types of atoms present in a

molecule but contain no

information about their

arrangement.

o Structural and line-bond formulas


Structural FormulasStructural formulas show the arrangement ofatoms in an organic compound.

o In expanded structural formulas, all the individual bonds are drawn.

o In condensed structural formulas, each carbon is written with the H atoms connected to it.

H H| |

H—C— = CH3— methyl; — C— = —CH2 —| |H H


Line-bond Formulas

o Because each C atom has

a tetrahedral arrangement,

the geometrical

arrangement of carbon

atoms is not a straight line.

o A line-bond formula

abbreviates the carbon

chain and shows only the

zigzag pattern of bonds

from carbon atom to

carbon atom


Glucose – Expanded And

Condensed Structural Formulas

o Structural formulas of glucose

o The carbohydrate glucose is a

structure with many functional groups

• On the left is the expanded

structural formula and on the right

is the condensed geometric

formula

• They are both the same molecule,

glucose

• In the condensed formula, there

are 5 C atoms and 1 O in the ring

and one C atom above the ring;

the atom H is assumed as shown

in Fig. 2.13 (Tortora and

Derrickson, 2014)


Naming Organic Compounds

o Common names

• There are well-established common names that remain in

general usage

• Common names are not based on any internationally agreed

system

o The IUPAC system

• International Union of Pure and Applied Chemistry establishes

the rules for naming organic compounds systematically

o In either system, the naming is based on the functional

group


The IUPAC System Basics

The IUPAC system of naming

indicates:

o The length of the parent

carbon chain by the ‘stem’

(eg meth-, eth-, prop-, but-

etc)

o The functional group by the

ending (eg –ane for alkanes, -

ene for alkenes)

o A ring shape (cyclo)

o Branches (eg alkyl groups)

and their position on the

parent chain by numbering

Number

of C

atom

Molecular

formula

Condensed formula Name

1 CH4 CH4 Methane

2 C2H6 CH3-CH3 Ethane

3 C3H8 CH3-CH3-CH3 Propane

4 C4H10 CH3-CH3-CH3-CH3 Butane

5 C5H12 CH3-CH3-CH3-CH3-CH3 Pentane

IUPAC names of commalkane,

Refer to Timberlake, 2016, p. 480


Naming OverviewIn the IUPAC system:

o The longest C chain is named as the main chain.

o Any carbon branches use their alkyl names, in Table 11.5 (Timberlake, 2010, p. 424; 2013, p. 421)

o For side chains, which branch off from a given carbon in the main chain, number the main chain carbon that contains the branch

o The main chain is numbered in the direction that gives lower set of numbers

o Branches are listed in alphabetical order.


Names And Formulas Of Some

Common Alkyl Groups

Many carbon branches use their alkyl group names. Timberlake 2016, p.485

© 2016 Pearson Education, Inc.


Learning Check, Naming Example

The structural formula is drawn from the IUPAC name.

2, 3-dimethylpentane

2, 3 dimethyl pentaneLocation of Two CH3- groups 5 carbon main chain

branches on attached with single C-C bonds

Solution, Naming example


Polarity of organic compounds

o Alkanes are non polar

o An organic compound is water soluble only if it contains

one polar functional group that can hydrogen bond with

water

o The polar functional groups include the following

groups, hydroxyl (OH), carboxyl (COOH), thiol (SH),

amine (NH2), ether (C-O-C), ketone (C=O), ester

(-COO-).

o If the carbon chain is long even if it has polar group, will

not be soluble in water due to hydrophobic interaction.


HydrocarbonsAlkanes:

o Have only single C—C bonds

o Have the maximum number of Hydrogens attached (saturated)

o Have a general formula of CnH2n +2.

o Name ends in “ane”

o Cycloalkanes have the C atoms in a ring (egcyclopropane)

Alkenes have double bonds

Alkynes have triple bonds


Cycloalkanes

• are cyclic alkanes.

• have two fewer hydrogen atoms than the open chain form.

• are named by using the prefix cyclo before the name of the

alkane chain with the same number of carbon atoms.

propane (C3H8) cyclopropane (C3H6)

H2C

H2C

CH2H3C

H2C

CH3

Refer to Table 12.4 (Timberlake, 2016, p. 482

Cycloalkanes


Classification of Carbon Atoms

Carbon atoms are classified according to the number of attached carbon atoms.

o Primary (1°) bonds to one carbon atom.

o Secondary (2°) bonds to two carbon atoms.

o Tertiary (3°) bonds to three carbon atoms.CH3|

CH3 —CH2—CH2—CH3 CH3—CH—CH3

secondary primary tertiary


Alkenes And Alkynes

o Alkenes contain a

double bond between

adjacent carbon atoms.

• IUPAC name ends in

“ene”

o Alkynes contain a triple

bond

• IUPAC name ends in

“yne”


Haloalkaneso In a haloalkane, one or more H atoms in an alkane is

replaced by a halogen atom.

o For example

Cl Br

| |CH3—CH—CH2—CH—CH2—CH3

4-bromo-2-chlorohexane


Alcohols, Ethers And Thiols

o An alcohol contains the hydroxyl (-

OH) functional group

• IUPAC - ends in (-ol); (methanol)

In an ether, an oxygen atom is bonded to

two carbon atoms

–C–O–C– .

(IUPAC –alkoxy alkane), (ethoxy

ethane)

o A thiol has a S atom instead of an O

bonded to two carbon atoms

• IUPAC - ends in (-thiol), (methane

thiol)

From 11.5 Functional groups, Alcohols, Thiols and

Ethers(Timberlake, 2010, p. 435)


Phenols

A phenol contains

o A hydroxyl group

(—OH) attached

to a benzene ring.

o Benzene (C6H6) is

a stable structure

o They are aromatic

compounds

From Section 13.1 Alcohols,

Phenols, & Thiols (Timberlake,

2010, p. 480)


Benzene Ring And

Common SubstituentsBenzene (C6H6) is a stable

structure

Some common names have been

in use for many years. – toluene,

aniline and phenol – these names

have been taken into the IUPAC

system

From Section 12.8 Aromatic Compounds

(Timberlake, 2016, p. 506)


Aromatic compound- Benzene

Substitution Reactionso In a substitution

reaction, a hydrogen

atom on a benzene

ring is replaced by an

atom or group of

atoms;

o halogenation

(halogen),

o nitro group (—NO2)

and

o sulfonation (—SO3H

group)

ChlorobenzeneBenzene

FeCl3 HCl+

Cl

Cl2+

H

NitrobenzeneBenzene

H2SO4 HOH+

NO2

HNO3+

H


Aldehydes And Ketoneso An aldehyde contains a carbonyl

group (C=O), which is a carbon atom with a double bond to an oxygen atom, attached to at least one hydrogen.• IUPAC - ends in (-al); (ethanal)

o In a ketone, the carbon of the carbonyl group is attached to two other carbon atoms• IUPAC - ends in (-one), (propanone)

Copyright © 2007 by Pearson Education, Inc.

Publishing as Benjamin Cummings

Adapted from Timberlake

(2010, p. 435 ; 2013, p.

509)


Carboxylic Acids And Esters

o Carboxylic acids contain the

carboxyl group, which is a

carbonyl group attached to a

hydroxyl group.

• IUPAC - ends in (-oic acid)

(ethanoic acid)

O

— C—OH

o An ester contains the carboxyl

group between carbon atoms

• IUPAC - ends in (-oate); (ethyl

methanoate)

Adapted from Timberlake ( 2010; p. 436;

2013, p. 577)


Amines And Amides

o In amines, the functional

group is a nitrogen atom.

|

— N —

IUPAC - ends in (-amine),

(methanamine)

o In amides, the hydroxyl

group of a carboxylic acid is

replaced by a nitrogen group.

• IUPAC - ends in (-amide);

(ethanamide)

Section 18.1 Amines and Section

18.4 Amides (Timberlake, 2010, p.

645, p.658 )


Functional Groups In Everyday

Items

Methyl amine (fish)

Environmental Note: Functional

Groups in Familiar Compounds

(Timberlake, 2010, p. 438; 2013,

pp 436-7))

Esters in fruit; carboxylic

acid group in acetic acid;

methylamine in fish; ether

and many hydroxyl

groups in glucose


Isomerism

o Organic compounds that have identical molecular formula but

different arrangement of atoms (structure).

o The isomers interact differently with the receptor molecules and

induce different sensations.

o The two isomers of the amino acid, leucine, for have different tastes,

L -leucine is bitter, whereas D-leucine is sweeter.

o Structural isomers

• Have different bonding arrangements (Ethyl alcohol and dimethyl

ether, it is a constitutional or functional group isomerism)

o Stereoisomers

• Contain the same functional groups and differ only in the

arrangement of atoms in space (cis trans isomerism).

• Cis and trans fatty acid (unsaturated with C = C (double bond) in

the chain.


Structural Isomers

o What are structural (constitutional)

isomers?

• Molecules that have the same molecular

formula, but different bonding

arrangements

• They can have different physical and

chemical properties

e.g. butane and methyl propane see Fig.

11.5

Section 11.5 Functional Groups:

Alcohols, Thiols and Ethers

(Timberlake, 2010, p. 435; 2013, p.

420 )

ethanol vs dimethyl ether


Stereoisomers

Cis-trans isomers:

o cis isomer - groups are

attached on the same side of

the double bond.

trans isomer - the groups are

attached on opposite sides

Enantiomers – chiral

molecules (mirror images

cannot be superimposed; D

and L forms of glucose, D

form is biologically active)


Chirality

o Chiral compounds have the same number of atoms

arranged differently in space.

o A chiral carbon atom is bonded to four different groups.

o The mirror images of chiral compounds cannot be

superimposed.

o The mirror images of achiral compounds can be

superimposed.

180° rotation in 3-D, then

superimpose = achiral


Mirror Images

o The mirror images of chiral compounds cannot be

superimposed.

o For example, when the H and I atoms are aligned, the Cl

and Br atoms are on opposite sides as in Fig. 14.9

(Timberlake, 2016, p. 564)


Achiral Structures are

Superimposableo When the mirror image of an achiral structure is rotated,

the structure can be aligned with the initial structure. Thus this mirror image is superimposable in Fig. 14.9 (Timberlake, 2016, p. 564).


Learning Check, Chiral Carbons

o Identify each as a chiral or achiral compound.

C

Cl

CH3H

CH2CH3

C

Cl

CH3H

H

A B

C

Cl

CH3H

Br

C


Solution, Chiral Carbons

o Identify each as a chiral or achiral compound.

Chiral Achiral Chiral

C

Cl

CH3H

CH2CH3

C

Cl

CH3H

H

A B

C

Cl

CH3H

Br

C


Concept Map, Introduction to

Organic Chemistry


Post-session Summary /

Revision Questions:Introduction to Organic Chemistry:

1. Define organic chemistry.

2. Explain how carbon can combine to make so many compounds.

3. Describe the tetrahedral structure of carbon.

4. Use the IUPAC system to name hydrocarbons and learn the names of the

first ten.

5. Draw the full, condensed and very condensed structure of alkanes.

6. Draw and name cycloalkanes using the IUPAC naming system.

7. Understand and draw structural isomers of alkanes.

8. Discuss the polarity of organic molecules.

9. Describe carbon classification – primary, secondary, tertiary

10. Explain the concept of isomers and explain the difference between

structural and stereoisomers.

11. Briefly describe and draw the functional groups of alkenes, alkynes,

alcohols, ethers, phenols, aldehydes, ketones, amines, carboxylic acids,

amides, esters and name common examples of each.


References & Diagramso Timberlake, KC 2016, General, organic, and biological

chemistry: structures of Life, 5th edn, Pearson, Boston.

o Timberlake, KC 2013, General, organic, and biological

chemistry, 4th edn, Pearson Benjamin Cummings,

Boston.

o Timberlake, KC 2010, General, organic and biological

chemistry, 3rd edn, Pearson Benjamin Cummings

o Timberlake, KC 2007, General, organic and biological

chemistry, 2nd edn, Pearson Benjamin Cummings


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Biochemistry for Complementary Therapists Session 5 Introduction to Organic Chemistry ... · · 2016-08-11Biochemistry for Complementary Therapists Session 5 ... Introduction to