Download BIOO211 SN05 Lecture OrganicChem

BIOO211
Biochemistry for Complementary Therapists
Session 5
Introduction to Organic Chemistry
Department of Bioscience
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Biochemistry for Complementary
Therapists
Session 5 Introduction
to Organic Chemistry
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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
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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
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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
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Comparing Organic And Inorganic
Compounds
See Table 12.1, Some typical properties of organic and inorganic compounds (Timberlake, (2016, p. 477)
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Properties Of Organic Compounds
Typical organic compounds
o Have low boiling
points/evaporate easily.
Oil (organic) and
water (inorganic)
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))
© 2016 Pearson Education, Inc.
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Bonding with Carbon
o Carbon has 4 valence electrons; hydrogen has 1.
•
•
C•
H•
•
o To achieve an octet, carbon forms four bonds.
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Organic Molecules
o In organic molecules, valence electrons form
covalent bonds between carbon atoms.
H H
H H
••
••
••
••
HCCH
H H
|
|
|
|
H—C—C—H
H H
Ethane, CH3—CH3
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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
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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
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Types of Organic Compounds
o Organic compounds are divided into different
types based on their functional groups
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Functional Groups
o
o
o
o
Carbon combines with other elements to form functional groups.
Site of chemical reactions
Particular functional groups undergo similar chemical reactions
Used to classify and name organic compounds.
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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
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Structural Formulas
Structural formulas show the arrangement of
atoms 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
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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
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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)
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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
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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-, butetc)
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
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Naming Overview
In 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.
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Names And Formulas Of Some
Common Alkyl Groups
Many carbon branches use their alkyl
group names. Timberlake 2016, p.485
© 2016 Pearson Education, Inc.
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Learning Check, Naming Example
The structural formula is drawn from the IUPAC name.
2, 3-dimethylpentane
2, 3
Location of
branches on
dimethyl
Two CH3- groups
attached
pentane
5 carbon main chain
with single C-C bonds
Solution, Naming example
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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.
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Hydrocarbons
Alkanes:
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 (eg
cyclopropane)
Alkenes have double bonds
Alkynes have triple bonds
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Cycloalkanes
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)
H2
H2
C
C
H3C
CH3
H2C
CH2
Refer to Table 12.4 (Timberlake, 2016, p. 482
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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
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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”
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Haloalkanes
o 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
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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)
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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)
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Benzene Ring And
Common Substituents
Benzene (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)
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Aromatic compound- Benzene
Substitution Reactions
o 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)
H
+
Cl
Cl2
FeCl3
Benzene
+
HCl
Chlorobenzene
H
+ HNO3
NO2
H2SO4
Benzene
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+
HOH
Nitrobenzene
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Aldehydes And Ketones
o 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)
Adapted from Timberlake
(2010, p. 435 ; 2013, p.
509)
Copyright © 2007 by Pearson Education, Inc.
Publishing as Benjamin Cummings
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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)
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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 )
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Functional Groups In Everyday
Items
Environmental Note: Functional
Groups in Familiar Compounds
(Timberlake, 2010, p. 438; 2013,
pp 436-7))
Methyl amine (fish)
Esters in fruit; carboxylic
acid group in acetic acid;
methylamine in fish; ether
and many hydroxyl
groups in glucose
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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.
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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
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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)
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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
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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)
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Achiral Structures are
Superimposable
o 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).
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Learning Check, Chiral Carbons
o
Identify each as a chiral or achiral compound.
Cl
H C CH3
CH2CH3
A
Cl
H C CH3
Cl
H C CH3
H
Br
B
C
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Solution, Chiral Carbons
o Identify each as a chiral or achiral compound.
Cl
Cl
H C CH3
H C CH3
H
CH2CH3
Chiral
A
Cl
Achiral
H C CH3
Br
Chiral
B
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Concept Map, Introduction to
Organic Chemistry
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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.
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References & Diagrams
o 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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