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98 VII. ORGANIC AND BIOCHEMISTRY / A. Introduction to Organic Compounds
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VII. ORGANIC AND BIOCHEMISTRY
A. Introduction to Organic Compounds
1. Classifications
ORGANIC
HYDROCARBONS
HETERO ATOMS
NUMEROUS FUNCTIONAL GROUPS
SATURATED
UNSATURATED
AROMATIC
2. Carbon is unique since it can bond with itself to form long continuous chains, or
branched chains. This is why life is based on carbon; there is no limit to the number
of compounds.
3. Number of Bonds
a) Carbon always forms 4 covalent bonds since it can achieve 4 unpaired electrons.
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C
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sp3
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C
C
C
sp2
sp
sp
b) Hydrogen always forms 1 covalent bond, since it has one unpaired electron.
c) Oxygen always forms 2 covalent bonds, 2 unpaired electrons.
O
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sp3
O
sp2
d) Nitrogen always forms 3 covalent bonds, 3 unpaired. (We will only see single
bonds.)
N
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sp3
H
99 VII. ORGANIC AND BIOCHEMISTRY / A. Introduction to Organic Compounds
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e) Often, for the sake of simplicity, the hydrogen atoms are not shown in the structure,
and the molecules are drawn linearly. To fulfill the bonding requirements of C, O, and N (as
well as some other atoms) we correctly assume that the un-shown bonds are to hydrogens.
Example(1): Fill in the H atoms in the molecules below:
CCCC
CCCCC
CCCCC
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C
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C
Example(2): Fill in the H atoms in the molecules below:
COC
CCCO
CCNC
CCCN
CCCC
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O
4. Molecular Shapes (You should be able to predict bond angles by applying what you
learned in the previous chapter about predicting molecular shapes.)
Example(3): Determine all of the bond angles in CCCC .
100 VII. ORGANIC AND BIOCHEMISTRY / A. Introduction to Organic Compounds
Example(4): Determine all of the bond angles in COC .
5. Condensed Structural Formulas
Example(5): Write the condensed structural formulas of the molecules below:
CCCC
CCCCC
CCCCC
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C
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C
Example(6): Write the condensed structural formulas of the molecules below:
COC
CCCO
CCCN
CCCC
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O
CCNC
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101 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
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B. Hydrocarbons and Isomers
1. Saturated Hydrocarbons
a) Alkanes: have only single bonds between carbons.
e.g. CCCC
b) Cycloalkanes: are cyclic and have only single bonds between carbons.
e.g.
C
C
C
C
C
2. Unsaturated Hydrocarbons
a) Alkenes: have a double bond between 2 carbons. e.g. CCCC
b) Alkynes: have a triple bond between 2 carbons. e.g. CCCCC
c) Unsaturated Cyclic Compounds: have one or more multiple bonds between C’s .
e.g
C
C
C
C
C
d) Aromatic compounds: are cyclic and have alternating double bonds. e.g.
C
C
C
C
C
C
3. Alkanes
a) General formula: CnH2n+2
H H H H H H
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HCCCCCCH
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H H H H H H
Each C has 2 H’s, and then an extra H on the left
and right end of the carbon chain.
102 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
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b) Naming “straight chained” alkanes”. The name is the root name +ane
1C
2 C’s
3 C’s
4 C’s
5 C’s
methane
ethane
propane
butane
pentane
6 C’s
7 C’s
8 C’s
9 C’s
10 C’s
hexane
heptane
octane
nonane
decane
c) Branched alkanes and structural isomers
Isomers: different molecules that by coincidence have the same chemical formula.
Example(1): Draw the two different molecules with the formula C4H10
Example(2): Draw three different molecules with the formula C5H12
Note: there is no such thing as a branch on an end carbon.
d) Naming branched alkanes
i) Find the longest continuous carbon chain, the name of the chain is its root name +
ane.
ii) If there is one or more branches on the chain, number the chain from the end
closest to a branch.
iii) Each branch must have a locating number and a name. A branch is named with
its root name + yl.
103 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
Example(3): Name the following compounds:
C
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CCCC
CCCC
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C
Example(4): Name the following compounds:
C
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CCCC
C
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CCC
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C
Example(5): Name the following compounds:
CCCCCC
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C C
CCCCC
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C
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C
4. Alkenes
a) General formula: CnH2n
e.g.
H H H H
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HCCCCH
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H
H
b) Unsaturated: carbons are not completely filled or saturated with hydrogen.
Anytime there is one or more multiple bonds between carbons, the
compound is unsaturated.
c) Hydrogenation: The addition of hydrogen to an unsaturated compound.
(done at high pressure and with a catalyst.)
Alkene + H2  Alkane
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104 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
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Example(6): What product is produced when CH3CHCHCH3 is hydrogenated?
Example(7): What product is produced when CH2CHCH2CH2CH3 is hydrogenated?
d) Structural isomers of alkenes
Example(8): Which molecule or molecules are structural isomers of:
CCCC
CCCC
CCCC
C
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CCC
e) Geometric isomers of alkenes
Example(9): Draw the 2 geometric isomers of CCCC
f) Naming alkenes
Alkenes are named like alkanes: you must find and number the longest carbon chain
containing the double bond. The numbering begins from the end closest to the double bond.
The longest chain is name by its root name + ene.
Example(10): Name the following compounds:
CCCC
C
C
CC
C
CC
C
105 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
5. Alkynes
a) General formula: CnH2n-2
e.g.
H
H
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HCCCCH
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H
H
Example(11): If an alkyne has 6 carbon atom, how many hydrogen atoms will it have?
b) Hydrogenation
Alkyne + 2H2  Alkane
Example(12): What product is produced when CH3C≡CCH2CH3is completely hydrogenated?
Example(13): What product is produced when CH3C≡CCH3 is partially hydrogenated?
c) Isomers
Example(14): Draw the unbranched isomers of C5H8
d) Naming Alkynes
Alkynes are named like alkenes: you must find and number the longest carbon chain
containing the triple bond. The numbering begins from the end closest to the triple bond.
The longest chain is name by its root name + yne.
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106 VII. ORGANIC AND BIOCHEMISTRY / B. Hydrocarbons and Isomers
Example(15): Name the following compounds:
CCCC
CCCC
Example(16): Name the following compounds:
CCCC
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C
CCCC
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C
6. Aromatic Compounds
a) Aromatic Hydrocarbons: are cyclic planer compounds with alternating double
bonds.
Example(17): Draw the two resonance structure of the cyclic compound benzene, C6H6 Show the
shorthand representation.
Example(18): Draw the three resonance structure of the bicyclic compound naphthalene, C10H8 Show
the shorthand representation.
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107 VII. ORGANIC AND BIOCHEMISTRY / C. Oxygen Functional Groups
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C. Oxygen Functional Groups
1. Functional Group: is a special group of atoms other than singly bonded carbons or
hydrogens.
2. Preview of Oxygen Functional Groups
Oxygen always forms 2 bonds: –O– or O=
hydrocarbon–O–H
Alcohol
hydrocarbon–O–hydrocarbon
Ether
O
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hydrocarbon–C–H
Aldehyde
O
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hydrocarbon–C–hydrocarbon
Ketone
O
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hydrocarbon–C–O–H
Acid
O
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hydrocarbon–C–O–hydrocarbon
Ester
3. Alcohols contain one O atom singly bonded to one carbon.
Example(1): Add the H atoms to the molecules below.
CCCO
CCC
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O
a) Any hydrocarbon with a covalently bonded –O–H is no longer a hydrocarbon, but
an alcohol.
b) A covalently bonded –O–H is called a hydroxyl group. (An ionicly bonded OH-1 is a
hydroxide ion.)
c) General structure: R–O–H, where R stands for the rest of the molecule, usually a
hydrocarbon.
d) Naming Alcohols
Find and number the longest carbon chain containing the hydroxyl (alcohol function). The
numbering begins from the end closest to the hydroxyl. In the IUPAC system: # + root + anol.
108 VII. ORGANIC AND BIOCHEMISTRY / C. Oxygen Functional Groups
STRUCTURE
IUPAC
Common System Name
COH
methanol
methyl alcohol (poisonous)
CCOH
ethanol
ethyl alcohol (drinkable but
poisonous in large quantities)
CCCOH
1-propanol
propyl alcohol
CCC
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O
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H
2-propanol
isopropyl alcohol
(rubbing alcohol)
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Example(2): Name the compounds below using the IUPAC system.
CCC
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O
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H
CCCC
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O
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H
4. Ethers contain one O atom singly bonded between two carbon groups.
CCOC
CCCOCC
a) General structure: ROR’
b) Naming ethers
Common System: name the R groups as branches off of the ether function.
CCOC
CCCOCC
CCOCC
ethyl methyl ether
ethyl propyl ether
(or propyl ethyl ether is OK)
diethyl ether (common ether)
5. Aldehydes contain one O atom doubly bonded on an end carbon.
O
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a) General structure: RCH
109 VII. ORGANIC AND BIOCHEMISTRY / C. Oxygen Functional Groups
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Example(3): Add the H atoms to the molecules below.
O
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CCCCC
O
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CCCC
CCCC
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C=O
b) Naming Aldehydes DO NOT HAVE TO DO
c) Common Aldehydes
formaldehyde R = H
acetaldehyde R = CH3
the root name form is an old name for 1 carbon
the root name acet is an old name for 2 carbon
Example(4): Draw the structure of formaldehyde and acetaldehyde.
6. Ketones contain one O atom doubly bonded on any interior carbon (i.e. not on an end
carbon).
a) General structure
O
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RCR’
b) Naming ketones
Common System: name the R groups as branches off of the ketone function.
Example(5): Name the compounds below using the common system.
O
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CCCCC
O
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CCCC
CCC
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O
110 VII. ORGANIC AND BIOCHEMISTRY / C. Oxygen Functional Groups
7. Carboxylic Acids
O
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a) General structure: RCOH
b) Naming carboxylic acids
IUPAC system: Find the longest carbon chain containing the carboxyl (acid function). Name
with the root name + anoic.
Example(6): Name the following acids:
CHOOH
CH3COOH
CH3CH2COOH
CH3CH2CH2COOH
Example(7): What are the common names of CHOOH and CH3COOH ?
c) Acid property
All carboxylic acids are weak in water, and have Ka’s of about 1x 10‾5
Example(8): a)Write the equation for the ionization of CH3COOH in water.
b) Show the two resonance structures of the resulting anion.
c) Show the shorthand notation for the resonance.
8. Esters
O
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a) General structure: RCOR
b) Formation
Esterfication: dehydration between an alcohol and an acid.
alcohol + acid → ester + H2O
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111 VII. ORGANIC AND BIOCHEMISTRY / C. Oxygen Functional Groups
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Example(9): Give the structure of the ester which forms by the reaction of 1-propanol and acetic acid.
( This is the ester that give pears their flavor.)
JUST FOR FUN:
Octyl acetate
Oranges
Isoamyl acetate
Banana
Ethyl Butyrate
Pineapple
Butyl acetate
Apple
Methyl trans-cinnamate
Strawberry
112 VII. ORGANIC AND BIOCHEMISTRY / D. Nitrogen Functional Groups
D. Nitrogen Functional Groups
1. Amines
a) General Structure
i) primary amine R–N–H
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H
ii) secondary amine R–N–R’
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H
iii) tertiary amine R–N–R’
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R’’
Example(1): a)What is the hybridization of the N in an amine?
b) What are the bond angles in an amine?
b) Nomenclature
Common System: The hydrocarbon(s) are named as branches off of the amine function.
Example(2): Name the following amines using the common system.
CH3CH2NH2
CH3CH2NH
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CH3
CH3CH2N CH2CH3
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CH2CH2CH3
c) Base properties
All amines are weak bases in water, and have Kb’s of about 1x 10‾4
Example(3): Show the reaction of CH3NH2 with water. (Kb = 3.6 x 10ˉ4)
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113 VII. ORGANIC AND BIOCHEMISTRY / D. Nitrogen Functional Groups
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JUST FOR FUN:
2. Amides
a) General Structure
O
║
R–N–C–R
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R
b) The amide functional group is found in proteins (and many other compounds as
well). In a protein it is sometimes referred to as the peptide bond.
3. The structure is below containing two functional groups. What class of compound is it
classified as?
a) General Structure
H O
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H–N—C—C—O–H
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H R
114 VII. ORGANIC AND BIOCHEMISTRY / E. Triglycerides
E. Triglycerides
1. Triglycerides: are esters made from glycerol and three fatty acid molecules.
They are commonly referred to as fats or oils.
a) Glycerol: is a 3 carbon, 3 hydroxyl compound
(propane–1,2,3 triol)
C―O―H
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C―O―H
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C―O―H
b) Fatty Acids: are “straight” chain carboxylic acids. The most common naturally
occurring fatty acids have from 16 to 20 carbon atoms. They can be
saturated or unsaturated.
Two examples are (you do not have to know these):
Stearic acid: CH3(CH)13COOH, Oleic acid: CH3(CH2)7CHCH(CH2)7COOH
(saturated)
(unsaturated)
c) Recall an alcohol and an acid form an ester through dehydration.
d) Block diagram:
g
l
y
c
e
r
o
l
part
fatty acid part
fatty acid part
fatty acid part
Example(1): Draw the structure of the triglyceride formed from glycerol and 3 stearic acid molecules.
e) Triglycerides can be broken in to glycerol and 3 fatty acids by hydrolysis.
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115 VII. ORGANIC AND BIOCHEMISTRY / E. Triglycerides
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Example(2): In general terms, what products, and how many of each, are formed by the hydrolysis of a
triglyceride.
f) Triglycerides which are solid at room temperature are called fats. Those that are
liquid are oils. Whether it is a fat or oil depends on several factors. The most common factor
is the degree of saturation of the hydrocarbon chains. The more saturated the hydrocarbon
chains, the higher the melting point.
g) Hydrogenation: the addition of hydrogen at the site of a double (or triple) bond in a
hydrocarbon chain. (Done at high pressure H2 and with a catalyst.)
Oil + H2 → Fat
116 VII. ORGANIC AND BIOCHEMISTRY / F Carbohydrates
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F. Carbohydrates
1. Classifications
a) Monosaccharides: are simple sugars with a general formula of CnH2nOn. the most
common monosaccharides have n=3 to 6.
Block diagram:
Example(1): Write the formula of a monosaccharide with 5 carbon atoms.
b) Disaccharides: are formed by bonding together two monosaccharides through the
process of dehydration.
Block diagram:
Example(2): Write the formula of a disaccharide made from 2 monosaccharides, each containing 6
carbons. (Remember dehydration occurs between the monosaccharides.)
c) Polysaccharides: contain many monosaccharides; anywhere from 100 to 3000.
They can be “straight chained” or branched.
Block diagram:
2. Monosaccharides are either polyhydroxyl aldehydes or polyhydroxyl ketones (when they
are in their open form).
Example(3): Using the definition of a monosaccharide, draw any five carbon monosaccharide with an
aldehyde function in the “open form”.
117 VII. ORGANIC AND BIOCHEMISTRY / F Carbohydrates
Example(4): Using the definition of a monosaccharide, draw any six carbon monosaccharide with an a
ketone function in the “open form”.
a) Classification of monosaccharides
The classification is base on the two criteria: the functional group, and the number of carbons:
i) If the functional group is an aldehyde, its classification is an aldo.
If the functional group is a ketone, its classification is a keto.
ii) 3 carbons is a triose.
4 carbons is a tetrose.
5 carbons is a pentose.
6 carbons is a hexose.
Example(5): Classify the two monosaccharides you drew in the previous two examples.
b) Closed form of monosaccharides
H
O
C
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HC―OH
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HO―CH
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HC―OH
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HC―OH
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6 CH2OH
1
H
O
C
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HC―OH
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HO―CH
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HC―OH
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HC―OH
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6 CH2OH
1
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118 VII. ORGANIC AND BIOCHEMISTRY / F Carbohydrates
alpha glucose
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beta glucose
c) Some common monosaccharides:
i) Glucose (dextrose) is the primary fuel that our bodies burn. It is an aldohexose.
ii) Galactose is found in the brain and nervous tissue. It is an aldohexose.
iii) Fructose is fruit sugar. It is a ketohexose
3. Disaccharides
a) Recall that a dicassharide is formed by dehydration between two monosaccharides.
b) Some common disaccharides
119 VII. ORGANIC AND BIOCHEMISTRY / F Carbohydrates
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i) Sucrose is table sugar. It is made from glucose and fructose.
ii) Maltose is malt sugar. It is made from glucose and glucose.
iii) Lactose is milk sugar. It is made from glucose and galactose.
c) Disaccharides can be broken into monosaccharides by hydrolysis.
Example(6): What products are produced by the hydrolysis of lactose?
4. Polysaccharides are polymers of thousands of monosaccharides. The most important
polysaccharides are based on glucose.
a) Starch is a mixture of two polysaccharides, amylose and amylopectin.
i) Amylose is unbranched, and is made from alpha glucose.
ii) amylopectin is branched and is also made from alpha glucose.
Amylose
b) Cellulose is made from beta glucose, and is unbranched. It is plant fiber.
c) Glycogen is a branched polysaccharide made from alpha glucose. It is the form in
which glucose is stored in our bodies.
120 VII. ORGANIC AND BIOCHEMISTRY / G. Proteins
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G. Proteins
1) Proteins: are polymers of amino acids. The amino acids go together by dehydration
between the acid function on one molecule, and the amine function on
another molecule
a) Drawing an amino acid.
i) Start with a single carbon atom, which we will call the central atom (even though it
is not physically in the center)
ii) Add a primary amine to the central carbon:
H–N―C
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H
iii) Add a carboxylic acid function to the same carbon atom
O
║
H–N―C―C–O–H
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H
iv) Add a hydrogen atom and an R group to the central carbon.
H O
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H–N―C―C–O–H
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H R
b) The 20 naturally occurring amino acids differ only in their R group.
The simplest R group is a H atom, the next simplest is a CH3 group. Some R groups contain
functional groups of their own: acid function, amine function, alcohol function, amide function,
and others.
2. Dipeptide: is made from putting together two amino acids by dehydration. The
dehydration occurs between the acid function on one molecule and the
amine function on the other
121 VII. ORGANIC AND BIOCHEMISTRY / G. Proteins
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The amino acids are faced head to tail (i.e. acid to amine.
Example(1): Draw the two possible dipeptides that can be formed from two amino acids. One amino
acid with R=H, the other with R= CH3
3. Polaypeptide: is many amino acids (usuall defined as less than 100) bonded together.
4. Proteins: are unbranched polypeptides with molecular weighs ranging from about
5000 g/mol into millions of g/mol.
5. Hydrolysis:
The peptide bonds in a protein, polypeptide or dipeptide can be broken by hydrolysis to yield
the individual amino acids.