ORGANIC CHEMISTRY

Organic chemistry is the chemistry of carbon

compounds Carbon is in the group 4 or 14 of the

periodic table.

Carbon always forms covalent bonds.

Covalent Bond - a chemical bond that involves the sharing of electron pairs between
atoms
Valence is the number of covalent bonds an atom can form. It is usually equal to the number
of electrons required to complete the atom's outermost (valence) electron shell.
Carbon has a valence of 4 and can form many types of large molecules.

As carbon has 4 electrons in its valence level (2,4) it forms 4 covalent

bonds. When all of them are single bond, they have a tetrahedral
arrangement.
In organic molecules:
• Carbon always forms 4 bonds.

• Oxygen forms 2 bonds

• Halogen and Hydrogen form 1 bond

 Homologous Series

A homologous series is a series of compounds with the same functional group, in which
each member differs from the next by -CH2-.
Features of homologous series:
• Successive compounds differ from each other by a -CH2- group (methylene
group)
• The compounds can all be represented by a general formula

• The compounds have similar chemical properties.

• Successive compounds have physical properties that vary in a regular manner
as the
number of carbon atoms present increases.

Example: Alkanes

CnH2n + 2 (n ≥ 1)
methane
CH4 – one carbon and 4 hydrogen
ethane
C2H6 – two carbon and 6 hydrogen

propane
C3H8 – three carbon and 8 hydrogen
butane
C4H10 – four carbon and 10 hydrogen

pentane
C5H12 – five carbon and 12 hydrogen
hexane
C6H14 – six carbon and 14 hydrogen

As the number of carbon atoms in a molecule in a particular homologous series

increases the boiling point increases.
The boiling point of straight chain alkanes increases when a methylene group is
added.

Recall:

methylene group is any part of a molecule that consists of

two hydrogen atoms bound to a carbon atom, which is connected to the remainder of
the molecule by two single bonds.

Reaso
n:

• As the relative molecular mass of the alkane increases the strength of the Van
der
Waals forces between molecule increases.
• The boiling point of the alcohols(-OH) tend to be higher due to the
presence of hydrogen bonding.
• Other functional groups such as carboxylic acid (-COOH), amine(-NH2) and
amide(- CONH2) also gives rise to hydrogen bonding

The physical properties, especially the melting and boiling point, depend on
intermolecular forces. Therefore, they have higher melting and boiling point than non-
polar or polar organic compounds of similar molar masses.
Likewise, branched chain isomers have lower boiling point then straight chain isomers.
• Reason: Branches prevent the main chains from getting as close together and
so Van
der Waals forces are weaker between the molecules
.
The Different Appearance of a Compound

• Empirical formula: The simplest whole number ratio of the elements present in a
compound.

• Molecular formula: The total number of atoms of each element present in the molecule
of the
compound.
 • A structural formula indicates in a fixed manner how the atoms are arranged in the
molecule

• The condensed structural formula

Isomers are different compounds which have the same molecular formula.
Different isomers have different chemical and physical properties
Structural isomers: Two or more compounds in which the atoms are joint in a different order
so that they have the same molecular formula but different structural formula.

Position isomers: Have the same hydrocarbon skeleton and the same
functional group Example: Propan-1-ol and propan-2-ol

Functional group isomers: is joined to a different part of the skeleton.

Hydrocarbon chain isomers: Have different hydrocarbon skeletons that the functional group is attached
to.

Example: Butane and methylpropane

Functional group isomers: Some functional groups will usually have isomers containing another
functional group.

Example: Alcohols usually have an alcoxyalkane that is isomeric to them hence ethanol has an
isomer methoxymethane

Stereoisomers: The order that the atoms are joined together is the same, but the molecules a
different arrangement of atoms in space and hence 3-d shapes.
• Saturated-Carbon has a single bond can be eight In an open or closed system
• Unsaturated: Carbon has a double bond/triple bond. In an open or closed system.
ALCOHOLS

Alcohols are organic molecules containing a hydroxyl functional group connected to an alkyl or
aryl group (ROH), The functional group of alcohol is -OH.

• The general molecular formula is CnH2n+1OH.

primary alcohol - the hydroxyl carbon only has a single R
group secondary alcohol - it has two R groups
tertiary alcohol- it has three R groups

• Alcohols have a much higher boiling point than alkanes as a result of hydrogen bonding.
• The lower members are soluble in water because of hydrogen bonding

Alcohols burn readily in air to form carbon dioxide and water, hence they are used for fuels in the
presence of excess oxygen
 Primary alcohols

• Primary alcohols are oxidized first of all to an aldehyde (partial oxidation)

• Then the aldehyde is oxidized further to a carboxylic acid (complete oxidation)
CARBOHYDRATES
Functions:
Providing dietary calories
Storage form of energy
Cell membrane components that mediate some form of intercellular communication
Structural component
Cell wall of bacteria
Exoskeleton of insects
Cellulose of plants

Monosaccharides
-number of carbon atoms they contain
-type of carbonyl group they contain
Aldoses = aldehyde =CHO
Ketoses = Ketoses = CO “ul”

ISOMERS – same chemical formula but different structure

EPIMERS – carbohydrate isomers that differ in configuration
around only one specific carbon atom, except the carbonyl carbon

ENANTIOMERS = mirror images

 D-isomer = -OH group on the asymmetric carbon farthest from the carbonyl carbon is on the right
L-isomer

ISOMERASES – enzyme that interconvert D- and L- isomers

MONOSACCHARIDED CYCLIZATION
ACYCLIC = monosaccharides in open-chain forms <1%
CYCLIC FORM = RING FORM = the aldehyde/keto group reacted with a hydroxyl group on the same sugar,
making the carbonyl carbon asymmetric (Carbon 1 for aldose, carbon 2 for ketose)

ANOMERS = creation of an anomeric carbon generates a new pair of isomers = alpha and beta configuration of the
sugars
Alpha and beta forms are not mirror images = DIASTEREOMERS
 Alpha and beta can be distinguished by enzymes
Ex: glycogen = synthesized from alpha-D-glucopyranose
Cellulose = synthesized from beta-D—glucopyranose

MUTAROTATION = cyclic alpha and beta anomers of a sugar solution spontaneously forming an equilibrium
mixture

REDUCING SUGARS: = sugar acting as a reducing agent = react with chromogenic agents
The rings are open because the hydroxyl grp on the anomeric carbon of a cyclized sugar is not linked to
another compound by a glycosidic bond

MONOSACCHARIDES are all reducing sugars

Fructose is a reducing sugar because it can be isomerized to an aldose.
A colorimetric test can detect a reducing sugar

MONOSACCHARIDE JOINING
GLYCISIDIC BONDS = link monosaccharides to create larger structures
Attach carbohydrates to non carbohydrate structures
N-glycosidic link = -NH2
O-glycosidic link = -OH
O-type linkage = all sugar-sugar binds

GLYCOSYL TRANSFERASE = enzymes = use nucleotide sugars (activated sugars) a substrates. Ex of activated sugar:
uridine diphosphate glucose
NAMING: according to the numbers of the connected carbons
Position of the anomeric hydroxyl group of the first sugar involved in the bond
Alpha bond
Beta bond
DISACCHARIDES:
Lactose= galactose + glucose
Sucrose = glucose + fructose
Maltose = glucose + glucose

OLIGOSACCHARIDES
2-10 monosaccharides
Low molecular weight carbohydrates which can be hydrolyzed by enzymes or acids to yield
monosaccharides
Powdery or crystalline, water soluble and sweet
Classified according to the number of monosaccharides they contain
Disaccharide
Trisaccharide
Tetrasaccharides
Pentasaccharides
May be reducing or non-reducing

POLYSACCHARIDES
Joined by glycosidic bonds
Hydrolyzed by enzymes or acids
Insoluble in water, tasteless, linear or branched
Classified according
kind of monosaccharides present: homoglycans or heteroglycans
function: storage and structural
Branched glycogen
Starch
Unbranched Cellulose
Lipids
• soluble in non polar solvents & solvents with low polarity
• most diverse class of biochemical

CLASSIFICATION BY FUNCTION
1. Storage
▪ The burning of fat produce more than produces more than twice
the amount of energy
2. Separate cellular compartments of aqueous solution
▪ hydrophobic
3. Chemical messengers
▪ Primary messengers – steroid hormones
▪ Secondary messengers– prostaglandins and thromboxane
CLASSIFICATION BY STRUCTURE
1. Simple lipids – fats oils and waxes
2. Complex lipids
3. Steroids
4. Prostaglandins
FATTY ACIDS
▪ unbranched carbon chain with a carboxyl group at one end
▪ Amphipathic
• Hydrocarbon tail is hydrophobic
• Carboxyl group hydrophilic
▪ Groups:
• Saturated
• Unsaturated
▪ Rarely found free in nature
▪ Form parts of many commonly occurring lipids
▪ A trans bond creates a straight chain and a cis bond results in a
chain that is bent

RECALL: Cis and Trans Isomers

▪ Nomenclature
▪ The systematic name takes into account the number of carbons in
the hydrophobic chain
▪ The symbol nomenclature takes into account the number of
carbons in the chain and the number of unsaturated bonds.
▪ Delta – starts in the carboxylic acid
▪ Omega – starts in the carbon end
 Linoleic Acid 18:2 (6,9)

Characteristics of the most abundant fatty acids

1. Nearly all fatty acids have an even number of carbon atoms, most between
12 and 20, in an unbranched chain.
2. The three most abundant fatty acids in nature are:
• palmitic acid (16:0)
• stearic acid (18:0)
• oleic acid (18:1)
3. In most unsaturated fatty acids, the cis isomer predominates. The trans
isomer is rare.
4. Unsaturated fatty acids have lower melting points than their saturated
counterparts.
- The greater the degree of unsaturation, the lower the melting point.

TRIGLYCERIDES
Recall: Esters = alcohol part + acid part
o Trimesters of glycerol and fatty acids
o Alcohol part: glycerol + Acid part: fatty acids
o Most common lipid material
o Complex mixture
o Hydrophobic due to the long hydrocarbon chains of the fatty acid
component.

Properties of Triglycerides

a. Physical state
 ▪ Fats from animals = solid -> saturated fatty acids
▪ fats from plants or fish = liquid -> unsaturated fatty acids
▪ ESSENTIAL FATTY ACIDS = cannot be synthesized
▪ POLYUNSATURATED – oil with an average of more than one
double bond per fatty acid chain
b. Hydrogenation
1. Hydrogenation – adding hydrogen across the double bond of
unsaturated fatty acids/to produce saturated fatty acids.
• Plant oils are liquid because they have higher proportions
of unsaturated fatty acids
▪ Partial hydrogenation

COMPLEX LIPIDS
2 Groups of Complex Lipids
1. Phospholipids = alcohol + two fatty acids + phosphate group
a. Glycerophospholipids: alcohol = glycerol
b. Sphingolipids: alcohol=sphingosine
2. Glycolipids = contains carbohydrate
LIPIDS & MEMBRANE STRUCTURE

Lipid part = barrier

The degree of fluidity increases when more unsaturated fatty acids occur
Protein

➢ Peripheral proteins
➢ Integral proteins

GLYCEROPHOSPHOLIPDS
➢ Membrane components of cells
➢ Backbone: glycerol
Phosphatidylcholines = lecithin
• One end is always saturated and the middle one is always unsaturated
• Negatively charged phosphate group, positively charges quaternary
nitrogen from choline

Cephalins – ethanolamine or serine as the alcohol

 Phosphatidyl-inositol (PI)
▪ Inositol is bonded by a phosphate ester bond

SPHINGOLIPIDS

- Backbone: sphingosine
- The terminal hydroxyl of the sphingosine is esterified to a phosphorylcholine o
phosphoryl-ethanolamine molecule

CERAMIDE = fatty acid + sphingosine

Sphingomyelin – most important lipid in the myelin sheaths of nerve cells

GLYCOLIPIDS

- Contains carbohydrates and ceramides

- Groups:
 1. Cerebrosides = ceramide+ mono or oligosaccharides
▪ the fatty acid of the ceramide part may contain either 18-
carbon or 24-carbon chains
▪ glucose or galactose carbohydrate unit forms a b-1-glycosidic
bond with the ceramide portion of the molecule.
▪ occur primarily in the brain (accounting for 7% of the brain’s dry
weight) and at nerve synapses
2. Gangliosides = more complex carbohydrate structure

STEROIDS

= three cyclohexane rings + cyclopentane

1. Cholesterol
▪ Plasma membrane
▪ Raw material for synthesis of other steroids
▪ Free form and Esterified form
▪ Manufactured in the liver
2. Lipoproteins: Carriers of Cholesterol
▪ HDL
▪ LDL
▪ VLDL
▪ Chylomicrons
3. Transport of Cholesterol in LDL
▪ apoB-100 - endocytosis and degradation
4. Transport of Cholesterol in HDL
▪ Removes cholesterol from the blood stream – binds to the liver to transfer its
cholesteryl ester -> bile acids and steroid hormones
5. Levels of LDL and HDL
• Atherosclerosis -> Myocardial Infarction
• Familial hypercholesterolemia
6. Membrane Cholesterol Functions
• Growth factor receptor for Interleukin-3 = promotes division and multiplication of
many types of immune cells

Physiological Roles of Steroid

- Adrenocorticoid Hormones – adrenal glands

▪ Mineralocorticoids – ion concentration
▪ Aldosterone - controls tissue swelling
▪ Glucocorticoids – carbohydrate metabolism
▪ Cortisol – increase glucose and glycogen concentration in the body
▪ Cortisones – ketone derivative = anti inflammatory
- Sex Hormones
▪ Testosterone
 ▪ Estradiol – synthesized from testosterone by aromatization of the A-ring

▪ Progesterone
▪ Luteinizing Hormone

Bile Salts

- Oxidation products of cholesterol

Taurine
- Powerful detergents
- Remove excess cholesterol
1. Breakdown products of cholesterol
2. Solubilize the deposited cholesterol

Prostaglandins, Thromboxane, and Leukotrienes

- synthesized from arachidonic acids

Prostaglandins

Cyclooxygenase (COX)

COX-1 -> normal physiological production of prostaglandins

– Stimulate uterine contractions and induce labor

– Lowers blood pressure
– Treats asthma

COX-1 -> response to inflammation

Thromboxane – induce platelet aggregation

Leukotrienes – act to mediate hormonal responses

Molecular Transport Across Membranes

Transport - Semipermeable barriers

Catalysis
Receptor property

Passive transport = same direction as the concentration gradient

Simple diffusion
Facilitated diffusion – larger molecules
-carrier protein is used

Active Transport = against the concentration gradient

Carrier protein + energy source
Sodium-potassium ion pump
Hydrolysis of ATP to ADP + phosphate ion