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Topic 1:Chemicals of life
1. Molecules and Atoms
2. Water
3. Carbon and Other elements
3. Carbon and Other Elements
3.1 Organic Chemistry
3.2 Bonding with Carbon
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Carbon Chains
Hydrocarbons
Isomers
3.3 Functional Groups
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Hydroxyl
Carboxyl
Carbonyl
Amino
Sulfhydryl
Phosphate
All living organisms
are made up of
chemicals based
mostly on the
element carbon,
besides water
• the study of carbon
compounds
• carbon compounds
can be simple or
very complex
The Concept of Vitalism
• organic compounds arise only within living organisms
• disproven in 1953 when Miller synthesized the
compounds in the laboratory
C
• carbon has four
valence electrons
• it can form four
covalent bonds with a
variety of atoms
Carbon can make molecules of different length
Name and
Comments
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
H
(a) Methane
CH4
H
C
H
H
(b) Ethane
C2H6
H
C
C
H
H
H
(c) Ethene
(ethylene)
H
H
C2H4
H
C
H
H
C
H
Space-Filling
Model
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
N
C
H
O
Carbon can bond covalently to many different elements
Carbon can make Chains and Rings
(a) Length
H
H
H
C
C
H
H
H
H
Ethane
H
H
H
C
C
C
H
H
H
H
Propane
H
H
(b) Branching
H
H
H
H
H
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
H
H
(d) Rings
C
C
C
H
C
C
C
H
C
C
C
H
H
H
H
2-methylpropane
(commonly called isobutane)
H
H
H
H
H
H
C
C
C
C
H
1-Butene
H
H
H
H
H
H
Butane
(c) Double bonds
C
H
H
2-Butene
H
H
H
H
H
Cyclohexane
H
C
C
C
C
H
C
Benzene
• the skeletons of most organic molecules contain carbon
• carbon skeletons vary in length, shape, and type of bonds
Hydrocarbons
methane
ethane
propane
butane
molecules consisting of only carbon and hydrogen
Fat droplets (stained red)
100 µm
(a) A fat molecule
(b) Mammalian adipose cells
Hydrocarbons are found in many of a cell’s organic molecules
Isomers
(a) Structural isomers
H
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
X
C
H
H
H
C
C
C
H
H
H
C
H
C
X
H
H
CO2H
CO2H
C
C
H
NH2
CH3
H
X
C
C
H
(c) Enantiomers
H
X
C
(b) Geometric isomers
H
H
H
H
H
NH2
CH3
molecules with the same molecular formula but
different structures and properties
Structural Isomers
molecules with the same chemical formula,
but different arrangement of the atoms
C4H10
They have different physical properties, ex. Melting point
Geometric Isomers
molecules with the same chemical formula,
but atoms are arranged on different sides of a
bond or ring
Enantiomers are important in the pharmaceutical industry.
Caused by the presence of asymmetric carbon atoms
L-Dopa
D-Dopa
(effective against
Parkinson’s disease)
(biologically
inactive)
Estradiol
OH
CH3
HO
the chemically
reactive groups of
atoms within an
organic molecule
that give it its
chemical properties
Female lion
OH
CH3
CH3
O
Male lion
Testosterone
Six functional groups are important in the
chemistry of living things
hydroxyl
carbonyl
carboxyl
amino
sulfhydryl
phosphate
Hydoxyl Group
formula
structure – a H atom bonded to an O atom that is
bonded to the carbon skeleton
compounds – alcohols (names end in –ol)
example
H
H
H
C
C
H
H
OH
ethanol – in alcoholic beverages
properties – polar, attracts H2O molecules, dissolves
organic compounds
Carbonyl Group
formula
structure – a C joined to an O by a double bond
compounds – ketones (if the carbonyl is in a carbon
skeleton, non-terminal carbon)
aldehydes (if the carbonyl is at the end
of a carbon skeleton, terminal carbon)
H
example
H
O
C
C
H
H
C
H
H
H
H
C
C
H
H
O
C
H
H
acetone (simple ketone)
propanol (an aldehyde)
Carboxyl Group
formula
structure – an O is double bonded to a C that is
also bonded to an OH
compounds – carboxylic acids
example
H
H
C
H
O
C
OH
acetic acid (vinegar)
properties – acidic properties
Amino Group
formula
structure – a N atom bonded to two H atoms and to
the carbon skeleton
compounds – amines
H
O
example
C
HO
C
H
N
H
H
glycine
properties – acts as a base, can pick up a proton from
solution
Sulfhydryl Group
formula
structure – a S atom bonded to an atom of H
compounds – thiols
example
H
H
H
C
C
H
H
SH
ethanethiol
properties – can help stabilize protein structure by
forming covalent bridges: disulfide bridges.
Phosphate Group
formula
structure – a P atom is bonded to four O atoms,
one O atom is bonded to the carbon skeleton
compounds – organic phosphates
OH OH H
example
H
C
C
C
H
H
H
O
O
P
O
O
glycerol phosphate
properties – makes molecule into an anion, transfers
energy between organic molecules