Ch 4
Molecular Basis of Living Organisms
• After water, cells consists mostly of carbon-based
compounds= organic molecules
•
• Examples
• Carbohydrates, lipids, proteins, nucleic acids (DNA, RNA)
Carbon Bonds
• Four valence electrons--> allows 4 covalent
single bonds
• Or 2 double bonds
• Consequence:
– Potential to form complex molecules
LE 4-3
Molecular
Formula
Methane
Ethane
Ethene (ethylene)
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
Shape of carbon complex
• Tetrahedron
– When C bonded to 4 other groups
• Groups can rotate around single bonds
• Linear/Flat/Planar
– When C is double bonded to another C
• Unable to rotate
Common Carbon Bonding Partners
in Biological Molecules
• Hydrogen
• Oxygen
• Nitrogen
Molecular Diversity of Organic Molecules
Due in part to
• Formation of carbon chain
• Differences in length and organizationof chain
LE 4-5
Ethane
Propane
Butane
2-methylpropane
(commonly called isobutane)
Length
Branching
1-Butene
Double bonds
2-Butene
Note: molecular
abbreviation
Cyclohexane
Rings
Benzene
Isomers
• Compounds with same molecular formula but
different structures/ properties
Structural isomers
different covalent arrangements of atoms
Geometric isomers
same covalent arrangements;different spatial
arrangements
Enantiomers
mirror images of each other
LE 4-7
Structural isomer
Structural isomers differ in covalent partners, as shown in
this example of two isomers of pentane.
Geometric
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
Geometric isomers differ in arrangement about a double
bond. In these diagrams, X represents an atom or group of
atoms attached to a double-bonded carbon.
Enantiomers
Stereoisomers
Mirror images
L
isomer
D
isomer
Enantiomers differ in spatial arrangement around an
asymmetric carbon, resulting in molecules that are mirror
images, like left and right hands. The two isomers are
designated the L and D isomers from the Latin for left and
right (levo and dextro). Enantiomers cannot be
superimposed on each other.
LE 4-8
Enantiomers
L-Dopa
D-Dopa
(effective against
Parkinson’s disease)
(biologically
Inactive)
Functional Groups
• Molecules attached to carbon chains that
are involved in reactions
• Determine distinctive properties of organic
molecule
LE 4-9
Estradiol
Female lion
Testosterone
Male lion
• The six functional groups that are most
important in the biological chemistry:
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Phosphate group
– Sulfhydryl group
LE 4-10aa
STRUCTURE
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized) (ionized)
Ionized, with a charge of 1+,
under cellular conditions
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
Thiols
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
Structure.
LE 4-10bc
Cccccccccc
ccccccc
ccc
Questions?
Ch 5 Overview: The Molecules of Life
• Within cells
– small organic molecules bond together to form
larger molecules
• Macromolecules
– large molecules composed of thousands of
covalently connected atoms
What is the structure of most organic macromolecules?
Polymer
long molecule consisting of similar building blocks
called monomers
• Three of the four classes of life’s organic molecules
are polymers:
– Carbohydrates
– Proteins
– Nucleic acids
LE 5-2
Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water
molecule, breaking a bond
Hydrolysis of a polymer
The Synthesis and Breakdown of Polymers
• Synthesis (Construction)
– Monomers link together through
– dehydration reactions
• Breakdown
• Polymers disassemble to monomers by
hydrolysis (reverse of dehydration)
Carbohydrates
Functions
Fuel
Construction and support
Structure
Simple sugars: monosaccharides
Formula CH2O
Polymers
Disaccharides (relatively short)
Polysaccharides (long)
LE 5-3
Triose sugars
(C3H6O3)
Pentose sugars
(C5H10O5)
Hexose sugars
(C5H12O6)
Glyceraldehyde
Ribose
Galactose
Glucose
Dihydroxyacetone
Ribulose
Fructose
• Monosaccharides
• Functions
– major fuel for cells
– raw material for building molecules
• Structures
• linear ---> ring
LE 5-4
Linear and
ring forms
Abbreviated ring
structure
• Disaccharide
– forms by a dehydration reaction between two
monosaccharides
• Nomenclature of bond
– glycosidic linkage
LE 5-5
Disaccharide formation
Dehydration
reaction in the
synthesis of maltose
1–4
glycosidic
linkage
Glucose
Glucose
Dehydration
reaction in the
synthesis of sucrose
Maltose
1–2
glycosidic
linkage
Glucose
Fructose
Sucrose
Polysaccharides
Storage Polysaccharides
• Starch
– Fuel storage molecule in plants
• Polymer of glucose
 -glycosidic linkage
• Stored in chloroplasts and other plastids
LE 5-6a
Chloroplast
Starch
1 µm
Amylose
Amylopectin
Starch: a plant polysaccharide
LE 5-7
Glucose
 Glucose
and  glucose ring structures
Starch
Starch: 1–4 linkage of  glucose monomers.
Cellulose: 1–4 linkage of  glucose monomers.
• Glycogen
– storage polysaccharide in animals
– Stored in liver and muscle
LE 5-6b
Mitochondria Glycogen granules
0.5 µm
Glycogen
Glycogen: an animal polysaccharide
Structural Polysaccharides
– Cellulose found in plant cell walls
– Polymer of glucose
-glycosidic linkages
LE 5-7
Glucose
 Glucose
and  glucose ring structures
Starch: 1–4 linkage of  glucose monomers.
Cellulose
Cellulose: 1–4 linkage of  glucose monomers.
LE 5-8
Cellulose microfibrils
in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose
molecules
 Glucose
monomer
Structural difference of glucose isomers
• Polymers of alpha glucose
• helical
• Polymers with beta glucose
•
•
•
•
Straight
Pack together well in microfibrils
Stabilized by H-bonds
Strong
Many animals
-unable to breakdown cellulose
-lack hydrolytic enzymes
- in human: insoluble fiber results
• Some bacteria
– Possess enzymes to breakdown cellulose
– Live in symbiotic relationship in guts of animals (from
cow to termite)
• Chitin
– structural polysaccharide
– in the exoskeleton of arthropods
– cell walls of many fungi
• Chitin
– used as surgical thread!