Download Carbon and the Molecular Diversity of Life Chapter 4: 1. Organic Molecules

Chapter 4:
Carbon and the Molecular
Diversity of Life
1. Organic Molecules
2. Chemical Groups
1. Organic Molecules
Chapter Reading – pp. 57-62
Elements in Biological Molecules
Biological macromolecules are made almost
entirely of just 6 elements:
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
Phosphorus (P)
Sulfur (S)
The central element of macromolecules is Carbon!
Valence of the 4 Main Elements
The most abundant elements in macromolecules
are Carbon, Hydrogen, Oxygen and Nitrogen:
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
H
O
N
C
The valence (i.e., number of “unpaired” electrons)
of these elements determines how many covalent
bonds each will form.
The Element Carbon
Carbon has key properties necessary for the
formation of complex biological macromolecules:
• each carbon atom can form 4 covalent bonds
• equally spaced bond angles (tetrahedral, 109.5o)
• no unshared electron pairs in outer shell
• free rotation around single bonds
• intermediate electronegativity
• covalent bonds relatively non-polar, stable in water
• its abundance in nature!
Organic Chemistry
Organic chemistry is the study of carbon-based
compounds, in particular hydrocarbons (CnHn)
and their derivatives.
• hydrocarbon derivatives have something else
in place of one or more hydrogens:
e.g., CH4 vs CH3Cl
Organic molecules contain C & H:
• methane (CH4), glucose (C6H12O6) are organic
• water (H2O), carbon dioxide (CO2) are inorganic
• organic molecules are typically derived from living
things, hence the term “organic”
Hydrocarbon Structure
Hydrocarbons come in an almost limitless variety with
some of the simpler hydrocarbons shown below:
Name
(a) Methane
(b) Ethane
(c) Ethene
(ethylene)
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
Carbon Skeletons
Ethane
Propane
1-Butene
(a) Length
Butane
(b) Branching
2-Butene
(c) Double bonds
2-Methylpropane
(commonly called isobutane)
Cyclohexane
Benzene
(d) Rings
Hydrocarbons and their derivatives are
essentially carbon skeletons “filled in” with
hydrogen atoms or other chemical groups
Isomers
Isomers are molecules with identical molecular
formulas yet different structural formulas:
(C4H10)
(C4H10)
Structural Isomers
Structural isomers have different structural
arrangements of their carbon skeleton:
Pentane
(a) Structural isomers
2-methyl butane
cis-trans Isomers
cis-trans isomers involve different arrangements of
non-hydrogen atoms or chemical groups around
carbons connected by a double bond:
cis = “same side”
trans = “opposite side”
cis isomer: The two Xs are
on the same side.
(b) cis-trans isomers
trans isomer: The two Xs are
on opposite sides.
Enantiomers
Enantiomers are isomers with asymmetric
carbons that are mirror images of each other:
• asymmetric carbons are connected to 4 different
atoms or groups and have 2 possible arrangements
L isomer
(c) Enantiomers
D isomer
2. Chemical Groups
Chapter Reading – pp. 62-64
Chemical Groups
Chemical groups are common groups or
arrangements of atoms that substitute for
hydrogen on carbon skeletons:
Estradiol
Testosterone
The Hydroxyl Group
Hydroxyl
STRUCTURE
(may be written
HO—)
EXAMPLE
Ethanol
Alcohols
(Their specific
names usually
end in -ol.)
NAME OF
COMPOUND
• Is polar as a result
of the electrons
spending more
time near the
electronegative
oxygen atom.
FUNCTIONAL
PROPERTIES
• Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
polar
The Carbonyl Group
Carbonyl
STRUCTURE
Ketones if the carbonyl
group is within a
carbon skeleton
NAME OF
COMPOUND
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
• A ketone and an
FUNCTIONAL
PROPERTIES
aldehyde may be
structural isomers
with different properties,
as is the case for
acetone and propanal.
EXAMPLE
Acetone
Propanal
• Ketone and aldehyde
groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
groups).
polar
The Carboxyl Group
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
NAME OF
COMPOUND
EXAMPLE
• Acts as an acid; can
FUNCTIONAL
PROPERTIES
donate an H+ because the
covalent bond between
oxygen and hydrogen is so
polar:
Acetic acid
Nonionized
Ionized
• Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion.
acidic
The Amino Group
Amino
STRUCTURE
Amines
EXAMPLE
•
NAME OF
COMPOUND
Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
FUNCTIONAL
PROPERTIES
Glycine
Nonionized
•
Ionized
Found in cells in the
ionized form with a
charge of 1.
basic
The Sulfhydryl Group
Sulfhydryl
Thiols
STRUCTURE
NAME OF
COMPOUND
(may be
written HS—)
EXAMPLE
Cysteine
•
Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
•
Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
FUNCTIONAL
PROPERTIES
polar
Disulfide Bonds
Two sulfhydryl groups can undergo a reduction
reaction to form a disfulfide bond or bridge:
sulfhydryl
groups
disulfide
bond
The Phosphate Group
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
•
FUNCTIONAL
Contributes negative
charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
•
Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
Glycerol phosphate
NAME OF
COMPOUND
acidic
The Phosphate Groups of ATP
Adenosine
ATP
The terminal phosphate group of ATP (adenosine
triphosphate) provides the energy that fuels cell
cellular activities.
Reacts
with H2O
Adenosine
Adenosine
ATP
inorganic
phosphate
ADP
Energy
The Methyl Group
Methyl
STRUCTURE
Methylated compounds
NAME OF
COMPOUND
EXAMPLE
•
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
FUNCTIONAL
PROPERTIES
•
Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
nonpolar
Key Terms for Chapter 4
• organic vs inorganic
• isomers: structural, cis-trans, enantiomer
• hydroxyl group
• carbonyl group
• carboxyl group
Relevant Chapter
Questions
• amino group
• sulfhydryl group, disulfide bond
• phosphate group
• methyl group
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