Download Carbon and the Molecular Diversity of Life

LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 4
Carbon and the Molecular
Diversity of Life
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
Overview: Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based
compounds
• Carbon is unparalleled in its ability to form large,
complex, and diverse molecules
• Proteins, DNA, carbohydrates, and other
molecules that distinguish living matter (versus
inanimate objects) are all composed of carbon
compounds
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Concept 4.1: Organic chemistry is the study
of carbon compounds
• Organic chemistry is the study of compounds
that contain carbon
• Organic compounds range from simple
molecules to colossal ones
• Most organic compounds contain hydrogen
atoms in addition to carbon atoms
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• Vitalism, the idea that organic compounds
arise only in organisms, was disproved when
chemists synthesized these compounds
– In the mid-1800’s, Herman Kolbe made the organic
compound acetic acid from inorganic substances
that could be prepared directly from pure elements.
• Mechanism is the view that all natural
phenomena are governed by physical and
chemical laws
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• Can organic molecules form under
conditions believed to simulate those on
the early Earth?
– Sea
– Mixture of Gases
– Lightening
Organic Molecules and the Origin of Life
on Earth
• Stanley Miller’s classic experiment
demonstrated the abiotic (non-living)
synthesis of organic compounds
• Experiments support the idea that abiotic
synthesis of organic compounds, perhaps
near volcanoes, could have been a stage in
the origin of life
• Organic chemistry was redefined as the
study of carbon compounds, regardless of
origin.
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Figure 4.2
EXPERIMENT
2. the “atmosphere”
contained a mixture
of hydrogen gas,
methane, ammonia,
and water vapor.
“Atmosphere”
CH4
Water vapor
Electrode
3. Sparks were
discharged to
mimic lightening.
Condenser
Cooled “rain”
containing
organic
molecules
1. “sea” water was
heated; vapor
entered the
“atmosphere” flask
H2O
“sea”
4. A condenser
Cold cooled the
water
atmosphere,
raining water and
any dissolved
molecules down
into the flask.
5. As material cycled
through the apparatus,
Miller periodically
Sample for chemical analysis collected samples for
analysis.
Concept 4.2: Carbon atoms can form diverse
molecules by bonding to four other atoms
• Electron configuration is the key to an atom’s
characteristics
• Electron configuration determines the kinds
and number of bonds an atom will form with
other atoms
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The Formation of Bonds with Carbon
• With four valence electrons, carbon can form
four covalent bonds with a variety of atoms
• A valence electron is an electron that is
associated with an atom, and that can participate
in the formation of a chemical bond
• This ability makes large, complex molecules
possible
• In molecules with multiple carbons, each carbon
bonded to four other atoms has a tetrahedral
shape
• However, when two carbon atoms are joined by
a double bond, the atoms joined to the carbons
are in the same plane as the carbons
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H
H
C
H
H
• Methane CH4
• 1 carbon and 4 hydrogen
• When a carbon atom has four single bonds to other
atoms, the molecule is tetrahedral (tetra = 4)
• The electron configuration of carbon gives it
covalent compatibility with many different
elements
• The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are
the “building code” that governs the
architecture of living molecules
• A carbon atom can also use one or more
valence electrons to form covalent bonds to
other carbon atoms, linking the atoms into
chains of infinite variety!
© 2011 Pearson Education, Inc.
Figure 4.3
Name and
Comment
Molecular
Formula
Structural
Formula
Ball-andStick Model
(a) Methane
CH4
Tetrahedral
(b) Ethane
C2H6
Tetrahedral (2)
(c) Ethene
(ethylene)
C2H4
1 plane
Space-Filling
Model
Figure 4.4
Figure 4.4 Valences of the major elements of organic
molecules.
Hydrogen
(valence  1)
Oxygen
(valence  2)
Nitrogen
(valence  3)
Carbon
(valence  4)
To determine the valence number, ask: how many more
electrons does it need to fill the outermost shell? That is how
many chemical bonds the atom can have.
What is a double bond?
• Carbon atoms can partner with atoms other than
hydrogen; for example: Can someone go up to
– Carbon dioxide: CO2
the board and draw the
electron distribution
diagram for CO2 ?
Is CO2 considered organic?
Why or why not?
– Urea: CO(NH2)2
Urea
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Molecular Diversity Arising from Carbon
Skeleton Variation
• Carbon chains form the skeletons (or backbone)
of most organic molecules
• Carbon chains (carbons linked together) vary in
length and shape
© 2011 Pearson Education, Inc.
Animation: Carbon Skeletons
Right-click slide/select “Play”
© 2011 Pearson Education, Inc.
Figure 4.5
Figure 4.5 Four ways that carbon skeletons can vary.
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Hydrocarbons
Hydrocarbons are the major components
of petroleum, which is called a fossil fuel.
Why do we call them fossil fuels? THINK,
PAIR, SHARE!
• Hydrocarbons are organic molecules
consisting of only carbon and hydrogen
• Many organic molecules, such as fats, have
hydrocarbon components
• Hydrocarbons can undergo reactions that
release a large amount of energy
What common role does petroleum for cars and the
fat in our bodies play? THINK, PAIR, SHARE!
© 2011 Pearson Education, Inc.
Figure 4.6
Nucleus
Fat droplets
Long hydrocarbon
tails attached to a
nonhydrocarbon
component.
10 m
(a) Part of a human adipose cell
(b) A fat molecule
• Hydrocarbons are not prevalent in most living organisms, but
many of a cell’s organic molecules have regions consisting of
only carbon and hydrogen.
• Why is fat considered hydrophobic? THINK PAIRE SHARE!
Isomers
• Isomers are compounds with the same
molecular formula but different structures and
properties
– Structural isomers have different covalent
arrangements of their atoms
– Cis-trans isomers have the same covalent
bonds but differ in spatial arrangements
– Enantiomers are isomers that are mirror
images of each other
We will discuss “trans fats”
in the next chapter.
© 2011 Pearson Education, Inc.
Animation: Isomers
Right-click slide / select “Play”
© 2011 Pearson Education, Inc.
Figure 4.7
(a) Structural isomers
(b) Cis-trans isomers
To help you
remember: Cis
and Same both
start with an
“S” sound.
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
Latin for left is
levo and for
right is dextro
• Enantiomers are important in the
pharmaceutical industry
• Two enantiomers of a drug may have different
effects
• Usually only one isomer is biologically active
• Differing effects of enantiomers demonstrate
that organisms are sensitive to even subtle
variations in molecules
© 2011 Pearson Education, Inc.
Figure 4.8
Drug
Condition
Ibuprofen
Pain;
inflammation
Albuterol
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma
• Ibuprofen reduces inflammation and pain. It is commonly sold
as a mixture of 2 enantiomers. The S is 100X more effective
than the other.
• Albuterol is used to relax bronchial muscles, improving airflow.
Only R is synthesized and sold as a drug.
Concept 4.3: A few chemical groups are key
to the functioning of biological molecules
• Distinctive properties of organic molecules
depend on the carbon skeleton and on the
molecular components attached to it
• A number of characteristic groups can
replace the hydrogens attached to skeletons
of organic molecules
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The Chemical Groups Most Important in
the Processes of Life
• Functional groups are the components of
organic molecules that are most commonly
involved in chemical reactions
• The number and arrangement of functional
groups give each molecule its unique
properties
© 2011 Pearson Education, Inc.
Figure 4.UN02
Estradiol
Testosterone
The female and male sex hormones have the same basic
shape, but they differ in functional groups. Even our sexuality
has its biological basis in variations of molecular architecture!
• The seven functional groups that are most
important in the chemistry of life:
–
–
–
–
–
–
–
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group
These are hydrophilic and
can increase the solubility
of organic compounds in
water.
Methyl is not reactive.
© 2011 Pearson Education, Inc.
Figure 4.9-a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
Alcohols (Their specific names
usually end in -ol.)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic acids
Aldehydes if the carbonyl group
is at the end of the carbon skeleton
EXAMPLE
EtOH’s polarity came
into question during
our last lab…
Ethanol
Propanal
FUNCTIONAL
PROPERTIES
• Is polar as a result of the
electrons spending more time
near the electronegative oxygen
atom.
• Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
Acetic acid
Acetone
Which is a ketone?
• A ketone and an aldehyde may be
structural isomers with different
properties, as is the case for
acetone and 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).
• Acts as an acid; can donate an
H+ because the covalent bond
between oxygen and hydrogen
is so polar:
Nonionized
Ionized
• Found in cells in the ionized form
with a charge of 1 and called a
carboxylate ion.
Figure 4.9-b
Amino
Sulfhydryl
Phosphate
Methyl
(may be
written HS—)
Amines
Organic phosphates
Thiols
Sulfhydryls
have -SH
AmiNo groups
have Nitrogens
Cysteine
Glycine
• Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Nonionized
Ionized
• Found in cells in the
ionized form with a
charge of 1+.
Methylated compounds
PhOsphates have
P’s and O’s
Glycerol phosphate
• Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
• Contributes negative charge to
the molecule of which it is a part
(2– when at the end of a molecule,
as above; 1– when located
internally in a chain of
phosphates).
• 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.
• Molecules containing phosphate
groups have the potential to react
with water, releasing energy.
5-Methyl cytidine
• Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
• Be able to recognize these groups and
some of their characteristics!
• Which functional group is not present in
this molecule?
• Which chemical group is most likely to
be responsible for an organic molecule
behaving as a base?
– Hydroxyl
– Carbonyl
– Carboxyl
– Amino
– Phosphate
ATP: An Important Source of Energy for
Cellular Processes
• One phosphate molecule, adenosine
triphosphate (ATP), is the primary energytransferring molecule in the cell
• ATP consists of an organic molecule called
adenosine attached to a string of three
phosphate groups
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Figure 4. UN04
Adenosine
Figure 4. UN05
Adenosine Triphosphate (ADP)
Reacts
with H2O
Adenosine
Adenosine
ATP
Inorganic
phosphate
Energy
ADP
Adenosine Diphosphate (ADP)
The Chemical Elements of Life: A Review
• The versatility of carbon makes possible the
great diversity of organic molecules
• Variation at the molecular level lies at the
foundation of all biological diversity
© 2011 Pearson Education, Inc.