Download Lecture #3 – Carbon and the Molecular Diversity of Life

Lecture 003 – Carbon and the Molecular Diversity of Life
1. CARBON AND THE MOLECULAR DIVERSITY OF LIFE
2. MEET CARBON – OUR HERO
a. LIVING BEINGS ARE MADE MOSTLY OF CHEMICALS BASED ON CARBON.
b. CARBON ENTERS OUR BIOSPHERE WITH THE HELP OF PLANTS THAT USE
LIGHT ENERGY TO TRANSFORM ATMOSPHERIC CARBON (CO2) INTO THE
MOLECULES THAT ARE CONSUMED BY ANIMALS THAT FEED ON PLANTS.
AND SO BEGINS THE CYCLE....
3. Why is carbon so significant? What are some important features of carbon?
4. CARBON
a. ORGANIC CHEMISTRY is the study of carbon compounds (regardless of their
origin) though most naturally occurring organic compounds are produced by
organisms.
b. Organic Compounds (sometimes defined as): Compounds with covalent
bonds between carbon and hydrogen atoms.
c. Inorganic: describing a molecule that does not contain both carbon and
hydrogen. Examples?
d. Carbon dioxide (CO2) and all molecules without carbon. Name one we have
discussed in detail?
5. ORGANIC CHEMISTRY BACKGROUND HIGHLIGHTS
6. ARE ORGANIC COMPOUNDS SYNTHESIZED BY “VIS-VITALIS?”
a. “Vis vitalis”: literally SOUL or life force.
b. Vitalism: the belief that life in living organisms was caused and sustained by
a vital force that is distinct from all physical and chemical forces.
c. Vitalism: the belief that life is, in part, self-determining and self-evolving.
d. FOUNDATION FOR BELIEF:
e. Complex organic molecules could not be produced in the laboratory…only
extracted from living matter.
f. Heat “killed” organic substances and original state could not be restored.
g. Plato points to the heavens for truth.
h. Aristotle points to earth "experience is the only truth".
7. INCREASED DATA BASE and EXPLANATIONS CAN BECOME BASED IN FACT
a. Scientists in the 1590's utilized early microscopes and developed the Germ
Theory.
b. Early microscopes and the Germ Theory changed understanding of cellular
composition and the molecular analysis of the maintenance of life.
c. Life’s processes could be described in CHEMICAL or PHYSICAL terms.
d. IMAGE: early scientific drawings of cells
e. IMAGE: Death by Cholera
Student notes
003 Carbon
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8. ORGANIC COMPOUNDS
a. Berzelius: One of the “father’s of modern chemistry”.
b. 1828: Wohler (student of Berzelius) synthesizes urea from inorganic
compounds.
c. Urea, an “organic compound” present in the urine of animals was
synthesized using potassium cyanate and ammonium sulfate in the
laboratory.
d. The cyanate had been extracted from animal blood…vitalism held.
e. Kolbe (student of Wohler) synthesizes acetic acid from indisputably inorganic
compounds.
9. DIFFERING VIEWS
a. Louis Pasteur presents a famous rebuttal on spontaneous generation (life
from nothing) but believes fermentation is a “vital action” that occurs ONLY
in living cells. Rejects Berzelius.
b. Berzelius had claimed fermentation resulted from chemical agents or
catalysts within cells.
c. Vitalism continues to crumble as a theory.
10.
CAN ORGANIC MOLECULES FORM UNDER CONDITIONS BELIEVED TO
SIMULATE THOSE ON THE EARLY EARTH?
a. In 1953, Stanley Miller set up a closed system to simulate conditions
thought to be found on early earth.
b. Recent work allows for slightly different early earth conditions, although the
same organic compounds were created.
c. Organic chemistry was redefined and biological thought moved to
MECHANISM.
11.
MECHANISM
a. Mechanism: physical and chemical laws govern all natural phenomenon's,
including the processes of life.
b. VITALISM CRUMBLES???!!!....
12.
Ernst Walter Mayr
July 5, 1904– February 3, 2005
WERE VITALIST'S WRONG? HAS SCIENCE ANSWERED THE QUESTION OF THE
EMERGENT PROPERTY WE KNOW AS LIFE?
a. One of the 20th century’s leading evolutionary biologists.
b. Renowned taxonomist.
c. His work contributed to the conceptual revolution that led to the modern
evolutionary synthesis of Mendelian genetics, systematics, and Darwinian
evolution, and to the development of the biological species concept.
13.
14.
Student notes
WHAT ARE SOME IMPORTANT FEATURES OF CARBON?
CONVENIENT TO WRITE OUT MOLECULES FLAT, NOT THE REAL PICTURE.
a. Ball and stick model AS well as space filling model of butane.
b. How we often draw butane.
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15.
THE ELECTRON CONFIGURATIONS OF CARBON AND ITS MOST FREQUENT
PARTNERS.
a. The four major atomic components of organic molecules.
16.
WHAT ARE SOME IMPORTANT FEATURES OF CARBON?
17.
MOLECULAR DIVERSITY THROUGH CARBON SKELETON VARIATION
Variation of Length
Branching
Double Bonds
Rings
a.
b.
c.
d.
18.
CARBON
a. HYDROCARBON: An organic molecule consisting only of carbon and
hydrogen.
19.
ISOMERS
a. ISOMER: One of several compounds with the same molecular formula but
different structures and therefore different properties. The three types of
isomers are structural isomers, geometric isomers, and enantiomers.
b. We will first look at a structural isomer, two compounds that both have the
molecular formula C5H12 – they are isomers – but with very different shapes.
c. BELOW ARE MOLECULES – THESE ARE NOT ISOMERS!!! THEIR STRUCTURES
ARE NOT DIFFERENT – THEY HAVE SIMPLE ROTATED AROUND A SINGLE
BOND!!
20.
STRUCTURAL ISOMER: One of several compounds that have the same
molecular formula but differ in the covalent arrangements of their atoms.
21.
ISOMERS
a. CIS-TRANS ISOMER/GEOMETRIC ISOMER: One of several compounds that
have the same molecular formula and covalent arrangements but differ in
the spatial arrangements of their atoms owing to the inflexibility of double
bonds. Term is considered obsolete by IUPAC though used as a synonym for
cis-trans isomerism.
i. Two different groups on the left-hand end of the bond and two
different groups on the right-hand end. It doesn't matter whether the
left-hand groups are the same as the right-hand ones or not.
22.
CIS AND TRANS
a. CIS: (from Latin) “on the same side”.
b. TRANS: (from the Latin) “on the other side” or “across”.
c. It describes the orientation of functional groups within a molecule. In
general, such isomers contain double bonds, which cannot rotate, but they
can also occur in ring structures, those bonds are also greatly restricted.
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003 Carbon
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d. Cis and Trans: Isomers occur both in organic and inorganic coordination
complexes.
23.
NOT ISOMERS
a. There is free rotation around a single bond, therefore, though the first would
appear to be trans and the second cis, they are not held in place by the
double bond. THESE ARE THE SAME MOLECULES!! THEY CAN ROTATE!
24.
ISOMERS
a. ENANTIOMERS: One of two compounds that are mirror images of each
other.
b. The middle carbon is called the asymmetric carbon because it is attached to
four different atoms or groups of atoms.
c. The four groups can be arranged around the asymmetric carbon in TWO
DIFFERENT ways that are MIRROR images of each other. Another way of
saying left and right handed images.
25.
ENANTIOMERS AND PHARMACOLOGICAL IMPORTANCE
26.
Thalidomide baby: an unfortunate and irresponsible side effect of a
medication used in pregnant women during the late 1950’s and early 1960’s to
control morning sickness.
a. One enantiomer had desired effect, the other caused birth defects. Even in
purified form, the good would convert to the bad in the body.
27.
SMALL DIFFERENCES, BIG CHANGES
a. Note the differences in the ring structure to the left.
b. The arrangement of the carbon skeleton is only part of the story!
c. Another SIGNIFICANT characteristic is what is ATTACHED to the skeleton!
28.
A FUNCTIONAL FAMILY
a. FUNCTIONAL GROUPS: A specific configuration of atoms commonly attached
to the carbon skeletons of organic molecules and usually involved in
chemical reactions.
b. Note carbon skeleton abbreviations.
29.
FUNCTIONAL GROUPS - Hydroxyl
a. Hydroxyl group (the party animal): Organic compounds containing
hydroxyl groups are called alcohols, and their specific names usually end in
–ol as in ethanol in alcoholic beverages. A hydrogen bonded to an oxygen.
b. Seen as –OH or HO- . Do not confuse with our hydroxide ion OH-!
(Remember acids and bases).
30.
FUNCTIONAL GROUPS - Carbonyl
a. Carbonyl – Look for a carbon atom double bonded to one oxygen.
b. The red-headed step-child – not included in some books.
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c. When carbonyl is on the end of a carbon skeleton, the organic compound is
called an aldehyde (formaldehyde – lab specimens). Otherwise, it is called
a ketone (within the structure) [acetone – removes nail polish].
d. Acetone, the simplest ketone
e. Propanal, an aldehyde
31.
a.
b.
c.
d.
FUNCTIONAL GROUPS – CARBOXYL
CARBOXYL GROUP: (The acid-tongued relative); Look for -COOH as his
nickname.
Compounds containing carboxyl groups are carboxylic acids or organic acids
– acetic acid the acid of vinegar.
Carboxyl group 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
32.
FUNCTIONAL GROUPS - Amino
a. AMINO GROUP: (Your “basic” relative) -NH2 a nitrogen atom bonded to
two hydrogen atoms and the carbon skeleton. Organic compounds in this
group are called amines.
b. Because glycine has an amine group and a carboxylic acid, compounds with
both are called something very important – amino acids – the building blocks
of PROTEINS.
c. Why is it the basic relative? It likes to act as a base. Can pick up a H+ ion
from the surrounding solution (water in living organisms).
d. See non-ionized and ionized.
33.
Proteins are polymers of amino acids, joined by peptide bonds.
a. They are composed of a central carbon atom bonded to an amino group (NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable group of
atoms denoted by the letter “R”.
34.
SICKLE CELL ANEMIA – ONE BASE PAIR CHANGE
a. Glutamic Acid – an amino acid with an electrical charge - acidic
b. Valine – a non-polar amino acid. Replaced by valine.
c. How? DNA mutations inherited from the parents lead mRNA to send the
wrong message, and the wrong amino acid is put into the protein.
Ribosomes.
35.
FUNCTIONAL GROUPS- Sulfhydryl
a. SULFHYDRYL GROUP: Consists of a sulfur atom bonded to an atom of
hydrogen; resembles a hydroxyl group in shape.
b. The Long-Suffering Relative – these compounds are referred to as Thiols.
c. EXAMPLE Ethanethiol. Cysteine is an important sulfur-containing amino acid.
36.
FUNCTIONAL GROUPS - Phosphate
a. PHOSPHATE GROUP: (The backbone of the family); -H2PO3-2. A phosphorus
atom is bonded to four oxygen atoms.
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003 Carbon
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b. Combined with a deoxyribose sugar, the phosphate group makes up the
back bone of the double helix DNA molecule.
37.
FUNCTIONAL GROUPS - Methyl
a. Methyl – The oily relative. Big on making molecules hydrophobic – lipids.
b. Both of these substances have methyl groups. It consists of a carbon bonded
to 3 hydrogen atoms. The methyl group may be attached to a carbon or to a
different atom.
38.
A FIRST MEETING WITH ATP
a. ATP: (adenosine triphosphate) an adenine containing nucleoside
triphosphate that releases free energy when its phosphate bonds are
hydrolyzed. This energy is used to drive endergonic reactions in cells.
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003 Carbon
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