Nerve activates contraction

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CHAPTER 4 CARBON AND THE MOLECULAR DIVERSITY OF
LIFE

• -Organic chem. study of carbon compunds.
• -70-90 cell is water, other consists of
  carbon-based compounds. DNA, Protein,
  carbohydrates etc.
• -Carbon and its ability to form a variety of
  different bonds basis of diversity of organic
  molecules
• -H hydrogen, O oxygen, N nitrogen , S sulfer, P
  phosphorous common ingredients in organic
  molecules.

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Beginnings of organic chemistry

• The Swedish chemist Berzelius
• distinguished living things from non-living
  things by separating
• organic chemicals present in living things and
  inorganic chemicals present in non-living

Vitalism Early 19th century
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Vitalism

• Initially it was believed that organic compounds
  have to be made by living things.
• Such as
• Simplest CO2 or CH4 to
• - Complex macromolecules
• (milk protein, sugars
• Cellulose, pigments)
• Only half a century later it was found not to be
  true e.g.

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• Organic compounds can be synthesized in lab
• 1828 Friedrich Wöhler urea using inorganic
  starting materials.
• In 1953, Stanley Miller simulated chemical
  conditions on the primitive Earth
• synthesized organic compounds
• such as amino acids, simple sugars etc.

Fig. 4.1
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• Organic chemistry was redefined as the study of
  carbon compounds regardless of origin.
• The important points are
• 1) Living things have innate capability to make
  organic compounds in an amazing diversity and
  complexity
• 2) One can synthesize the same organic compounds
  outside the living things environment such as lab
  conditions and now in factories.

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• Advanced Biotech Co. Patterson, NJ

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Carbon atoms are the most versatile building
blocks of molecules

• Carbon has 6 electrons
• 4 in the outer most valance shell
• Cannot transfer / or gain 4 electrons
• Shares four electrons
• Forming 4 bonds
• tetravalence by carbon makes large, complex
  molecules possible.

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Carbons tetravalence gives rise to many covaent
bonding alternatives
H-C-C-H

• 4 single bonds
• Two double bonds
• One double, two single bonds
• One triple, one single bond

H-CCC-H
H-CC-H
H-CC-H
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Bonding
Double bond
Single bonds
Triple bond
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• Examples of small organic molecules
• 1) CO2
• In atmosphere
• 2) Urea
• Found in urin

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CO2 Double bonds
O
C
H
H
N
N
H
H
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How can carbon generate such diverse organic
molecules?

• 1) Variation in Length/shape/size of the carbon
  chain
• 2) Formation of Isomers
• 3) Bonding with various functional groups

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1) Variation in Length/shape/size of the carbon
chain

• The skeletons may
• 1) vary in length and may be straight, branched,
  or arranged in closed rings.
• 2) may also include double and triple bonds.
• Double and triple bonds have different bond
  lengths change shape of molecule due to bond
  length

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Straight chains, simple carbon backbones

• Hydrocarbons carbon and hydrogen atoms only!
• Hydrocarbons are the major component of
  petroleum.
• Hydrocarbons NOT present in living cells, but are
  regions of fat molecules.
• Hydrophobic!!

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• Fats are biological molecules that have long
  hydrocarbon tails attached to a non-hydrocarbon
  component.

Fig. 4.5
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Rings

• Carbon skeletons can form ring structures
• There can also be multiple rings such as steroid
  molecule

steroid
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Branched, other shapes (examples)

• Carbon backbone can be highly branched and a mix
  of rings, straight chains, branched areasall
  lend to great variety of molecules

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• Isomers
• are such compounds that have same molecular
  formula
• but different structural formula different
  chemical properties
• Different types of isomers
• 1) Structural isomers
• 2) Geometrical isomers
• 3) Enantiomers

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• Structural Isomers
• molecules with the same molecular formula
• but differ in the covalent arrangement of atoms.

C4H10
Fig. 4.6a
-as Benjamin Cummings
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• Geometric isomers
• same covalent molecular formula
• but differ in their spatial arrangement around a
  carbon-carbon double bond.
• The double bond does not allow atoms to rotate
  freely around the bond axis.

-as Benjamin Cummings
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• Biological example of geometric isomer
• The biochemistry of vision involves a
  light-induced change in the structure of
• rhodopsin in the retina from one geometric isomer
  to another.

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• Enantiomers
• molecules that are mirror images of each other
• Enantiomers are only possible if there are four
  different atoms or groups of atoms bonded to a
  carbon.
• Center carbon is called asymmetric carbon.

-as Benjamin Cummings
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• Like left-handed and right-handed versions.
• Usually one is biologically active, the other
  inactive.
• Cell can distinguish one over the other!
• The following is an example of amino acid of
  which only one isomer is biologically active

• Known as
• R and S
• or
• D and L

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• Biological example of enantiomers
• Thalidomide reduced morning sickness, its
  desired effect,
• -but the other isomer caused severe birth
  defects.
• The L-Dopa isomer is an effective treatment of
  Parkinsons disease,
• but the D-Dopa isomer is inactive.

1957
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Functional groups attachments that replace one
or more hydrogen atoms to the carbon skeleton of
the hydrocarbon

• Each functional group has unique chemical
  properties
• The common property shared by all these
  functional groups is
• they are hydrophilic therefore increase
  solubility of organic compounds in water.

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• There are six functional groups that are most
  important to the chemistry of life
• hydroxyl -OH
• carbonyl -CO
• carboxyl -COOH
• Amino -NH2 OR NH3
• sulfhydryl -SH
• phosphate groups. -PO4

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• Hydroxyl group (-OH),
• Organic compounds with hydroxyl groups are
  alcohols and their names typically end in -ol.
• Found in carbohydrates

-as Benjamin Cummings
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• Carbonyl group (-CO) consists of an oxygen atom
  joined to the carbon skeleton by a double bond.
• 2 types
• Aldehyde carbonyl group is _at_ end of the
  skeleton
• Ketone carbonyl group in not at the end.

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• Carboxyl group (-COOH)
• carbon atom with a double bond with an oxygen
  atom
• single bond to a hydroxyl group.
• ACIDIC! carboxylic acids

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• Amino group (-NH2) consists of a
• nitrogen atom attached to two hydrogen atoms

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• Organic compounds with amino groups are amines.
• Forms basic, charged molecules.
• Amino acids the building blocks of proteins, have
  amino and carboxyl groups.

amino acid structure
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• A sulfhydryl group (-SH)
• sulfur atom bonded to a hydrogen atom
• Organic molecules with sulfhydryl groups are
  thiols.
• Important in protein folding

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• A Phosphate group (-OPO42-)
• phosphorus bound to
• four oxygen atoms (three with single bonds and
  one with a double bond).
• Phospholipids, DNA, RNA, ATP

2 negative charges!
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IDENTIFY THE FUNCTIONAL GROUPS