Lecture 2: Introduction to Bioorganic Chemistry

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Lecture 2Introduction to Bioorganic Chemistry

• Yiu-Kay Lai
• 2007.3.13

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Chemistry of Biomolecules

• A biomolecule is a chemical compound that
  naturally occurs in living organisms.
• Biomolecules consist primarily of carbon and
  hydrogen, along with nitrogen, oxygen, phosphorus
  and sulfur.
• Other elements sometimes are incorporated but are
  much less common.

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The Six Most Abundant Elements of Life
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Valence ?

• Each element has a characteristic valence that
  determines the number of covalent bonds it can
  form.
• A shared electron pair is called a covalent bond
  (???). The number of covalent bonds that each
  element can form is called its valence.

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Organic Molecules Hydrocarbons
Hydrocarbons (?????), the simplest organic
molecules, contain only carbon and hydrogen atoms.
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Isomers

• Organic molecules exist in three-dimensional
  space, and the same set of atoms can be put
  together in many recognizably different ways,
  resulting in molecules called isomers.
• ???????,?????????
• 1. Structural isomers Variations in the
  position at which different atoms are joined
  together.
• 2. Geometric isomers Variations in the
  placement of atoms around carbon atoms joined by
  double covalent bonds.
• 3. Enantiomers Left-handed and right-handed
  variations resulting from the tetrahedral
  geometry of carbon.

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Isomers
(a) Structural isomers
(b) Geometric isomers
(c) Enantiomers
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Enantiomers are important in the pharmaceutical
industry
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Polarity ??
Many combinations of different elements Result in
unequal electron sharing, called polar
bonding. The sharing of electrons in covalent
bonds is not always equal. In a covalent bond,
atoms such as oxygen contain a higher
localization of negative charge density than
their atomic partners. As a result, the electron
distribution is asymmetric, or polar, and the
oxygen atom is said to be electronegative. This
asymmetry results in regions of slight negative
and positive charge in different regions of the
molecule, denoted by the Greek symbol d, for
"partial" charge.                          
                         
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The Functional Groups
The properties of different biological molecules
depend on certain characteristic groupings of
atoms called functional groups. The names of the
six most important functional groups are

• Hydroxyl
• Carbonyl
• Carboxyl
• Amino
• Sulfhydryl
• Phosphate

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Hydroxyl Group
OH

• In a hydroxyl group (OH), a hydrogen atom is
  bonded to an oxygen atom, which in turn is bonded
  to the carbon skeleton of the organic molecule.
  (Do not confuse this functional group with the
  hydroxide ion, OH).
• Hydroxyl groups are not highly reactive, but they
  readily form hydrogen bonds and contribute to
  making molecules soluble in water.
• Alcohols and sugars are "loaded" with hydroxyl
  groups.

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Carbonyl Group

• Carbonyl group consists of a carbon atom joined
  to an oxygen atom by a double bond (symbolized as
  CO).
• Like hydroxyl groups, carbonyl groups contribute
  to making molecules water-soluble. All sugar
  molecules have one carbonyl group, in addition to
  hydroxyl groups on the other carbon atoms.

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Two Forms of Carbonyl Groups Aldehydes and
Ketones
Propanal, an aldehyde
Acetone, a ketone

• Aldehyde groups, where the CO group is at the
  end of an organic molecule. A hydrogen atom is
  also located on the same carbon atom.
• Keto groups, where the CO group is located
  within an organic molecule. All sugars have
  either a keto or an aldehyde group.
• An aldehyde and a ketone may be structural
  isomers with different properties, as is the case
  for acetone and propanal.

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Carboxyl Group (Acids)
Acetic Acid
Acetate

• The carboxyl group (symbolized as COOH) has both
  a carbonyl and a hydroxyl group attached to the
  same carbon atom, resulting in new properties.
• Carboxyl groups are weak acids, dissociating
  partially to release hydrogen ions.

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Amino Group (Bases)

• The amino group (NH2) consists of a nitrogen
  atom bonded to two hydrogen atoms and to the
  carbon skeleton.
• Acts as a base can pick up a proton from the
  surrounding solution.
• Ionized, with a charge of 1, under cellular
  conditions.

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Sulfhydryl Group
SH

• The sulfhydryl group (SH) consists of a sulfur
  atom bonded to an atom of hydrogen resembles a
  hydroxyl group in shape.
• Two sulfhydryl groups can interact to help
  stabilize protein structure called disulfide bond
  (symbolized as -S-S-).

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Phosphate Group (Acids)

• In a phosphate group, a phosphorus atom is bonded
  to four oxygen atoms one oxygen is bonded to the
  carbon skeleton two oxygens carry negative
  charges abbreviated P . The phosphate group
  (OPO32-) is an ionized form of a phosphoric acid
  group (OPO3H2 note the two hydrogens).
• Makes the molecule of which is a part an anion
  (negatively charged ion).
• Can transfer energy between organic molecules
  (e.g., ATP).

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The Functional Groups

• Functional groups are the chemically reactive
  groups of atoms within an organic molecule.
• Give organic molecules distinctive chemical
  properties.
• Most Important in the Chemistry of Life