Chapter 18 Amino Acids and Proteins

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Chapter 18Amino Acids and Proteins
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Introduction to Biochemistry

• Biochemistry The study of the chemical
  substances and vital processes occurring in
  living organisms biological chemistry
  physiological chemistry.
• Biomolecules Proteins, carbohydrates, lipids,
  nucleic acids.

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• Protein A polymer formed from amino acid units.

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Amino acids
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• Amino acid In biochemistry when we refer to
  amino acids we really mean a-amino acids. As the
  name implies, an amino acid contains a carboxylic
  acid group (-COOH) and an amino group (-NH2).
  Both groups are attached to the same carbon atom
  (the a carbon). In addition, there are diverse R
  groups attached to this carbon as well

The a carbon
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• There are 20 amino acids in all living organisms
  19 of them differ only in the identity of the R
  group, or side chain, attached to the a carbon.
  The other amino acid, proline, is a secondary
  amine whose nitrogen and a carbon atoms are
  joined in a five atom ring.
• The 20 amino acids are classified as neutral,
  acidic or basic according to the nature of the
  side chain. Neutral amino acids (15) are further
  subdivided into polar and nonpolar depending on
  the polarity of the side chain as well.

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• Nonpolar side chains are also known as
  hydrophobic (water-fearing) while the polar,
  acidic and basic chains are referred to as
  hydrophilic (water-loving).
• We defined proteins as polymers made out of
  amino acids. In such chains we can have diverse
  combinations of hydrophobic and hydrophilic amino
  acids. Remember that living organisms contain
  large amounts of water in such an environment,
  proteins will tend to adopt conformations such
  that the hydrophobic amino acids are facing
  inwards while the hydrophilic ones are outwards
  facing the solvent.

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• Because amino acids contain both an acidic end
  and a basic end, they can undergo an
  intramolecular (within the same molecule)
  acid-base reaction in this reaction, a proton is
  transferred from the COOH group to the NH2
  group.
• The dipolar ion generated is called a zwitterion
  (from the german zwitter meaning hybrid).

A Zwitterion
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• In acidic solution (excess of H) amino acid
  zwitterions accept a proton on the COO- group.
  In basic solution (excess of OH-) a proton is
  lost from the NH3 end

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• Because amino acids are normally in the
  zwitterion form, they have similar properties to
  salts pure amino acids form crystals with high
  melting points that are soluble in water but not
  in nonpolar solvents.
• In solution, the charge on an amino acid depends
  on the particular amino acid (i.e the side chain)
  and the pH of the medium.
• Isoelectric point pH at which the net positive
  charge equal the net negative charge in a sample
  of the amino acid, that is, the total charge is
  zero.

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• Objects like your hands or feet are equal in
  structure but they are not identical one cannot
  super-impose one on top of the other. They are
  mirror images.
• We call an object that cannot be super-imposed
  to its mirror image chiral.

Chiral Cannot be super-imposed to its mirror
image.
Achiral Can be super-imposed to its mirror image.

• Such objects are also said to be handed or to
  posses handedness.

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• The figure on the left shows a C atom (black)
  connected to four different substituents (color
  spheres). Not matter how much you try, the mirror
  image of this molecule cannot be superimposed on
  itself A carbon atom with four different
  substituents is a chiral molecule.

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• A carbon atom with four different substituents
  is said to be a chiral carbon atom or chirality
  center.

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Chiral Carbon atom

• For 19 of the 20 amino acids, the a-carbon is
  joined to 4 different substituents. Thus, these
  19 amino acids are chiral.
• The only exception is Glycine in which the R
  group is a Hydrogen atom.

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• For historical reasons, pairs of molecules that
  are mirror images are labeled with the prefixes
  L- and D- indicating a right handed or left
  handed molecule.

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• Notice that two molecules that are mirror images
  of one another have the same formula and
  connections but nevertheless they are different.
  Thus, they are isomers.
• In particular, we refer to pairs of molecules
  that are mirror images as enantiomers or optical
  isomers.

A pair of enantiomers
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• If two molecules are isomers some of its
  properties will be different.
• In the case of enantiomers we find that all
  physical properties (melting point, boiling
  point, density, etc.) are identical Yet, being
  isomers we know there must be some difference
  other than structure.

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• Normal light consists of electromagnetic waves
  oscillating in all planes perpendicular to the
  direction of propagation. When ordinary light is
  passed through a polarizer, only the waves in one
  plane get through. We say that this light is
  polarized.

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• When polarized light is passed through a sample
  containing only one of a pair of enantiomers, we
  find that the plane of the polarized light is
  changed by a certain amount. If we conduct the
  experiment using the other enantiomer, we find
  exactly the same deviation but in the opposite
  sense.

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• Enantiomers Pair of isomers whose structures are
  mirror images of one another. The only physical
  property that is different in a pair of
  enantiomers is the change of rotation in the
  plane of polarized light that they induce. This
  change is of equal magnitude but of opposite
  direction.

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• Enantiomers are just a special case of a more
  general case called stereoisomers.
• Stereoisomers Molecules with the same
  connections, same formulas, but different spatial
  arrangement of the atoms.
• What other case of stereoisomers do we know?

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• At the level of chemical properties we also find
  that pair of enantiomers react differently with
  other chiral molecules.
• At the most fundamental level, living organism
  are just a collection of chemical reactions.
  Because amino acids are the building blocks of a
  large portion of the chemical compounds found in
  living systems, it is not surprising then that
  chirality effects are involved in many of these
  chemical processes.

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• Chirality has an effect in the biological
  activity of compounds. Pairs of enantiomers
  often differ in the way they smell, taste or in
  their effects as drugs.
• Aspartame (shown above) is made of the D-
  enantiomers of the amino acids Aspartate and
  Phenylalanine and it is used as a substitute for
  sugar. Changing one or two of the enantiomers to
  the L- form produces a substance that tastes
  bitter.

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• Because each amino acid contains and amino group
  and a carboxylic acid group they can react
  forming and amide bond
• In Biochemistry amide bonds are referred to as
  peptide bonds. Two amino acids can react to form
  a dipeptide (like above), three will form a
  tripeptide, and so on. With 4 and above you
  normally call the structure a polypeptide.