The Chemistry of Villin Gary Benz and Claudia Winkler

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The Chemistry of VillinGary Benz and Claudia
Winkler
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The Chemistry of Villin

• Villin is a protein
• Proteins are macromolecules (polymers) formed by
  a defined sequence of small similar molecules
  (monomers) of amino acids
• Amino acids are organic compounds containing at
  least one amino group (NH3) and one carboxyl
  group (-COOH).
• 20 different amino acids make up all proteins

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The amino-acid alphabet

• Biologists represent each amino acid with a
  capital letter
• For instance
• DAspartic Acid, EGlutamic Acid,
  FPhenylalanine, KLysine, AAlanine, VValine,
  FPhenylalanine
• All amino acids are made of 4 elements Carbon,
  Hydrogen, Oxygen, Nitrogen. Two also contain
  Sulfur.

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Villins Single Chain

• Biologists describe the sequence of amino acids
  that make villin as
• DEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFMLS
• Although villin is made of a chain of 36 letters,
  only 16 different letters are needed to describe
  villin
• In the next slides we shall look at the
  individual amino acids that make up villin

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D Aspartic Acid
Name Info Looks
Aspartic acid, Letter D Abbreviation Asp 4 oxygen 4 carbon 6 hydrogen 1 nitrogen
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E Glutamic Acid
Name Info Looks
Glutamic acid Letter E Abbreviation Glu 5 carbon 8 hydrogen 4 oxygen 1 nitrogen
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F Phenylalanine
Name Info Looks
Phenylalanine Letter F Abbreviation Phe 9 carbon 11 hydrogen 1 nitrogen 2 oxygen
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K Lysine
Name Info Looks
Lysine Letter K Abbreviation Lys 6 carbon 14 hydrogen 2 nitrogen 2 oxygen
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A Alanine
Name Info Looks
Alanine Letter A Abbreviation Ala 3 carbon 7 hydrogen 1 nitrogen 2 oxygen
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V Valine
Name Info Looks
Valine Letter V Abbreviation Val 5 carbon 11 hydrogen 1 nitrogen 2 oxygen
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G Glycine
Name Info Looks
Glycine Letter G Abbreviation Gly 5 carbon 11 hydrogen 1 nitrogen 2 oxygen
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M Methionine
Name Info Looks
Methionine Letter M Abbreviation Met 5 carbon 11 hydrogen 1 nitrogen 2 oxygen 1 suphur
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T Threonine
Name Info Looks
Threonine Letter T Abbreviation Thr 4 carbon 9 hydrogen 1 nitrogen 3 oxygen
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R Arginine
Name Info Looks
Arginine Letter R Abbreviation Arg 6 carbon 14 hydrogen 4 nitrogen 2 oxygen
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S Serine
Name Info Looks
Serine Letter S Abbreviation Ser 3 carbon 7 hydrogen 1 nitrogen 3 oxygen
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N Asparagine
Name Info Looks
Asparagine Letter N Abbreviation Asn 4 carbon 8 hydrogen 2 nitrogen 3 oxygen
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L Leucine
Name Info Looks
Leucine Letter L Abbreviation Leu 6 carbon 13 hydrogen 1 nitrogen 2 oxygen
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P Proline
Name Info Looks
Proline Letter P Abbreviation Pro 5 carbon 9 hydrogen 1 nitrogen 2 oxygen
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W Tryptophan
Name Info Looks
Tryptophan Letter W Abbreviation Trp 11 carbon 12 hydrogen 2 nitrogen 2 oxygen
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Q Glutamine
Name Info Looks
Glutamine Letter Q Abbreviation Gln 5 carbon 10 hydrogen 2 nitrogen 3 oxygen
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Elements

• Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen
  (N) and Sulfur (S) are the only chemical elements
  that make up all villins amino acids.
• We shall review some of their properties in the
  next pages.

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Carbon

• (Latin carbo, charcoal) Carbon, an element of
  prehistoric discovery, is very widely distributed
  in nature. It is found in abundance in the sun,
  stars, comets, and atmospheres of most planets.
• Carbon is the source of energy for life through
  carbohydrates, just like a burning log is a
  source of energy to a cold room.

Atomic number 6
Atomic Symbol C
Atomic mass 12.011 u
Electron Configuration He2s22p2
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Hydrogen

• (Greek hydro, water, and genes, forming)
  Hydrogen is the most abundant of all elements in
  the universe.
• The heavier elements were originally made from
  Hydrogen or from other elements that were
  originally made from Hydrogen.
• Used in rocket fuel.

Atomic number 1
Atomic symbol H
Atomic mass 1.0070 u
Electron Configuration 1s1
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Oxygen

• Greek oxys, sharp, acid, and genes, forming
  acid former) Oxygen is the third most abundant
  element found in the sun. Oxygen is vital to the
  respiration of living organisms.
• Oxygen is responsible for the bright red and
  yellow-green colors of the Aurora.
• Essential element for combustion (i.e. burning).

Atomic number 8
Atomic symbol O
Atomic mass 15.9994 u
Electron Configuration He2s22p4
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Nitrogen

• (Latin Nitrum, Greek. Nitron, native soda genes,
  forming).
• Nitrogen gas (N2) makes up 78.1 of the Earths
  air, by volume.
• Nitrogen is found in all living systems as part
  of the makeup of biological compounds.
• Ammonia (NH3) is the most important commercial
  compound of nitrogen, with a very pungent smell,
  used in cleaning supplies.

Atomic number 7
Atomic symbol N
Atomic mass 14.00674
Electron Configuration He2s22p3
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Sulfur

• (Sanskrit, sulvere Latin sulpur) Known to the
  ancients referred to in Genesis as brimstone.
• Sulfur occurs native in the vicinity of volcanoes
  and hot springs.
• It is widely distributed in nature in various
  minerals (iron pyrites, galena, sphalerite,
  cinnabar, stibnite, gypsum, epsom salts,
  celestite, barite, etc.)
• Sulfur is found in meteorites.

Atomic number 16
Atomic symbol S
Atomic mass 32.6
Electron Configuration Ne3s23p4
Yellowstone hot springs
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Molecules, Bonds

• Atoms are bonded together to form molecules and
  molecules are bonded together to form
  macromolecules.
• The next slides shows some characteristics of
  chemical bonds.

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Chemical Bonds
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Peptide Bond

• Amino acids join together via a special bond
  called peptide bond.
• In a peptide bond, two molecules (amino acid 1
  and amino acid 2) are joined together with the
  accompanying removal of a molecule of water.

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Activity

• Knowing that villin is made of the following
  sequence of amino acids
• DEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFMLS
• Compute the molar mass of villin.
• Compute the percentage by number of each atom
  component.
• Compute the percentage by mass of each atom
  component.
• (Remember that amino acids are joined together
  through peptide bonds.)
• Lesson Plan