Biochemistry

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Biochemistry

• Proteins

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Proteins

• Derived from amino acids - compounds containing
  an amine group - NH2 , an R group, a H atom and
  a carboxylic acid group (COOH) all bonded to
  same carbon atom (called alpha carbon atom)
• R group stands for any combination of atoms
  usually involving C and H
• Natural amino acids use 20 R-groups

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Components of an Amino Acid
(BASE)
(ACID)
Joesten, World of Chemistry 2nd, Saunders FL,
1996, 460
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Amino acid as an Acid/Base

• An acid is a proton (H) donor and a base is a
  proton (H) acceptor
• Amino acid is both an acid and a base
• The carboxylic acid part of amino acid (COOH) can
  donate H to the amine base part of the amino
  acid (NH2) giving RCH(NH3) COO - as a second
  form for an amino acid

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The 20 Amino Acids Found in Natural Proteins
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C.
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C.
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D.
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Formation of Proteins
Proteins result when 50 or more amino acids are
joined together by peptide bonds to form a chain
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Structures of Proteins - Phone Cord Analogy
Hill/Kolb,Chemistry for Changing Times, 7th,
Prentice Hall, NJ, 1995, 468
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Primary Structure of Proteins

• Primary - the linear order of amino acids held
  together by peptide bonds
• Usually represented by the three letter
  abbreviations for proteins such as
  gly-val-ala-asp for a short tetra-peptide
  containing, in order, the amino acids glycine,
  valine, alanin, and aspartic acid

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Secondary Structure of Proteins

• Secondary - repetitive pattern established by the
  backbone (the chain containing the peptide bonds)
  due to H-bonding between backbone atoms
• Two common structures are helix if H-bonding is
  between nearby atoms in the same chain, or
  pleated-sheet if between atoms in parallel chains

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Secondary Protein Structure - alpha helix
H-bonding between backbone atoms on nearby
segments of one protein chain
Tro, 410
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Secondary Protein Structure - pleated sheet
Hydrogen bonding between parallel segments of
several protein chains
Joesten, World of Chemistry 2nd, Saunders FL,
1996, 471
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Tertiary Structures of Proteins

• Tertiary - refers to how a chain is folded by
  interactions between its R-groups
• Four common interactions causing folding are
  hydrogen bonding, ionic bonding, covalent bonding
  involving S-linkages, and hydrophobic interaction
  (London Dispersion Force)

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Tertiary Structure of Proteins
Ionic bonding
Four types of interactions that maintain tertiary
structures
Hill/Kolb, "Chemistry for Changing Times",
7th,Prentice Hall, NJ, 1995, 469.
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Globular Structure
Protein chain often folds with non-polar groups
on the inside (red) where they are held together
by dispersion forces. Hydrophobic region The
outside has polar groups extending into the water
(blue). Hydrophilic region
Hill/Kolb, "Chemistry for Changing Times",
7th,Prentice Hall, NJ, 1995, 470.
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Tertiary Protein Structure of Myoglobin - globule
Hill/Kolb,Chemistry for Changing Times, 7th,
Prentice Hall, NJ, 1995, 468
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Quaternary Structure of Proteins

• Quaternary - arrangement of subunits of a protein
  that consists of two or more subchains
• Frequently involve same four kinds of
  interactions as tertiary

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Quaternary Structure of Hemoglobin Protein
Molecule
Tro, 412
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Sickle-Cell Anemia

• Results from mutant gene that changes 2 amino
  acids out of the 574 that make up hemoglobin
  (Hb) valine (non-polar R) replaces glutamic acid
  (polar R)
• London Force causes Hb molecules to aggregate
  into shapes that inhibit blood flow thus clogging
  arteries and causing anemia and severe pain

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Amino Acids Involved in Sickle-Cell Anemia
Chang, Chemistry, 6th, McGraw-Hill, 1998, 985
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Locations of valine groups shown by red dots
Chang, Chemistry, 6th, McGraw-Hill, 1998, 986
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Normal (round) and Sickle Cells
Brown et al, Chemistry, 8th, Prentice Hall, NJ,
2000,498
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Function of Proteins Enzymes

• Catalyst is a substance that increases the rate
  of a reaction without undergoing permanent
  change itself
• Enzymes are folded proteins that function as
  catalysts and enable living systems to metabolize
  food in hours rather than years

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Zumdahl, Chemical principles, Heath,MA, 1992, 697
The folded structure of the enzyme
carboxypeptidase-A which contains 307 amino acids
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Function of Proteins Enzymes

• Enzymes react by molecular recognition, i.e, they
  "recognize" their partners by size, shape, and
  complementary intermolecular forces
• Substrate is a molecule that is attracted to and
  fits a specific enzyme
• Enzymes lower Ea for a specific reaction and thus
  increase its rate

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Lock and Key Analogy for Enzymes
Hill/Kolb, Chemistry for Changing Times, 6th,
Prentice Hall, NJ, 1995, 471
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Protein-substrate interaction
Zumdahl, Chemical principles, Heath,MA, 1992, 697
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Enzyme
Zumdahl, Chemical principles, Heath,MA, 1992, 678
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Prions

• Prions are proteins that have folded incorrectly
  resulting in a tertiary structure that cannot
  fulfill its biological function (Mad Cow's
  Disease)
• The primary structure appears to be correct so
  the cause of the incorrect folding is unknown and
  is an area of current active research