Condensation Reactions

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Condensation Reactions

• Two molecules combine with the generation of a
  smaller molecule

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Condensation Reactions

• Reaction of Acetic Acid and Ethanol

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Looking at the Reaction Mechanism

• The carbonyl carbon is
• Electron deficient
• In a trigonal planar geometry
• 120º between substituents
• The carbonyl oxygen is pulling electrons towards
  it
• Resonance stabilization
• The Lone Pair of the alcohol oxygen can react
  with the carbonyl carbon to set the whole thing
  in motion
• Remember your VSEPR Geometry

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Condensation Reactions Making Lipids from
Sugars and Fatty Acids

• Your cells can synthesize lipids from glycerol
  and fatty acids in a condensation reaction

?
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Condensation Reactions Polymerizing
Carbohydrate Monomers
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Condensation Reactions Forming a Peptide Bond

1. What are the amino acids in the figure?
2. What function group is formed?

Its not really this simple, but it illustrates a
point!
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Hydrolysis The Opposite of Condensation

• In a hydrolytic reaction, we add the elements of
  water (H and OH-) across a bond
• Many enzymes use this kind of reaction to degrade
  polymers
• Lipases Hydrolyze lipid esters
• Glycosidases Hydrolyze carbohydrate polymers
• Peptidases Hydrolyze peptide bonds
• Compound Name ase Usually indicates a
  hydrolase (but not always!)
• If it isnt a compound name and ase, then it
  usually does something else
• Lyase
• Reductase
• Kinase
• Transferase

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Hydrolysis of Sugar Polymers

• We add water across the Glycosidic Bond of
  Maltose to break it and generate 2 monomers
• Catalyzed by a glycosidase (Maltase perhaps?)

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Hydrolysis of Peptides

• Dipeptide (What are the amino acids) is
  hydrolyzed to ???
• Catalyzed by a peptidase or a protease

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Amino Acids

• Amino acids are the building blocks of proteins
• They consist of an amino group bonded to an
  ?-carbon, a hydrogen bonded to the ?-carbon and a
  carboxylic acid

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Amino Acids and Stereochemistry

• The ?-carbon is all amino acids except for
  glycine is chiral
• Stereoisomers exist that is non-superimposable
• Any carbon with 4 different substituents can be
  chiral
• We describe the chirality of the ?-carbon as
  being Levorotary or Dextrorotary
• L- or D-
• Refers to how the molecule rotates polarized light

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Amino Acids and Stereochemistry
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Amino Acid Side Chains Where the Action is!

• The amino acids are classified according to the
  chemical character of the R-grop attached to the
  ?-carbon
• Important Criteria
• Polar or Nonpolar side chains
• Acidic or Basic
• Charged or uncharged Polar residues

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Side Chain Classification

• Nonpolar (hydrophobic) Amino Acids
• G, A, V, L, I, P, F, W, M
• These amino acids have aliphatic side chains
• Phenylalanine and Tryptophan are aromatic
• Proline is cyclic
• Induces turns in proteins

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Side Chain Classification

• Polar, Uncharged Amino Acids
• S, T, Y, C, N, Q
• S, T, Y have hydroxyl groups (-OH)
• C has a sulfhydryl (-SH)
• N and Q have amide side chains
• Uncharged at neutral pH

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Side Chain Classification

• Acidic Amino Acids
• D and E have carboxylic acids on their side
  chains
• The side chains are negatively charged at neutral
  pH
• This means the pKas of the side chains are less
  than 7

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Side Chain Classification

• Basic Amino Acids
• H, K and R have side chains that are positively
  charged at neutral pH
• Because these side chains have basic groups, they
  accept protons at pH values lower than the pKa of
  the side chain

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Titrating Amino Acids

• Free amino acids can have up to 3 pKa values
  associated with them
• Carboxylic acid
• Amino group
• R-group
• The carboxylic acid group has the lowest pKa
  (2.0)
• The pKa of the ?-amino is around 9-10
• D, E, H, C, Y, K and R have R-groups that can
  ionize and their pKas range from 4 to 12

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Titrating and Amino Acid Alanine

• Well start at a pH of 1
• The carboxylic acid and the amino group are
  protonated
• As we start adding base, more and more of the
  carboxylic acids start losing protons until we
  reach pH 2.34 (the pKa of COOH)
• At this concentration, NH3CHCH3COOHNH3CHCH3C
  OO- (same as we learned with regular titrations)
• As we add more base, we deprotonate all the
  carboxylic acids
• Midway up the sharp slope increase
• For alanine, this is the isoelectric point
• As we add more base, well start deprotonating
  the ?-amino group until we reach pH9.69 (the pKa
  of the group)
• NH3CHCH3COO-NH2CHCH3COO-
• Finally we can keep adding base until the only
  species is NH2CHCH3COO-

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Titrating and Amino Acid Histidine

• Well start at a pH of 1, the only species is the
  fully protonated form.
• pK1 (COOH) 1.82
• pK2 (Imidazole nitrogen) 6.0
• pK3 (Amino) 9.17
• As we start adding base, the pH increases as the
  carboxylic acid converts to carboxylate
• At pK1, the concentration of the carboxylate
  specie equals the concentration of the carboxylic
  acid species
• As we add more base, we start deprotonating the
  imidazole nitrogen
• At pK2, the conc. of the deprotonated imidazole
  group equals that of the protonated state
• The pI is reached then the imidazole group is
  completely deprotonated
• As we add more base, well start deprotonating
  the ?-amino group until we reach pH9.17 (the pKa
  of the group)

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Amino Acid Titrations

• At the isoelectric point, the molecule has zero
  net charge
• The pH where this occurs is called the pI
• We can calculate the pI of an amino acid using
  the following equation
• We average the pK values from the higher pKa that
  lost a hydrogen and the lowest pKa that is still
  protonated
• For example Histidine
• pK1 1.82
• pK2 6.0
• pK3 9.17
• Wed use the last two values
• Usually it will be the alpha amino and the R
  group pKs that are used

But we must take care to use the correct pK
values!
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The Peptide Bond

• Amino acids are joined together in a condensation
  reaction that forms an amide known as a peptide
  bond

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The Peptide Bond

• A peptide bond has planar character due to
  resonance hybridization of the amide
• This planarity is key to the three dimensional
  structure of proteins