Transcript Lecture 6

Condensation Reactions
• Two molecules
combine with the
generation of a
smaller molecule
Condensation Reactions
• Reaction of Acetic Acid and Ethanol
Looking at the Reaction Mechanism
1. The carbonyl carbon is:
•
•
Electron deficient
In a trigonal planar geometry
•
120º between substituents
2. The carbonyl oxygen is pulling electrons
towards it
•
Resonance stabilization
3. The Lone Pair of the alcohol oxygen can
react with the carbonyl carbon to set the
whole thing in motion
4. Remember your VSEPR Geometry
Condensation Reactions: Making Lipids from Sugars
and Fatty Acids
• Your cells can
synthesize
lipids from
glycerol and
fatty acids in a
condensation
reaction

Condensation Reactions: Polymerizing Carbohydrate
Monomers
Condensation Reactions: Forming a Peptide Bond
1.
2.
What are the
amino acids in
the figure?
What function
group is
formed?
Its not really this
simple, but it
illustrates a
point!
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 isn’t a compound name and ase, then it usually does something else:
•Lyase
•Reductase
•Kinase
•Transferase
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?)
Hydrolysis of Peptides
•
•
Dipeptide (What are
the amino acids) is
hydrolyzed to ???
Catalyzed by a
peptidase or a
protease
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
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
Amino Acids and Stereochemistry
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
Side Chain Classification
1. 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
Side Chain Classification
2. 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
Side Chain Classification
3. 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 pKa’s of the side chains are less
than 7
Side Chain Classification
4. 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
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 pKa’s range from ~4 to
12
Titrating and Amino Acid: Alanine
1.
We’ll start at a pH of 1
•
The carboxylic acid and the amino group are
protonated
2.
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,
[NH3+CHCH3COOH]=[NH3+CHCH3COO-]
(same as we learned with regular titrations)
3.
As we add more base, we deprotonate all
the carboxylic acids
•
Midway up the sharp slope increase
•
For alanine, this is the isoelectric point
4.
As we add more base, we’ll start
deprotonating the -amino group until we
reach pH=9.69 (the pKa of the group)
•
[NH3+CHCH3COO-]=[NH2CHCH3COO-]
5.
Finally we can keep adding base until the
only species is: NH2CHCH3COO-
Titrating and Amino Acid: Histidine
1.
We’ll 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
2.
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
3.
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
4.
As we add more base, we’ll start
deprotonating the -amino group until we
reach pH=9.17 (the pKa of the group)
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:
pK1 + pK 2
pI =
2
But we must take care to
use the correct pK values!
• We average the pK values from the higher pKa that lost a
hydrogen and the lowest pKa that is still protonated
 Histidine
• For example:
–
–
–
–
–
pK1 = 1.82
pK2 = 6.0
pK3 = 9.17
We’d use the last two values
Usually it will be the alpha amino and the R group pK’s that are used
The Peptide Bond
• Amino acids are
joined together
in a
condensation
reaction that
forms an amide
known as a
peptide bond
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