Notes Amino Acids and Proteins
Proteins are about 50% of the dry weight of most cells, and are the most structurally complex
molecules known. Each type of protein has its own unique structure and function.
Polymers are any kind of large molecules made of repeating identical or similar subunits called
monomers. The starch and cellulose we previously discussed are polymers of glucose, which in that
case, is the monomer. Proteins are polymers of about 20 amino acids monomers.
The amino acids all have both a single and triple letter abbreviation. Here is an example.
Alanine = A = Ala
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Each amino acid contains an "amine" group, (NH2) and a "carboxylic acid" group (COOH)
(shown in black in the diagram).
The amino acids vary in their side chains (indicated in blue in the diagram).
The eight amino acids in the orange area are nonpolar and hydrophobic.
The other amino acids are polar and hydrophilic ("water loving").
The two amino acids in the magenta box are acidic ("carboxylic" group in the side chain).
The three amino acids in the light blue box are basic ("amine" group in the side chain).
Amino Acids: shown in another structural formula format
H O
H O
NH2
C C OH
CH3
NH2
CH
H3C CH3
alanine
ala – A
C C OH
NH2
C C OH
NH2
C C OH
CH2
CH2
NH2
leucine
leu – L
H O
NH2
isoleucine
ile – I
NH2
methionine
met – M
H O
tryptophan
trp – W
C C OH
H O
NH2
C C OH
CH OH
CH2
CH3
SH
OH
tyrosine
tyr – Y
threonine
thr – T
cysteine
cys – C
NH2 C C OH
NH2 C C OH
CH2
H O
NH2
C C OH
CH2
O C
OH
aspartic acid
asp – D
NH2
C C OH
H O
NH2
CH2
glycine*
gly – G
H O
NH2
C C OH
O C
O C
NH2
OH
glutamic acid
glu – E
NH 2
C C OH
CH2
CH2
CH2
NH
CH2
NH2
histidine
his – H
H O
NH2
lysine
lys – K
C C OH
CH2
CH2
O C
NH2
asparagine
asn – N
CH2
N
serine
ser – S
CH2
C C OH
CH2
OH
H
H O
H O
H O
H O
CH2
NH
C C OH
proline
pro – P
*
C C OH
CH3
CH2
CH2 CH2
CH2
CH3
S
NH 2
C C OH
H O
CH2
phenylalanine
phe – F
NH
CH2
CH
H3C CH3
H O
C C OH
CH CH3
CH2
valine
val – V
H O
H O
NH2
C C OH
H O
H O
glutamine
gln – Q
H O
NH 2
C C OH
CH2
CH2
CH2
NH
NH C
NH2
arginine
arg – R
Amino acids are named as such because each amino acid consists of an amine portion and a
carboxylic acid part, as seen below.
H O
NH2
C C OH
R
Compare this structure to the above structures of each of the amino acids. Each amino acid has this
general structure.
The side chains are sometime shown as R-groups when illustrating the backbone.
In the approximately 20 amino acids found in our bodies, what varies is the side chain. Some side
chains are hydrophilic while others are hydrophobic. Since these side chains stick out from the
backbone of the molecule, they help determine the properties of the protein made from them.
The amino acids in our bodies are referred to as alpha amino acids. The reason is that the central
carbon is in an alpha position in relation to the carbonyl carbon. The carbon adjacent to the carbonyl
carbon is designated the alpha carbon. Each carbon in the chain will be designated with a different
letter of the Greek alphabet. See the example below.
carbonyl carbon
O
beta
delta
CH3CH2CH2CH2CH2 CH
epsilon
gamma
alpha
H O
+
NH3
-
C C O
R
zwitter ion
You may have noticed that the general form for the amino acid is often drawn with the acidic
hydrogen attached to the amine group. This occurs because amine groups are basic. So, the amino
acid has performed an acid-base reaction on itself. When the amino acid is in this form it is referred
to as a Zwitter ion. When amino acids are in solution this is the form that they will be found.
Protein Functions:
Type of Protein
Structure
Function
structural support
Contractile
Transportation
Storage
muscle movement
movement of compounds
nutrient storage
Examples
collagen in tendons and cartilage
keratin in hair and nails
actin, myosin, tubulin and kinesin proteins
hemoglobin carries O2 and lipoproteins carry lipids
ferritin stores iron is spleen and liver
casein stores proteins in milk
Hormone
Enzyme
chemical communication
Catalyze biological reactions
Protection
Recognized and destroy
foreign substances
insulin regulates blood sugar
lactase breaks down lactose
trypsin breaks down proteins
immunoglobulins stimulate immune system
Reactions of Amino Acids:
To form protein, the amino acids are linked by dehydration synthesis to form peptide bonds. The
chain of amino acids is also known as a polypeptide.
Test Reagents for Amino Acids:
Xanthoproteic Test:
 positive test for benzene rings which have amino or hydroxyl groups, such as that present in
tryptophan and tyrosine
 addition of concentrated HNO3 .
 gives yellow color and is intensified to orange-yellow by the addition of a base
Cysteine Test:
 positive test for cysteine
 addition of cyanide salt to reduce disulfide bonds
 addition of nitroprusside to from a colored complex with sulfhydryl groups
 gives a pink to purple color intensity increases with concentration of –SH groups
 if no nitroprusside is used a black ppt will indicate positive test
nitroprusside
Biuret Test:
 positive test for peptide bonds
 Biuret Reagent is made of sodium hydroxide and copper sulfate
 blue reagent turns violet in the presence of proteins
 pink color persists with short-chain polypeptides
 color intensity varies with concentration of peptides
Ninhydrin Test:
 positive test for amino acids, not peptides
 all amino acids give blue
 except proline which gives a yellow color
Sanger Reagent:
 Reagent for the determination of the N-terminal amino acid in a peptide.
 In the first step the amino group is coupled to 1-fluoro-2,4-dinitirobenzene (by a nucleophilic
aromatic substitution).
 Then the peptide is hydrolytically cleaved. If the hydrolysis is mild enough (which can be quite
annoying), then the whole peptide can be degradated via this reaction.

After the cleavage the dinitrophenyl residue is still connected to the N-terminal amino acid. That
can easily be separated and analyzed by e.g. chromatography
Edman Degradation:
 Degradation of the N-terminal amino acid of a peptide.
 Then the amino acid can be identified e.g. with chromatographic methods or melting point.