Lec Notes

BIOCHEM
LEC NOTES – PROTEINS

Amino Acids
Structural formula of amino acids
H
l
NH3 -‐ C -‐ COO-‐
+
l
R

§ type of intermolecular force: Van der Waals (non polar)
§ (+) Ninhydrin test: presence of an α–NH2 group (all AA except proline and hydroxyproline)

§ type of intermolecular force: pi-‐pi complex (aromatic)
CONFIRMATORY TESTS:
§ (+) FeCl3 test: presence of phenol (only tyrosine)
§ (+) Hopkin’s Cole test: presence of indole ring (only tryptophan)
§ (+) Xanthoproteic test: presence of benzene ring (only phe-‐tyr-‐trp)

§ type of intermolecular force: salt bridge (negative and positive ions)
§ CONFIRMATORY TEST: (+) Sakaguchi test – presence of guanido group (only arginine)

§ type of intermolecular force: disulfide bond (thiol group)
§ CONFIRMATORY TEST: (+) Lead acetate test -‐ presence of thiol group (only cysteine)

Zwitterion form
H
l
NH3 -‐-‐ C -‐ COO -‐
+
l
R
§ dipolar form of an amino acid at its isoelectric point (pH at which a protein molecule or an amino acid
precipitates)
§ at the isoelectric point there is a net equal charge; unlike charges attract and the protein molecule/
amino acid becomes INSOLUBLE
§ before & beyond the isoelectric point , there is repulsion of like charges and the protein molecule/
amino acid becomes SOLUBLE

Buffer action
H
l
NH3 -‐-‐ C -‐ COO -‐
+
l H+
R
§ in the presence of an acid (at low pH), the carboxylate ion absorbs the H+ and forms -‐COOH in the
reaction: -‐COO-‐ + H+ → -‐COOH
§ +1 charge results from –NH3+ and the amino acid DISSOLVES
H
l
NH3+ -‐-‐ C -‐ COO -‐
l
R
+ -‐
H + OH → H2O
§ in the presence of a base (at high pH), the ammonium ion absorbs the OH-‐ and forms –NH2 in the
reaction: -‐NH3+ + OH-‐ → -‐NH2 + H2O
§ -‐1 charge results from –COO-‐ and the amino acid DISSOLVES

Protein Structures
Primary structure: Peptide bond

§ peptide bond is formed between carboxyl group (-‐COOH) of the first AA and amino group
(-‐NH2) of the second AA by eliminating H2O
§ peptide bond is an amide bond that can undergo hydrolysis
O
II
NH2 – CH – C – NH – CH – COOH
I I
R1 R2
§ two AA – dipeptide; NEGATIVE in the Biuret test
three AA and above – tripeptide and other polypeptides give (+) Biuret test

Secondary structure:
H – bond (α – helix)

H – Bond (β – pleated sheet)

Tertiary Structure

§ involves the intermolecular forces among the amino acid side chains
aliphatic AA – Van der Waals acidic & basic AA – salt bridge
aromatic AA – pi-‐pi complex -‐SH group AA – disulfide bond
-‐OH group AA – H-‐bond
-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐-‐
HW
1) Given the zwitterion form, draw the predominant structure at: a) low pH b) high pH
aspartic acid
NH3+ -‐ CH – COO-‐
l
CH2-‐COOH

2) Given the zwitterion form, draw the predominant structure at: a) low pH b) high pH
lysine
NH3+ -‐ CH -‐ COO-‐
l
(CH2)4-‐NH2

3) a) Given the following AA, draw its primary structure.
b) Encircle the N-‐terminal, C-‐terminal and peptide/ amide bond.

NH3+ CH-COO-

CH3 CH2

CH CH - NH3+
CH3 COO-

OH

4) a) Draw the structure of the dipeptide based on the following amino acids.
b) Describe the side chains (polar, non polar, acidic or basic)
NH3+ CH-COO-
SH - CH2 CH - NH3+
CH2
COO-

For nos. 5 & 7, refer to the given illustration. Below are two tripeptide strands linked together by bonds A, B
and C.

A
B C

5) For bond A:
a) Identify bond A if it is an amide, H-‐bond or an intermolecular force
b) Is this bond a 1O, 2 O or 3 O protein structure?

6) For bond B:
a) Identify bond B if it is an amide, H-‐bond or an intermolecular force
b) Is this bond a 1O, 2 O or 3 O protein structure?

7) a) Identify the force of attraction between the side chains of the two amino acids:
NH2 – CH – COOH and NH2 – CH – COOH
l l
CH2 – COOH CH2 – CO-‐ NH2
b) This force of attraction illustrates a 1O, 2 O or 3 O protein structure?

8) a) Identify the force of attraction between the side chains of the two amino acids:
NH2 – CH – COOH and NH2 – CH – COOH
l l
CH2 – SH (CH2)2-‐S-‐CH3
b) This force of attraction illustrates a 1O, 2 O or 3 O protein structure?

Lec Notes

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BIOCHEM

LEC NOTES – PROTEINS

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