This document discusses proteins and amino acids. It begins by describing the general structure of amino acids, including that they contain a central carbon atom bonded to an amino group, carboxyl group, hydrogen atoms, and a side chain. It then discusses the condensation reaction of amino acids to form polypeptides, and describes the primary, secondary, tertiary, and quaternary structures of proteins. Methods for analyzing proteins using chromatography and electrophoresis are also summarized. The document concludes by listing the major functions of proteins in the body, such as providing structure, acting as enzymes and hormones, transporting molecules, and serving as an energy source.

1. HUMAN
BIOCHEMISTRY
-fatin
-hanis
-bella

2. B1.1: CALCULATE THE ENERGY VALUE OF A
FOOD FROM ENTHALPHY OF COMBUSTION
DATA
∆H = mc∆T
Keys:
m = mass
c = specific heat of water (4.18 Jg-1C°-1)
∆T = change in temperature

3. Example:
1.00 g cereal raises the temperature of 400 cm3
water in an insulated food calorimeter from
23.7 C° to 33.4 C°. Calculate the energy value
per gram of the cereal, assuming the heat
capacity of the calorimeter is negligible and
given the specific heat of water = 4.18 Jg-1C°-1
(answer: 16.2 kJ per gram of cereal)

4. B2.1: DRAW THE GENERAL FORMULA OF
2-AMINO ACIDS
• Central carbon of amino acids is made up of
hydrogen (H), amino group (-NH), carboxylic
acid group (-COOH) and side chain (R)

6. B2.2: DESCRIBE THE CHARACTERISTIC
PROPERTIES OF 2-AMINO ACIDS
• Amino acids are:
– Colorless
– Crystalline solids
– Exist as zwitterions (dipolar ions)
– Relatively high melting points
– More soluble in water than organic solvents
– Are amphoterics (capable of behaving as acids or
bases)

7. H2NCHRCOOH + H2O H3N+CHRCOOH + OH-
At lower pH, H+ added reacts with OH- and the
forward reaction is favoured to replace some of
the OH- used up. Thus, in an acidic solution, the
-NH2 group is protonated.

8. H2NCHRCOOH + H2O H2NCHRCOO- + H3O+
At higher pH, the base added react with H3O+
and the forward reaction is favoured to replace
some of the H3O+ used up. Thus, in an alkaline
solution, the carboxylic acid group donates a
proton and converted to the carboxylate ion.

9. When a strong acid is added to an
aqueous solution of amino acid, the
zwitterions accepts the proton thus
minimizing the effect of the acid added.

10. If a strong base is added, the zwitterion
donates H+ to neutralize the base to form
water.

11. B 2.3 : DESCRIBE THE CONDENSATION
REACTION OF
2 - AMINO ACID TO FORM POLYPEPTIDES

12. Amino acid contain both an amine functional group and a
carboxylic acid function group.
When they are both attached to the same carbon atom, they
known as 2-amino acid or α–amino acid
diagram of 2-amino acid or α–amino acid :
H
H₂N C COOH
R
-2-amino acid-

13. There are about twenty 2-amino acid that
occur naturally.
All the twenty 2-amino acid are the basic
“building block” of protein in our body.
It consist of long polypeptides which
formed by condensation reaction
between amino acid.
All amino acid have both a carboxyl group
and an amino group which they able to
undergo condensation reaction to form
substituted amides.

14. This process call as condensation reaction as it involve the formation of
water molecule.
The reaction between two amino acid result in the formation of a
dipeptide and water.
Definition of dipeptide : a product which is a substituted amide made up
of two amino acid joined by a peptide bond or peptide linkage.
The two amino acid residues are joined by a strong carbon - nitrogen
bond.

15. The process of condensation polymerization is repeated until
long chain of amino acids is formed that is known as
polypeptides.

16. One example of alanine and glycine, can form two
dipeptides:
NOTE:
 Alanine : have CH₃ on carbon molecule.
 Glycine : just have H on the carbon molecule.

17. B 2.4 : DESCRIBE AND
EXPLAIN THE STRUCTURE
OF PROTEIN

18. PRIMARY STRUCTURE :
 Definition : Linear sequences of amino acids in
polypeptides chain.
 Primary structure of protein is determined by the
sequence of bases in gene that codes for protein.
 If there is changing if a single amino acid due to a
mutation in DNA of its gene will alter its properties
drastically. Example: sickle anaemia cell.
 Each protein has its own unique primary sequence if
amino acid.
 Primary structure of protein gives the protein ability to
carry out its characteristic function.
 Eg : a tripeptide containing the amino acid :
 lysine, glycine and leucine lys-gly-leu

19. SECONDARY STRUCTURE :
Secondary structure is the chain of amino acid that
folds itself due to the intramolecular hydrogen bond.
Two type of secondary structure :
 α-helix : the protein is twist in a spiralling manner like
coiled spring.
 β pleated sheet : give a sheet- like structure.
Example of :
 α-helix : keratin that found in nail and hair
 β pleated sheet : silk fibre

20. TERTIARY STRUCTURE :
 Tertiary structure is the overall folding of chain by interaction between
distant amino acid and gives protein its three-dimensional shape of
single protein.
(when the secondary structure is folded further to form 3D shape of
globule)
 Tertiary sturucture of protein is folded each other because of they have
attraction between amino acid in polypetides
 The interaction that involve :
 Hydrogen bond
 Van Der Waal’s between non polar side group
 Ionic attraction between polar groups
 Disulphide bridge
 Example of tertiary structure of protein :
 Immunoglobin
 Antibody
 Enzyme
 Insulin (Protein based hormone)

21. QUARTERNARY STRUCTURE :
Quaternary structure : separate
polypeptides chains can interact together to give a
more complex structure.
Eg : Haemoglobin
has quaternary structure that include 4 protein
chain ( two α– chains and two β - chains) which
is grouped together around four haem groups

22. B 2.5 Explain how proteins can be analyzed by
chromatography and electrophoresis.
Chromatography.
•Primary structure of protein can be identified by chromatography paper or
electrophoresis.
•However, protein must be hydrolyzed first by hydrochloric acid to successively
release amino acids.
Procedure :
1. A small spot of an unknown amino acid sample is placed in a solvent (eluent)
placed in developing tank with cover.
2. Eluent rises up the paper due to capillary action.
3. When it meets the sample spot, the different amino acid partition
themselves between the eluent and the paper to some extents
4. The move up at different rates.
5. When the eluent almost reach the top, the paper is removed from the tank,
dried up, and sprayed with organic dyes (ninhydrin) to develop
chromatogram by coloring acids.
6. Compare the position of all spots.

23. Rf value = =
x y

24. Alternative ways :
If sample of known amino acid is not available, Rf
value (retention factor) can be measured and
compared with known values as each amino acid
had a different Rf value.
Sometimes, we may found that two acids have the
same Rf value using the same solvent, but using a
different solvent may result different Rf value.
Chromatogram can be turned through 90o and run
again using the second solvent.

25. Electrophoresis
• Structure of amino acid changes at different value of
pH.
• At low pH (acidic medium), amine group will be
protonated.
• At high pH (alkaline medium), the carboxylic group will
lose a proton.
• This is why amino cid can act as buffers.
• If H is added, they are removed as –NH and if OH is
added, -COOH will lose a proton to remove OH- ions in
water.
• For each amino acid, there is a unique pH value named
isoelectric point where the acid exists as zwitterions.

26. Procedures :
• Electrophoresis is carried out in polyacrylamide gel as
medium. Hence, the process is called PAGE (polyacrylamide
gel electrophoresis)
• The sample is placed in the centre of the gel and potential
different is applied across it.
• Depending on the pH of amino acid, the sample will move
at different rates toward the negative and positive
electrodes.
• At isolelectric point, a particular amino acid will stop
moving as its charge is balanced already.
• When separation is completed, the acids can be sprayed
with ninhydrin and identified by comparing distances they
have travelled with standard samples or from comparison
of their isoelectric point.

28. B2.6 List the major functions of proteins
in the body.
1. Structural
• Protein such as collagen (found under the skin) and keratin (found in hair and nails) provide
structure and strength.
2. Biological catalysts
• Enzymes act as biological catalyst that speed up the reaction in human body by providing alternate
pathways for the reaction. It lowers the activation energy of the reaction.
3. Hormones
• Insulin is essential for human body.
4. Antibodies
• Types of protein produced result to presence of any foreign materials in human body. It provide
immunity against the diseases. For example, immunoproteins.
5. Transport
• Haemoglobin in red blood cells carry oxygen from lungs to the cell. It also carries carbon dioxide
from cells to lung to be excreted out.
6. Energy.
• Protein can also be a source of energy for human. Instead of carbohydrates and fats, protein can
also be metabolized to provide energy under certain condition.