1. Amino Acids
“Amino Acid”
Amino Acids are the building units of proteins. Proteins are
polymers of amino acids linked together by what is called “
Peptide bond” (see latter).
 There are about 300 amino acids occur in nature. Only 20 of
them occur in proteins.
Structure of amino acids:
Each amino acid has 4 different groups attached to α- carbon
( which is C-atom next to COOH). These 4 groups are : amino
group, COOH gp,
Hydrogen atom and side
Chain (R)
R

2. • At physiological PH (7.4), -COOH gp is dissociated forming a
negatively charged carboxylate ion (COO-) and amino gp is
protonated forming positively charged ion (NH3+) forming
Zwitter ion
• N.B. Proline is an imino acid not amino acid (see latter)
Classification of amino acids
I- Chemical classification: According to number of COOH and
NH2 groups i.e. according to net charge on amino acid.
A- Monobasic, monocarboxylic amino acids i.e. neutral or
uncharged:
R

3. (Lecture 2):
B- Basic amino acids: Contain two or more NH2 groups or
nitrogen atoms that act as base i.e. can
bind proton.
At physiological pH, basic amino acids will be positively charged.
e.g.
a- Lysine
b- Arginine: contains guanido group
c- Histidine: is an example on basic heterocyclic amino acids

4. C- Acidic Amino acids: at physiological pH will carry negative
charge.
e.g. Aspartic acid (aspartate) and Glutamic acid (glutamate). see
structures in hand out.
Aspargine and Glutamine: They are amide forms of aspartate and
glutamate in which side chain COOH groups are amidated.
They are classified as neutral amino acids.

5. II- Classification according to polarity of side chain (R):
A- Polar amino acids: in which R contains polar hydrophilic group so
can forms hydrogen bond with H2O. In those amino acids, R may
contain:
1- OH group : as in serine, threonine and tyrosine
2- SH group : as in cysteine
3- amide group: as in glutamine and aspargine
4- NH2 group or nitrogen act as a base (basic amino acids ): as lysine,
arginine and histidine
5- COOH group ( acidic amino acids): as aspartic and glutamic .
B- Non polar amino acids:
R is alkyl hydrophobic group which can’t enter in hydrogen bonf
formation. 9 amino acids are non polar ( glycine, alanine, valine, leucine,
isoleucine, phenyl alanine, tryptophan, proline and methionine)

7. IV- Metabolic classification: according to metabolic or degradation
products of amino acids they may be:
1- Ketogenic amino acids: which give ketone bodies . Lysine and
Leucine are the only pure ketogenic amino acids.
2- Mixed ketogenic and glucogenic amino acids: which give both
ketonbodies and glucose.These are: isoleucine, phenyl alanine,
tyrosine and tryptophan.
3- Glucogenic amino acids: Which give glucose. They include the
rest of amino acids. These amino acids by catabolism yields products
that enter in glycogen and glucose formation.

8. Amphoteric properties of amino acids: that is they have both basic
and acidic groups and so can act as base or acid.
Neutral amino acids (monobasic, monocarboxylic) exist in aqueous
solution as “ Zwitter ion” i.e. contain both positive and negative
charge. Zwitter ion is electrically neutral and can’t migrate into electric
field.
Isoelectric point (IEP) = is the pH at which the zwitter ion is formed.
e.g IEP of alanine is 6
Chemical properties of amino acids:
1- Reactions due to COOH group:
-Salt formation with alkalis, ester formation with alcohols, amide
formation with amines and decarboxylation
-2- Reactions due toNH2 group: deamination and reaction with
ninhydrin reagent.
-Ninhydrin reagent reacts with amino group of amino acid yielding
blue colored product. The intensity of blue color indicates quantity of
amino acids present.

9. Ninhydrine can react with imino acids as proline and hydroxy
proline but gives yellow color.
3- Reactions due to side chain (R):
1- Millon reaction: for tyrosine gives red colored mass
2- Rosenheim reaction: for tryptophan and gives violet ring.
3- Pauly reaction: for imidazole ring of histidine: gives yellow to
reddish product
4- Sakagushi test: for guanido group of arginine andgives red
color.
5- Lead sulfide test (sulfur test): for sulfur containing amino
acids as cysteine give brown color.

12.  These nonessential nutrients -- some
prefer the term "dispensable" -- can be
manufactured from other amino acids
or from simpler compounds already
present in your body.
alanine glutamic serine
acid
asparagine glutamine tyrosine
aspartic glycine arginine
acid
cysteine proline

13. Glutamic
Asparagine acid
Aspartic
acid
proline
serine glycine
tyrosine

14.  Are obtained from dietary sources.
Although you do not have to consume
these amino acids on a daily basis --
they are recycled, to some extent -- you
cannot remain healthy if you are
deprived of them for very long.

15. histidine
lysine methionine
isoleucine
Phenylalanine
Tryptophan
Threonine

22. Ques:
Name the dipeptides below using the two letter amino
acid abbreviations separated by hyphen.
Ο O
|| ||
H₂N―CH―C―NH―CH―C―OH
| |
CH₂ CH₂
| |
CH₂ OH
|
C=O
|
OH

24.  Proteins –is a naturally occuring
,unbranched polymer in which the
monomer units are amino acids.
-is a peptide in which atleast amino
acid residues are present.
Proteins are classified as monomeric or
multimeric.

25.  Monomeric  Multimeric protein
protein -is a protein on
-is a protein in which more than one
peptide chain is
which only one
present.
peptide chain is
present.

26. -a protein in
which only amino -is a protein that has one or
acid residues are more non-amino acid
present. residues are present.

28. • is the order in • Is the
which amino arrangemen
acids are linked t in
together in a spaceadopt
protein. edby the
backbone
portion of a
protein.

29.  The alpha helix  Beta pleated sheet
-is a protein -is a protein
secondary structure secondary structure
in which a single in which two fully
protein chain adopts extended protein
a shape that chain segment in the
resembles a coiled same or different
spring(helix)with the molecules are held
coil configuration together by
maintained by hydrogen bonds.
hydrogen bond.

30.  Beta pleated
 Alpha helix
sheet

31. Question:
Draw the secondary structure of a-
helix and b-pleated sheet.

32. Is the overall three dimensional
shape of a protein that results from
the interactions between amino acid
side chains (R group ) that are widely
separated from each other within a
peptide chain.

34.  Interactions responsible for tertiary
structure”
Four types of attractive interactions contribute to the tertiary
structure of a protein:
1. Covalent disulfide bonds
2. Electrostatic attraction(salt bridges)
3. Hydrogen bonds
4. Hydrophobic bonds

35.  The strongest of the
tertiary –structure
interactions ,result from  Also called salt
the –SH groups of two bridges,always involve
cysteine residues the interaction between
reacting with each other acidic side chain (R
to form a covalent group )and a basic side
disulfide bond. chain (R Group)
 Cysteine-is the only
amino acid that
contains a sulfhydryl
group (-SH)

36.  INTERACTIONS RESPONSIBLE FOR TERTIARY
STRUCTURE

37. Questions :
What is the only a-amino acid that
contains sulfhydryl group?

39. Questions:
Identify the following and name its
structure:
(a.) (b.)
(c.) (d.)

40.  Protein classification based on function
 Catalytic proteins
 Defense proteins
 Transport proteins
 Messenger proteins

42.  Globular Proteins
- consist of polypeptides folded into the
shape of a ball.
- are soluble in water or form colloidal
dispersions and active globulins.
- ex. Hemoglobin, albumin, and the
globulins.

43. - consist of parallel polypeptide chains
that are coiled and stretch out.
- are insoluble in water.
- ex. Collagen, fibrin, and myosin.

44.  Colloidal Nature
- proteins form colloidal dispersions in
water.
- proteins present in the bloodstream
and cannot pass through membranes.
-the presence of protein in the urine
indicates damage to the membranes in
the kidneys.

45. - A protein refers to the unfolding and
rearrangement of the secondary and
tertiary structures of a protein without
breaking the peptide bonds.
- A protein that is denatured loses its
biologic activity.

46.  Alcohol
 Salts of Heavy Metals
 Heat

52. Give some reagents or conditions that
cause denaturation?