Structure of Amino Acid

Amino Acid is the building block of proteins B. Polar, uncharged side chain
-Two functional groups: amino 1.Hydrophilic : Zero charged at neutral pH
(NH2) and carboxyl groups 2.Contain:
(COOH). i.Polar OH group
-R group (side chain) determines -Participate in hydrogen bond with water
amino acid its unique structure -site of attachment for structure , ie phosphate group
and properties. ii.sulfhydryl group (SH) - Disulfide bond - active sites of enzymes
a. Stereoisomers 3. Location: interior of membrane associated proteins
carbon chiral : Exist as enantiomers (mirror image of one another) – L and D C. Acidic side chain- negative charged
forms. Only L isomers used as building block in protein 1.Proton donors
b. Amphoteric Molecule – behaving as both acid & base 2.Contain carboxylate group (COO-)
3.Location: interior of membrane associated proteins
D. Basic side chain- positive charged
1.Accept protons (protonated)
2.Location: interior of membrane associated proteins
Why you should know the different type of aa?
-contribution to the formation various bond ie
hydrophobic, electrostatic and Van der Waal‟s
interactions to establish protein conformation.
 Human genetic code directly encodes 20 a.a.
c. Exist as Zwitterions  All have a common structure except for the R group

d. Has it’s own pK values

•pH at which amino group or carboxyl group 50% ionises.
•pk1 of carboxylic group of all aa is ~ 2 (1.8-2.4) - acidic
•Pk2 of all amino groups is ~9.5 (8.8-11.0) – base PEPTIDES
e. Has it’s own isoelectric point  Amino acids are joined by the peptide bond to form peptide chains.
Isoelectric Point (pI): pH at which an  Peptide, dipeptide, tripeptide (Gluthathione), oligopeptide and polypeptide
amino acid has no NET charge  The main chain of polypeptide is sometimes termed backbone
Classification of amino acid A) Polypeptide chain
•Based on the properties of side chain:
-A sequence of amino acid.
1)Non polar side chain
-Polypeptide chains have direction:
2)Polar, uncharged side chain
3)Acidic side chain Polar, Charged •Begin: Amino terminal
4)Basic side chain •End: carboxyl terminal
- Polarity – unequal/uneven distribution -Example: Insulin (86 amino acids)
charges on the two ends of any PROTEIN STRUCTURE
molecule(ie H20), hydrophilic
1. Primary Structure : Unique
A. Non polar side chain
1.Does not bind or donate
sequence of amino acid
protons/participate in hydrogen or  Sequence determined during
ionic bonds. DNA replication
2.So cannot form hydrogen bond with  A slight change in primary
water. structure can affect a
3.Promotes hydrophobic interactions – protein’s conformation and
stabilizing protein structure
ability to function
4.Location: on surface of membrane
2. Secondary Structure :
proteins, interacts with lipid
Polypeptide chain can fold into
–Coils = alpha helix
–Lie parallel to each other
=beta pleated sheet
•Hydrogen bonds at regular
intervals along the polypeptide
backbone
 a) Secondary structure: The α-helix COLLAGEN
 Hydrogen bonds form between NH (amide hydrogen) and CO  Most abundant protein in human
(carbonyl oxygen) group in the same strand  Three polypeptides : alpha-helix
 The α-helix coils at every 4th amino acid  Consist glycine, hydroxylproline (x),
b) Secondary Structure: β- Pleated Protein hydroxylysine(y)
 H+ bond is formed b/w amino and co gp on an adjacent strand.  Aggregation of collagen into long fiber:
 Polypeptide strand lie in the same direction: parallel tough and tensile strength
 Polypeptide strand lie in the opposite direction: antiparallel b. Globular Protein The importance of primary structure
3. Tertiary Structure : Refers to the helical form coiled into a ball •Form functional components of the cells  Determined by the nucleotide sequence in
like structure = 3D structure of protein •They are compactly folded and coiled. the gene for the polypeptide or protein.
 The functional unit called the domain. •Examples are:  Determines the 3-D conformation through
 The folding of a protein into its domains is related to the -insulin,plasma albumin,globulin, enzymes folding patterns
hydrophilic or hydrophobic properties of its amino acids. 2. Classification based on composition:  A slight change in primary structure can
 Example : myoglobin = Single polypeptide chain of 154 aa a. Simple protein: Composed of entirely aa. affect tertiary conformation of the cells
The forces that hold 3º structure together are: -Example: and ability to function
a.van der Waals interaction d.ionic i. Albumin, Globulin Example: Sickle Cell Anemia
b.Hydrogen-bonds e.disulphide linkages - present in egg, milk and blood  Abnormal hemoglobin formation because
c.hydrophobic interactions -High biological value i.e. contain all of a single amino acid substitution.
MYOGLOBIN essential amino acids and easily digested.  causes hemoglobin to crystallize,
 Single polypeptide unit that form into several alpha helixes (folded) = 3D ii. Globulins (Histones): deforming the red blood cells and leading
structure, |154 amino acid |Attach to heme -Basic proteins rich in histidine amino acid to clogs in blood vessels.
 Function: Oxygen storage in muscle -Combine with DNA
4. Quaternary Structure : Refers to more than one ball like globular  α1 globulin: antitrypsin: protease inhibitor
structures held together by weak interactions  α2 globulin: haptoglobin: protein that
 Two or more polypeptide chains join in aggregate, they form a binds hemoglobin to prevent its excretion
quaternary structure; eg hemoglobin, DNA polymerase. by the kidney
 Often quaternary proteins are complexed with a different  β-globulin: transferrin: protein that
molecule; ie a mineral. Hemoglobin contains iron, for example. transport iron
 Hemoglobin structure : 2 alpha and 2  γ-globulins = Immunoglobulins
beta subunits (antibodies): responsible for immunity
 Alpha unit= 146 amino acid, beta b. Complex or Conjugated Proteins
unit = 141 amino acid  Made up of aa & other organic compound
 each chain is associated w 1 heme gp  The non-aa group is termed as the
 Function: Oxygen transportation prosthetic group.

c. Derived Protein
 denatured proteins that are derived from
simple & conjugated proteins that occur
after inactive proteins & enzymes are
broken down initially to peptides by
intracellular proteolytic enzymes.
 then degraded to amino acids within the
Classification of proteins: a.Fibrous Protein cell for re-synthesis of new proteins.
1.Based on shape (structural):  form structural comp in the body
a.Fibrous protein  Exhibit special mechanical
b.Globular protein properties = unique structure but
2.Based on composition : simple
a.Simple  Long, rod-shape molecules,
b.Conjugate
 Spiral and helical and are cross
c.Derived protein
linked by disulfide & hydrogen bond
3.Based on biological function
 Physically tough
a. Movement
•Example:
b. Structure
1.Collagen: skin, cartilage, ligament
c. Signaling
2.Keratin: hair, skin, nails
d. Transport
3.Elastin: Wall or blood vessels
e. Catalysis
4.Fibrin: blood clots
f. Protection