AMINO ACID

 Component that builds protein.

 A protein is composed of 20 amino acids, although not all proteins
entirely composed of all the twenty mentioned.
 There are 200 free amino acids in the nature.
 One protein to another is composed by different amino acids,
leading to them having different properties and structure.
 The structure of amino acid is as below.

α-amino acid is the basis component that made up proteins. The α-

carbon (Ca) is asimetrically. Carbon binding the other group
covanently.
R is a side chain that differs from one amino acid to another.
 Amino acid classification
1. Based on side chain and interaction with water.
Category Properties AA

HYDROPHOBIC

Hidrophobic  Straight chain ALA ILE LEU PRO

alipathic  Hidrophobic VAL

Alanine

Isoleucine

Leucine

Methionine
 Proline

Valine

Hidrophobic  Side chain PHE TRP TYR

aromatic aromatic (ring
form) Phenylalanine
 Hidrophobic
 Side chain of
tyrosine contains
of phenolic group
that ionized alkali Tyrosine
pH.

Tryptophan

HYDROPHILIC: dissolve in water

Negative charged  Hydrophilic ASP GLU

polar  Side chain
contained Aspartate
carboxyl group
that can form
negative charged
and acid, in pH
neutral. Glutamate

Positive charged  Hydrophilic ARG HIS LYS

polar  In neutral pH,
 arginine and
lysine is slightly
base.
Arginine

Histidine

Lysine

Polar, uncharged  Uncharged side Serine

chain, hydrophilic
 Polarity of serine
and threonine is
caused by
hydroxyl group Threonine
that has the
ability to bind
between
hydrogen and
water.
 Amide group of Asparagine
asn and gln can
bind hydrogen to
water.
 Sistein dalam
protein biasanya
ada dalam
bentuk sistin
Glutamine
yaitu dua
molekul sistein
saling berikatan
melalui ikatan Cysteine
disulfida
 R as atom H Polar, hydrophilic Glycine
Glycine turns
slightly positive-
charged in neutral
pH.

Negative  Uncharged  Positive

2. Based on the nutrition and physiological properties.
a. Essential; Valine, leucine, isoleucine, phenylalanine,
tryptophan, methionine, threonine, histidine (esensial bagi
bayi dan anak-anak), lysine and arginine (“semi-esensial”)
b. Non-essential; glycine, alanine, proline, serine, cysteine,
tyrosine, asparagine, glutamine, aspartic acid and glutamic
acid.
 PROLIN
 A unique amino acid as it is the only one who form cyclic
structure due to imino group (NH 2) form a cyclic bond with α-
carbon. Imino group structure is as below.

 Side chain (propil) bond covalently with α-carbon and α-imino

group form pyrolidine ring.
 Commonly found in gelatine proline and hydroxyproline.
 STEREOCHEMISTRY
 All α-carbon in the amino acid is asimetric, unless glycine, due
to them binding to different groups. It made them has a
polarization (optically-active property). Amino acid—unless
glycine, isoleucine, and threonine—have two enantiomers (L
and D).
 Isoleucine and threonine have four enantionmers, each two
from α-C and β-C. Both carbons are asimetric.
 ACID-BASE PROPERTIES
 Amino acids are amphoteric due to the carboxyl group (acid)
and amino group (base).
 Glycine, as the simplest amino acid, have three ionization
conditions depends on the pH.


 In neutral condition, the ionization condition is called
zwitter/dipolar ion, due to the compound has both positive and
negative charged. Both carboxyl and amino groups are
ionized. The pH value of the neutral condition is called
isoelectric point (pI).
 In acidic titration, COO- bind H atom/protonized.
The pH value when COOH concentration equals with COO -,
[COOH] = [COO-], is called pKa1.
 In base titration, COO- release H atom/deprotonized.
The pH value when NH2 concentration equals with NH3, [NH2]
= [NH3], is called pKa2.

 Lysine, arginine, histidine, aspartate, glutamate, cysteine, and

tyrosine side chain contains group that able to ionized.
 Isoelectric point of amino acid can be predicted from pK a1,
pKa2, and pKa3.
Amino acid with uncharged side chain
( pKa1+ pKa 2)
pI =
2
 Amino acid with acid side chain
( pKa1+ pKa3)
pI =
2

Amino acid with base side chain

( pKa2+ pKa 3)
pI =
2

 REACTIVITY
The reaction between ninhydrin and an amino acid, leading to the
production of a dark purple compound known as Ruhemann’s
purple.

O-Phthaldialdehyde, in the presence of reduced sulfhydryl

groups, reacts with the primary amino groups found in terminal
amino acids and the e-amino group of lysine to form fluorescent
moieties.
PEPTIDE
 Peptide is a compound formed by bond between amino acids
through peptide bond.
 On the other side, free amino acids are released when facing a
peptide hydrolysis.

 NAME
 3-9 amino acids that bind together is called oligopeptide.
 More than 10 amino acids that bind together is called
polypeptide.
 Transition between peptide and protein is still undefined.
 Commonly, protein is when there are >100 amino acids.
 Naming peptide is based on the composition of amino acids.

 ACID-BASE PROPERTIES
 Acid-base properties of peptide are lower than that of free AA.
 The name of peptides impacted the acid-base properties.
e.g., glycine-alanine is different with alanine-glycine.

 SENSORY PROPERTIES
 Aren’t linked to the AA that composed the peptide.
 Commonly are bitter, but there are some that can be a
sweetener (aspartame from aspartate-phenylalanine).
  Peptide with salty taste can be an alternative for NaCl.

 FUNCTIONS
 Glutation (Glu-Cys-Gly) as a coenzyme in metabolic enzymes
of a body.
 Carnosine, Anserine, Belanine: to detected meat extraction.
 Nisyne, which comes from Streptococcus lactis, is
preservative.
 Peptide from lysine can prevent Browning reaction.
PROTEIN
 Similar to peptide, protein is made up from amino acids bind by
peptide bonds.
 Besides amino acid, they can be composed of:
1. Phosphoprotein, contains of ester phospate. (casein, fosvitine)
2. Glycoprotein, contains of carbohydrate. (collagen, blood serum
proteins, white egg)
3. Lipoprotein, a protein that bind lipid. (HDL-cholesterol)
 STRUCTURE
Five bonds that determined the protein structure:
1. Peptide bond -CO—NH-
2. Hydrogen bond -H—H-
3. Disulfide bond -S—S-
4. Ionic bond -Glu—Lys-
5. Hydrophobic -Val—Phe-

 Primary structure
 Linear structure of amino acids in a polypeptide chain.
 Peptide bond is formed between α-carbonyl amino acid in “i”
and α-amino amino acid in “i+1”.
 If the amount of AA in a protein is “n”, then the amount of
peptide bond in that same protein is “n-1”.
 N terminal: the end of a chain that bind into free α-amino acid
group.
 C terminal: the end of a chain that bind into free α-carboxyl
group.
 Secondary structure
 Organized conformation from polypeptide chain, space
structure that form repeated amino acid.
 Organized conformation is classified into two groups, α-helix
and β-sheet. Another structure which is unorganized is called
random coil.
 α-helix, commonly found structure in the protein.
o Right-handed are more stable than left-handed.
o Stabilized by hydrogen bond, which can be found every
3,6 residues of AA.
o Each of NH group from an AA bind hydrogen bond to
C=O from another AA.
o R-group pointed outside.
o Most of this structure are amphilic. One side is
hydrophobic (non-polar, inside of protein) and another is
hydrophilic (polar, outside of protein)
 β-sheet
 o Formed due to C=O group and N-H perpendicular
towards chain, allowing hydrogen bond to only form
between segments.
o R-group is either on top or below the chain.
o β-strand is composed of 5-15 residue of AA. Two β-
strands interact by hydrogen bond and form sheet-like
structure  β-pleated sheet.
o Β-pleated sheet is classified by the orientation of NH and
C=O: antiparallel and parallel. Antiparallel structure
allows hydrogen bond of -NH—C=O- in a straight line, 0 0.
Meanwhile, parallel structure has an angle.
“Antiparallel has higher stability than parallel”
o β-sheet is more stable than α-helix. In a protein with big
fraction of β-sheet, the denaturation temperature is
high.
 Tertiary structure
 Three-dimentional structure from pleated polypeptides.
Commonly found in globular form (rough circle with irregular
topography).
 Formed due to interaction between polypeptide bonds using the
lowest energy. Hydrophobic interaction, van der Waals, ionic,
and hydrogen bonds between AA side chain cause the energy in
protein to be minimum.
 Stabilized by bonds between one R-group/side chain and another
 hydrogen, disulfide, ionic, and hydrophobic bond.
Bond Explanation Pictures
Hydrogen o Weak
bond o Easy to be broken 
easier to experience
reformation.
This leads to the arise
possibility of changing
structure, resulting in
functional properties of
protein molecules.
Disulfide o Covalent bond
bond between sulfur atoms
in two cysteine.
 Ionic bond o Ion in side chain
formed a salt bridge
by this bond.

Hydrophobic o Formed between R-

bond side chains.
o Very weak, but if
there’s a large scale
of hydrogen bonds, it
can lead to a
stabilized structure.
o Reject polar/charged
compounds.

 Kinds of tertiary structure:

o Fiber protein (fibrillar, fibrous, scleroproteins, protein in
collagen)
o Globular protein/folded protein (protein in white eggs),
40-50% covered by nonpolar amino acid residues.
 Hydrophobic residues of AA are located inside, while the
hydrophilic residues of AA are located outside.
 Quartenary structure
 Biological properties of protein depended on polypeptide chains
or multimeric protein.
 Complex quartenary structure composed of either homogenous
subunit or heterogenous subunit.
 Can be in a dimer, trimer, tetramer, and many other forms.
 The polypeptide chain can have homogen properties and
heterogen properties.
 β-lactoglobulin has homogen quartenary structure, where in
pH of 5-8 it is in dimer form, in pH 3-5 it’s in octomer form,
and in pH>8 it’s in monomer form.
 Hemoglobin has tetramer property, which has α chain and β
chain.


  Arrangement of protein space that composed from few
polypeptide chains. From secondary structure to a more complex
structure.
 Structure has a potential to change in response of environment
settings.
 Random coils

 Irregular repeated units.

 Random coil of a protein has specific structure.
 Commonly found with connecting loop region.
 Structure is determined by bond from R-chain (not always
hydrogen bond).