Detailed Amino acid structure, Zwitter ions, acid base properties of Amino acids, Chirality, L and D forms of amino acids,standard and non standard amino acids, Essential and non essential amino acids,Learn all amino acids, their properties in detail,methods to quantify amino acids

1. Amino acids structure and
properties
Dr. Lakshmi

2. Class Learning Objectives (CLO)
At the end of the lecture, students should :
• Describe the general structure of amino acids.
• Recognize the importance of genetic code in the formation
of Peptide bonds
• Understand the acid/base properties of AA.
• Examine the chirality and Stereo chemical representations of
AA
• Differentiate the L and D forms of Amino acids
• Differential standard and non standard amino acids
• Classify amino acids based on their property.

3. Amino acids are monomers (single units) and join to
form polymers (many units) of proteins
Basic concepts

4. Making and Breakdown of Polymers
Basic concepts
A dehydration or condensation
reaction occurs when two
monomers (amino acids join)
bond together through the loss of
a water molecule (Making of a
protein)
(Making of a polymer)
Polymers are disassembled to
monomers by hydrolysis, a
reaction that is essentially the
reverse of the dehydration
reaction (Breaking of protein to
give Amino acids)
(Breaking of polymer)

5. Formation of Peptide Bonds
• Amino acids are monomers and get joined by the formation
of a peptide bond (CONH).
• Amino group of one molecule reacts with the carboxyl group
of other, resulting in elimination of water and formation of
dipeptide bond.
• A condensation reaction (loss of water) forms a peptide bond
between two amino acids
• A dehydration reaction occurs when two monomers bond
together through the loss of a water molecule.

6. • Protein synthesis is the process in which cells
make proteins. It occurs in two stages: transcription
and translation.
• Transcription is the transfer of genetic instructions in
DNA to mRNA in the nucleus. It includes three steps:
initiation, elongation, and termination.
• Protein synthesis takes place in ribosomes
• Instruction and Information on the kind of protein
synthesis comes from genes .

7. • When joined in a series of peptide bonds AA are called residues to distinguish it from free form and forms found
in proteins.
• Peptide: short sequence of residues
• Polypeptide: longer chain of residues of known sequence and length

8. Amino acids
• GENETIC CODE SPECIFIES 20 AMINO ACIDS:
• All 20 Amino acids are encoded by nucleotide triplets
called codons
• Codon is a 3 letter genetic code (AUG)
• Genetic codon is Redundant meaning several AA are
specified by multiple codons
• There are 22 genetically encoded (proteinogenic) amino
acids, 20 in the standard genetic code and an additional 2 that
can be incorporated by special translation mechanisms.
• Selenocysteine (Sec) and pyrrolysine (Pyl) are rare amino
acids that are cotranslationally inserted into proteins and
known as the 21st and 22nd amino acids in the genetic code.
• Sec and Pyl are encoded by UGA and UAG codons,
respectively, which normally serve as stop signals

9. Amino acids (AA) are building blocks of proteins
• All proteins are made of 20 different AA, and form building
blocks of proteins.
• There are only five atoms that will appear in your amino acid
variable groups: H, C, N, O, and S.
• The term amino acid is short for α-amino [alpha-amino-]
carboxylic acid.
• It is called alpha amino acid because amino group is attached to
the alpha carbon, the carbon next to carbonyl group
• Amino acid is any of a group of organic molecules that consist of
a basic amino group (―NH2),
• All AA contain key elements such as carbon, hydrogen, nitrogen
and oxygen except the two amino acids with sulfur atoms in their
side chains: cysteine and methionine.
AA is represented by a skeletal
diagram as Zwitterion state at
neutral pH.

10. Basic Structure of an Amino Acid
• All amino acids include five basic parts:
• A central carbon atom (the alpha carbon or chiral carbon): All amino acids
contain a carbon atom in the middle of the molecule, the alpha-carbon,
The first carbon is the part of the carboxyl group. The second carbon, to
which is attached the amino group, is called the α-carbon.
• One is a basic amine group -NH2: an amino group - consisting of a nitrogen
atom (nitrogen is a proton acceptor so it is basic) and two hydrogen atoms.
• The second one is acidic carboxyl group –COOH: a carboxyl group -
consisting of a carbon atom, two oxygen atoms and one hydrogen atom(H
is a proton donor so it is acidic)
• A hydrogen atom
• The third group is denoted by R group or side chain. This is the variable
radical group and is different for every amino acid. This R group makes the
amino acid unique. They can be hydrophobic or hydrophilic, aliphatic or
aromatic etc

11. • Amino acids containing an amino group bonded directly to
the alpha carbon are also referred to as alpha amino acids.
• All amino acids found in proteins have this basic structure,
differing only in the structure of the R-group or the side
chain. It is the R-group or side chain that differs between
the 20 amino acids.
• The simplest, and smallest, amino acid found in proteins is
glycine for which the R-group is a hydrogen (H) and where
the α-carbon is symmetric, because in glycine the R group
is just hydrogen
• There are 1000s of amino acids in nature but only about 20
amino acids form a part of the proteins in the human body.
• These twenty acids will be our focus here.
What difference did you notice
between these 2 amino acids
R group here is methyl
group
Important points to note on Amino acids

12. Zwitterions - Amino Acids
• A zwitterion is a molecule with functional groups, of which at least one
has a positive and one has a negative electrical charge. The net charge of
the entire molecule is zero.
Amino acids are the best-known examples of zwitterions. :
• They contain an amine group (basic- proton acceptors) and a carboxylic
group (acidic- proton donors).
• There is an internal transfer of a hydrogen ion from the -COOH group to the
-NH2 group to leave an ion with both a negative charge and a positive
charge. This is called a zwitterion.
• The -NH2 group is the stronger base, and so it picks up H+ from the -COOH
group to leave a zwitterion (i.e. the amine group de-protonates the
carboxylic acid)
• The (neutral) zwitterion is the usual form amino acids exist in
solution and as solids. It is electrically neutral and carries no net
charge
• In the physiological pH range (5-8), the α carboxyl and α-amino
groups of amino acids are completely ionized

13. Depending on the change in pH,
AA can exist in 2 forms
Adding an acid to AA solution decrease the pH(low
pH – 2,acidic condition)
If the pH is lower, than the isoelectric point then the amino
acid acts as a base and accepts a proton (H) at the amino
group. This gives it a positive change.
The -COO- part of the zwitter ion picks up hydrogen ion.
During electrophoresis, AA would move towards the
cathode (the negative electrode) as Cations are
(positively charged).
1.CATIONS +++ 2.ANIONS (-ve)
Adding an alkali to AA solution(high pH-12)
increases the pH
Increase pH of solution of AA by adding hydroxide
ions
Hydrogen ion is removed from the -NH3
+ group.
In electrophoresis, these negative ions (anions)
of AA negative ion flow toward the anode

15. THE ACID BASE PROPERTIES OF AA
 Amino acids are amphiprotic: Meaning they can
accept or donate protons.
 Amino acids are amphoteric: AA can react
with acids or bases, The carboxyl group is able to lose a
proton and the amine group is able to accept a proton
 Amino acids are dipole: meaning it is an electrically
neutral molecule carrying a positive and a negative
charge but no net charge and at this pH the AA will not
migrate to anode or cathode in electrophoresis. This pH
is called the isoelectric point or pI
 Amino acids are called zwitterion: For each amino
acid there is a particular pH, the isoelectric point, at
which the amino acid exists as the neutral zwitter ion.
 Depending on the pH, AA exist in 3 forms as cations, anions
and as zwitter ions.
 AA functions as buffers.
It is important to study acid base
properties of AA as it finally
influences the behavior of proteins,
helps us in methods of identification
of different types of AA and to
understand AA reactions

16. Chirality (means hand) and Stereoisomerism
Chiral atoms not super imposable
on mirror image.
Click here to watch the video (ctrl plus click): https://youtu.be/0cfX72BT2Ww

17. • Amino Acids are optically active except glycine. (mirror images of each other
and rotate plane polarized light but not super imposable).
• The α-carbon of most amino acids is joined by covalent bonds to 4 different
groups.
• The four bonds of the central (alpha) carbon (C) of an amino acid are directed
towards the four corners of a tetrahedron.
• Therefore, this carbon atom is also called a chiral carbon or central of chirality
or as a stereocenter.
• A chiral carbon has 4 unique groups attached to it, so it is asymmetrical
carbon.
• In other words, if you pass plain polarized light at an amino acid, then because
the carbon is chiral, it would rotate the light. Chirality is an optical activity.
Chirality

18. If a molecule contains one asymmetrical carbon, 2 distinguishable
stereoisomers exist; these are non super imposable mirror images of one
another or called enantiomers as seen in figure.
Stereoisomers are designated D (dextro-rotatory) or L (levo-rotatory) according
to the direction in which the crystalline forms rotate polarized light, to the
right and left, respectively.
Naturally-occurring proteins comprise exclusively the L forms of amino acids.
The L and D can be distinguished from one another experimentally because
their solutions rotate the plane of polarized light in opposite directions, so also
called as optical isomers
In this example, Alanine has a CH3 as a radical group. If you imagine holding
the model with the COOH at the top and the NH2 at the bottom,
the CH3 radical group in the D form will be on your right. In the mirror
image L form, it will be on the left.
Another way to project AA structure is by using Fisher projection, It highlights
the 4 groups around chiral carbon.
Look at the Amino group if its on Left
then it is L amino acid and if Amino is on
right side then D AA

19. AA is represented by a stereochemical view showing the arrangement
of atoms.
It represents the position in space of each atom.
The amino, carboxyl, hydrogen and R groups are arranged
tetrahedrally around central alpha carbon.

20. Why more of L form?
• Reason not clearly known.
Speculations:
• Repetitive substructure in proteins (helices,
sheets, turns) require all amino acids have the
same configuration.
• Apparently, living systems evolved from L amino
acids based upon an initial random choice
• AA with D configuration can be found in
microorganisms (e.g. in the bacterial cell
wall and in antibiotic peptides) and in
certain animals (e.g. the frog skin
peptide ‘dermorphin’) BUT NEVER
FOUND IN PROTEINS

21. Amino acids are
represented using
one and three letter
abbreviations while
representing them
in a sequence of
peptides or protein

22. Some easy ways of remembering the one letter code for amino acids
C=Cys=Cysteine
H= His=Histidine
I=Ile=Isoleucine
M=Met=Methionine
S= Ser=Serine
V=Val = valine
If more than one amino acid begins with a certain letter,
that letter is given to most commonly occurring amino acid
A= Ala = Alanine
G=Gly=Glycine
L=Leu=Leucine
P=Pro=Proline
T=Thr=Threonine
In others letters close to the initial is used
Amides have a leter in middle of alphabet
D= Asp=Aspartic acid (near A)
E= Glu=glutamic acid (near G)
Q= Gln=Glutamine (Qtamine)
N=Asn=Asparagine (contain N)
K=Lys=Lysine (near L)
Some are phenotypically suggestive
F= Phe= Phenylalanine
R= Arg=aRginine
Y= Tyr=tYrosine
W= Trp=Trypotophan (double ring in molecule)

23. Types of Amino acids
Standard Amino acids /Proteinogenic or Natural Amino
acids
Nonstandard amino acid
• A standard amino acid is an amino acid organisms use in
the synthesis of peptides.
• A nonstandard amino acid is an amino acid that occurs
naturally in cells but do not participate in peptide
synthesis.
• There are 22 amino acids which are naturally occurring
and are incorporated into polypeptides. They are called
Proteinogenic or Natural Amino acids
• They are generated by modification of standard amino
acids in the peptide molecule ( post-translational
modification).
• Out of the 22 standard amino acids, 20 are alpha amino
acids encoded by universal genetic code; remaining 2 are
incorporated into proteins by unique synthetic
mechanism.
• Not encoded in the universal genetic code.
• Selenocysteine (Sec) and pyrrolysine (Pyl) are rare amino
acids that are cotranslationally inserted into proteins and
known as the 21st and 22nd amino acids in the genetic
code.
• Sec and Pyl are encoded by UGA and UAG codons,
respectively, which normally serve as stop signals
• Example:
• Significant proportions of the amino acids in collagen are
modified forms of proline and lysine: 4-hydroxyproline
and 5-hydroxylysine.
• GABA and L- DOPA)

24. 1. When isolated from proteins, AA are
white crystalline solids.
2. AA have high melting and boiling
points (not common for other organic
compounds)
3. AA have electrical conductivity
4. AA have high solubility
All last 3 properties are because of the
presence of charged groups. An positive
charged Amino NH3 and carboxyl group
COO- attached to alpha carbon
PROPERTIES OF AMINO ACIDS

25. Classification of Amino Acids based on nutritional requirements
Essential Amino acids or Indispensable AA Non-essential amino acids or dispensable AA
Amino Acids are those that cannot be synthesized by
the body on its own
AA that your body can produce, specifically by the
liver, without any outside help.
Must be obtained from diet.
Does not store them so required on daily basis
Do not have to be taken in diet, body can make it.
Most of them are produced from glucose.
Number
There are 9 essential amino acids
Number
There are 11 of them
Function:
As precursor for neurotransmitter in brain,
Build and repair muscle tissue
Function:
Removal of toxins, anti ageing, wound healing etc
Provides 55% of daily energy requirement
Source
Has to be taken with food, animal proteins such as egg,
meat, chicken, plant products such as soy
Source
Can be manufactured in the body from carbohydrates
and other amino acids. Also available in food
Deficiencies
Can occur if your diet is inadequate; weak immune
system due to less antibodies, lack of neurotransmitter
Starvation.
Rare but can occur with illness

26. Classification of Amino Acids based on nutritional requirements
Semi essential Amino Acids
They are formed in the body but not in sufficient amount for body
requirement; especially in children and sick people.
Example: Arginine and Histidine can be formed by adults but not kids

27. • All amino acids found in proteins have this basic structure, differing only
in the structure of the R-group or the side chain.
• It is the R-group or side chain that differs between the 20 amino acids
and accounts for the physical properties of protein.
• Basic structure for all 19 AA is same except proline ,which has an unusual
cyclic ring formed by the side chain bonding directly to amide nitrogen.
• The simplest, and smallest, amino acid found in proteins is glycine for
which the R-group is a hydrogen (H) and where the α-carbon is
symmetric, because in glycine the R group is just hydrogen
• There are 1000s of amino acids in nature but only about 20 amino acids
form a part of the proteins in the human body.
• These twenty acids will be our focus here.
What difference did you notice
between these 2 amino acids
R group here is methyl
group
Important points to note on Amino acids

28. Basic amino acid structure
NH3+ ---------CH--------COO-
R group
Letz learn and draw the 20 AA and their chemical and physical properties of Amino acid
Only R groups have to be
replaced

29. Amino acids with Aliphatic side chains
• Aliphatic implies that the protein side
chain contains only carbon or hydrogen
atoms.
• Aliphatic amino acids are non-polar
and hydrophobic.
• Hydrophobicity increases as the
number of carbon atoms on the
hydrocarbon chain increases.
• Most aliphatic amino acids are found
within protein molecules

30. 1. Lets replace this R with hydrogen, you will get
simplest amino acid called Glycine.
2. It is represented as Gly in 3 letter word and as G
in one letter word.
3. The R or side chain has hydrogen and so is
uncharged
4. Does not have chiral alpha carbon.
5. Not a stereoisomer
6. It is superimposable
7. Smallest amino acid
8. not essential AA
H
Amino acid 1: Glycine – Gly----G
NH2 ---------CH--------COOH

31. 1. Letz replace this R with methyl group
2. It is non polar (cannot form hydrogen bonds)
3. Are hydrophobic (Hate water, does not dissolve
in water)
4. Aliphatic means carbon atoms form open chains
not aromatic rings.
5. Always look for C or H in side chains, then it is
non polar
6. Non essential
CH3
Amino acid 2: Alanine – Ala----A
NH2 ---------CH--------COOH

32. 1. Letz replace this R or side is hydrophobic with CH-
CH3-CH3
2. It is non polar (cannot form hydrogen bonds)
3. Are hydrophobic (Hate water, does not dissolve in
water)
4. Aliphatic means carbon atoms form open chains
not aromatic rings.
5. Always look for C or H in side chains, then it is non
polar
6. It is a member of the branched-chain amino acid
family, along with leucine and isoleucine.
7. Essential AA
8. Valine differs from threonine by replacement of the
hydroxyl group with a methyl substituent,
CH
Amino acid 3: Valine– Val----V
CH3 CH3
NH2 ---------CH--------COOH

33. 1. It has one additional methylene group in its side
chain (R) compared with valine.
2. It is non polar (cannot form hydrogen bonds)
3. Are hydrophobic (Hate water, does not dissolve
in water)
4. Aliphatic means carbon atoms form open chains
not aromatic rings.
5. Always look for C or H in side chains, then it is
non polar
6. Leucine is an essential amino acid, which means
that humans cannot synthesize it, so it must be
ingested
CH 2
Amino acid 4: Leucine– Leu----L
CH3 CH3
CH
NH2 ---------CH--------COOH

34. 1. It has one additional methylene group in its side
chain (R) compared with valine.
2. It is non polar (cannot form hydrogen bonds)
3. Are hydrophobic (Hate water, does not dissolve
in water)
4. Aliphatic means carbon atoms form open chains
not aromatic rings.
5. Always look for C or H in side chains, then it is
non polar
6. Iso Leucine is an essential amino acid, which
means that humans cannot synthesize it, so it
must be ingested
NH2 ---------CH--------COOH
CH
Amino acid 5: IsoLeucine– Ile----I
CH3
CH3
CH2

35. Ans1:Alanine, Valine, Isolecine and leucine
Ans2:Glycine
Ans 3: Valine, leucine and isoleucine.
Revision Questions
1. Give examples of AA with aliphatic side chains?
2. Which amino acid is Not a stereoisomer and is superimposable?
3. Which AA have branched-chain amino acid?

37. 1. R or side chain has OH group (hydroxyl group) so
polar
2. Serine and threonine are the two AA having
hydroxyl containing amino acids.
3. Serine and Threonine are Hydrophilic due to the
hydrogen bonding capacity of the hydroxyl group.
4. Both Serine and threonine are site of
phosphorylation (addition of phosphate) and
glycosylation which is important for enzyme
regulation and cell signaling.
5. Addition of phosphates to create phosphoserine
and phosphothreonine occurs as post translational
modification.
6. Non essential AA.
OH
Amino acid 6: Serine –Ser ----S
CH2
OH
NH2 ---------CH--------COOH

38. 1. amino acids with polar side chains.
2. Hydrophilic
3. It differs from serine by having in the R group a
methyl substituent in place of one of the
hydrogens on the β carbon.
4. R or side chain has OH group (hydroxyl group)
so polar
5. Threonine and Serine are site of
phosphorylation and glycosylation which is
important for enzyme regulation and cell
signaling.
6. Threonine is an essential amino acid,
NH2 ---------CH--------COOH
OH
Amino acid 7: Threonine– Thr ----T
CH CH2
OH

39. 1. Amino acids with polar side chains.
2. Has a thiol group (SH)
3. It is a Sulphur containing AA
4. Because of its high reactivity, the thiol group of
cysteine has numerous biological functions.
5. It serves as a potent nucleophile and metal ligand
(particularly for iron and zinc)
6. Specialty or best known for its ability to form
disulfide bonds, which often make an important
contribution to the stability of extracellular proteins.
7. Cysteine is a very important amino acid when it comes
to tertiary and quaternary structure.
8. Cysteine is a non-essential amino acid
Amino acid 8: Cysteine– Cys----C
CH2
SH

40. 1. Amino acids with polar side
chains.
2. Has a thiol group (SH)
3. It is a Sulphur containing AA
4. Methionine is hydrophobic
amino acid
5. Found buried within the
interior of a protein.
6. It is an essential amino acid.
Amino acid 9: Methionine – Met----M
SH- thiol

41. Ans1: Serine and threonine
Ans2: Threonine is an essential amino acid
Ans 3: Threonine and Serine .
Revision Questions
1. Give examples of two AA having hydroxyl (OH).
?
2. Which among the 2 AA Threonine or Serine is an essential amino
acid?
3. Phosphorylation and glycosylation is important for enzyme
regulation and cell signaling.
Name any one of the AA

42. Acidic amino acids and their amides
• Aspartic acid and glutamic
acid are the only amino
acids that carry negative
charge (anions) at pH7.
hence these amino acids
are often referred to as
aspartate and glutamate Aspartic acid refers to the protonated acidic form of the
amino acid. When deprotonated, you’ll often see the
conjugate base salt referred to as aspartate. This is the
standard nomenclature for carboxylic acids.

43. 1. Aspartic acid is an electrically charged amino
acids with acidic side chains COOH.
2. Generally located on the surface of the protein.
3. Aspartic acid and glutamic acid play important
roles as general acids in enzyme active centers,
as well as in maintaining the solubility and ionic
character of proteins.
4. Aspartic acid (sometimes referred to as
asparate depending on pH).
5. is non-essential AA
Amino acid 10: Aspartate – Asp ---- DCOO
charged

44. 1. Glutamic acid is an electrically charged amino
acids.
2. It also contain a carboxylic acid group in its side
chains.
3. These acids play important roles as general
acids in enzyme active centers, as well as in
maintaining the solubility and ionic character of
proteins.
4. Glutamic acid is commonly referred to
as glutamate, because its carboxylic acid side
chain will be deprotonated and thus negatively
charged in its anionic form at physiological pH.
5. It is a non-essential amino acid
Amino acid 11: Glutamate –Glu ---- ECOO
charged

45. Ans1: Aspartate and Glutamate/aspartic acid
and glutamic acid
Ans2: Cysteine and Methionine
Ans 3: True.
Revision Questions
1. Give examples of two AA having COOH or carboxyl group (OH).
?
2. Which among the 2 AA has a thiol or SH group?
3. True or False
Cysteine is a non-essential amino acid

46. Amino acid 12: –Asparagine ---- Asn----N
1. Has an amide functional group like glutamine
2. Because of the hydrogen bonds in amide groups
they are polar.
3. Presence of amide group makes it polar
4. They provide many of the functional groups
found in proteins.
5. Asparagine is a common site for attachment of
carbohydrates in glycoproteins.
6. Asparagine is amide derivative of aspartic acid.
Asparagine is not essential AA for humans.
carbonyl group bonded to a nitrogen

47. Amino acid 13: –Glutamine ---- Q
1. Has an amide functional group like Asparagine
2. Generally amide groups are unreactive, but polar
3. The polarity causes it to act as hydrogen bond donor
and acceptor .
4. Presence of amide group makes it polar so it is amino
acids with polar side chains.
5. It is an important carrier of ammonia and contributes
it to the formation of urea and purines.
6. Glutamine is not recognized as an essential amino
acid but may become conditionally essential in certain
situations, including intensive athletic training or
certain gastrointestinal disorders.

49. Amino acid 14: Lysine-----Lys-- K
1. It is a basic amino acid along with Arginine.
2. There are 4 methylene (CH2) groups and amine /
amino group (NH2)
3. Lysine is an electrically charged amino acids with basic
side chains.
4. Lysine is a base, as are arginine and histidine.
5. The amino group is highly reactive and often
participates in reactions at the active centers of
enzymes.
6. Lysine plays an important role in coordinating
negatively charged ligands.
7. It is an essential amino acid, which means that
humans cannot synthesize it, so it must be ingested.
amino---4 3 2 1

50. Amino acid 15: Arginine-----Arg------ R ----
1. Arginine is an electrically charged AA with basic side chains.
2. It is similar to lysine, instead of 4 methylene (CH2) there is only 3 methylene group then to amino group (NH2), then carbon double bonded to (NH2), and
(NH2).
3. It has a lot of Nitrogen atoms and so basic
4. As a group the charged amino acids are important for making proteins soluble.
5. These residues are generally located on the surface of the protein.
6. Arginine is well designed to bind the phosphate anion, and is often found in the active centers of proteins that bind phosphorylated substrates.
7. As a cation, arginine, as well as lysine, plays a role in maintaining the overall charge balance of a protein.
8. Although arginine is considered an essential amino acid (it must be obtained through the diet, semi essential), this is true only during the juvenile period in
humans.
3 2 1
Only 3 methyl groups

51. amino acids that have an aromatic ring in the side-chain

52. 1. Similar to alanine structure but instead of the
CH3 replace the Hydrogen from CH3 to CH2 and
add a benzene ring to it.
2. Since the benzene ring (more carbon and
hydrogen) is there, it is aromatic and non polar.
3. Phenylalanine is hydrophobic amino acids with
aromatic side chain.
4. It is quite hydrophobic and even the free amino
acid is not very soluble in water.
5. Phenylalanine is large aromatic residue that is
normally found buried in the interior of a
protein and is important for protein stability.
6. It is an essential amino acid.
Amino acid 16: ---Phenyl alanine---Phe---F

53. 1. Similar to phenylalanine, but here you will find a hydroxyl group
attached to the aromatic benzene ring so it has a polar OH
group and a benzene ring which is non polar.
2. Tyrosine is hydrophobic amino acids with aromatic side chain.
3. Tyrosine is large aromatic residue that is normally found buried
in the interior of a protein and is important for protein stability.
4. Tyrosine has special properties since its hydroxyl side chain may
function as a powerful nucleophile in an enzyme active site
(when ionized) and is a common site for phosphorylation in cell
signaling cascades.
5. Tyrosine absorbs ultraviolet radiation and contributes to the
absorbance spectra of proteins.
6. It is not essential AA
Amino acid 17: ---- Tyrosine -- Y

54. 1. Proline is different from other AA because there is no freeNH3, as here
nitrogen becomes a part of a heterocyclic side chain.
2. It is non polar as the R group has more hydrocarbons (C and H).
3. Proline has an aliphatic side chain with a distinctive cyclic structure.
4. The secondary amino (imino) group of proline residues is held in a rigid
conformation that reduces the structural flexibility of polypeptide regions
containing proline.
5. Proline is formally NOT an amino acid, but an imino acid (both an amide
and a carboxyl group), bonded to the alpha carbon molecule.
6. When proline is in a peptide bond, it does not have a hydrogen on the
α amino group, so it cannot donate a hydrogen bond to stabilize an α helix
or a β sheet.
7. It is not an essential amino acid,
Amino acid 18: ---- Proline---Pro--- P--

55. 1. Unlike Proline, it is similar to other AA structure,
to the methylene group we find a 5 numbered
heterocyclic aromatic ring attached.
2. It is electrically charged and because of the high
number of nitrogen is basic in nature.
3. Histidine is an electrically charged amino acids
with basic side chains.
4. It is an essential amino acid
Amino acid 19: ----Histidine _His--H

56. 1. To the alpha carbon a methylene is attached to
which 2 aromatic rings can be found, one is
heterocyclic ring and other is a benzene ring.
2. Tryptophan is hydrophobic amino acids with
aromatic side chain. It is non polar.
3. important for protein stability.
4. It has spectral properties that make it the
best inherent probe for following protein
folding and conformational changes
associated with biochemical processes
5. . It is an essential amino acid
Amino acid 20: ----Trypotophan—Trp--W

57. Ans1: Proline
Ans2: Asparagine and glutamine
Ans 3: NO they don’t have same structure but
have similarities in structure. It is Similar to alanine structure
instead of the CH3 replace the
Hydrogen from CH3 to CH2 and add a benzene ring to it.
Revision Questions
1. Which amino acid is not technically an amino acid or Give
example of imido acid
?
2. Give examples of AA which contains amide residues
3. Does Analine and Phenylanaline have same structure?

58. Methods to quantify proteins
depends on amino acids
Amino acid side
chain reactions
Concentration of
Amino acid
1. Using Beer lamberts law
2. Using Ellmans reagent tp detect reaction
between thiol groups of cysteine
3. UsingNinhydrin, fluroscemine, nitrophenol
Using BCA or Bicinchoninic acid-
colorimetrically detects colour changes
Using Biurette reagent;reaction based on
the properties of polypeptide back bone
Using Folin lowry method(old) uses cupric
sulphae and tartarate in aqueous solution.
It forms a blue water soluble product
which can be measured at 750nm
Using Coomassie brilliant blue (Bradford
assay)Negatively charged coomasie blue
bind to positively charged proteins. When
no proteins present inn sample dye
absorbs 465nm and has ted colour.when
protein is present it changes to blue at
595nm