Amino acids essenatial and non essential .classification ,structufe ,proteins

1. Amino Acids and Proteins
A comprehensive study of Amino acid structure and
function and their role in Protein formation

2. Amino acids and Proteins
• Proteins mediate every process that takes place inside a cell.
• Most abundant biological macromolecules in cells.
• All proteins, regardless of organism, are composed of the same set of
20 amino acids.
• Due to the nearly limitless variety in the sequences of amino acids in
proteins, nearly all imaginable functions can be encoded in proteins

3. Amino acids
• Functions
• Common features
• Configuration
• Classification and structure
• Physical and Chemical properties
• Modified Amino acids
Proteins
• Functions
• Classification
• Structure
• Structural hierarchy
• Denaturation
• Solubility
Class outline….

4. • Building blocks for all living things : Crucial for life as
they contain peptides and proteins
• The linear sequence of amino acid residues in a
polypeptide chain determines the three-dimensional
configuration of a protein, and the structure of a protein
determines its function.
Functions
Amino acids
Protein
function
3 D
configuration
and structure
of protein
Linear
sequence of
Amino acid

5. Imperative for sustaining the health of the human body
Amino acids

6. Functions
Amino acids
Amino acids
(Derived from breakdown of dietary and tissue proteins)
Nitrogen containing
substrates
Carbon skeletons
Biosynthesis of purines,
pyrimidines,
neurotransmitters, hormones,
porphyrins, and nonessential
amino acids
Fuel source in the citric acid
cycle, used for
gluconeogenesis,
or in fatty acid synthesis

7. Common Features
•There are 20 "standard" amino acids
•All amino acids contain an a carbon to which typically 4 different
substituent groups are attached
•These groups are the α-amino group, the a-carboxyl group,
hydrogen, and the variable R group (side-chain).
•In glycine, the R group consists of another hydrogen atom (symmetric
carbon atom). In the other 19 amino acids the  carbon is a chiral center
and asymmetric.)
•The α -amino and α -carboxyl groups are charged at neutral pH
Amino acids

8. Configuration
•There are two possible
configurations for these four
substituents--the "D" and "L"
stereoisomers, which are mirror
images of each other
(enantiomers)
•The standard amino acids have
the L-configuration.
Amino acids

10. Numbering of Carbons
The conventions for labeling the carbon atoms in amino acids is
illustrated using lysine in the figure. The  carbon is always carbon-2 of
the amino acid. The -carboxyl group is always carbon-1
Amino acids

11. Classification based on R Group
Amino acids are collected into different categories based on
similarities in the properties of their R groups. One such
classification scheme relies heavily on the polarity of the R groups.
The amino acids classified into five categories based on the properties
of their R groups:
Amino acids
I. Nonpolar and aliphatic
II. Aromatic
III. Polar and uncharged
IV. Positively charged
V. Negatively charged

12. I - Nonpolar, Aliphatic Amino Acids
The amino acids in this group lack polar functional groups and aliphatic in
their side chains. Due to the hydrophobicity of their R groups, they
often cluster together within the interior of proteins, stabilizing
protein structure via hydrophobic interactions.

13. II - Aromatic Amino Acids
The side-chains of the aromatic amino acids, Phenylalanine,
Tyrosine, and Tryptophan (Indole group), overall are very
hydrophobic. The R group of tyrosine also contains a polar hydroxyl
group that can participate in H bonding interactions. The R groups of
tyrosine, and particularly tryptophan, absorb ultraviolet light at a
maximum of 280 nm wavelength.
Indole

14. III - Polar, Uncharged Amino Acids
• The R groups of the polar,
uncharged amino acids all
contain polar functional groups
that can hydrogen bond with
water.
• Serine and Threonine contain
hydroxyl groups,
• Asparagine and Glutamine
contain amide groups. Amide
forms of the two negatively
charged amino acids Aspartate
and Glutamate.
• Cysteine contains a sulfhydryl
group, whose polarity is quite
weak

15. Cysteine and Disulfide Bonds
The thiol groups of two cysteine residues are readily oxidized to form
a covalently linked dimeric amino acid known as cystine. In cystine,
the two cysteines are joined by a disulfide bond. The disulfide-linked
cystine residue is strongly hydrophobic. In proteins, disulfide
bonds form covalent links between different parts of a polypeptide
chain (intra disulphide), or between two different polypeptide chains
(inter disulphide).

16. IV- Positively Charged Amino Acids
The most hydrophilic R groups are those that are either positively or
negatively charged. The side-chains of lysine and arginine are fully
positively charged at neutral pH. In lysine, a primary amino group is
attached to the  carbon of the side-chain. In arginine, the
guanidinium group of the side-chain is postively charged. The
histidine R group contains an aromatic imidazole group that is
partially positively charged at neutral pH. Histidine residues function in
many enzyme-catalyzed reactions as proton donors and/or acceptors.
Quanidinium
Imidazole

17. V - Negatively Charged Amino Acids
The R groups of Aspartate and Glutamate contain carboxyl groups
that are fully negatively charged at neutral pH In aspartate, the
carboxyl group is attached to the ß carbon of the amino acid backbone.
In glutamate, the carboxyl group is attached to the  carbon.

18. Classification based on Nutrition
Essential Amino Acids:
Need to supplied in daily diet
1. Lysine
2. Leucine
3. Isoleucine
4. Methionine
5. Tryptophan
6. Phenylalanine
7. Threonine
8. Valine
9. Histidine
Nonessential Amino Acids:
Need not be supplied in daily diet
1. Alanine
2. Asparagine
3. Glycine
4. Tyrosine
5. Serine
6. Proline
7. Cysteine
8. Cystine
9. Glutamine(conditionally essential)
10. Arginine(conditionally essential)
11. Glutamate
Amino acids

19. Properties : Physical
• Amino acids are colorless, crystalline solid.
• All amino acids have a high melting point greater than
200o C
• Solubility: They are soluble in water, slightly soluble in
alcohol and dissolve with difficulty in methanol, ethanol, and
propanol. R-group of amino acids and pH of the solvent play
important role in solubility.
• On heating to high temperatures, they decompose.
• All amino acids (except glycine) are optically active.
• Peptide bond formation: Amino acids can connect with a
peptide bond involving their amino and carboxylate groups.
Amino acids

20. Peptide Bonds
Peptide bonds are amide linkages that join amino acids in
oligopeptides, polypeptides, and proteins. Peptide bonds are formed by
condensation reactions in which the elements of water are
removed (dehydration) from the reacting -amino and -carboxyl
groups that come together to form the bond The term oligopeptide
refers to polymers with relatively few amino acid residues. The term
polypeptide signifies polymers of generally less than 10,000 mw,
whereas the term protein refers to longer polymers.
Peptide bonds are planar
and partially ionic

23. Dipeptide - TWO amino acids linked together by ONE peptide bond.
Glycyl alanine
Glutaminyl argininyl methionine
Tripeptide - THREE amino acids linked together by TWO peptide bond.
N terminal C terminal

24. Structure of (Oligo)peptides
When an amino acid sequence of a peptide, polypeptide, or protein is
shown, by convention the amino-terminal (N-terminal) end is placed on
the left, and the carboxyl-terminal (C-terminal) end is place on the
right. The amino acid sequence is read left-to-right beginning with the N-
terminal end.
Seryl glycyl tyrosyl alanyl leucine (Ser-Gly-Tyr-Ala-Leu, SGYAL)

25. Properties: Chemical properties
1. ZWITTER ION AND AMPHOTERIC PROPERTY
•Amino acids form internal salts called zwitterions
•In the pure solid state and in aqueous solution near neutral
pH, amino acids exist almost completely as zwitterions
Amino acids

26. The -carboxyl and -amino groups of all amino acids, along with the
ionizable R groups of 7 amino acids, function as weak acids and bases
in aqueous solutions. When dissolved in water at neutral pH, its -
carboxyl group is negatively charged, and its -amino group is positively
charged. Such dipolar ions (total charge equals 0) are called
ZWITTERIONS. Substances having this dual (acid-base) nature are
amphoteric and are often called AMPHOLYTES.
Amino Acid Ionization
Zwitter ion
Cation Anion

27. Amino Acid Ionization
• The zwitterionic form predominates at neutral pH.
• The nonionic form does not occur in significant amounts in aqueous
solution at any pH.
• A zwitterion can act as either an acid (proton donor) or a base
(proton acceptor).
Proton donor
proton acceptor

29. Acid-base titration of amino acids
The ionic form of the amino acid present in an aqueous
solution is dependent upon the solution’s pH. An acid-
base titration is used to identify an unknown amino acid.
Simple amino acids, like glycine, have two dissociation
steps:
(1) the loss of H+ from the acidic carboxyl group at low pH
(2) the loss of H+ from the more basic amino group at high
pH.

30. The pKa value for each dissociable group of an amino acid can be
determined from such a titration curve by extrapolating the midpoint of
each buffering region (the plateau) within the curve.
Acid-Base Titration curve of Glycine
A point on the curve where the amino acid behaves as a neutral salt.
Specifically, this point is known as the isoelectric point (pI), and is loosely
defined as the pH where the amino acid is predominantly a zwitterion.
https://www.youtube.com/watch?v=UT_YFQItvhM
pKa = – log[Ka]
pI is defined as the mean of the
pKa values for a molecule. So, the
pI of a protein is determined by the
pKa of every amino constituent
amino acid.

31. Titration of Simple Amino Acids
TITRATION CURVES OF GLYCINE
• The curves have two plateaus,
which correspond to the dissociation
and titration of the -carboxyl
group (pK1) and the -amino group
(pK2).
• Low pH : is the fully protonated
form, +H3N-CH2-COOH (net charge
= +1),
• High pH : H2N-CH2-COO- (net
charge -1) predominates
• In between the two plateaus, the
zwitterionic form, +H3N-CH2-
COO- (net charge = 0) predominates.
• The curve shows that glycine has two
regions of buffering power centered
±1 pH unit above pK1 and pK2

32. Titration of Simple Amino Acids
TITRATION CURVES OF GLYCINE
• The Henderson-Hasselbalch
equation can be used to
calculate the amounts of the
conjugate acid and
conjugate base species in
solution at any pH.
• The pH at which the zwitterionic
(0-charged) species of glycine
predominates (one equivalent of
OH- added) is called the
isoelectric point or isoelectric pH
(pI).
• The isoelectric pH is exactly
halfway between the two pKas
for glycine.

33. Titration curve of Glutamatic acid
• The acidic amino acid glutamate, has
a second carboxyl group present in
its side-chain.
• Thus the titration curve for glutamate
has three plateaus, each one
corresponding to the dissociation of a
proton from the amino acid
• Since the R group carboxyl group
has a pKR between that of the pK1
and pK2, the second plateau
corresponds to the titration of this
group.
• The zwitterionic form of glutamate
occurs at a pH midway between that
of pK1 and pKR.
• Thus the pI for glutamate is 3.22.

34. 2. NINHYDRIN TEST
• Amines (including α-amino acids) react with
ninhydrin to give a blue-purple coloured
product.
• It can be used qualitatively (e.g. for
chromatographic visualisation) or quantitatively
(e.g. for peptide sequencing).
• Proline, a secondary amine, gives a yellow-
orange product.
• The test is sensitive enough that ninhydrin can
be used for the visualisation of fingerprints.
Amino acids: Chemical properties
Ruhemann's
purple

35. Step 1

36. Step 2

37. 3. REACTION WITH ALKALIES AND ALCOHOLS

38. Edman is a method of sequencing amino acids in a peptide. The amino-terminal
residue is labeled and cleaved from the peptide without disrupting the peptide
bonds between other amino acid residues.
4. REACTION WITH EDMAN’S REAGENT

39. 5. XANTHOPROTEIC TEST
The xanthoproteic test is performed for the detection of aromatic
amino acids Tyr and Trp in a protein solution. The nitration of
benzoid radicals present in the amino acid chain occurs due to
reaction with nitric acid, giving the solution yellow coloration.

40. Sanger’s reagent (1-fluoro-2, 4-dinitrobenzene) reacts
with a free amino group in the peptide chain in a mild
alkaline medium under cold conditions.
Sanger's reagent, was first used by Sanger to detect free amino
acids of Insulin. DNFB undergoes nucleophilic aromatic substitution
with the N-terminal amino group of a peptide or protein. ... DNFB is
hence used in protein sequencing to determine N-terminal amino acid.
6. REACTION WITH SANGER’S REAGENT

41. Biologically Active (Modified) Amino Acids
CHEMICAL MESSENGERS : Neurotransmitters and
Hormones
Γ amino butyric acid (GABA)
neurotransmitter
Hormone
Amino acids

42. Seratonin - Neurotransmitter
Hormone involved in
skin pigmentation
CHEMICAL MESSENGERS : Neurotransmitters and
Hormones

43. Glutathione : Γ Glutamyl Cysteinyl Glycine
Glutathione is a tripeptide present in most mammalian tissue. It acts as an
antioxidant, a free radical scavenger and a detoxifying agent.
Detoxifying agent and antioxidant

44. Precursor for other molecules
Metabolic intermediates
Arginine, Citrulline and
Ornithine are
intermediates of urea
cycle (amino acid
metabolism)
Arginine

45. Modified amino acids present in polypeptides
• Modified amino acids are present in polypeptides after protein
synthesis
• Serine, Threonine and Tyrosine can be phosphorylated
• Gamma carboxy glutamate seen in Prothrombin
• 4 hydroxy Proline and 5 hydroxy lysine found in Collagen

46. Artificial sweetner: Aspartame
Naturally occurring peptides range in length from two to many thousands
of amino acid residues. Even small peptides can be biologically active. For
example, the commercially synthesized dipeptide L-aspartyl-L-
phenylalanine methyl ester is the sweetener called aspartame or
NutraSweet.

47. Short biologically active peptides
THYROTROPIN-RELEASING FACTOR (three amino acid residues
Glu –His-Pro-NH2

48. Pepsin Hemoglobin Collagen
Most structurally & functionally diverse group of multi-purpose biomolecules

49. Size
• The lengths of polypeptide chains in proteins vary.
• While the great majority of proteins contain fewer than 2,000 amino
acids, some are much larger.
• The largest known protein is titin (26,926 amino acids), which is a
component of vertebrate muscle.
• Some proteins consist of a single polypeptide chain, whereas others
called multisubunit proteins have two or more associated
polypeptides.
• The individual polypeptide chains in a multisubunit protein can be
identical or different.
• If at least two subunits are identical, the protein is said to be
oligomeric and the identical units (consisting of one or more
polypeptide chains) are referred to as protomers.
Proteins

50. Size

51. Amino Acid Compositions
Proteins

53. Classification
Based on
1. Physical properties or structure
2. Function
3. Composition and nature
Proteins

55. – Keratin : hair and nails, wool, feathers, spider web
– Collagen and Elastin: supports ligaments, tendons, and skin
Fibrous proteins

57. Egg albumin Globular Antibodies
Histones
Protamines
in spermiogenesis
Globular
proteins

60. CLASSIFICATION BASED ON COMPOSITION AND NATURE
[Insoluble in neutral solvents]

62. Conjugated proteins

64. Metabolism
Few examples of significant proteins:
Enzymes
– Biological catalysts – speed up chemical reactions
• Digestive enzymes aid in hydrolysis
» Lipase
» Amylase
» Lactase
» Protease
• Molecular Biology
» Polymerase
» Ligase
• Industry
» Dairy, infant formulas, rubber, beer, photography, contact
lens cleaner

65. Transport
Channel and carrier proteins in the cell membrane
– Allows substances to enter and exit the cell
Transport molecules in blood
– Hemoglobin – transports oxygen in the blood

66. Defense
Antibodies
– Combat bacteria and viruses

67. Regulation
Hormones
– Intercellular messengers that influence
metabolism
– Insulin – regulates the amount of glucose in the
blood and in cells
– Human growth hormone determines
the height
Receptor Proteins
– Built into the membranes of nerve cells
– Detect chemical signals released by
other nerve cells

68. Contractile proteins : Movement
Actin and myosin – make up muscle fibers
- Motor proteins within the cell
– Allow cell components to move from place to
place.
– Flagella- move the cell.
– Cilia- move contents around the cell

69. Structure & function relationship
Proteins
PROTEIN Structure:
– monomer = amino acids
• 20 different amino acids [ 11 made by body and
9 essential amino acids]
– polymer = polypeptide
• protein can be one or more polypeptide chains
folded & bonded together
• large & complex molecules
• complex 3-D shape

70. Structure & function
Function depends on structure
– 3-D structure
• twisted, folded, coiled into unique shape
hemoglobin collagen
pepsin

71. Order of amino acids in chain
– amino acid sequence determined by
gene (DNA)
– slight change in amino acid sequence
can affect protein’s structure & it’s
function
lysozyme: enzyme
in tears & mucus
that kills bacteria

72. Even just one amino acid change can make all the difference!
Sickle cell anemia

73. Structure hierarchy and Organization
Proteins
1 2
3 4

74. 1. Primary Structure
• The primary structure of a protein
refers to its linear amino acid
sequence.
• Amino acids in peptides (<30 aas)
and proteins (typically 200 to
1,000 aas) are joined together by
peptide bonds (amide bonds)
between the carboxyl and amino
groups of adjacent amino acids.
• The backbone of all proteins
consists of a [-N-Cα(R)-C(O)-]
repetitive unit.
• Only the R-group side-chains vary.
• By convention, protein sequences
are written from left-to-right, from
the protein’s N- to C-terminus.
N
C(R)

75. 2. Secondary Structure
α Helix
Secondary structure refers to short-range,
periodic folding elements that are
common in proteins.
These include the α helix, the β sheet, and
turns.
In the α helix, the backbone adopts a
cylindrical spiral structure in which there are
3.6 aas per turn.
The R-groups point out from the helix, and
mediate contacts to other structure elements
in the folded protein.
The  helix is stabilized by H-bonds between
backbone carbonyl oxygen and amide
nitrogen atoms that are oriented parallel to
the helix axis.

76. protofibril

77. Secondary Structure: β sheets & β turns
In ß sheets (pleated sheets), each ß
strand adopts an extended conformation.
ß strands tend to occur in pairs or multiple
copies in ß sheets that interact with one
another via H-bonds directed
perpendicular to the axis of each
strand.
Carbonyl oxygens and amide nitrogens in
the strands form the H-bonds.
Strands can orient antiparallel or parallel
to one another. R-groups of every other
amino acid point up or down relative to the
sheet. Most ß strands in proteins are 5 to 8
aas long.
ß Turns consist of 3-4 amino acids that
form tight bends. Glycine and proline are
common in turns. Longer connecting
segments between ß strands are called
loops.
ß turn

78. Secondary (2°) structure

79. Silk fibroin:
β pleated
sheet

80. Secondary Structure Motifs
Secondary structure motifs are evolutionarily conserved collections of
secondary structure elements which have a defined conformation. They
also have a consensus sequence because the aa sequence ultimately
determines structure. A given motif can occur in a number of proteins where
it carries out the same or similar functions. Some well known examples such as
the coiled-coil, EF hand/helix-loop-helix, and zinc-finger motifs. These
motifs typically mediate protein-protein association, calcium/DNA
binding, and DNA or RNA binding, respectively.

81. 3. Tertiary Structure
Tertiary structure refers to the folded 3D structure of a protein.
It is also known as the native structure or active conformation.
Tertiary structure mostly is stabilized by noncovalent interactions
between secondary structure elements and other internal sequence regions.
The folding of proteins is thought to be driven by the need to place the most
hydrophobic regions in the interior out of contact with water.
The structures of hundreds of proteins have been determined by techniques
such as x-ray crystallography and NMR.

82. Tertiary (3°) structure
“Whole molecule folding”
– created when the secondary structure fold
and form bonds to stabilize the structure into
a unique shape
– determined by interactions
between R groups
• Hydrophobic interactions
• anchored by disulfide bridges
• Ionic Bonds between R groups
• Hydrogen bonds between backbones
• Van der Waals Force
• Globular (spherical) proteins
have tertiary structure

83. Tertiary structure of Myoglobin
• Myoglobin is an iron and oxygen
binding protein found in the cardiac
and skeletal muscle tissue of vertebrates
and in mammals
• Single polypeptide with 154 amino
acids, folded into 8 α
helices connected by loops.
• Non-polar amino acids at the core of the
globulin, where the heme group is
non-covalently bounded with the
polypeptide of myoglobin.

84. 3. Quaternary Structure
• Multi-subunit (multimeric) proteins have another level of
structural organization known as quaternary structure.
• Quaternary structure refers to the number of subunits,
their relative positions, and contacts between the individual
monomers in a multimeric protein.
• Two or more tertiary folded peptide subunits bonded
together to make a functional protein

85. Quaternary Structure of Hemoglobin and
Collagen
• Hemoglobin consists of 4
subunits (tetramer). Two α and
two β polypeptide chains, each
chain with a heme group for
binding Oxygen.
• Collagen found in skin and
tendons is made up of 3
polypeptide chains. Triple
helical structure

86. Quaternary (4°) structure
two or more tertiary folded peptide subunits bonded
together to make a functional protein
– Hemoglobin – 4 polypeptides
– Collagen – 3 polypeptides
hemoglobin
collagen =
skin & tendons

87. Protein structure (review)
1°
2°
3°
4°
aa sequence
peptide bonds
determined
by DNA
R groups
hydrophobic
interactions,
disulfide
bridges, ionic
bonds
Multiple polypeptides
hydrophobic interactions
H bonds

88. Protein denaturation
Proteins

91. Chemical agents
1. Ionizing radiations
2. Organic solvents (acetone, alcohol)
3. Detergent Sodium dodecyl sulphate (SDS)

92. • Solubility influenced by pH
• Solubility is lowest at Isoelectric point and increases
with increasing acidity or alkalinity
• This is because when the pH is changed, proteins exist
as cations or anions, repulsive forces between ions are
high, therefore they will be more soluble than in iso
electric state
Solubility of proteins
Proteins

93. Factors
affecting
solubility
Amino acid
composition
Protein
structure
pH
Temperature
Salt
concentration
Ionic strength
Hydrophobic
interaction
Denaturation

94. “Salting in” and “salting out”

95. Low ionic
strength
High ionic
strength