AMINO ACIDS AND PROTEINS(Dr.GIREESH KM)

BIOCHEMISTRY

2. Chemistry of amino acids
and proteins
MAHE INSTITUTE OF DENTAL SCIENCES & HOSPITAL
Gireesh Kumar K.M
Assistant Professor
Department of Biochemistry

3. Functions of proteins
Proteinsarethemostabundantmacromoleules
inlivingcell
Proteinisthemostimportantofcell
constituents
Allenzymesareproteins
Manyhormonesareproteins(insulin)
Defensefunctionex:immunoglobulins(antibodies)

4. Protiens carry (transport) compounds across cell
membrane
Proteins act as buffers to maintain pH of the cell

5. Amino acids
Amino acids are the simplest units of a protein
molecule
They form the building block of protein
An amino acid has an amino group and a carboxyl
group
Carbon atom which –
COOH group is attached is
called αcarbon
In amino acids , both
amino and COOH group
are attached toαcarbon .

6. Proteinsarethechainsofaminoacidsthatare
linkedbypeptidebonds
Eachproteinhasspecificanduniquesequence
ofaminoacid.
20aminoacidsareinvolvedinformationof
proteins
TheydifferintheRgroup.

7. Peptide bond
In proteins successive amino acids are joined by
peptide bonds
A dipeptide contain one peptide bond
If the first amino acid is alanine and the second
amino acid is glycine a dipeptide can be written as
Ala-Gly
TripeptideGlu-Cys-Gly(Glutamate –cysteine –
glycine)

8. Amino acid exhibit two types of isomerism due to the
presence of assymetric carbon
Stereoisomerism
Optical isomerism
Stereoisomerism
All amino acids except glycine exist in D and L forms
In D amino acids, -NH2 group is on the right side , in L
it is on left
Only L amino acids are utilized in our body

9. Optical isomerism
All amino acids except glycine exhibit optical activity
as they rotate the plane polarised light.
Glycine ,Gly(optically inactive amino acid)

10. Importance of amino acids
formation of proteins
Some amino acids are converted to carbohydrate and
are called glucogenic amino acids
Enzyme activity
Transport and storage form of ammonia
Detoxification reactions
Formation of biologically important
compounds(explanation later)

11. Classification of amino acids
Based on structure
Based on nutritional status
Based on metabolic fate
Based on side chain

12. 1. Based on structure
According to this type , amino acids are classified
as
Aliphatic aminoacids
Mono amino mono carboxylic amino acids
Simple amino acids
Branched chain amino acids
Hydroxy aminoacids
Sulphur containing amino acids
Amino acids with amide group
Dicarboxylic acid and their amides
Diamino acids
Aromatic amino acids
Heterocyclic amino acids
Imino acids

14. Simple amino acids
Glycine ,Gly(optically inactive amino acid)
Alanine, Ala
Branched chain
Valine , val (branch chain)
Leucine (branch chain, Leu
Isoleucine (branch chain,Ile

15. Aliphatic amino acids
Branched chain
Valine , val (branch chain)
Leucine (branch chain, Leu
Isoleucine (branch chain,Ile

17. Hydroxy aminoacids
Amino acids having –OH group in the side chain
Serine , Ser
Threonine, Thr
Tyrosine , Tyr(aromatic also)

19. Sulphur containing amino acids
Cysteine, Cys
Methionine, Met

20. Amino acid with amide group
Glutamine(amide of glutamic acid), Gln
Aspargine (amide of aspartic acid), Asn

21. mono amino Dicarboxylic acid
Amino acids having carboxylic acids in their side
chain(COOH >NH2)-acidic amino acids
Glutamic acid, Glu
Aspartic acid, Asp

22. (Diamino acids)
Di amino monocarboxylic acids
-Lysine, Lys
-Arginine,Arg
-Histidine , His (aromatic also)

23. Aromatic amino acids
Contain aromatic ring
Phenylalanine,(Phe)-contain benzene ring
Tyrosine , (Tyr)-contain phenol group
Tryptophan (Trp)-indole group
Histidine (His)-imidazole group

24. Heterocyclic amino acids
Tryptophan (Trp)-indole group
Histidine (His)-imidazole group

25. Imino acids or heterocyclic
Amino acids have secondary amino(imino,-NH)
group
Eg proline

27. Special groups in amino acids
Phenylalanine,(Phe)-contain benzene ring
Tyrosine , (Tyr)-contain phenol group
Tryptophan (Trp)-indole group
Histidine (His)-imidazole group
Proline-pyrrolidine group
Arginine –guanidium group

28. Based on nutritional status

29. According to this type amino acid classified as
Nutritionally essential or indispenible amino
acids
Nutritionally non essential or dispensible
Semi essential amino acids

30. Essential amino acids
Amino acids cannot be synthesized by the body and
must be essentially supplied through the diet
Tryptophan
Valine
Threonine
Isoleucine
Lysine
Leucine
Phenyl alanine
Methionine
T.V TILL 8
P.M

31. 31
MAHTT VIL PhLy
Mmethionine
A arginine
Tthreonine
Ttryptophan
Vvaline
Iisoleucine
Lleucine
Phphenylalanine
Lylysine
H Histidine

32. SEMI ESSENTIAL
HISTIDINE AND ARGININE are called semi
essential amino acids because they are not
synthesised only in small quantities
So the synthesis is not suffecient during the
period of growth
So GROWING CHIDREN REQUIRE THEM IN
FOOD

33. NON ESSENTIAL
THE REMAINING 10 AMINO ACIDS ARE NON
ESSENTIAL
THEY CAN BE SYNTHESIZED BY THE BODY
THEY ARE REQUIRED FOR NORMAL PROTEIN
SYNTHESIS
GLYCINE,ALANINE, PROLINE, SERINE,
GLUTAMIC ACID,
GLUTAMINE,TYROSINE,CYSTEINE,
ASPARTIC ACID, ASPARGINE

34. BASED ON METABOLIC FATE

35. Aftertheremovalofaminogroupofaminoacid.If
thecarbonskeltoncanbeconvertedtoglucosethey
arecalledPURELYGLUCOGENIC AMINO ACIDS-
(Thosewhichcanbeconvertedintoglucose)
Aftertheremovalofaminogroupofaminoacid.If
thecarbonskeltoncanbeconvertedtoketonebody
thentheyarecalledPURELY KETOGENIC
AMINOACIDS -Thosewhichcanbeconvertedinto
ketonebodies

36. After the removal of amino group of amino acid .
If the carbon skelton splits in to two parts, one of
which can be converted to glucose and other
parts become ketone body such amino acids are
BOTH GLUCOGENIC AND KETOGENIC -Those
which can be converted in to both types

37. KETOGENIC BOTH KETOGENIC
AND GLUCOGENIC
(I like Aromatic
amino acids)
GLUCOGENIC
LEUCINE(purely
ketogenic)
LYSINE
ISOLEUCINE
PHENYL LANINE
TYROSINE
TRYPTOPHAN
GLYCINE
ALANINE
SERINE
ASPARTIC ACID
ASPARGINE
GLUTAMIC ACID
GLUTAMINE
PROLINE
HISTIDINE
ARGININE
METHIONINE
THREONINE
VALINE

38. BASED ON SIDE CHAIN

39. ACCORDING TO THIS AMINO ACIDS ARE
CLASSIFIED IN TO 2
HYDROPHILIC OR POLAR AMIOACIDS
HYDROPHOBIC OR NON POLAR AMINOACIDS

40. HYDROPHILIC OR POLAR
The side chains of hydrophilic amino acids
contain polargroups that may be either
Charged
Uncharged
Positively charged side chains-Basic amino
acids
Negatively charged side chains-acidic amino
acids
Theseaminoacidsarerelativelyhydrophilic
(waterloving)becausetheypossesspolar
functionalgroups(insidechains)i.e.oxygenand
nitrogen,whichcanparticipateinhydrogen
bondingwithwatersocapableofinteractingwith
water

41. UNCHARGED HYDROPHILIC
The uncharged side chains of other amino acid have O,
S , N atoms enabling them to form hydrogen bond with
water
Threonine and serine-------OH gp in the side chain
Aspargine and glutamine------amide gp

42. HYDROPHOBIC –non polar
The side chain of hydrophobic amino acids interact
poorly with water
Side chains which have purehydrocarbonalkyl
groups (alkane branches) or aromatic (benzene rings)
arenon-polar
. Examples include valine, alanine, leucine, isoleucine,
phenylalanine

43. Protein classification

44. Classification on the basis of
Function
Shape and size
Physical and chemical properties
Nutritional classification.

45. Proteins
Shape
&size
Function
Soluability & physical
properties
Nutritional
classificaton
Fibrou
s
protei
n
Globul
ar
protein
Keratin
collagen
Myoglobi
n
Hb
Simple
protein
Conjugated
protein
Derived
protein
Albumin Glycoproteins Primary
Seconda
ry
Globulin Lipoproteins
Glutelin Nucleo proteins
Protamin
es
Chromoprotein
s
Histones Phosphoprotei
ns
Prolamin
es
Metalloproteins
Catalytic protein
Transport protein
Storage protein
Contractile protein
Structural protein
Defense protein
Regulatory Nutritionally rich
protein or
complete
Incomplete
protein
Poor protein

46. Based on function
1 ..Catalytic proteins or enzymes
Protein act as enzymes
Glucokinase
Dehydrogenases
Transaminases
Hydrolytic enzymes, pepsin,
trypsin

47. 2..Transport proteins
Involved in the process of
transportation
Hbtransports oxygen
Transferrintransports iron
Albumintransports fatty acids
and bilirubin

48. 3..Storage proteins
Proteins serves as storage form
Apoferritinstores iron in the form
of ferritin
Myoglobinstores oxygen in
muscles
Ovalbumin & glutelin

49. 4..Contractile proteins
Some proteins have the ability to
contract and function in the
contractile system of skeletal
muscle
Actin
Myosin

50. 5..Structural proteins
Many protein serves as supporting
frame work of cells to give
biological structure , strength or
protection
Collagenin bone
Elastinof ligaments
Keratinof hair, nail

51. 6..Defense protein
Many proteins involved in defense
mechanism against foreign
substances such as viruses,
bacteria
Immunoglobulinor antibodies
Fibrinogen and thrombin

52. 7..Regulatory proteins(hormonal protein)
Proteins regulate cellular or
physiological activity
Many hormones
Insulin, regulate sugar
metabolism
Growth hormone of pituitory
gland regulates growth of cells

53. 8.Protein as buffers
Plasma proteins are involved in
the buffringi in plasma
Hb is an important buffer inside
RBC

54. 9. PROTEIN AS TOXINS
Clostridium botulinum toxin which cause
bacterial food poisoning

55. 9.. Protein as antivitamin
Avidin of raw egg white which binds
biotin(vitamin) and interfere with its
absorption

56. Based on shape and size
Fibrous protein: they are elongated or
needle shaped molecules
Have axial ratio of length : width >10
Ex: keratins
Elastin
collagen

57. Globular proteins: they are spherical in
shape
Have axial ratio of length : width <10
Ex plasma globulins ,
fibrinogen,albumin, myoglobin, Hb etc


58. Based on physical and soluability(chemical)
properties of protein
Simple proteins
Conjugated proteins
Derived proteins

59. Simple Conjugated Derived
Albumin Nucleoprotein Primary
coagulated protein
Proteans
Metaproteans
Globulin Glycoprotein Secondary
Proteoses
Peptones
Peptides
Glutelin Chromo protein
Protamines Phospho protein
Histones Lipo protein
Prolamines metalloprotein
Scleroproteins

60. Simple proteins
Defined as those proteins that
upon hydrolysis, yield only amino
acids or their derivatives
They are classified according to
their solubility and heat
coagulability. They are

61. Name Soluability Examples
Albumin Soluble in water
Coagulated by heat
Egg albumin
Serum albumin
Lactalbumin
Globulin Insoluble in water, soluble in
dilute neutral salt solutions
Heat coagulable
Ovaglobulin of egg yolk
Serum globulin
Myosin of muscle
Glutelin Soluble in dilute acids and
alkalies
Insoluble in neutral solvents
Plant proteins
Glutelin of wheat
Oryzenin of rice
Prolamines Soluble in 70-80-% alcohol
Insoluable in water, neutral
solvent or absolute alcohol
Plant proteins
Zein of corn
Gliadin of wheat
Protamines Soluble in water
Not heat coagulable
Nucleoproteins
Sclero proteins Insoluable in water and salt
solution
Collagen and elastin
Histones Soluable in water Nucleoproteins

62. Conjugated proteins
Composed of simple protein combined
with some non protein
substances(prosthetic group)
Examples
Nucleoproteins
Glycoproteins
Chromoprotein
Phosphoprotein
Lipoprotein
Metaloproteins

63. Conjugated protein Non protein part Examples
Glycoproteins Carbohydrate Blood group antigens ,
serum proteins
Lipoproteins Lipids Serum, lipoproteun(HDL,
LDL
Nucleo proteins Nucleic acids Histones
Chromoproteins Colored group Hemoglobin ,
flavoprotein (riboflavin
yellow )
Phosphoproteins Phosphorus Casein of milk , vitellin of
egg yolk
Metalloproteins Metal ions Hb(iron), Carbonic
anhydrase(Zn), Xanthine
Oxidase(Molybdenum)

64. Derived proteins
Thisincludesthosesubstances
derivedfromsimpleand
conjugatedproteins
Derivedproteinsaredividedinto
two
Primary derived proteins
Secondary derived proteins

65. Primary derived proteins
Theseproteinderivativesareformed
byagents(heat,acids,alkalies)
whichcauseonlyslightchangesin
theproteinmoleculeandits
properties,withoutcleavageof
peptidebondexamplesare

66. Proteans–earliestproductofprotein
hydrolysisbytheactionofdilute
acidsorenzymeseg,fibrinfrom
fibrinogen
Metaproteins
Areformedbyfurtheractionof
acidsandalkaliesonproteins

67. Secondary derived proteins
Substancesareformedinthe
progressivehydrolyticcleavageof
peptidebondofmetaproteinsinto
smallermoleculesex.
Proteoses
Peptones
peptides

68. Note –Gelatin is another example
for deived protein , derived from
collagen(connective tissue
protein)

70. 70
CLASSIFICATION BASED ON
NUTRITIONAL VALUE

71. Class Definition Example
Nutritionally rich
proteins
They contain all essential
amino acids in required
proportion
casein of milk
Incomplete proteins They are protein which
lack one essential amino
acid.
Proteins from pulses
(defecient in methionine)
Protein from cereals ( def:
in lysine
Poor proteins They lack in many
essential amino acids:
zein of corn ( def: in
tryptophan and lysine

72. Properties of protein

73. The average nitrogen content of protein is 16%
•Solubility-Proteins form colloidal solution instead of true
solution in water
•Mol.wt-Proteins vary in the mol.wt, which depend on the
number of amino acid residues
Shape-Wide variation in shape-scleroproteins are in the form
of fibers
Isoelectric pH-At isoelectric pH protein exists as
ZWITTERIONS

74. Isoelectric pH of casein-4.6
Albumin 4.7
globulin -6.4

75. Hydration of proteins
Proteins when contact with water, it
absorbs and swell up
Polar groups of protein(COOH, NH2, OH)
binds with water to form hydrogen bonds to
hold a considerable amount of water
Thus a relatively immobile shell like layer
of water(solvation layer) is held around each
protein in aqueous medium

76. Precipitation of proteins
Thestabilityofproteininsolution
dependson
Chargeandhydrationofproteinmolecule
Thefactorswhichneutralizethechargeor
removehydration,causesPRECIPITATION
OFPROTEIN

77. Factors used for precipitation of protein
are
Precipitation by Salting out
Precipitation at Isoelectric pH
Precipitation by Organic solvents
Precipitation by Anionic or alkaloid
reagents
Precipitation by salt of heavy metals

78. Salting out
Theprocessofproteinprecipitationbythe
additionofneutralsaltsuchasammonium
sulfateisknownassaltingout.
Explainedonthebasisofdehydrationof
proteinsbysalts

79. Mineralionsattractwatermoleculesand
consequentlyremoveshellofhydration
(solvationlayer)aroundproteinmolecules
Sincewaterlayeraroundproteinmoleculeis
removed,proteinisprecipitated,calledsalting
out

80. Amountofsaltrequiredforproteinprecipitation
dependsonsize(mol.Wt)ofprotein
Highmol.Wtproteinrequirelesssaltto
precipitatethanlowmol.Wt
Albumin -69,000
Globulin -1,60,000

81. Serumglobulinsareprecipitatedbyhalf
saturationwithammoniumsulfatesolutionwhile
albuminisprecipitatedbyfullsaturationwith
solidammoniumsulfatecrystals.
PrecipitationatisoelectricpH
AllproteinsareleastsolubleattheirisoelectricpH
Precipitationbyorganicsolvents
Org.solventslikealcohol-dehydratesand
precipitatesproteins

82. Precipitation by salts of heavy metals
Heavymetaslikepb
2+,
Fe
2+,
Zn
2+,
Cd
2+
causeprecipitationofproteins.
Thesemetalsarepositivelycharged,when
addedtoaproteinsolution(-vely
charged)inalkalinemediumreults
preipitation

83. Precipitation by anionic or alkaloidal
reagents
Proteinscanbeprecipitatedbtrichoroaceticacid,
sulphosaliylicacid,Phosphotungsticacid,tannicacid
etc
Bytheadditionoftheseacids,proteinexistingas
cationsareprecipitatedbytheanionicformofacids
toproduceprotein-sulphosalicylate,protein-
tungstate,etc

84. Colour reactions of protein
Proteins give several colour reactions which are
used to identify the nature of amino acids present in
them .
Colour reactions are ;

85. Reaction Specific group/amino acid
Biuret reaction 2 peptide linkage
Ninhydrin reaction Alpha amino acids
Xanthoproteic reaction Benzene ring of aromatic amino
acids(phe, Tyr, Trp)
Millons reaction Phenolic group
Hopkins coles reaction
Aldehyde test
Indole ring(Trp)
Nitroprusside test Sulfhydril group(cys)
Sulphur test Sulfhydril group(cys)
Pauly’s test Imidazole ring(his)

86. Denaturation of protein
Thethreedimensionalconformation,the1
o
,2
o
,3
o
and
evensomecasesof4
o
structureischaracteristicsof
nativeprotein.(thenaturalbiologicalconformationofa
proteiniscallednativestate)
Theconformationcanupsetanddisorganized,onlyby
thebreakageofbondswhichstabilizethestructure
Thephenomenonofdisorganizationofnativeprotein
structureisknownasdenaturation

87. Agents of denaturation
Physical agents
Heat ,x-rays, uv rays can denature protein
Chemical agents
Acids, alkalies, and certain solutions of heavy
metals (Hg,Pb,detergents) organic solvents like
alcohol,ethers, urea etc denature protein
•Mechanical agents
Vigorous shaking and grinding leads to
denaturation

89. Characteristics of denaturation
Nativestructureofproteinislost
Denaturationresultsinthelossofsecondarystructure,
tertiaryandquaternarystructure
Primarystructureofproteinremainintact
Involveschangesinthephysical,chemicalandbiological
propertiesofprotein
Losesbiologicalactivity
Denaturedproteinbecomesinsolubleinsolvent,inwhichis
originallysoluble

90. ViscosityofDenaturedproteinincreases
Denaturedproteiniseasilydigested
Denaturedproteinisirreversible(omletcanbeprepared
fromeggproteinalbumin.Butthereversalisimpossible)
Sometimesreversible.(renaturation)
Hbundergodenaturationbysalicylate.Byremovalof
salicylate,Hbisrenatured.

91. Coagulation
Thetermcoagulumreferstosemisolidviscous
precipitateofaprotein
Irreversibledenaturationresultsincoagulation
Albuminandglobulinarecoagulableprotein
Heatcoagulationtestiscommonlyusedtodetect
thepresenceofalbumininurine

92. Structure of protein
(levels of
organization of
proteins )

93. Primary structure
Secondary structure
Teritiary structure
Quaternary structure

94. Primary structure of protein
Primarystructurereferstotheorderand
sequenceofaminoacidsinapolypeptidechain
andthelocationofdisulphidebonds,ifany
Eachaminoacidinapolypeptidechainis
calledaresidueormoiety

95. Eachpolypeptidechainishavingfree
aminogroupatoneendcalledN
terminalandfreecarboxylgroupat
otherendcalledCterminal

97. Thisaminoacidsequenceofaproteinis
referredasPRIMARYSTRUCTURE
Understandingofprimarystructureofaprotein
isimportantbecausemanygeneticdiseases
resultduetoanabnormalaminoacidsequence

98. Forces keeping the primary
structure
Peptide linkage
Disulphide linkage

99. Secondary structure of proteins
Forstabilityofprimarystructure,hydrogen
bondingbetweenhydrogenofNHand
oxygenofC=Ogroupsofpolypeptidechain
occurs,whichgiverisetofoldingortwisting
ofprimarystructure

100. Regularfoldingortwistingofpolypeptide
chainbyhydrogenbondingiscalled
structureiscalledsecondarystructureof
protein
2typesofsecondarystructuresare
-helix
ß-pleated

101. H -bonding

103. -helix
Mostcommon&stableconformation
-helixisaspiralstructure
Isatightlycoiledstructurewithaminoacids
sidechainsextentoutwardfromcentralaxis
Thepolypeptidebondsformsthebackbone

104. All the peptide bonds participate in H
bonding except first and last
Each turn of -helix contain 3.6 amino
acid and travels a distance of 0.54nm,
spacing of each amino acid is 0.15nm
Each turn has 3 complete amino acid and two atoms from the next one

105. The helix is stabilized by H bond between
the NH & C-O groups of the same chain.
N-O distance 2.8 A
o

106. ß pleated sheet structure
IntheßsheetsHbondsareformed
betweenNH&COgroupsindifferent
polypeptidechains.
Thepolypeptidechainsintheßsheets
maybearrangedeitherinparallel(same
direction)orantiparellel(opposite
direction)

107. Parellel pleated sheet
Thepolypeptidechainliesidebysideandinsamedirection(with
respecttotoNandCterminal),sothattheirNterminalresidues
areatthesameend(NterminalfacestoNterminal)andstabilized
byhydrogenbonding

108. Antiparellel sheet
Thepolypeptidechainlieinoppositedirection,ieN
terminalendofoneisnexttotheCterminalofother(N
terminalfacestoCterminal)andstabilizedbyhydrogen
bonding

109. Tertiary structure
Thepeptidechain,withitssecondarystructure,may
foldedandtwistedaboutitselfforming.Three
dimensionalarrangementofpolypeptidechainor
3-dimensionalstructureisformedwhenalphahelices
andbetasheetsareheldtogether
Hydrogenbonds
Hydrohphobicinteractions
VanderWaalsforce
Disulphidebond
Ionicbond
Stabilize tertiary structure

111. Quaternary structure
Some protein contain more than one polypeptide
chain.
They are known as oligomeric protein(multi
subunit)
Each subunit possesses primary,secondary,and
tertiary chain have quaternary structure

112. Whenthesesubunitsareheld
togetherbynoncovalent
interactionsorbycovalentcross
linked,itisreferredas
quaternarystructure

113. Certainpolypeptideswillaggregatetoform
onefunctionalprotein
Dependingonthenumberofmonomersthe
proteinmaybetermedasdimer(2),
tetramer(4)

114. Examples –glycolytic enzymes
Aldolase,LDH,PDH
Hemoglobin
Creatine kinase
Alkaline phosphatase
IMMUNOGLOBULIN
aspartatetranscarbamoylase
Collagen

115. Theforcesthatkeepthequaternarystructurearehydrogenbonds,
disulphidebonds,electrostaticbonds,hydrophobicbondsandvanderWaals
forces.

117. 117
Primary structure
Sequence of amino acids
Secondary structure
Alpha helix; Beta pleated sheets
Tertiary structure
3-dimensional structure is formed when alpha helices and beta
sheets are held together
Quaternary structure
consists of more than one
polypeptide chain
Levels of Organisations of Proteins