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Proteins
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2. Biological importance
Amino acids : Classification.
Introduction to peptides.
Proteins - Classification : simple and
conjugated; Globular and fibrous.
Charge properties - Buffer action.
Denaturation
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3. Most abundant organic molecules of the
living system
Its fundamental basis of structures and
function of life.
50 % of dry weight of every cell
It’s a polymer of L α-amino acids.
300 different amino acids occur in nature –
only 20 as standard amino acids.
21st amino acid added - Selenocysteine
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4. Beside forming long chain polypeptide unit of
protein, amino acids have additional functions
◦ nerve transmission
◦ biosynthesis of porphyrins, purines, pyrimidines,
and urea
◦ Short polymers of AA – peptides
◦ Neuroendocrine system - hormones, hormone
releasing factors, neuromodulators, or
neurotransmitters
◦ Microorganisms : D- and L-α-amino acids
Therapeutic value: antibiotics bacitracin and gramicidin A
and the antitumor agent bleomycin
Some may be toxic
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5. It’s a group of organic
compounds containing
two functional groups –
amino (-NH2) and
carboxyl group (-COOH)
Its also called Zwitter Ion–
both acidic and basic
functional group (dipolar
ion)
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• This property is known as amphoteric and
are often called ampholytes
• Neither humans nor any other higher animals
can synthesize 10 of the 20 common amino
acids – Essential Amino acids
6. Amino acid has been classified under various
ways
◦ Structure
With side chain containing Aliphatic Side Chains
With Side Chains Containing Hydroxylic (OH) Groups
With Side Chains Containing Sulfur Atoms
With Side Chains Containing Acidic Groups or Their Amides
With Side Chains Containing Basic Groups
Containing Aromatic Rings
Imino Acid
◦ Polarity
Non Polar
Polar
◦ Nutritional
Essential and Non-essential
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7. Simplest
amino acids
Contains
branched
chain of
hydrocarbon
s
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14. Non- polar group : No charge on R group. Ex:
Alanine, leucine. Isoleucine, valine, methionine,
phenylalanine, tryptophan and proline
Polar group
◦ No charge on R : no charge on R but posses group such
as hydroxyl, sulfhydryl and amide. Ex: Glycine, serine,
threonine, cysteine, glutamine, asparigine and tyrsoine
◦ Positive R- Lysine, arginine, and histidine
◦ Negative R – asparatic acid and glutamic acid
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15. It cant be synthesized in the body and therefore
need to be supplied through diet
Proper growth and maintenance of the individual
Ex. Arginine, Valine, Histidine, Isoleucine,
leucine, lysine, Methionine, Phenylalanine,
Threonine, Tryphtophan
Mnemonics : AV hill, MP TT
Semi-essential amino acid: Adults can synthesize
2 amino acid and not by growing children. Ex:
Arginine and histidine
So in all 8 are essential and 2 semi essential
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16. Two AA covalently joined
through a substituted
amide linkage – peptide
bond
Dehydration – removal of
H2O
◦ OH- Carboxyl group of one
AA
◦ H+ from amino group of
another AA
• Example of a
condensation reaction
– common biological
reactions
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17. Two AA reacts to form
dipeptides, Three AA can
be joined by two peptide
bonds to form a tripeptide
and so on.
Oligopeptide: When a few
AA are joined by various
peptide linkage
When many amino acids
are joined, the product is
called a polypeptide.
Proteins may have
thousands of amino acid
residues
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Tetrapeptide
18. Proteins catalyze metabolic reactions, power
cellular motion, and forms structural integrity to
hair, bones, tendons and teeth
Human proteins therefore reflects the
sophistication and diversity of their biologic roles
Therefore maturation of a newly synthesized
polypeptide into a biologically functional protein
◦ Requires folding into a specific three-dimensional
arrangement, or conformation
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19. During maturation, posttranslational
modifications may add new chemical groups or
remove it transiently
Genetic or nutritional deficiencies that impede
protein maturation are deleterious
to health.
Ex: Creutzfeldt Jakob disease, Scrapie,
Alzheimer’s disease, and bovine spongiform
encephalopathy
Scurvy - nutritional deficiency that impairs
protein maturation.
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20. The modular nature of protein synthesis and folding
are embodied in the concept of orders of protein
structure:
◦ Primary structure: linking amino acid residues in a
polypeptide chain
◦ Secondary structure: stable arrangements of amino acid
residues giving rise to recurring structural patterns into
geometrically ordered units; twisting resulting in α-helix or
pleated
◦ Tertiary structure: the three-dimensional assembly of
secondary structural units to form larger functional units
◦ Quaternary structure: It’s the arrangement in space of
protein having two or more polypeptide subunits
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22. Primary (1°) structure
Each protein has a
distinctive number and
sequence of amino acid
residues
These determines how it
folds up into a unique
three-dimensional
structure
This in turn determines
the function of
the protein
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Bovine Pancreatic
Ribonuclease A
23. 2° structures
Polypeptide chain can arrange
itself into characteristic helical or
pleated segments
◦ Given by Pauling and Corey
◦ hydrogen bonding interactions
between adjacent amino acid
residues
• Free rotation is possible
about only two of the three
covalent bonds of the
polypeptide backbone
α-carbon (Cα) to the carbonyl carbon
(Co) bond
Cα to nitrogen bond
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Psi (Ψ)
angle
Phi (Φ)
angle
24. α helix is twisted by
an equal amount about each α-
carbon
With a phi angle of approx. −570
and a psi angle of approx − 470
Complete turn of the helix
contains an average of 3.6
aminoacyl residues
Distance it rises per turn (pitch)
is 0.54 nm
R groups of each aminoacyl
residue in an α helix face
outward
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26. Stability of an α helix arises
primarily from hydrogen
bonds
Between the oxygen of
carbonyl and the hydrogen
atom of nitrogen of the 4th
residue down the
polypeptide chain
Supplemented by van der
Waals interactions
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27. Extended conformation of
polypeptide chains
Viewed edge-on, form a
zigzag or pleated pattern
in which the R groups of
adjacent residues point in
opposite directions
Stability from hydrogen
bonds between the
carbonyl oxygens and
amide hydrogens of
peptide bonds - adjacent
segments of β sheet
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28. Parallel:polypeptide chain proceed in the same
direction amino to carboxyl
Antiparallel: they proceed in opposite
directions
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29. Short segments of amino acids that join two
units of secondary structure – 3-4 units
Globular proteins - compact folded structure
Nearly one-third of the amino acid residues
are in turns or loops where the polypeptide
chain reverses direction
The structure is a 1800 turn involving four
amino acid residues
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30. Carbonyl oxygen of the
first residue forms a
hydrogen bond with the
amino-group hydrogen of
the fourth residue
The peptide groups of the
central two residues do
not participate in any
hydrogen bonding
Gly (small and flexible)
and Pro (readily assume
the cis configuration)
residues often occur in
turns
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31. Generally found on the surface of a protein
γ -turn - less common is the, a three residue
turn with a hydrogen bond between the first
and third residues.
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32. Entire 3-dimensional conformation of a
polypeptide
Beside H bond, sulfide bond (-S-S), ionic
interaction and hydrophobic bond
Consists of helices, sheets, bends, turns, and
loops— assemble to form domains
Domain is a section of protein structure -
perform a particular chemical or physical task
◦ binding of a substrate or other ligand
◦ anchor a protein to a membrane
◦ interact with a regulatory molecules
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33. Enzyme triose
phosphate isomerase
complexed with the
substrate analog 2-
phosphoglycerate
(red)
Elegant and symmetrical
arrangement of
alternating β sheets
(light blue) and a helices
(green), with the β
sheets forming a β-
barrel core surrounded
by
the helices
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34. Single domain - triose phosphate isomerase, myoglobin
Two domains - lactate dehydrogenase, quinone
oxidoreductase
A polypeptides with 200 amino acids normally consists of
two or more domains
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Tetrameric enzyme
lactate
dehydrogenase with
the substrates
NaDh (red) and
pyruvate (blue)
bound
35. Majority of proteins are composed of single
polypeptide chains
Some of protein consists of 2 or more
polypeptide chain which may be identical or
different
Such protein are termed as oligomers and poses
quaternary structures.
When it consists of 2 polypeptides - dimers
Homodimers contain two copies of the same
polypeptide chain, while in a heterodimer the
polypeptides differ
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36. Solublity: forms colloidal solution instead of true
solutions in water – large size of protein
Molecular Weight: depends on number of amino
acid
Shape: there is wide variety in shape –
globular(insulin), oval(albumin), fibrous or
elongated (fibrinogen)
Acidic and basic: depends on ratio of (lysine +
arginine) : (Glut + Asp). Ratios greater than 1 is
basic and vice-versa
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37. Protein are isoelectric
Nature of amino acids determines the pH of a
protein
Acidic amino acid (Asp, Glu) and basic amino acid
(His, lys, Arg) – determines the charge on protein
At isoelectric pH, the protein exist as Zwitter-
ions and dipolar ions
◦ Electrically neutral
◦ Minimum solubility
◦ Maximum precipitability
◦ Least buffering capacity
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38. Proteins are classified on the basis of
◦ Chemical nature and solubility
Simple
Conjugates
Derived
◦ Function
Structural
Enzyme or catalytic
Transport
Hormonal
Contractile
Storage
Genetic
Defense
Receptor
◦ Nutritional Importance
Complete
Partially incomplete
Incomplete
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39. They are composed of only amino acid
residues
They are again classified as
◦ Globular Protein : spherical or oval in shape, soluble
in water or other solvent and digestible
Globulin: soluble in neutral and salt solution. Ex:
serum globulin
Albumin: soluble in water and dilute salt solutions and
cogulated by heat. Ex: serum albumin, ova albumin,
lactalbumin
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40. Globular Protein (Cont)…
◦ Glutelins : soluble in dilute acids, alkalies and
mostly found in plants. Ex: Glutelin (wheat),
oryzenin (rice)
◦ Prolamines: soluble in alcohol. Ex: gliadin(wheat),
zein (maize)
◦ Histones: strongly basic proteins, soluble in water
and dilute acids but insoluble in dilute ammonium
hydroxide. Ex: thymus histone
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41. Fibrous Protein: fiber like in shape, insoluble
in water and resistant to digestion. It again of
3 types
◦ Collagen: connective tissue protein lacking
tryptophan. On heating with boiling water or acids
it turns to soluble gelatin
◦ Elastin: elastic tissues such as tendons and ateries
◦ Keratin: present in the exoskeleton structures. Ex:
hair, nails, horns
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42. Beside amino acid, it contains a non-protein
moiety known as prosthetic group or
conjugating group. Its again of 6 types
◦ Nucleoprotein: nucleic acid (DNA or RNA)
◦ Glycoprotein: prosthetic group is carbohydrate
which is less than 4 % and when it exceeds 4% its
called mucoprotein. Ex: mucin (saliva), ovamucid
(egg white)
◦ Lipoprotein: found in the conjugation with lipids.
Ex: serum lipoprotein, membrane lipoprotein
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43. Phosphoprotein: phosphoric acid as
conjugate. Ex: casein(milk), vitelline (egg
yolk)
Chromoprotein: prosthetic group is colored in
nature. Ex: Hemoglobins, cytochromes
Metalloprotein: it contains metal ions such as
Fe, Co, Zn, Cu, Mg,
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44. Denatured or degraded product of simple or
conjugated protein
Its of 2 types
◦ Primary derived protein: denatured or cogulated or first
hydrolyzed product of proteins. They are
Cogulated proteins: denatured protein produced by agents
such as heat, acids, alkalies
Proteans: earliest product of protein hydrolysis by enzymes,
dilute acids, alkalies etc. Insoluble in water
Metaprotein: second stage of protein hydrolysis obtained by
treatment with slightly stronger acids and alkalies
◦ Secondary derived protein: progressive hydrolytic
product of protein hydrolysis. Ex: proteoses, peptones,
polypeptides and peptides
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45. The phenomenon of disorganization of native
protein structure
It results in the loss of secondary, tertiary and
quaternary structure of proteins.
It involves the change of physical, chemical and
biological properties
Agents of Denaturation
◦ Physical agents: Heat, UV radiation, X-rays and violent
shaking (centrifuge)
◦ Chemical Agents: Acids, alkalies, organic solvents (ether,
alcohol), salts of heavy metals, urea, salicylate
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46. Primary structures remains intact i.e peptide
linkage are not broken
Loses its biological activity
Insoluble in solvent which was previously soluble
Viscosity increases while its surface tension
decreases
Its more easily digestible
Its usually irreversible, but careful denaturation
(renaturation) is reversible. Ex: Hemoglobin is
renatured on removal of salicylates
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47. Coagulation
◦ Irreversible denaturation of protein to semi-solid viscous
precipitate
◦ Albumins and globulins – coagulable proteins
Flocculation
◦ Protein precipitation at isoelectric pH.
◦ Precipitate is known as flocculum
◦ Casein – milk protein, prepared by adjusting isoelectric
pH by dilute acetic acid
◦ Its reversible, but on heating it turns to be irreversible
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48. Harper's Illustrated Biochemistry, 30E (2015)
Biochemistry - U. Satyanarayan and U.
Chakrapani 3rd edition
Lehninger Principles of Biochemistry, Fourth
Edition - David L. Nelson, Michael M. Cox
Biochemistry - Garrett And Grisham 2nd Ed
1998
Biochemistry Stryer 5th Edition repost
Color Atlas of Biochemistry 2005
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