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Proteins mediate virtually every process that takes place in a cell, exhibiting an almost endless
diversity of functions
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Proteins are the most abundant biological
macromolecules, occurring in all cells and all parts of cells
...
As the arbiters of molecular function,
proteins are the most important final products of the information pathways
...

All proteins, whether from the most ancient lines of bacteria or from the most complex forms of
life, are constructed from the same ubiquitous set of 20 amino acids, covalently linked in
characteristic linear sequences
...
Proteins are found in a wide range
of sizes, from relatively small peptides with just a few amino acid residues to huge polymers
with molecular weights in the millions
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AMINO ACIDS
Amino acids are the building blocks of proteins
...
Nineteen of
these are α-amino acids with a primary amino group (–NH3+) and a carboxylic acid (carboxyl; –
COOH) group attached to a central carbon atom, which is called the α-carbon atom (Cα)
because it is adjacent to the carboxyl group
...
The one exception to this general structure is Proline,
which has a secondary amino group and is really an α-imino acid
...
Thus, for example, proline is
abbreviated to Pro or P
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For six amino acids (CHIMSV), the first letter of the amino acid name is unique and thus is used as the
symbol
...
For another four, the letter used is
phonetically suggestive (RFYW: aRginine, Fenylalanine, tYrosine, tWiptophan)
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That left lysine
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Enantiomers: All of the amino acids, except for glycine, have four different groups arranged
tetrahedrally around the central Cα atom, which is thus known as an asymmetric center or chiral
center and has the property of chirality
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Enantiomers are physically and chemically indistinguishable by most techniques,

but can be distinguished on the basis of their different optical rotation of plane
plane-polarized light
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d- and l-amino
amino acids can also be distinguished by enzymes which usually only
recognize one or other enantiomer
...
The
absolute configurations of si
simple
sugars and amino acids are specified
byy the D, L system, based on the
absolute configuration
guration of the three
threecarbon sugar glyceraldehyde
aldehyde
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The functional
groups of L-alanine
nine are matched with those of L-glyceraldehyde
L
by aligning tthose that can be
interconverted by simple, one-step
step chemical reactions
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The Amino Acid Residues in Proteins
Protei are L Stereoisomers
Nearly all biological compounds
pounds with a chiral center occur
oc
naturally in only one
ne stereoisomeric
form, either D or L
...
D-Amino
Amino acid residues have been found in only a few,
few, generally small pep
peptides,
including
cluding some peptides of bacterial cell walls and certain peptide antibiotics
...
In a living system, D and L
isomers are as different as the right hand and the left
...
Cells are
re able to specifically synthesize L isomers off amino acids because
the active sites of enzymes are asymmetric,
asym
causing their catalytic reactions
ons to be stereo
stereospecific
...
They can be subdivided into smaller groupings on the basis of similarities in
the properties of their side-chains
...
They display different physicochemical properties depending
on the nature of their side-chain
...
The
aliphatic side-chains
chains of alanine (Ala, A), valine (Val, V), leucine (Leu, L), isoleucine (Ile, I) and
methionine (Met, M) are chemically unreactive, but hydrophobic in nature
...
The sulfur-containing
sulfur
side-chain of cysteine
steine (Cys, C) is also hydrophobic
and is highly reactive, capable of reacting with another cysteine to form a disulfide bond
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Tryptophan and tyrosine, and to a
much lesser extent phenylalanine, absorb ultraviolet light
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Polar, uncharged amino acids: The side-chains of asparagine (Asn, N) and glutamine (Gln, Q),
the amide derivatives of Asp and Glu, respectively, are uncharged but can participate in
hydrogen bonding
...

Polar, charged amino acids: The remaining amino acids all have polar, hydrophilic side-chains,
some of which are charged at neutral pH
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Side-chain of histidine (His, H) can be either positively charged or uncharged at neutral pH
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Uncommon Amino Acids: In addition to the 20 common amino acids, proteins may contain
residues created by modification of common residues already incorporated into a polypeptide
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The former is found in plant cell wall proteins, and both are
found in collagen, a fibrous protein of connective tissues
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Another important uncommon amino acid is γcarboxyglutamate, found in the blood-clotting protein prothrombin and in certain other proteins
that bind Ca2+ as part of their biological function
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Selenoeysteine is a special case
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It contains selenium rather than the sulfur of cysteine
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Selenocysteine is located in the active sites of enzymes that participate in oxidation–
reduction reactions, e
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glutathione peroxidase, thioredoxin reductase, iodothyronine deiodinase
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The addition of phosphoryl, methyl, acetyl, adenylyl, ADP-ribosyl, or other groups to particular
amino acid residues can increase or decrease a protein's activity
...
Some 300 additional amino acids have been
found in cells
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Ornithine
and citrulline deserve special note because they are key intermediates (metabolites) in the
biosynthesis of arginine and in the urea cycle
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When an amino acid lacking an ionizable R
group is dissolved in water at neutral pH, it exists in solution as the dipolar ion, or zwitterion
(German for "hybrid ion"), which can act as either an acid or a base
...
A simple monoamino monocarboxylic α-amino acid, such as alanine, is a diprotic

acid when fully protonated; it has two groups, the -COOH group and the –NH3 group that can
yield protons
...


Peptide bond: Proteins are linear sequences of amino acids linked together by peptide bonds
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Once two amino acids are joined together via a peptide bond to form a dipeptide, there
is still a free amino group at one end and a free carboxyl group at the other, each of which can in
turn be linked to further amino acids
...
When a few amino acids are joined in this fashion, the structure is
called an oligopeptide
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Proteins may have thousands of amino acid residues
...

Convention has it that peptide chains are written down with the free α-amino group on the left
(Amino or N-terminal), the free α-carboxyl group on the right (Carboxy or C-terminal) and a
hyphen between the amino acids to indicate the peptide bonds
...

Naturally occurring peptides range in length from two to marry thousands of amino acid
residues
...
Consider the
commercially synthesized dipeptide L-aspartyl-L-phenylalanine methyl ester, the artificial
sweetener better known as aspartame or NutraSweet
...
For example, a number of vertebrate hormones are small peptides
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Antidiuretic hormone (ADH), also known
as vasopressin, is a nine amino acid peptide secreted from the posterior pituitary
...


Protein classification
Simple proteins: Also known as homoproteins, they are made up of only amino acids
...
Simple proteins may be further divided into
2 classes on the basis of shape and solubility: fibrous and globular
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These proteins are insoluble in water as they contain
many hydrophobic amino acids, both internally and on their surface
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Globular proteins: They have a compact and more or less spherical structure, more
complex than fibrous proteins
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Most of the proteins belong to this class
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Unlike fibrous proteins, that have
structural and mechanical functions, they act as enzymes; hormones; membrane proteins;
transport proteins; immunoglobulins or antibodies; storage proteins etc
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Conjugated proteins: Sometimes also called heteroproteins, they contain in their structure a nonprotein portion
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Examples are glycoproteins, lipoproteins, metalloproteins
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This conformation is the three-dimensional spatial arrangement of atoms in the
structure and is determined by the amino acid sequence
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Proteins in any of
their functional, folded conformations are called native proteins
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Primary Structure: The primary level of structure in a protein is the linear sequence of
amino acids (and number) as joined together by peptide bonds
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Also included under primary
structure is the location of any other covalent bonds
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These covalent cross-links between separate polypeptide chains or between different parts of the
same chain are formed by the oxidation of the SH groups on cysteine residues that are juxtaposed
in space
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Disulfide bonds are often present in
extracellular proteins, but are rarely found in intracellular proteins
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Secondary Structure: The term secondary structure refers to any chosen segment of a
polypeptide chain and describes the local spatial arrangement of its main-chain atoms, without
regard to the conformation of its side chains or its relationship to other segments
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The most
prominent are the α-helix and β-conformations; another common type is the β-turn
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-helices: The simplest
arrangement
the
polypeptide chain can
assume, given its rigid
peptide bonds (but free
rotation around its
other, single bonds), is
a helical structure,
which Pauling and
Corey called the αhelix
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Hydrogen bonds are formed in orienting polar chemical groups such as the C:O and N-H groups
of the peptide bond
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The carbonyl oxygen of each peptide bond is
hydrogen bonded to the hydrogen on the amino group of the fourth amino acid away
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The repeating unit is a single turn of the helix, which
extends about 5
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6 amino acid residues
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β-pleated sheets: Pauling and Corey predicted a second type of repetitive structure, the βconformation
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In the β-conformation, the backbone of the polypeptide chain
is extended into a zigzag rather than helical structure
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In this arrangement, called
a β-sheet, hydrogen bonds form between adjacent segments of polypeptide chain
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R groups of adjacent residues protrude from the zigzag structure in opposite
directions, creating the alternating pattern
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Regions of the polypeptide chain that are not in a regular secondary structure are said to have a

coil or loop conformation
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-turns are often found connecting the ends of antiparallel -sheets
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Again, it is the sequence of amino acids that specifies this final 3-D
structure
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The
polypeptide chain folds spontaneously so that the majority of its hydrophobic side-chains are
buried in the interior, and the majority of its polar, charged side-chains are on the surface
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The electrostatic forces include salt bridges between oppositely
charged groups and the multiple weak van der Waals interactions between the tightly packed
aliphatic side-chains in the interior of the protein
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This level of
structure refers to the spatial arrangement of the polypeptide subunits and the nature of the
interactions between them
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g
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Protein stability
The native three dimensional conformation of a protein is maintained by a range of noncovalent interactions (electrostatic forces, hydrogen bonds, hydrophobic forces) and covalent
interactions (disulfide bonds) in addition to the peptide bonds between individual amino acids
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In addition, the noncovalent associations between electrically
neutral molecules, collectively referred to as van der Waals forces, arise from electrostatic interactions between permanent and/or induced dipoles, such as the carbonyl group in peptide bonds
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In biological systems the donor group is an
oxygen or nitrogen atom that has a covalently attached hydrogen atom, and the acceptor is either
oxygen or nitrogen
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Hydrogen bonds not only play an important role in protein structure, but
also in the structure of other biological macromolecules such as the DNA double helix and lipid
bilayers
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● Hydrophobic interactions: Hydrophobic effect is the name given to those forces that cause
nonpolar molecules to minimize their contact with water
...
Proteins, too,

find a conformation in which their nonpolar side-chains are largely out of contact with aqueous
solvent, and thus hydrophobic forces are an important determinant of protein structure, folding
and stability
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● Disulfide bonds: These covalent bonds form between Cys residues that are close together in
the final conformation of the protein and function to stabilize its three-dimensional structure
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It is not possible to predict the precise three-dimensional structure of a protein from its amino
acid sequence, unless its sequence is very similar to that of a protein whose three-dimensional
structure is already known
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The three-dimensional
structure of a protein can be determined to the atomic level by the techniques of X-ray
crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryoelectron microscopy
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As there is no need for external templates, this implies that the
primary structure of the protein dictates its three-dimensional structure
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It has also been observed that protein folding is driven primarily by
hydrophobic forces
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Although proteins can fold in vitro (in the laboratory) without the presence of accessory proteins,
this process can take minutes to days
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Folding for many proteins requires molecular chaperones, proteins that interact with partially
folded or improperly folded polypeptides, facilitating correct folding pathways or providing
microenvironments in which folding can occur
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Other proteins include the chaperonins,
lectins, calnexin and calreticulin
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Finally, the folding pathways of some proteins require two enzymes that catalyze isomerization
reactions
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Peptide prolyl cis-trans isomerase (PPI) catalyzes the interconversion of the cis and
trans isomers of Pro residue peptide bonds, which can be a slow step in the folding of proteins
that contain some Pro peptide bonds in the cis conformation
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In fact, protein misfolding is a substantial problem in all cells, and a quarter or more

of all polypeptides synthesized may be destroyed because they do not fold correctly
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Many
conditions, including type-2 diabetes, Alzheimer's disease, Huntington's disease, and Parkinson's
disease, arise from a common misfolding mechanism
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The diseases are collectively referred to as amyloidoses
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Conditions different from those in the cell can result in protein structural changes,
large and small
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The denatured state does not necessarily equate with complete unfolding of the protein and
randomization of conformation
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Most proteins can be denatured by
heat, which has complex effects on the weak interactions in a protein (primarily hydrogen
bonds)
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Each of these denaturing agents represents a relatively mild treatment in the sense that no
covalent bonds in the polypeptide chain are broken
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Protein separation and Analysis: A pure preparation is essential before a protein's
properties and activities can be determined
...
Some of the common procedures used for the purification and analysis of
proteins include Fractionation, Dialysis, Polyacrylamide gel electrophoresis (PAGE),
Chromatography, Mass-spectrometry, NMR etc

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