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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design

School of Chemical Engineering and Chemistry THE BIOMOLECULES

BIOMIMETICS
Biomimetics is the scientific method of learning new principles and processes based on systematic
study, observation and experimentation with live animals and organisms.
Biomimetics is a novel approach to developing designs and products or to solving human problems
by taking inspiration from nature.

Biomimetics at the molecular level:
Imitating and learning from nature, based on our understanding of molecular biology and
biochemistry will enable innovation and develop designs to solve human problems.

THE BIOMOLECULES
CARBOHYDRATES
Carbohydrates are the most abundant biological molecule and most of them consist of carbon, hydrogen
and oxygen in a 1:2:1 ratio (CH2O)n. Carbohydrates contain either an aldehyde moiety or a ketone moiety
with large quantities of hydroxyl groups. The presence of the hydroxyl groups allows carbohydrates to
interact with the aqueous environment and to participate in hydrogen bonding, both within and between
chains.

Cells use carbohydrates as: Occurrence:


structural materials Cell walls of bacteria and plants
transportable forms of energy Cell membranes of animals
storage form of energy Nucleotides sugar component

Major size classes of Carbohydrates:


a. MONOSACCHARIDES are the simplest sugars, having the formula (CH2O)n.

Monosaccharides can be categorized Fischer Projection formula of an aldose and ketose:


according to their value of 'n,' as shown below:

n Category
3 Triose
4 Tetrose
5 Pentose
6 Hexose

ISOMERISM in Carbohydrates

Stereoisomerism
H H
Enantiomers two molecules that are mirror-images to each
H OH H OH other and cannot be superimposed on each other
H OH HO H
D dextrorotatory, (+) clockwise rotation, position of hydroxyl
H OH H OH group on the reference carbon is on the right of the projection
H H formula
D-glyceraldehyde L-glyceraldehyde
L levorotatory, (-) counterclockwise rotation, position of the
* D-form monosaccharides are hydroxyl group on the reference carbon is on the left of the
used to construct carbohydrates. projection formula

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Haworth Projection formula: Cyclic form of aldose and ketose


Furanose five-membered ring
Pyranose six-membered ring

Example: Structures of -D-Glucose

Fischer Projection Haworth Projection (planar) Chair conformation (nonplanar)


H
C O OH
H OH
H OH H OH
H HO O
HO H OH H H
HO H H
H OH HO OH
H OH H OH OH
H OH
H2C OH -D-glucopyranose -D-glucopyranose

D-glucose

Application: Simple monosaccharides are reducing agents.


+3 +2
Glucose and other sugars are capable of reducing Fe or Cu and are called reducing sugars. Fehlings
test is a quantitative test to detect presence of reducing sugar (in diagnosis of diabetes mellitus).
OH OH
O OH
H H OH H H O
H H
OH 2Cu +2
+ 5OH
- OH + Cu2O + 3 H2O
HO H HO OH

H OH H OH

b. DISACCHARIDES are two monosaccharides joined covalently through Condensation reaction by an


O-glycosidic bond and the resultant molecules are called glycosides. Several physiologically important
disaccharides are sucrose, lactose and maltose.

Sucrose: prevalent in sugar cane and sugar beets, is composed of glucose and fructose through an -
(1,2)-glycosidic bond.

Lactose: is found exclusively in the milk of mammals and consists of galactose and glucose in a -(1,4)
glycosidic bond.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Maltose: the major degradation product of starch, is composed of 2 glucose monomers in an -(1,4)
glycosidic bond.

To describe disaccharides or oligosaccharides, the end of a chain that has a free anomeric carbon is
called the reducing end.

Condensation Reaction is involved in the formation of disaccharides.

c. POLYSACCHARIDES or glycans are polymers of monosaccharide units. Polysaccharides differ in the


composition of the monomeric unit, the linkages between them, and the ways in which branches from
the chains occur.
Homopolysaccharides - made up of only one kind of monomer
Heteropolysaccharides - made up of several kinds of monomers

HOMOPOLYSACCHARIDES
Storage Polysaccharides

a. Starch is the major form of stored carbohydrate in plant cells. It is actually a mixture of two
compounds, amylose (unbranched with glucose units linked (14) and amylopectin ( (14) links
with (16) links approximately every 25-30 glucose residues). Unbranched starch is called amylose;
branched starch is called amylopectin.

The unbranched structure of amylose causes the polymer to exist as a long, coiled helix under
conditions when it can be stabilized. One substance that will stabilize an amylose helix is iodine, which
fits into the hollow core of the structure. Binding of iodine to amylose helices produces an intense blue
color and has long been used as a qualitative test for starch. Polymers consisting solely of glucose are
called glucans.
Amylopectin is a polymer of glucose. It differs from amylose and resembles the animal storage
polysaccharide, glycogen, in containing (16) branches in addition to (14) links between glucose
units.

b. Glycogen is a branched polymer of glucose, consisting of main branches of glucose units joined in
(14) linkages. Every 7-20 residues, (16) branches of glucose units are also present. It is the
primary energy storage material in muscle. Individual glucose units are cleaved from glycogen in a
phosphorolytic mechanism catalyzed by glycogen phosphorylase.

Glycogen is a very compact structure that results from the coiling of the polymer chains. This
compactness allows large amounts of carbon energy to be stored in a small volume, with little effect on
cellular osmolarity.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Structural Polysaccharides

a. Cellulose is a glucan and is the major polysaccharide in


woody and fibrous plants. It is the most abundant single
polymer in the biosphere. Made up of units of D-glucose
linked in the 1-> 4 configuration, cellulose forms a planar
structure with individual parallel chains held together by
hydrogen bonds. Most animals cannot digest the 1->4
linkages in cellulose. Among the animals, only ruminants
(cows, horses, etc.) contain a symbiotic bacterium with an
enzyme, cellulase that can break cellulose down to
glucose. Fungi too contain cellulases. Cellulose is also
used as a structural component of some animal cells, such
as the marine invertebrates called tunicates.

Molecular arrangement in cellulose

b. Chitin is a polymer of of N-acetyl--D-glucosamine. The linkage between individual N-acetyl--D-


glucosamine units is -1,4, giving it a structure similar to that of cellulose, except that the hydroxyl on
carbon 2 of each residue is replaced by an acetylated amino group.

Chitin is widely distributed among the kingdoms of


organisms. It is a minor constituent in most fungi and
some algae, where it often substitutes for cellulose or
other glucans. In dividing yeast cells, chitin is found in
the septum that forms between the separating cells.
The best known role of chitin, in invertebrate animals
is it constitutes a major structural material in the
exoskeletons of many arthropods and mollusks. In
many of these exoskeletons, chitin forms a matrix on
which mineralization takes place.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

LIPIDS
- provide energy reserves, predominantly in the form of triacylglycerols.
- serve as structural components of biological membranes.
- both lipids and lipid derivatives serve as vitamins and hormones.

STORAGE LIPIDS

a. FATTY ACIDS

Numerical Common Name Structure Melting temp., C


Symbol
14:0 Myristic acid CH3(CH2)12COOH 53.9
16:0 Palmitic acid CH3(CH2)14COOH 63.1
16:19 Palmitoleic acid CH3(CH2)5CH=CH(CH2)7COOH 0.5
18:0 Stearic acid CH3(CH2)16COOH 69.6
18:19 Oleic acid CH3(CH2)7CH=CH(CH2)7COOH 13.4
18:29,12 Linoleic acid CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH 5
18:39,12,15 Linolenic acid CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH 11
20:45,8,11,14 Arachidonic acid CH3(CH2)3(CH2CH=CH)4(CH2)3COOH 49.5

Physical Properties of Fatty acids


Length of hydrocarbon chain
Degree of unsaturation

Solubility to water
- FAs have poor solubility in H2O
*the longer the FA chain and fewer double bonds, the lower its solubility in water.
Ex: Arrange the ff. FAs accdg. to increasing solubility in water: 16:0; 20:0; 18:0; 16:1
9

Melting point
- unsaturated FAs have lower MP than saturated FAs.

% Fatty Acid
State at RT Saturated Unsaturated
25C C4-C12 C14 C16 C18 C16 + C18
Olive oil Liquid <2 <2 13 3 80
Butter Solid (soft) 11 10 26 11 40
Beef fat Solid (hard) <2 <2 29 21 46

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Triacylglycerols simplest lipids constructed from FAs which functions as energy storage and
insulation. TAG or fats are in form of solids and oil. Fats which are rich in unsaturated fatty acids are
typically oils. When lipid-rich foods are exposed too long to air, they become rancid as a result from the
oxidative cleavage of their double bonds in the chain.

TAGs yield 2x as much energy as CHOs (stored in adipocytes or fat cells; seeds in plants)
TAGs provide insulation: seals, walrus, penguins
TAGs have low density: in sperm whales, TAGs allows the animal to match the buoyancy of their
bodies to that of their surroundings.
Hydrolysis of TAGs produces soaps by heating them with NaOH or KOH. This process is called
+ +
saponification which produces glycerol and Na or K salts of the fatty acids known as the soap.
O O
+
H2C O C R1 H2C OH K -O C R1
O 3KOH O
+
HC O C R2 HC OH K -O C R2
O O
+
H2C O C R3 H2C OH K -O C R3

Salts of long-chain carboxylic acids or soap

How do soaps clean dirt and grease?


In water, soaps exist in soluble spherical
clusters called micelles
Micelles have the hydrophilic carboxylate
group of the fatty acid salt on the outside
exposed to water
Soaps clean by incorporating greasy
(hydrophobic) dirt molecules into the dirt
grease
hydrophobic alkyl portion of micelles
The polar carboxylate groups of the soap
micelles serve to suspend the micelle in
water so that it (with the enclosed dirt
molecules) can be washed away. dirt
grease

STRUCTURAL LIPIDS

Phospholipids
are a class of lipids that are a major component of all cell membranes or plasma membrane as they can
form lipid bilayers.

The cell membrane lipid bilayer is semi-permeable. It only allow small nonpolar molecules such as CO2
and O2 to pass through the membrane. Other molecules need a transporter in order to move across the
membrane.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

The Fluid Mosaic Model of the Cell Membrane

The cell membrane consists of two layers of phospholipids that arranged in a fashion by which the
nonpolar portions are sandwiched in between the polar portions. The lipid bilayer also consists of other
biomolecules such as peripheral protein and integral proteins that aid in transport of molecules;
carbohydrates for cell recognition; and cholesterol.

Carbohydrates and Lipids in Biomimetics

Chitosan has been used in many medical applications. It serves as biomimetic material of anti-
hemoglobin antibodies to create an imprinted recognition surface of hemoglobin beads.

Chitosan was proved to act as a thickener in cement mixtures.

Glycocalyx-mimetic peptoid is a modified polysaccharide that serves as antifouling agent on


surfaces.

Welan gum that exhibits high rheological property is used as admixtures for eco-efficient
construction materials e.g. concretes.

Biomimetic membranes may provide an alternative to current reverse osmosis and nanofiltration
membranes e.g. for industrial separation and wastewater treatment.

In the creation of biosensors, a lipid layer that mimics the cell membrane served as an
impermeable barrier around the wire where a membrane protein (bio-element) can be
incorporated.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

AMINO ACIDS
Amino acids are the building blocks of proteins. An amino acid consists of an asymmetric carbon (-
carbon) at the center with four different groups attached to it: an amino group, a carboxyl group, a
hydrogen atom and a variable group, R (except for glycine). Thus amino acids have chiral centers.

Essential amino acids Non-essential amino acids


Threonine, Thr (T) Alanine, Ala (A) Stereoisomers of alanine
Valine, Val (V) Asparagine, Asn (N)
Methionine, Met (M) Aspartic acid, Asp (D)
Isoleucine, Ile (I) Cysteine, Cys (C)
Leucine, Leu (L) Glutamic acid, Glu (E)
Lysine, Lys (K) Glutamine, Gln (Q)
Phenylalanine, Phe (F) Glycine, Gly (G)
Tryptophan, Trp (W) Proline, Pro (P)
Histidine, His (H) Serine, Ser (S)
Arginine, Arg (R) Tyrosine, Tyr (Y)
Essential amino acids are those the body cannot make and must be obtained from dietary sources.

PEPTIDES AND POLYPEPTIDES


Peptides are chains of amino acids joined by a peptide bond. The linkage of two amino acids is a
dipeptide and the reaction is an example of condensation reaction. When few amino acids are joined,
they are called oligopeptide, and thousands of it, they are called polypeptide.

Peptides are named from sequence of their constituent amino acids, beginning from the amino terminal
residue at the left proceeding toward the carboxyl terminus at the right.

Peptides undergo characteristic chemical reactions:


a. Hydrolysis by boiling with either strong acid or base
b. Hydrolysis by certain enzymes (proteases)

Some biologically important peptides have only few amino acid


residues like the commercially synthesized L-Aspartyl-L-
phenylalanyl methyl ester or better known as aspartame.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

PROTEIN
Proteins are biopolymers (called polypeptides) of L-amino acids.
Only L-amino acids are used to make proteins (rare exceptions of proteins in bacterial cell wall, which
contain some D-amino acids)
The process of putting amino acids together to make proteins is called translation. Translation relies on
the genetic code, in which three nucleotides in mRNA specify one amino acid in protein.
The difference between a polypeptide and a protein is that the term polypeptide refers simply to a chain of
amino acids. The term protein refers to the chain of amino acids after it folds properly and is (in some
cases) modified. Proteins may consist of more than one polypeptide chain.
Proteins are sometimes described as the "workhorses" of the cell because they do so many things -
catalyze reactions, provide structural integrity, transport molecules, provide movement, bind molecules,
and others.
Function of Proteins
a. Transport e. Defense
b. Nutrient and storage f. Regulation of cellular or physiological activity
c. Contraction g. Catalyst
d. Structure or support

Protein Structure
The order or sequence of amino acids distinguishes different proteins from each other. The sequence of
amino acids determines the 3-dimensional shape of the protein. Alterations to the amino acid sequence of
a protein changes its 3D shape.

Primary structure is the most basic level of protein structure. It is the linear sequence of amino acids.
The primary structure of a protein is specified by the order of bases in the genomic DNA. Different
sequences of the acids along a chain, however, affect the structure of a protein molecule in different
ways.
Secondary structures are stable and occur widely in proteins (globular and fibrous). Most prominent are
the -helix and -conformation. The simplest arrangement the polypeptide chain could assume with its
rigid peptide bonds is a helical structure that is right-handed.
-Helical structure (right-handed) is predominant in -
keratin. Secondary structures are stabilized by favorable
hydrogen bonding between residues and have been brought
into close juxtaposition by folding or coiling of the primary
structure. In the -conformation, the backbone of the
polypeptide chain is extended into a zigzag manner (-
pleated sheets) and the hydrogen bonding can either be
intrachain or interchain between peptide linkages of adjacent
polypeptide chains.

-keratin right-handed helix; rich in Phe, Ile, Val, Met, and


Ala.
collagen left-handed helix; rich in Gly, Ala, Pro and Hyp

Structure-properties of fibrous proteins:


-helix cross-linked by disulfide bonds tough, insoluble
protective structures of varying hardness and flexibility ex.
-keratin of hair, feathers and nails
-Conformation soft, flexible filaments ex. Fibrion of silk
Collagen triple helix high tensile strength, without stretch
ex. Collagen of tendons, bone matrix

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Tertiary structure (three dimensional


arrangement of atoms in protein) is formed
when forces cause the molecule to become
even more compact, as in globular proteins.
Each molecule of a particular protein has the
same conformation and this differs from
molecules of other proteins.

Myoglobin contains a single polypeptide chain


folded about a prosthetic group, the heme,
which contains the oxygen binding site. The
heme in myoglobin is in the form of an iron
complexed with protoporphyrin IX.
Myoglobin, by contrast with hemoglobin, is an
oxygen storage protein. Oxygen transported
to tissues must be released for utilization. In
tissues, such as muscle, with high oxygen
demands, myoglobin provides large oxygen
reserves.

Quaternary protein structure refers to the interaction between


subunits of oligomeric protein or large protein assemblies as in
hemoglobin and some enzymes. Four subunits of hemoglobin
exhibit cooperative interactions on oxygen-binding.

ENZYMES
- Most enzymes are proteins.
- They function as catalyst in biological reactions.
- Enzymes are globular proteins - their molecules are round
in shape.
- Each enzyme has a specific catalytic action.
- Their normal activity depends on their environment.
- Abnormal conditions cause reduced activity

How enzymes work.


Enzymes have an area - usually thought of as a pocket-shaped gap in the molecule - which is called the
active site.
Some enzymes are found inside cells (intracellular enzymes), and some - especially digestive enzymes -
are released so they have their effects outside the cell (extracellular enzymes).

(Only) the substrate (or substrates) fits/fit into the


active site.

The enzyme speeds up the process of conversion of


substrates (reactants) into products - usually so much
that the reaction does not take place in the absence of
enzyme.
Although the enzyme obviously joins with the
substrate for a short while, the enzyme and
substrate split apart afterwards, releasing the
enzyme. Thus the enzyme is not used up in the
process (unlike the substrate(s)), so it can
continue to react if more substrate is provided.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

NUCLEIC ACIDS
Nucleic acids are complex structures composed of nucleotide chains that are used to maintain genetic
information.

Component structures of nucleotide:


Pyrimidine and purine bases
Sugar
Phosphate

Pyrimidine bases Purine bases


NH2 O O H 2N O

CH3 N N
N HN HN HN HN

O N O N O N N N H2N N N
H H H H H

CYTOSINE (C) URACIL (U) THYMINE (T) ADENINE (A) GUANINE (G)

Nucleosides: Pyrimidine + sugar

NH2 O NH2
O O

CH3 N
N HN N C N
HN HN C
CH
CH
HC C
N O N O N C C
O N N N
H2N N
HO HO HO
O O HO HO
O O O

OH OH OH OH OH OH OH OH OH OH
CYTIDINE URIDINE THYMIDINE ADENOSINE GUANOSINE

Nucleotides: Nucleoside + Phosphate

C
P U T A G
O P P P P
O O O O

OH OH
OH OH OH OH OH OH OH OH
Cytidine Uridine Thymidine Adenosine Guanosine
monophosphate monophosphate monophosphate monophosphate monophosphate

Two common Nucleic Acids:


1. RNA Ribonucleic acid
RNAs are single-stranded polynucleotides that are used to express genetic information.
Three types of RNAs:
rRNA ribosomal RNA
mRNA messenger RNA
tRNA transfer RNA

2. DNA Deoxyribonucleic acid


DNAs are double-stranded polynucleotide helix that carries the genetic information.

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

Differences in the structure of RNA and DNA


RNA DNA
A, G, C, U type of bases used A G, C, T
Ribose sugar used Deoxyribose
Single polynucleotide strand double

Nucleic acids are formed through linkage of one nucleotide with another by forming a covalent
bond called 3,5-phosphodiester bond. The next nucleotide to be attached to the growing
polynucleotide chain is always added at the 3-end.

Nucleic acids are constructed starting from the 5-end going to the 3-end
Example: 5- ATG CCC GGG AAA GCG TTT CCG.-3

James Watson and Francis Cricks model of the DNA

The DNA molecule consists of 2 strands of polynucleotide held together through hydrogen bonding
interaction of the bases contained in the 2 strands. This pairing of bases is called complimentary base
pairs: A=T and CG

The orientation of the 2 strands is anti-parallel to each other.

Cytosine Guanine Thymine Adenine

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Mapua Institute of Technology Introduction to Biomimetics Engineering and Biocomponent Design
School of Chemical Engineering and Chemistry THE BIOMOLECULES

A-DNA B-DNA Z-DNA


Parameters A Form B Form Z Form
Direction of Right Right Left
helical
rotation
Residues 11 BP 10 BP 12 BP
per turn of
helix
Occurence Favored at Favored at high Favored at high
dehydrated water salt concentration
condition concentration

Proteins and Nucleic Acids in Biomimetics

Steel-Cable Technology in Muscles:


The load-bearing cables in suspension bridges are composed of bundles
of strands, just like the human muscles.

Fiberglass Technology in Crocodile Skin:


A crocodiles skin has much the same structure as fiberglass. Crocodile skin is impervious to arrows,
knives and sometimes, even bullets. The substance that gives crocodile skin its special strength is
the collagen protein fibers it contains.

DNA-inspired: World's first curved double helix bridge at Marina Bay, Singapore
Bridge measures 280 meters long made of a special stainless steel. If all the steel tubes forming the major
and minor helix are laid end to end, it will measure 2,250 meters long, and the entire structure weighs about
1,700 tons, which is equivalent to about 1,130 saloon cars.

DNA-inspired: DNA-Shaped Agora Garden Building (Taiwan)


The design creates more surface area, and enables suspended open-air gardens to hang from one level to
the next, unobtrusively.

References:
Yosef Bar Cohen, Biomimetics Biologically Inspired Technologies, CRC press, 2006.
Hyun Ok Ham, et al., J. Am. Chem. Soc., 2013, 135 (35), pp 1301513022.
Varinder Kaur, Manav B. Bera, Parmjit S. Panesar, Harish Kumar, J.F. Kenned, Int. Journ. of Biological
Macromolecule, 2014
M. Lasheras-Zubiate, I. Navarro-Blasco, J. M. Fernndez and J. I. Alvarez, Journal of Applied Polymer
Science, 2010.
Torben Lenau, Biomimetics as a Design Methodology, Intl Conf. on Engg Des. Stanford Univ., 2009
nd
Voet and Voet, Biochemistry 2 ed. Wiley Publication (2004).
rd
Voet, Voet and Pratt, Biochemistry 3 edition (2008), Wiley and Sons.
th
Starr and Taggart (2004). Biology. The Unity and Diversity of Life, 10 edition, Wadsworth Group,
Thomson Learning, Inc., California

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