4/30/2016

PROTEINS

BIO20-Introduction
to Biomimetics Prof. Ureah Thea A. Sevilla

Proteins
Proteins are the most diverse biological molecule
(structural, nutritious, enzyme, transport,
communication, and defense proteins)
Proteins are organic compounds composed of one
or more chains of amino acids

Amino acid
- Amino acids are the building blocks of proteins.

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Amino Acids
A small organic compound with an amine group (NH3+),
a carboxyl group (COO-, the acid), and one or more
variable groups (R group)

Amino acid Stereoisomers

COO- COO-
+ +
H3 N C H H C NH3
CH3 CH3
L-Alanine D-Alanine

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Essential Amino Acids

T - Threonine F - Phenylalanine
V - Valine W - Tryptophan
M - Methionine H - Histidine
I - Isoleucine R - Arginine
L - Leucine
K - Lysine

Non-Essential Amino Acids

G - Glycine D - Aspartic acid
A - Alanine E - Glutamic acid
P - Proline C - Cysteine
S - Serine Q - Glutamine
Y - Tyrosine N - Asparagine

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Aliphatic, Non-Polar R-groups

O GLYCINE Gly
H2N
OH
O ALANINE Ala
H3 C
OH
NH2

CH3 O VALINE - Val

H3C OH
NH2

Aliphatic, Non-Polar R-groups

O
H3C
OH
CH3 NH2
O
H
LEUCINE - Leu N
OH
CH3 O
H3C
OH PROLINE - Pro
NH2

ISOLEUCINE - Ile

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Uncharged Polar R-groups

O

HO OH O
NH2
HS OH
SERINE - Ser
NH2
CH3 O
Cysteine - Cys
HO OH
NH2

THREONINE - Thr

Uncharged Polar R-groups

O
S
H3C OH NH2 O
NH2
O OH
METHIONINE- Met
NH2
O
GLUTAMINE - Gln
H2N
OH
O NH2

ASPARAGINE - Asn

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Aromatic R-groups
O

OH
O
NH2
OH
PHENYLALANINE - Phe
NH2
NH

O TRYPTOPHAN - Trp
OH
NH2
HO

TYROSINE - Tyr

Positively Charged R-groups

O
H2N
OH O
NH2 H
N OH
LYSINE - Lys NH2
N

NH2 O HISTIDINE - His

HN NH OH
NH2

ARGININE - Arg

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Negatively Charged R-groups

O
HO
OH
O NH2
ASPARTIC ACID - Asp

O O

HO OH
NH2

GLUTAMIC ACID - Glu

PEPTIDES ARE CHAINS OF AMINO ACIDS

R R
+
H3N CH C OH H2N CH C O-

O O

Peptide bond
H OH
R R
+
H3N CH C NH CH C O-

O O

Condensation Reaction

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Peptide bond

Peptides
Oligopeptides
Commercially impt. Olipeptides:
Aspartame
Glutathione
Polypeptides

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Function of Proteins
Transport ex. hemoglobin
Storage ex. myoglobin
Contraction ex. actin and myosin
Structure or support ex. keratin and collagen
Defense ex. immunoglobulins
Regulation of cellular or physiological activity
insulin
Biological catalyst enzymes

Hemoglobin structure

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Myoglobin structure

Myosin and Actin Structures

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Immunoglobulin Structure

Catalyst: -amylase structure

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Levels of Protein Structure

Primary structure
The unique amino acid sequence of a protein

Secondary structure
Thepolypeptide chain folds and forms hydrogen bonds
between amino acids

Levels of Protein Structure

Tertiary structure
A secondary structure is compacted into structurally
stable units called domains
Forms a functional protein

Quaternary structure
Some proteins consist of two or more folded
polypeptide chains in close association
Example: hemoglobin

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a Protein primary structure: Amino acids bonded as a polypeptide

chain.

Fig. 3-17a, p. 45

Regular Secondary Structure:

The -helix and -sheets

Alpha helix Beta Sheets

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Keratins A coiled coil (2structure)

Two important classes of proteins that have similar

amino acid sequences and biological function are
called - and -keratins.
-keratins - major proteins of hair and fingernails
and compose a major fraction of animal skin.
-keratins - contains much more -sheet structure
-keratins are found mostly in birds and reptiles, in
structures like feathers and scales.

Such twisted cables are stretchy and

flexible, but in different tissues -keratin is
hardened, to differing degrees, by the
introduction of disulfide cross-links within
the several levels of fiber structure.

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Collagen A Triple Helix (2structure)

Collagen is the most abundant single protein in most

vertebrates. In large animals, it may make up a third of
the total protein mass.
Collagen fibers form the matrix, or cement, material in
bone, on which the mineral constituents precipitate. These
fibers constitute the major portion of tendons. A network
of collagen fibers is an important constituent of skin.
Basically, collagen holds most animals together.
The basic unit of the collagen fiber is the tropocollagen
molecule, a triple helix of three polypeptide chains, each
about 1000 residues in length.

Plantar Fascia - highly organized, dense

networks of collagen fibers.
Plantar fascia is a connective tissue
band which extends from the heel
bone to the ball of the foot. It
supports a tremendous amount of
weight. As the heel lifts off the
ground when walking, the plantar
fascia tightens, like a dynamic
rope under tension.
This increases the rigidity of the foot and improves
efficiency as the calf muscles contract and propel the
body forward.

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Plantar Fascia - highly organized, dense

networks of collagen fibers.
The plantar fascia is composed of highly
organized, dense networks of collagen fibers.
Collagen is essentially woven together (or coiled) in
strands, and then organized into bundles. This
arrangement is what increases the strength of the
plantar fascia.

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Silk Fibroin sheets (2structure)

Silkworm fibroin contains long regions of

antiparallel sheet, with the polypeptide chains
running parallel to the fiber axis. The sheet
regions comprise almost exclusively multiple
repetitions of the sequence

[Gly - Ala - Gly - Ala - Gly - Ser - Gly

- Ala - Ala - Gly - (Ser - Gly - Ala - Gly
- Ala - Gly)]

Silk Fibers

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Protein Tertiary Structure

Protein tertiary
structure: A chains
coils, sheets, or both
fold and twist into
stable, functional
domains such as
barrels or pockets.

Fig. 3-17c, p. 45

Globular
Proteins

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Protein Quaternary Structure

Protein quaternary structure:

two or more polypeptide
chains associated as one
molecule.

Fig. 3-17d, p. 45

Aquaporins
Aquaporins are integral
membrane proteins that
form pores in
membranes of
biological cells.
It selectively conducts
water molecules in and
out of the cell, while
preventing the passage
of ions and
other solutes.

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Biomimetic Solar Fuels

Developing biomimetic molecular systems to efficiently

convert photons to fuels.
Natural photosynthesis serves as a paradigm for the
design of molecular systems that embody these features.

Biomimetics in Desalination
Seawater (salt water)
molecules pass through
channels made of
aquaporins proteins that
efficiently conduct water in
and out of living cells. A
positive charge near each
channels center repels salt.

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

Biomimetics in Infrastructures
Similar to the muscle fibers or
collagen fibers, each metal wire
is a left hand helix and
intertwined in a right hand
direction.

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Biomimetics in Infrastructures
A crocodiles skin has much the same structure as
fiberglass. Crocodile skin are impervious to arrows,
knives and sometimes, even bullets.

The substance that

gives crocodile
skin its special
strength is the
collagen protein
fibers it contains.

References:
Yosef Bar Cohen, Biomimetics Biologically Inspired
Technologies, CRC press, 2006.
Voet and Voet, Biochemistry 2nd ed. Wiley Publication
(2004).
Starr and Taggart (2004). Biology. The Unity and
Diversity of Life, 10th edition, Wadsworth Group,
Thomson Learning, Inc., California

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