Biopolymers structure and properties

Biopolymers/Natural polymers
Definition: Natural polymers are formed in nature during the growth cycles of all organisms, hence they are also referred to as biopolymers.
Their synthesis generally involves enzyme-catalyzed, chain growth polymerization reactions of activated monomers, which are formed typically within cells by complex metallic processes

Types
Polysaccharide based polymers
Starch, Cellulose in higher plants, Chitin/Chitosan

Protein based polymers

Protein collagen in animals, Gelatin, Silk Proteins, Albumin etc.

Microbial polyesters
Poly--hydroxyalkanoates

Collagen

Types of collagen Structure of collagen Biosynthesis of collagen

COLLAGEN
Collagen is the most abundant fibrous protein, which occur in vertebrates.
A typical collagen molecule is a long, rigid structure in which three polypeptides "chains" are wound around one another in a rope-like triple-helix

 Although collagen molecules are found throughout the body, their types and organization are dictated by the structural role collagen plays in a particular organ.
In some tissues, collagen may be dispersed as a gel support to the structure, as in the extracellular matrix or the vitreous humor of the eye.

 In other tissues, collagen may be bundled in tight, parallel fibers great strength, as in tendons.

In the cornea of the eye, collagen is stacked transmit light with a minimum of scattering. Collagen of bone occurs as fibers arranged at an angle to each other resist mechanical shear from any direction.

A. Types of collagen
The collagen superfamily of proteins includes more than 20 collagen types, and proteins that have collagen-like domains. The three polypeptide -chains are held together by hydrogen bonds between the chains.

 Variations in the amino acid sequence of the -chains structural components that are about the same size (approximately 1000 amino acids long), but with slightly different properties. These -chains are combined to form the various types of collagen found in the tissues.

1. Fibril-forming collagens:
Types I, II, and Ill are the fibrillar collagens, and have the rope-like structure described before for a typical collagen molecule.
In the electron microscope, these linear polymers of fibrils have characteristic banding patterns reflecting the regular staggered packing of the individual collagen molecules in the fibril
(Figure 4.3).

 Type I collagen fibers are found in supporting elements of high tensile strength (e.g. tendon and cornea).
Fibers formed from type II collagen molecules are restricted to cartilaginous structures. Fibrils derived from type Ill collagen are prevalent in more distensible tissues, such as blood vessels.

2. Network-forming collagens:
Types IV and VII form a three-dimensional mesh, rather than distinct fibrils (Figure 4.4). For example, type IV molecules assemble into a sheet or meshwork that constitutes a major part of basement membranes. [ Basement membranes are thin, sheet-like structures that provide mechanical support for adjacent cells, and function as a semipermeable filtration barrier for macromolecules in organs such as the kidney and the lung.]

3. Fibril-associated collagens:
Types IX and XII bind to the surface of collagen fibrils, linking these fibrils to one another and to other components in the extracellular matrix (Figure 4.2).

B. Structure of collagen
1. Amino acid sequence:
Collagen is rich in proline and glycine, both of which are important in the formation of the triple-stranded helix. Proline facilitates the formation of the helical conformation of each -chain because its ring structure "kinks" in the peptide chain.

proline

glycine

carbon nitrogen oxygen

 Glycine, the smallest amino acid, is found in every third position of the polypeptide chain. It fits into the restricted spaces where the three chains of the helix come together.

 The glycine residues are part of a repeating sequence. GlyXY, where X is frequently proline and Y is often hydroxyproline or hydroxylysine (Figure 4.5).
Most of the .- chain can be regarded as a polytripeptide whose sequence can be represented as (GlyXY) 333

2. Triple-helical structure:
Unlike most globular proteins that are folded into compact structures, collagen, a fibrous protein, has an elongated, triple-helical structure that places many of its amino acid side chains on the surface of the triple-helical molecule.

[This allows bond formation between the exposed R-groups of neighboring collagen monomers aggregation into long fibers]

3. Hydroxyproline and hydroxylysine:

Collagen contains hydroxyproline (hyp) and hydroxylysine (hyl), which are not present in most other proteins. These residues result from the hydroxylation of some of the proline and lysine residues after their incorporation into polypeptide chains
(Figure 4.6).

 The hydroxylation is, thus, an example of posttranslational modification . Hydroxyproline is important in stabilizing the triple-helical structure of collagen because it maximizes interchain hydrogen bond formation.

4. Glycosylation:
The hydroxyl group of the hydroxylysine residues of collagen may be enzymatically glycosylated.

Most commonly, glucose and galactose are sequentially attached to the polypeptide chain prior to triple-helix formation
(Figure 4.7).

C. Biosynthesis of collagen
The polypeptide precursors of the collagen molecule are formed in fibroblasts (or in the related osteoblasts of bone and chondroblasts of cartilage), and are secreted into the extracellular matrix. After enzymic modification, the mature collagen monomers aggregate and become cross-linked collagen fibrils.

1. Formation of pro- -chains:

Collagen is one of many proteins that normally function outside of cells.

Like most proteins produced for export, the newly synthesized polypeptide precursors of chains contain a special amino acid sequence at their N-terminal ends.
This acts as a signal that the polypeptide being synthesized is destined to leave the cell.

 The signal sequence:

facilitates the binding of ribosomes to the rough endoplasmic reticulum (RER) directs the passage of the polypeptide chain into the cisternae of the RER. is rapidly cleaved in the endoplasmic reticulum precursor of collagen called a pro--chain (Figure 4.7).

2. Hydroxylation:
The pro- -chains are processed by a number of enzymic steps within the lumen of the RER while the polypeptides are still being synthesized (Figure 4.7). Proline and lysine residues found in the Yposition of the GlyXY sequence can be hydroxylated hydroxyproline and hydroxylysine residues.

 These hydroxylation reactions require molecular oxygen and the reducing agent vitamin C the hydroxylating enzymes, prolyl hydroxylase and lysyl hydroxylase, are unable to function without vit. C
(Figure 4.6).

 In the case of vit.C deficiency (therefore, a lack of prolyl and lysyl hydroxylation), collagen fibers cannot be cross-linked, greatly the tensile strength of the assembled fiber.
Vit.C deficiency disease known as scurvy. Patients with vit.C deficiency often show bruises on the limbs as a result of subcutaneous extravasation of blood (capillary fragility) ( Figure 4.8)

3. Glycosylation:
Some hydroxylysine residues are modified by glycosylation with glucose or glucosylgalactose (Figure 4.7).

4. Assembly and secretion:

After hydroxylation and glycosylation, pro-chains form procollagen , a precursor of collagen that has a central region of triple helix flanked by the nonhelical amino- and carboxyl-terminal extensions called propeptides.
(Figure 4.7).

 The formation of procollagen begins with

formation of interchain disulfide bonds between the C-terminal extensions of the pro-- chains. This brings the three -chains into an alignment favorable for helix formation.

 The procollagen molecules are translocated to the Golgi apparatus, where they are packaged in secretory vesicles.
The vesicles fuse with the cell membrane release of procollagen molecules into the extracellular space.

5. Extracellular cleavage of procollagen molecules: After their release, the procollagen molecules are cleaved by N - and C pro collagen peptidases remove the terminal propeptides releasing triple-helical collagen molecules.

6. Formation of collagen fibrils:

Individual collagen molecules spontaneously associate form fibrils.

They form an ordered, overlap ping, parallel array, with adjacent collagen molecules arranged in a staggered pattern.
Each collagen molecule overlaps its neighbor by three-quarters of its length.
(Figure 4.7).

7. Cross-link formation: The fibrillar array of collagen molecules serves as a substrate for lysyl oxidase. This extracellular enzyme oxidatively deaminates some of the lysyl and hydroxylysyl residues in collagen.

 The reactive aldehydes that result (allysine and hydroxyallysine) condense with lysyl or hydroxylysyl residues in neighboring collagen molecules form covalent cross-links (Figure
4.9). This cross-linking is essential for achieving the tensile strength necessary for the proper functioning of connective tissue. Any mutation that interferes with the ability of collagen to form cross-linked fibrils affects the stability of the collagen].

Contribution of Collagen
The major fraction of connective tissue is collagen This component is important because it contributes significantly to toughness in mammalian muscle Gelatin serves as the functional ingredient in temperature Dependent Gel-type desserts

Solubility
Some of the collagen is soluble in neutral salt solution Some in soluble in acid Some is insoluble

The collagen triple helix A case of structure following composition

The unusual amino acid composition of collagen is unsuited for alpha helices or beta sheets But it is ideally suited for the collagen triple helix; three intertwined helical strands Much more extended than alpha helix, with a rise per residue of 2.9 Angstroms 3.3residues per turn Long stretches of Gly-Pro-Pro/Hyp

The Fabric of Collagen

The collagen monomer is a long cylindrical protein about 2800 long and 14-15 in diameter It consists of three poly peptide chains wound around each other in a suprahetical fashion

Collagen degradation
Collagen can be degraded by the enzyme called collagenase. Activity of collagenase will be reduced if collagen is crosslinked with metal ions which act as a enzyme poisons. Gelatin is the byproduct of collagen degradation by acid or alkaline digestion

Stability of collagen
Affected by dehydration
Contact with reagents which reduce hydrophobic interaction Heat Mucopolysaccharides

Contents: Elastin
Structure of elastin

ELASTIN
In contrast to collagen, which forms fibers that are tough and have high tensile strength, Elastin is a connective tissue protein with rubber-like properties.

 Elastic fibers composed of elastin and glycoprotein microfibrils are found in the lungs, the walls of large arteries, and elastic ligaments.
They can be stretched to several times their normal length, but recoil to their original shape when the stretching force is relaxed.

A. Structure of elastin
Elastin is an insoluble protein polymer synthesized from a precursor, tropoelastin, ( a linear polypeptide composed
of about 700 amino acids that are primarily small and nonpolar) (e.g. glycine,

alanine, and valine).

 Elastin is also,
rich in proline and lysine, contains a little hydroxyproline contains no hydroxylysine. Tropoelastin is secreted by the cell into the extracellular space. There, it interacts with specific glycoprotein microfibrils, such as fibrillin, which function as a scaffold onto which tropoelastin is deposited.

 Some of the lysyl side chains of the tropoelastin polypeptides are oxidatively deaminated by lysyl oxidase forming allysine residues. 3 of the allysyl side chains + one unaltered lysyl side chain from the same or neighboring polypeptides form a desmosine cross-link.
(Figure 4.12).

This produces Elastin - an extensively interconnected, rubbery network that can stretch and bend in any direction when stressed connective tissue elasticity
(Figure 4.13).

Elastin is stable to relatively high temperatures and chemical reagents due to low content of amino acids with polar side chains. The enzyme elastase, hydrolyses elastin at peptide bonds after small hydrophobic residues, particluarly alanine.

Mechanical properties of elastin and collagen fibers

Fibers Modulus of elasticity Mpa Elastic fibers 0.6 Collagen 1000 fibers Tensile strength Mpa 1 50-1000 Ultimate elongation %

100 10

mechanics of BIO materials

61

Extracellular Macromolecules

1. Glycosaminoglycans Proteoglycans Glycoproteins Mucins

Extracellular Macromolecules
macromolecule glycosaminoglycans* (GAGs) proteoglycans* glycoproteins fibrous proteins
Examples of functions: mechanical support cushioning cell spacers lubrication adhesives selective filters

% carb. 100 90-95 2-30 1-2

1 * aka mucopolysaccharides, mucoproteins, respectively

Extracellular matrix in tissues

ground substance + fibers macromolecules between cells
ground substance molecules GAGs/proteoglycans (mostly carbohydrate) fibers fibrous proteins: epithelial cells structural adhesive adhesion
basal lamina
molecules

especially abundant in connective tissue

2

extracellular matrix

underlying cells
Adapted from Hypercell

GAG structure
exist as:
independent molecules e.g., hyaluronate & heparin parts of larger structures e.g., in proteoglycans

O C HO HO

A sugar
O OH OH

H2C OH HO HO

B sugar
O OH NH2

heteropolysaccharides

where A is usually 1 uronic acid (hexose with C6 as COO ) & B is 1 glycosamine (amino sugar) derivative

repeating structure: disaccharide (AB)n ABABAB

unbranched

glycosidic linkage anomeric C of 1 unit linked to hydroxyl of adjacent unit

GAG structure: repeating units

GAG
hyaluronate

A sugar
glucuronate
O C O O H O

B sugar
N-acetyl glucosamine
H2C OH O
5 2

O HO O OH 1,3

1,4 O O

NH H3C

GAG structure: repeating units

GAG
hyaluronate

A sugar
glucuronate
O C O O H O

B sugar
N-acetyl glucosamine
H2C OH O
5 2

chondroitin sulfate dermatan sulfate heparan sulfate heparin keratan sulfate

3C glucuronate N-Ac H galactosamine 4-SO4 O iduronate " glucuronate glucosamine N-SO3, 6-SO4 iduronate 2-SO4 " galactose N-Ac glucosamine 6-SO4

O HO O OH 1,3

1,4 O

NH

*opposite configuration in iduronate glucuronate/iduronate: epimers at C5 glucose/galactose: epimers at C4

9.5 Proteoglycans
Example: syndecan - transmembrane protein inside domain interacts with cytoskeleton, outside domain interacts with fibronectin

Hyaluronate (aka hyaluronan)

mol wt: 106 107 (5000 50,000 monosaccharide units) very polar: 2 hydroxyls/unit 6 heteroatoms/unit Display of HA COO every other unit in motion + ++ binds cations: Na , Ca

1 4 5 6

(glucuronateN-acetyl glucosamine)3 (glcUAglcNAc)3

Proteoglycan Functions
Modulation of cell growth processes
Binding of growth factor proteins by proteoglycans in the glycocalyx provides a reservoir of growth factors at the cell surface

Cushioning in joints
Cartilage matrix proteoglycans absorb large amounts of water. During joint movement, cartilage is compressed, expelling water!

 composed of as many as 200 GAG chains covalently bonded to a core protein via serine side chains molecular weight range: 105 107 GAG chains: chondroitin sulfate, heparan sulfate, dermatan sulfate, keratan sulfate

Proteoglycans (PGs)

Examples

decorin

perlecan

many connective tissues binds type I collagen, TGF-

basal laminae structural & filtering function

from Alberts et al. Fig. 19-57

aggrecan syndecan (slide 13)

GAG chains

core protein

Alberts T 19-3: Dcrn GAG chndSO4 /drmSO4

Proteoglycans: aggrecan
~100 GAG chains/molecule ~100 monosaccharides/GAG chain each "bristle" = 1 GAG chain each GAG chain is either chondroitin sulfate or keratan sulfate GAG chains linked to ser side chains of core protein
core protein

11

GAG chains

An aggregate of aggrecans & hyaluronan

major GAGPG in cartilage link proteins bind noncovalently with bound H2O, disperses shocks, compressive force ~ cell size adhesion proteins link to collagen & cells hyaluronan degraded by chondroitin sulfatase, etc keratan
sulfate
1m

core protein

link proteins

12

chondroitin sulfate Alberts et al. Fig. 19-41

Proteoglycans: syndecan
cell-surface PG core protein domains
intracellular transmembrane extracellular 5 GAGs attached
GAG chains

outside

functions
interactions cell-cell cell-matrix growth factor receptor
13

inside
core protein
Lehninger et al. Fig. 9-22