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Collagen fiber

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Collagen is one of the long, fibrous structural proteins whose functions are quite different from those of globular proteins such as enzymes; tough bundles of collagen called collagen fibers are a major component of the extracellular matrix that supports most tissues and gives cells structure from the outside, but collagen is also found inside certain cells. Collagen has great tensile strength, and is the main component of fascia, cartilage, ligaments, tendons, bone and teeth. Along with soft keratin, it is responsible for skin strength and elasticity, and its degradation leads to wrinkles that accompany aging. It strengthens blood vessels and plays a role in tissue development. It is present in the cornea and lens of the eye in crystalline form. It is also used in cosmetic surgery and burns surgery.

[edit] Composition and structure

The structure of Collagen eluded scientist for decades. Many prominent scholars, including Nobel laureates like Watson and Crick and Linus Pauling were known to have been working on collagen structure when it was finally discovered.^[6] The triple helical structure that is known to be correct in the essentials was proposed by G. N. Ramachandran and Gopinath Kartha in the year 1954. ^[7]^[8] This proposed structure came to be known as the Madras helix.

The tropocollagen or “collagen molecule” subunit is a rod about 300 nm long and 1.5 nm in diameter, made up of three polypeptide strands, each of which is a left-handed helix, not to be confused with the commonly occurring alpha helix, which is right-handed. These three left-handed helices are twisted together into a right-handed coiled coil, a triple helix or “super helix”, a cooperative quaternary structure stabilized by numerous hydrogen bonds. Tropocollagen subunits spontaneously self-assemble, with regularly staggered ends, into even larger arrays in the extracellular spaces of tissues. There is some covalent crosslinking within the triple helices, and a variable amount of covalent crosslinking between tropocollagen helices, to form the different types of collagen found in different mature tissues — similar to the situation found with the α-keratins in hair. Collagen’s insolubility was a barrier to study until it was found that tropocollagen from young animals can be extracted because it is not yet fully crosslinked.

Collagen fibrils are collagen molecules packed into an organized overlapping bundle. Collagen fibers are bundles of fibrils.

A distinctive feature of collagen is the regular arrangement of amino acids in each of the three chains of these collagen subunits. The sequence often follows the pattern Gly-X-Pro or Gly-X-Hyp, where X may be any of various other amino acid residues. Gly-Pro-Hyp occurs frequently. This kind of regular repetition and high glycine content is found in only a few other fibrous proteins, such as silk fibroin. 75-80% of silk is (approximately) -Gly-Ala-Gly-Ala- with 10% serine — and elastin is rich in glycine, proline, and alanine (Ala), whose side group is a small, inert methyl. Such high glycine and regular repetitions are never found in globular proteins. Chemically-reactive side groups are not needed in structural proteins as they are in enzymes and transport proteins. The high content of Proline and Hydroxyproline rings, with their geometrically constrained carboxyl and (secondary) amino groups, accounts for the tendency of the individual polypeptide strands to form left-handed helices spontaneously, without any intrachain hydrogen bonding.

Because glycine is the smallest amino acid, it plays a unique role in fibrous structural proteins. In collagen, Gly is required at every third position because the assembly of the triple helix puts this residue at the interior (axis) of the helix, where there is no space for a larger side group than glycine’s single hydrogen atom. For the same reason, the rings of the Pro and Hyp must point outward. These two amino acids thermally stabilize the triple helix — Hyp even more so than Pro — and less of them is required in animals such as fish, whose body temperatures are low.

In bone, entire collagen triple helices lie in a parallel, staggered array. 40 nm gaps between the ends of the tropocollagen subunits probably serve as nucleation sites for the deposition of long, hard, fine crystals of the mineral component, which is (approximately) hydroxyapatite, Ca₅(PO₄)₃(OH), with some phosphate. It is in this way that certain kinds of cartilage turn into bone. Collagen gives bone its elasticity and contributes to fracture resistance.

[edit] Types of collagen and associated disorders

Collagen occurs in many places throughout the body. There are 28 types of collagen described in literature.

Collagen diseases commonly arise from genetic defects that affect the biosynthesis, assembly, postranslational modification, secretion, or other processes in the normal production of collagen.

Type	Notes	Gene(s)	Disorders
I	This is the most abundant collagen of the human body. It is present in scar tissue, the end product when tissue heals by repair. It is found in tendons, the endomysium of myofibrils, fibrocartilage, and the organic part of bone.	COL1A1, COL1A2	osteogenesis imperfecta, Ehlers-Danlos Syndrome
II	Hyaline cartilage, makes up 50% of all cartilage protein	COL2A1	Collagenopathy, types II and XI
III	This is the collagen of granulation tissue, and is produced quickly by young fibroblasts before the tougher type I collagen is synthesized. Reticular fiber. Also found in artery walls, intestines and the uterus	COL3A1	Ehlers-Danlos Syndrome
IV	basal lamina; eye lens. Also serves as part of the filtration system in capillaries and the glomeruli of nephron in the kidney.	COL4A1, COL4A2, COL4A3, COL4A4, COL4A5, COL4A6	Alport syndrome
V	most interstitial tissue, assoc. with type I, associated with placenta	COL5A1, COL5A2, COL5A3	Ehlers-Danlos syndrome (Classical)
VI	most interstitial tissue, assoc. with type I	COL6A1, COL6A2, COL6A3	Ulrich myopathy and Bethlem myopathy
VII	forms anchoring fibrils in dermal epidermal junctions	COL7A1	epidermolysis bullosa
VIII	some endothelial cells	COL8A1, COL8A2	-
IX	FACIT collagen, cartilage, assoc. with type II and XI fibrils	COL9A1, COL9A2, COL9A3	-
X	hypertrophic and mineralizing cartilage	COL10A1	-
XI	cartilage	COL11A1, COL11A2	Collagenopathy, types II and XI
XII	FACIT collagen, interacts with type I containing fibrils, decorin and glucosaminoglycans	COL12A1	-
XIII	transmembrane collagen, interacts with integrin a1b1, fibronectin and components of basment membranes like nidogen and perlecan.	COL13A1	-
XIV	FACIT collagen	COL14A1	-
XV	-	COL15A1	-
XVI	-	COL16A1	-
XVII	transmembrane collagen, also known as BP180, a 180 kDa protein	COL17A1	Bullous Pemphigoid and certain forms of junctional epidermolysis bullosa
XVIII	source of endostatin	COL18A1	-
XIX	FACIT collagen	COL19A1	-
XX	-	COL20A1	-
XXI	FACIT collagen	COL21A1	-
XXII	-	COL22A1	-
XXIII	-	COL23A1	-
XXIV	-	COL24A1	-
XXV	-	COL25A1	-
XXVI	-	EMID2	-
XXVII	-	COL27A1	-
XXVIII	-	COL28A1	-

In addition to the above mentioned disorders, excessive deposition of collagen occurs in Scleroderma.

[edit] Synthesis

[edit] Amino acids

Collagen has an unusual amino acid composition and sequence:

Glycine (Gly) is found at almost every third residue
Proline (Pro) makes up about 9% of collagen
Collagen contains two uncommon derivative amino acids not directly inserted during translation. These amino acids are found at specific locations relative to glycine and are modified post-translationally by different enzymes, both of which require vitamin C as a cofactor.
- Hydroxyproline (Hyp), derived from proline.
- Hydroxylysine, derived from lysine. Depending on the type of collagen, varying numbers of hydroxylysines have disaccharides attached to them.

[edit] Collagen I formation

Most collagen forms in a similar manner, but the following process is typical for type I:

Inside the cell
1. Three peptide chains are formed (2 alpha-1 and 1 alpha-2 chain) in ribosomes along the Rough Endoplasmic Reticulum (RER). These peptide chains (known as preprocollagen) have registration peptides on each end; and a signal peptide is also attached to each
2. Peptide chains are sent into the lumen of the RER
3. Signal Peptides are cleaved inside the RER and the chains are now known as procollagen
4. Hydroxylation of lysine and proline amino acids occurs inside the lumen. This process is dependent on Ascorbic Acid (Vitamin C) as a cofactor
5. Glycosylation of specific hydroxylated amino acid occurs
6. Triple helical structure is formed inside the RER
7. Procollagen is shipped to the golgi apparatus, where it is packaged and secreted by exocytosis
Outside the cell
1. Registration peptides are cleaved and tropocollagen is formed by procollagen peptidase.
2. Multiple tropocollagen molecules form collagen fibrils, and multiple collagen fibrils form into collagen fibers
3. Collagen is attached to cell membranes via several types of protein, including fibronectin and integrin.

[edit] Synthetic pathogenesis

Vitamin C deficiency causes scurvy, a serious and painful disease in which defective collagen prevents the formation of strong connective tissue. Gums deteriorate and bleed, with loss of teeth; skin discolors, and wounds do not heal. Prior to the eighteenth century, this condition was notorious among long duration military, particularly naval, expeditions during which participants were deprived of foods containing Vitamin C. In the human body, a malfunction of the immune system, called an autoimmune disease, results in an immune response in which healthy collagen fibers are systematically destroyed with inflammation of surrounding tissues. The resulting disease processes are called Lupus erythematosus, and rheumatoid arthritis, or collagen tissue disorders.^[10]

Many bacteria and viruses have virulence factors which destroy collagen or interfere with its production.

Additional images

Collagen

Action of lysyl oxydase (in French)

Keratin

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Keratins are a family of fibrous structural proteins; tough and insoluble, they form the hard but nonmineralized structures found in reptiles, birds, amphibians and mammals. They are rivaled as biological materials in toughness only by chitin.

There are various types of keratins within a single animal.

Variety of animal uses

Keratins are the main constituent of structures that grow from the skin:

the α-keratins in the hair (including wool), horns, nails, claws and hooves of mammals
the harder β-keratins in the scales and claws of reptiles, their shells (chelonians, such as tortoise, turtle, terrapin), and in the feathers, beaks, and claws of birds. (These keratins are formed primarily in beta sheets. However, beta sheets are also found in α-keratins.)^[1]

Arthropods such as crustaceans often have parts of their armor or exoskeleton made of keratin, sometimes in combination with chitin.

The baleen plates of filter-feeding whales are made of them.

They can be integrated in the chitinophosphatic material that makes up the shell and setae in many brachiopods.

Keratins are also found in the gastrointestinal tracts of many animals, including roundworms (who also have an outer layer made of keratin).

Although it is now difficult to be certain, the scales, claws, some protective armour and the beaks of dinosaurs would, almost certainly, have been composed of a type of keratin.

In Crossopterygian fish, the outer layer of cosmoid scales was keratin.

[edit] Cornification

In mammals there are soft epithelial keratins, the cytokeratins, and harder hair keratins. As certain skin cells differentiate and become cornified, pre-keratin polypeptides are incorporated into intermediate filaments. Eventually the nucleus and cytoplasmic organelles disappear, metabolism ceases and cells undergo a programmed death as they become fully keratinized.

Cells in the epidermis contain a structural matrix of keratin which makes this outermost layer of the skin almost waterproof, and along with collagen and elastin, gives skin its strength. Rubbing and pressure cause keratin to proliferate with the formation of protective calluses — useful for athletes and on the fingertips of musicians who play stringed instruments. Keratinized epidermal cells are constantly shed and replaced (see dandruff).

These hard, integumentary structures are formed by intercellular cementing of fibers formed from the dead, cornified cells generated by specialized beds deep within the skin. Hair grows continuously and feathers moult and regenerate. The constituent proteins may be phylogenetically homologous but differ somewhat in chemical structure and supermolecular organization. The evolutionary relationships are complex and only partially known. Multiple genes have been identified for the β-keratins in feathers, and this is probably characteristic of all keratins.

[edit] Molecular biology and biochemistry

The properties which make structural proteins like keratins useful depend on their supermolecular aggregation. These depend on the properties of the individual polypeptide strands, which depend in turn on their amino acid composition and sequence. The α-helix and β-sheet motifs, and disulfide bridges, are crucial to the conformations of globular, functional proteins like enzymes, many of which operate semi-independently, but they take on a completely dominant role in the architecture and aggregation of keratins.

[edit] Glycine and alanine

Keratins contain a high proportion of the smallest of the 20 amino acids, glycine, whose “side group” is a single hydrogen atom; also the next smallest, alanine, with a small and noncharged methyl group. In the case of β-sheets, this allows sterically-unhindered hydrogen bonding between the amino and carboxyl groups of peptide bonds on adjacent protein chains, facilitating their close alignment and strong binding. Fibrous keratin molecules can twist around each other to form helical intermediate filaments.

Limited interior space is the reason why the triple helix of the (unrelated) structural protein collagen, found in skin, cartilage and bone, likewise has a high percentage of glycine. The connective tissue protein elastin also has a high percentage of both glycine and alanine. Silk fibroin, considered a β-keratin, can have these two as 75–80% of the total, with 10–15% serine, with the rest having bulky side groups. The chains are antiparallel, with an alternating C → N orientation.[1] A preponderance of amino acids with small, nonreactive side groups is characteristic of structural proteins, for which H-bonded close packing is more important than chemical specificity.

[edit] Disulfide bridges

In addition to intra- and intermolecular hydrogen bonds, keratins have large amounts of the sulfur-containing amino acid cysteine, required for the disulfide bridges that confer additional strength and rigidity by permanent, thermally-stable crosslinking—a role sulfur bridges also play in vulcanized rubber. Human hair is approximately 14% cysteine. The pungent smells of burning hair and rubber are due to the sulfur compounds formed. Extensive disulfide bonding contributes to the insolubility of keratins, except in dissociating or reducing agents such as urea.

The more flexible and elastic keratins of hair have fewer interchain disulfide bridges than the keratins in mammalian fingernails, hooves and claws (homologous structures), which are harder and more like their analogs in other vertebrate classes. Hair and other α-keratins consist of α-helically-coiled single protein strands (with regular intra-chain H-bonding), which are then further twisted into superhelical ropes that may be further coiled. The β-keratins of reptiles and birds have β-pleated sheets twisted together, then stabilized and hardened by disulfide bridges.

[edit] Silk

The silk fibroins produced by insects and spiders are often classified as keratins, though it is unclear whether they are phylogenetically related to vertebrate keratins.

Silk found in insect pupae, and in spider webs and egg casings, also has twisted β-pleated sheets incorporated into fibers wound into larger supermolecular aggregates. The structure of the spinnerets on spiders’ tails, and the contributions of their interior glands, provide remarkable control of fast extrusion. Spider silk is typically about 1 to 2 micrometres (µm) thick, compared with about 60 µm for human hair, and more for some mammals. (Hair, or fur, occurs only in mammals.) The biologically and commercially useful properties of silk fibers depend on the organization of multiple adjacent protein chains into hard, crystalline regions of varying size, alternating with flexible, amorphous regions where the chains are randomly coiled.^[2] A somewhat analogous situation occurs with synthetic polymers such as nylon, developed as a silk substitute. Silk from the hornet cocoon contains doublets about 10 µm across, with cores and coating, and may be arranged in up to 10 layers; also in plaques of variable shape. Adult hornets also use silk as a glue, as do spiders.

[edit] Pairing

A (neutral-basic)	B (acidic)	Occurrence
keratin 1, keratin 2	keratin 9, keratin 10	stratum corneum, keratinocytes
keratin 3	keratin 12	cornea
keratin 4	keratin 13	stratified epithelium
keratin 5	keratin 14, keratin 15	stratified epithelium
keratin 6	keratin 16, keratin 17	squamous epithelium
keratin 7	keratin 19	ductal epithelia
keratin 8	keratin 18, keratin 20	simple epithelium

[edit] Clinical significance

Some infectious fungi, such as those which cause athlete’s foot and ringworm, feed on keratin.

Diseases caused by mutations in the keratin genes include

Amino acid

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Amino acid

Alpha-amino acids are the building blocks of proteins. A protein forms via the condensation of amino acids to form a chain of amino acid “residues” linked by peptide bonds. Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins.

Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. These twenty amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.

[edit] Functions in proteins

See also: Primary structure and Posttranslational modification

A polypeptide is a chain of amino acids.

Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or longer chains either called polypeptides or proteins. The process of such formation from an mRNA template is known as translation which is part of protein biosynthesis. Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues and responding to oxygen starvation. Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.

[edit] Non-protein functions

The twenty standard amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.^[2] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.^[3] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.^[4]

Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms. Microorganisms and plants can produce uncommon amino acids. In microbes, examples include 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged alanine dimer. Both these amino acids are both found in peptidic lantibiotics such as alamethicin.^[5] While in plants, 1-Aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.^[6]

In humans, non-protein amino acids also have biologically-important roles. Glycine, gamma-aminobutyric acid and glutamate are neurotransmitters and many amino acids are used to synthesize other molecules, for example:

Tryptophan is a precursor of the neurotransmitter serotonin
Glycine is a precursor of porphyrins such as heme
Arginine is a precursor of nitric oxide
Carnitine is used in lipid transport within a cell,
Ornithine and S-adenosylmethionine are precursors of polyamines,
Homocysteine is an intermediate in S-adenosylmethionine recycling

Also present are hydroxyproline, hydroxylysine, and sarcosine. The thyroid hormones are also alpha-amino acids.

Some amino acids have even been detected in meteorites, especially in a type known as carbonaceous chondrites.^[7] This observation has prompted the suggestion that life may have arrived on earth from an extraterrestrial source.

[edit] General structure

Further information: List of standard amino acids

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.

In the structure shown to the right, the R represents a side chain specific to each amino acid. The central carbon atom called C_α is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached. Amino acids are usually classified by the properties of the side chain into four groups. The side chain can make them behave like a weak acid, a weak base, a hydrophile if they are polar, and hydrophobe if they are nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are catalogued in the list of standard amino acids.

The phrase “branched-chain amino acids” or BCAA is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear, these are leucine, isoleucine and valine. Proline is the only proteinogenic amino acid whose side group links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed an imino acid, but this is not correct in the current nomenclature.^[8]

The two optical isomers of alanine.

[edit] Isomerism

Most amino acids can exist in either of two optical isomers, called D and L. The L-amino acids represent the vast majority of amino acids found in proteins. D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails.^[9] They are also abundant components of the peptidoglycan cell walls of bacteria.^[10]

The L and D conventions for amino acid configuration do not refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde having the same stereochemistry as the amino acid. S-Glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and so S-amino acids are called L- even if they are not levorotary, and R-amino acids are likewise called D- even if they are not dexterorotary.

There are two exceptions to these general rules of amino acid isomerism. Firstly, glycine, where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Secondly, in cysteine, the L = S and D = R assignment is reversed to L = R and D = S. Cysteine is structured similarly (with respect to glyceraldehyde) to the other amino acids but the sulfur atom alters the interpretation of the Cahn-Ingold-Prelog priority rule.

[edit] Reactions

As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group. The multiple side chains of amino acids can also undergo chemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in the articles dealing with each specific type of amino acid.

[edit] Peptide bond formation

The condensation of two amino acids to form a peptide bond.

For more details on this topic, see Peptide bond.

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly, instead the amino acid is activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.^[11] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.^[12] As a result of this mechanism, all proteins are synthesized starting at their N-terminus and moving towards their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.^[13] In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.^[14]

In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.^[15]

[edit] Zwitterions

An amino acid, in its (1) normal (unionized) and (2) zwitterionic forms.

As amino acids have both the active groups of an amine and a carboxylic acid they can be considered both acid and base (though their natural pH is usually influenced by the R group). At a certain pH known as the isoelectric point, the amine group gains a positive charge (is protonated) and the acid group a negative charge (is deprotonated). The exact value is specific to each different amino acid. This ion is known as a zwitterion, which comes from the German word Zwitter meaning “hybrid”. A zwitterion can be extracted from the solution as a white crystalline structure with a very high melting point, due to its dipolar nature. Near-neutral physiological pH allows most free amino acids to exist as zwitterions.

[edit] Hydrophilic and hydrophobic amino acids

Depending on the polarity of the side chain, amino acids vary in their hydrophilic or hydrophobic character. These properties are important in protein structure and protein-protein interactions. The importance of the physical properties of the side chains comes from the influence this has on the amino acid residues’ interactions with other structures, both within a single protein and between proteins. The distribution of hydrophilic and hydrophobic amino acids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. For example, soluble proteins have surfaces rich with polar amino acids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic amino acids that anchors them into the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Recently a new scale of hydrophobicity based on the free energy of hydrophobic association has been proposed^[16]

Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of amino acids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophilic glycoproteins.

[edit] Table of standard amino acid abbreviations and side chain properties

Main article: List of standard amino acids

Amino Acid	3-Letter	1-Letter	Side chain polarity	Side chain acidity or basicity	Hydropathy index^[17]
Alanine	Ala	A	nonpolar	neutral	1.8
Arginine	Arg	R	polar	basic (strongly)	-4.5
Asparagine	Asn	N	polar	neutral	-3.5
Aspartic acid	Asp	D	polar	acidic	-3.5
Cysteine	Cys	C	polar	neutral	2.5
Glutamic acid	Glu	E	polar	acidic	-3.5
Glutamine	Gln	Q	polar	neutral	-3.5
Glycine	Gly	G	nonpolar	neutral	-0.4
Histidine	His	H	polar	basic (weakly)	-3.2
Isoleucine	Ile	I	nonpolar	neutral	4.5
Leucine	Leu	L	nonpolar	neutral	3.8
Lysine	Lys	K	polar	basic	-3.9
Methionine	Met	M	nonpolar	neutral	1.9
Phenylalanine	Phe	F	nonpolar	neutral	2.8
Proline	Pro	P	nonpolar	neutral	-1.6
Serine	Ser	S	polar	neutral	-0.8
Threonine	Thr	T	polar	neutral	-0.7
Tryptophan	Trp	W	nonpolar	neutral	-0.9
Tyrosine	Tyr	Y	Nonpolar	neutral	-1.3
Valine	Val	V	nonpolar	neutral	4.2

In addition to the normal amino acid codes, placeholders were used historically in cases where chemical or crystallographic analysis of a peptide or protein could not completely establish the identity of a certain residue in a structure. The ones they could not resolve between are these pairs of amino-acids:

Ambiguous Amino Acids	3-Letter	1-Letter
Asparagine or aspartic acid	Asx	B
Glutamine or glutamic acid	Glx	Z
Leucine or Isoleucine	Xle	J
Unspecified or unknown amino acid	Xaa	X

Unk is sometimes used instead of Xaa, but is less standard.

[edit] Nonstandard amino acids

The amino acid selenocysteine.

Aside from the twenty standard amino acids, there are a vast number of “non-standard” amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.^[18] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG.^[19]

Examples of nonstandard amino acids that are not found in proteins include lanthionine, 2-aminoisobutyric acid, dehydroalanine and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids - for example ornithine and citrulline occur in the urea cycle, part of amino acid catabolism.^[20]

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine, ^[21] while dopamine is synthesized from l-DOPA, and hydroxyproline is made by a posttranslational modification of proline.^[22]

[edit] Uses in technology

Amino acid derivative	Use in industry
Aspartame (aspartyl-phenylalanine-1-methyl ester)	Low-calorie artificial sweetener
5-HTP (5-hydroxytryptophan)	Treatment for depression and the neurological problems of phenylketonuria.
L-DOPA (L-dihydroxyphenylalanine)	Treatment for Parkinsonism.
Monosodium glutamate	Food additive that enhances flavor. Confers the taste umami.

[edit] Nutritional importance

Further information: Protein in nutrition

Of the 20 standard proteinogenic amino acids, 8 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.^[23] Cysteine, tyrosine, histidine and arginine are considered as semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.^[24]

Essential	Nonessential
Isoleucine	Alanine
Leucine	Asparagine
Lysine	Aspartate
Methionine	Cysteine*
Phenylalanine	Glutamate
Threonine	Glutamine*
Tryptophan	Glycine*
Valine	Proline*
Arginine*	Serine*
Histidine*	Tyrosine*

(*) Essential only in certain cases.^[25]^[26]

Several common mnemonics have evolved for remembering the ten amino acids often described as essential. PVT TIM HALL (”Private Tim Hall”) uses the first letter of each essential amino acid, excluding arginine.^[27] Another mnemonic that frequently occurs in student practice materials is “These ten valuable amino acids have long preserved life in man”.^[28]

The Hormones : Corticoids Construction and Production

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The coagulation cascade.

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Image:Coagulation full.svg

From Wikipedia, the free encyclopedia

Eicosanoid synthesis

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Synthesis of Eicosanoids

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Synthesis of Eicosanoids

Contents of this page:
Prostaglandins and related compounds
Cyclic pathway: Prostaglandin-H₂ Synthase (cyclooxygenases)
Linear pathway (leukotriene synthesis): Lipoxygenase
EET synthesis: Cytochrome P₄₅₀ epoxygenase

Prostaglandins and related compounds are “local hormones” that are synthesized from the polyunsaturated fatty acid arachidonate. They have specific effects on target cells close to their site of formation. They are rapidly degraded, so they are not transported to distal sites within the body.

Examples include prostaglandins, prostacyclins, thromboxanes, leukotrienes, and epoxyeicosatrienoic acids. They have roles in inflammation, fever, regulation of blood pressure, blood clotting, immune system modulation, control of reproductive processes and tissue growth, and regulation of the sleep/wake cycle.

Prostaglandins and related compounds are collectively known as eicosanoids. They are produced from arachidonic acid, a 20-carbon polyunsaturated fatty acid (5,8,11,14-eicosatetraenoic acid).

Prostaglandins all have a cyclopentane ring, and are designated by a letter code, based on ring modifications (e.g., hydroxyl or keto groups). A subscript refers to the number of double bonds in the two side-chains.
Thromboxanes are similar but have instead a six-member ring

Prostaglandin E₂ (PGE₂) is shown at right.

Prostaglandin receptors: Prostaglandins and related compounds are transported out of the cells that synthesize them. Most affect other cells by interacting with plasma membrane G-protein coupled receptors. Depending on the cell type, the activated G protein may stimulate or inhibit formation of cAMP, or may activate a phosphatidylinositol signal pathway leading to intracellular Ca⁺⁺ release. Another prostaglandin receptor, designated PPARg, is related to a family of nuclear receptors with transcription factor activity.

Prostaglandin receptors are specified by the same letter code. For example:
Receptors for E-class prostaglandins are designated EP.
Thromboxane receptors are designated TP.
Multiple receptors for a prostaglandin are specified by subscripts (e.g., EP₁, EP₂, EP₃, etc.). Different receptors for a particular prostaglandin may activate different signal cascades. Effects may vary in different tissues, depending on which receptors are expressed.

The fatty acid arachidonate is often esterified to the hydroxyl on C2 of glycerophospholipids, especially phosphatidyl inositol, shown at right with arachidonate in blue.

Arachidonate is released from phospholipids by hydrolysis catalyzed by Phospholipase A₂. This enzyme hydrolyzes the ester linkage between a fatty acid and the hydroxyl at carbon 2 of the glycerol backbone, releasing the fatty acid (e.g., arachidonate) and a lysophospholipid as products.

Corticosteroids are anti-inflammatory because they prevent inducible Phospholipase A₂ expression, reducing arachidonate release.

There are multiple Phospholipase A₂ enzymes, subject to activation via different signal cascades.

The inflammatory signal molecule platelet activating factor is involved in activating some variants of Phospholipase A₂.
Attempts have been made to develop drugs that inhibit particular isoforms of Phospholipase A2, for treating inflammatory diseases. Success has been limited by the diversity of Phospholipase A2 enzymes, and the fact that arachidonate may give rise to inflammatory or anti-inflammatory eicosanoids in different tissues.

Phosphatidyl inositol signal cascades may lead to release of arachidonate. After phosphatidyl inositol is phosphorylated to PIP₂, cleavage of PIP₂ via Phospholipase C yields diacylglycerol (and IP₃). Arachidonate release from diacylglycerol is then catalyzed by Diacylglycerol Lipase.

Two major pathways of eicosanoid metabolism are summarized at right. Structures of examples of the compounds listed are shown on p. 962 of Biochemistry, by Voet & Voet, 3rd Edition.

Cyclic pathway:

Prostaglandin H₂ Synthase (PGH₂ Synthase) catalyzes the committed step in the “cyclic pathway” that leads to production of prostaglandins, prostacyclins, and thromboxanes. Different cell types convert PGH₂ to different compounds.

Prostaglandin H₂ Synthase is a heme-containing dioxygenase, bound to endoplasmic reticulum membranes. (A dioxygenase incorporates O₂ into a substrate.) PGH₂ Synthase exhibits two catalytic activities, Cyclooxygenase and Peroxidase. The enzyme expressing both activities is sometimes referred to as Cyclooxygenase, abbreviated COX.

The interacting cyclooxygenase and peroxidase reaction pathways are complex. A peroxide (such as that generated later in the reaction sequence) oxidizes the heme iron. The oxidized heme accepts an electron from a nearby tyrosine residue (Tyr385). The resulting tyrosine radical is proposed to extract a hydrogen atom from arachidonate, generating a radical species that reacts with O₂.

The signal molecule ·NO (nitric oxide) may initiate prostaglandin synthesis by reacting with superoxide anion (O₂·^-) to produce peroxynitrite, which oxidizes the heme iron enabling electron transfer from the active site tyrosine. Prostaglandin synthesis in response to some inflammatory stimuli is diminished by inhibitors of Nitric Oxide Synthase.

The membrane-binding domain of PGH₂ Synthase consists of 4 short amphipathic a-helices that insert into one leaflet of the lipid bilayer, facing the lumen of the endoplasmic reticulum.

Arachidonate, derived from membrane lipids, approaches the heme via a hydrophobic channel extending from the membrane-binding domain of the enzyme. In the image at right, the channel is occupied by an inhibitor, an ibuprofen analog.

Non-steroidal anti-inflammatory drugs (NSAIDs), such as aspirin and derivatives of ibuprofen, inhibit Cyclooxygenase activity of PGH₂ Synthase. They inhibit formation of prostaglandins involved in fever, pain and inflammation. They inhibit blood clotting by blocking thromboxane formation in blood platelets.

Ibuprofen and related compounds act by blocking the hydrophobic channel by which arachidonate enters the Cyclooxygenase active site. An iodinated analog of ibuprofen is seen in the structural diagram above, between the membrane-binding domain and the heme.

Aspirin acetylates a serine hydroxyl group near the active site, preventing arachidonate binding. The inhibition by aspirin is irreversible. However, in most body cells re-synthesis of PGH₂ Synthase would restore cyclooxygenase activity.

Thromboxane A₂ stimulates blood platelet aggregation, essential to the role of platelets in blood clotting. Many people take a daily aspirin for its anti-clotting effect, attributed to inhibition of thromboxane formation in blood platelets. This effect of aspirin is long-lived, because platelets lack a nucleus and do not make new enzyme.

Two isoforms of PGH₂ Synthase are designated COX-1 and COX-2 (Cyclooxygenase 1 & 2).

COX-1 is constitutively expressed at low levels in many cell types.
COX-2 expression is stimulated by growth factors, cytokines, and endotoxins.

Different localization of these isoforms within a cell, coupled to localization of enzymes that convert the product PGH₂ into particular prostaglandins or thromboxanes, may result in COX-1 and COX-2 yielding different ultimate products.

COX-1 is essential for thromboxane formation in blood platelets, and for maintaining integrity of the gastrointestinal epithelium.
Inflammation is associated with up-regulation of COX-2 and increased formation of particular prostaglandins. COX-2 levels increase in inflammatory diseases such as arthritis.
Increased COX-2 expression is seen in some cancer cells. Angiogenesis (blood vessel development), which is essential to tumor growth, requires COX-2. Overexpression of COX-2 leads to increased expression of VEGF (vascular endothelial growth factor). Regular use of NSAIDs has been shown to decrease the risk of developing colorectal cancer.

Most NSAIDs inhibit both COX-1 and COX-2.

Selective COX-2 inhibitors have been developed (e.g., Celebrex and Vioxx).

COX-2 inhibitors are anti-inflammatory & block pain, but are less likely to cause gastric toxicity associated with chronic use of NSAIDs that block COX-1.
A tendency to develop blood clots when taking some of these drugs has been attributed to:
- decreased production of an anti-thrombotic (clot blocking) prostaglandin (PGI₂) by endothelial cells lining small blood vessels
- lack of inhibition of COX-1-mediated formation of pro-thrombotic thromboxanes in platelets.

Some evidence suggests the existence of a third isoform of PGH₂Synthase, designated COX-3, with roles in mediating pain and fever, and subject to inhibition by acetaminophen (Tylenol). Acetaminophen has little effect on COX-1 or COX-2, and thus lacks anti-inflammatory activity.

Explore at right the structure of PGH₂ Synthase-1 (COX-1) crystallized with bound iodosuprofen, a derivative of ibuprofen.

PGH₂ Synthase

Linear Pathway:

The first step of the linear pathway for synthesis of leukotrienes is catalyzed by Lipoxygenase. Mammalian organisms have a family of Lipoxygenase enzymes that catalyze oxygenation of various polyunsaturated fatty acids at different sites. Many of the products have signal roles.

For example, 5-Lipoxygenase, found in leukocytes, catalyzes conversion of arachidonate to 5-HPETE (5-hydroperoxyeicosatetraenoic acid). 5-HPETE is converted to leukotriene-A₄, which in turn may be converted to various other leukotrienes (diagrams p. 966, 968).

A non-heme iron is the prosthetic group of Lipoxygenase enzymes. Ligands to the iron include 4 histidine nitrogen atoms and the C-terminal carboxylate oxygen. The arachidonate substrate binds in a hydrophobic pocket, adjacent to the catalytic iron atom. O₂ is thought to approach from the opposite side of the substrate than the side facing the iron, for a stereospecific reaction.

The reaction starts with extraction of a hydrogen from arachidonate, with transfer of the electron to the iron, reducing it from Fe³⁺ to Fe²⁺. The fatty acid radical reacts with O₂ to form a hydroperoxy fatty acid. Which hydrogen is extracted, & the position of the resulting hydroperoxy group, varies with different lipoxygenases (e.g., 5-Lipoxgenase shown at right, 15-Lipoxygenase, etc.) Additional reactions then yield the various leukotrienes.

Leukotrienes have roles in inflammation and asthmatic constriction of the bronchioles. Some leukotrienes act via specific G-protein coupled receptors in the plasma membrane.

Anti-asthma medications include inhibitors of 5-Lipoxygenase, such as Zyflo (zileuton), and drugs that interfere with leukotriene-receptor interactions. For example, Singulair (montelukast) and Accolate (zafirlukast) block binding of leukotrienes to their receptors on the plasma membranes of airway smooth muscle.

5-Lipoxygenase requires the presence of the membrane protein FLAP (5-Lipoxygenase-activating protein). FLAP binds arachidonate, facilitating its interaction with the enzyme.

A complex including 5-Lipoxygenase, FLAP, and Phospholipase A₂(which catalyzes release of arachidonate from phospholipids) forms in association with the nuclear envelope during leukotriene synthesis in leukocytes. A b-barrel domain at the N-terminus of Lipoxygenase enzymes has a role in binding to membranes.

Explore at right the structure of Lipoxygenase, with a substrate analog present at the active site.

Lipoxygenase

Cytochrome P₄₅₀ epoxygenase pathways:

Epoxyeicosatrienoic acids (EETs) and hydroxyeicosatrienoic acids are formed from arachidonate by enzymes of the cytochrome P₄₅₀ family. Other members of the cytochrome P₄₅₀ family participate in a variety of oxygenation reactions, including hydroxylation of sterols (to be discussed in the section on cholesterol synthesis and metabolism).

An example of an EET (14,15-epoxyeicosatrienoic acid), produced from arachidonate by activity of a cytochrome P₄₅₀ epoxygenase, is shown at right.

EETs are modified by additional enzyme-catalyzed reactions to produce many distinct compounds. They may be incorporated into phospholipids, and released by action of phospholipases. EETs have roles in regulating cellular proliferation, inflammation, peptide hormone secretion, and various cellular signal pathways relevant to cardiovascular and renal functions.

Fatty Acid Synthesis

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Fatty Acid Synthesis

One might predict that the pathway for the synthesis of fatty acids would be the reversal of the oxidation pathway. However, this would not allow distinct regulation of the two pathways to occur even given the fact that the pathways are separated within different cellular compartments.

The pathway for fatty acid synthesis occurs in the cytoplasm, whereas, oxidation occurs in the mitochondria. The other major difference is the use of nucleotide co-factors. Oxidation of fats involves the reduction of FADH⁺ and NAD⁺. Synthesis of fats involves the oxidation of NADPH. However, the essential chemistry of the two processes are reversals of each other. Both oxidation and synthesis of fats utilize an activated two carbon intermediate, acetyl-CoA. However, the acetyl-CoA in fat synthesis exists temporarily bound to the enzyme complex as malonyl-CoA.

The synthesis of malonyl-CoA is the first committed step of fatty acid synthesis and the enzyme that catalyzes this reaction, acetyl-CoA carboxylase (ACC), is the major site of regulation of fatty acid synthesis. Like other enzymes that transfer CO₂ to substrates, ACC requires a biotin co-factor.

The rate of fatty acid synthesis is controlled by the equilibrium between monomeric ACC and polymeric ACC. The activity of ACC requires polymerization. This conformational change is enhanced by citrate and inhibited by long-chain fatty acids. ACC is also controlled through hormone mediated phosphorylation (see below).

The acetyl groups that are the products of fatty acid oxidation are linked to CoASH. As you should recall, CoA contains a phosphopantetheine group coupled to AMP. The carrier of acetyl groups (and elongating acyl groups) during fatty acid synthesis is also a phosphopantetheine prosthetic group, however, it is attached a serine hydroxyl in the synthetic enzyme complex. The carrier portion of the synthetic complex is called acyl carrier protein, ACP. This is somewhat of a misnomer in eukaryotic fatty acid synthesis since the ACP portion of the synthetic complex is simply one of many domains of a single polypeptide. The acetyl-CoA and malonyl-CoA are transferred to ACP by the action of acetyl-CoA transacylase and malonyl-CoA transacylase, respectively. The attachment of these carbon atoms to ACP allows them to enter the fatty acid synthesis cycle.

The synthesis of fatty acids from acetyl-CoA and malonyl-CoA is carried out by fatty acid synthase, FAS. The active enzyme is a dimer of identical subunits.

All of the reactions of fatty acid synthesis are carried out by the multiple enzymatic activities of FAS. Like fat oxidation, fat synthesis involves 4 enzymatic activities. These are, b-keto-ACP synthase, b-keto-ACP reductase, 3-OH acyl-ACP dehydratase and enoyl-CoA reductase. The two reduction reactions require NADPH oxidation to NADP⁺.

The primary fatty acid synthesized by FAS is palmitate. Palmitate is then released from the enzyme and can then undergo separate elongation and/or unsaturation to yield other fatty acid molecules.

Origin of Cytoplasmic Acetyl-CoA

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Origin of Cytoplasmic Acetyl-CoA

Acetyl-CoA is generated in the mitochondria primarily from two sources, the pyruvate dehydrogenase (PDH) reaction and fatty acid oxidation. In order for these acetyl units to be utilized for fatty acid synthesis they must be present in the cytoplasm. The shift from fatty acid oxidation and glycolytic oxidation occurs when the need for energy diminishes. This results in reduced oxidation of acetyl-CoA in the TCA cycle and the oxidative phosphorylation pathway. Under these conditions the mitochondrial acetyl units can be stored as fat for future energy demands.

Acetyl-CoA enters the cytoplasm in the form of citrate via the tricarboxylate transport system (see Figure). In the cytoplasm, citrate is converted to oxaloacetate and acetyl-CoA by the ATP driven ATP-citrate lyase reaction. This reaction is essentially the reverse of that catalyzed by the TCA enzyme citrate synthase except it requires the energy of ATP hydrolysis to drive it forward. The resultant oxaloacetate is converted to malate by malate dehydrogenase (MDH).

Pathway for the movement of acetyl-CoA units from within the mitochondrion to the cytoplasm for use in lipid and cholesterol biosynthesis. Note that the cytoplasmic malic enzyme catalyzed reaction generates NADPH which can be used for reductive biosynthetic reactions such as those of fatty acid and cholesterol synthesis.

The malate produced by this pathway can undergo oxidative decarboxylation by malic enzyme. The co-enzyme for this reaction is NADP⁺ generating NADPH. The advantage of this series of reactions for converting mitochondrial acetyl-CoA into cytoplasmic acetyl-CoA is that the NADPH produced by the malic enzyme reaction can be a major source of reducing co-factor for the fatty acid synthase activities.

Synthesis of Triglycerides

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Synthesis of Triglycerides

Fatty acids are stored for future use as triacylglycerols in all cells, but primarily in adipocytes of adipose tissue. Triacylglycerols constitute molecules of glycerol to which three fatty acids have been esterified. The fatty acids present in triacylglycerols are predominantly saturated. The major building block for the synthesis of triacylglycerols, in tissues other than adipose tissue, is glycerol. Adipocytes lack glycerol kinase, therefore, dihydroxyacetone phosphate (DHAP), produced during glycolysis, is the precursor for triacylglycerol synthesis in adipose tissue. This means that adipoctes must have glucose to oxidize in order to store fatty acids in the form of triacylglycerols. DHAP can also serve as a backbone precursor for triacylglycerol synthesis in tissues other than adipose, but does so to a much lesser extent than glycerol.

The glycerol backbone of triacylglycerols is activated by phosphorylation at the C-3 position by glycerol kinase. The utilization of DHAP for the backbone is carried out through the action of glycerol-3-phosphate dehydrogenase, a reaction that requires NADH (the same reaction as that used in the glycerol-phosphate shuttle). The fatty acids incorporated into triacylglycerols are activated to acyl-CoAs through the action of acyl-CoA synthetases. Two molecules of acyl-CoA are esterified to glycerol-3-phosphate to yield 1,2-diacylglycerol phosphate (commonly identified as phosphatidic acid). The phosphate is then removed, by phosphatidic acid phosphatase, to yield 1,2-diacylglycerol, the substrate for addition of the third fatty acid. Intestinal monoacylglycerols, derived from the hydrolysis of dietary fats, can also serve as substrates for the synthesis of 1,2-diacylglycerols.

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