Structures and Chemistry of Proteins

Proteins can be separated into two major groups, fibrous proteins and globular proteins, depending upon their shapes. The fibrous proteins are long molecules that function as structural materials in animal tissues. Hydrogen bonding holds these water insoluble molecules together to form extended coiled chains. To this group belong collagen, protein of the connecting tissues; myosin, protein of the muscles; keratin, protein found in hair, nails, horns, and feathers; and fibroin, protein of silk fibers. Globular proteins are held by strong intramolecular hydrogen bonds in spherical or elliptical forms. Their intermolecular forces are weak and they are soluble in water and in dilute salt solutions. To this group of proteins belong enzymes, many hormones, egg albumin, and hemoglobin. Some proteins also contain a non-peptide portion that is attached chemically to the polyamide chain. The non-peptide moieties are called prosthetic groups, and the proteins with such groups are called conjugated proteins. Examples are hemoglobin and myoglobin that consist of polypeptide portions with iron–porphyrin prosthetic groups attached. This particular prosthetic group, called heme, is illustrated in Fig. 8.2. There are also a number of proteins that are associated with a nucleic acid. They are known as nucleoproteins. Numerous studies of protein structures have shown that the common conformations of the protein chains (fibrous) can be either as an a-helix, b-sheets, or random coils [26]. The steric arrangement or the conformations of the proteins are referred to as the secondary structure, while the composition of a amino acids in the polypeptide chains is called the primary structure [26]. Based on X-ray crystallogra phy data, Pauling et al. [24] deduced that an a-helix type configuration is formed because it accommodates hydrogen bonding of each nitrogen to a carbonyl oxygen (see Fig. 8.3). It allows space for all bulky substituents in amino acids and stabilizes the structure. The α-helix is probably the most important secondary structure in proteins [26]. The two a-helix illustrations are after Pauling et al. [24]. The one on the left shows right-handed helix. It is interesting to note that an a-helix conformation may

Fig. 8.2 Prostate group heme also occur in water solutions. This is due to van der Waal interactions [25], because water molecules interfere with hydrogen bonding that holds the helix together, as shown in Fig. 8.3. Not all proteins, however, form helical structures. If the substituent groups on the amino acids are small, as found in silk fibroin, then the polypeptide chains can line up side by side and form sheet-like arrangements. The chains tend to contract to accommodate hydrogen bonding and form pleated sheets. This is called b-arrangement. Such an arrangement can be parallel and antiparallel. The identity period of the parallel one is 6.5 A ˚ and that of the anti-parallel 7.0 A ˚. The secondary structures of proteins do not describe completely the arrangement of these macromolecules. There may, for instance, be sections that may exhibit some irregularity. Or, some sections may be linked chemically by sulfur–sulfur bonds of cystine groups. There may also be areas

Fig. 8.3 a-Helix structure of proteins where the folding of the helix is such that it allows hydrogen bonding between distant sites. The overall, three-dimensional picture of a protein structure is referred to as the tertiary structure. Disruption of the tertiary structure in proteins is called denaturation. When the protein is composed of more than a single peptide chain, the arrangement is called a quaternary structure. This associa tion results from non-covalent interactions. There is a relationship between the primary structures, or the amino acid content of many proteins, and the secondary structures [27]. The helical contents are inversely proportional to the amount of serine, threonine, valine, cysteine, and proline in the molecule. Conversely [28], valine, isoleucine, serine, cysteine, and threonine are non-helix-forming amino acids. Proline, due to its specific configuration, actually disrupts the helical structure when it is present in the polypeptide [29]. In addition, proteins that are composed of low ratios of polar to nonpolar amino acids have a tendency to aggregate [30]. Also, the globular protein, will, in an aqueous environment, tend to form shapes with nonpolar groups located inside the structure. This is due to the thermodynamic nature of the hydrophobic side chains. The polar ones, on the other hand, tend to be located outside, toward the water [31]. To date, much more information is available on some proteins than on others. Some of the more thoroughly explored proteins will be mentioned below. Keratins are proteins that are found in wool, hair, fur, skin, nails, horns, scales, feathers, etc. They are insoluble because the peptide chains are linked by disulfide bonds [32, 33]. Many keratins contain coils of a-helixes [34–36]. Some keratins, however, were found to consist of complicated b-helical structures. This apparently has not been fully explained. Wool keratin was shown to range in molecular weight from 8,000 to 80,000 [37]. The extensibility of a-keratins is believed to be due to the helical structures. The extent of keratin hardness (in claws, horns, and nails) is believed to be due to the amount of sulfur links. Silk fibers, which are obtained from the secretion of the silkworm, are double filaments that are enclosed by a coating of a gum (sericin) as they are secreted [40]. The amino acid sequence of the silk protein was shown to be (glycine–serine–glycine–alanine–glycine–alanine) n. The polypeptide chains are bound into antiparallel pleated b-sheet structures by hydrogen bonding [31, 39, 42]. The structures are also held together by van der Waal forces [31, 38].

The protein of skin and extracellular connective tissues in animals is collagen. The polymer is rigid and cross-linked. Mild hydrolysis disrupts the rigid secondary valence forces and produces gelatin [26]. The fundamental unit of collagen exists as a triple helix [41]. Three left-handed helices twist together to form a right-handed threefold super helix [31]. Collagen is composed mainly of glycine, proline, and hydroxyproline. Some other amino acids are also present in minor amounts. Aprotein that is similar to collagen is elastin, which is present in elastic tissues, such as tendons and arteries. Hydrolyses of elastin, which has rubber-like properties, however, do not yield gelatin. Mildly hydrolyzed elastin can be fractionated into two proteins [26]. Amongthe most studied globular proteins are myoglobin and hemoglobin. Myoglobin consists of a single chain of 153 amino acid residues and a prosthetic group that contains iron, called heme. Myoglobin polypeptides have eight helical segments that consist of right-handed a-helices that are interrupted by corners and non-helical regions. The overall shape resembles a pocket into which the heme group just fits. The pocket is hydrophobic because all but two side groups are nonpolar. The heme group’s two carboxylic acids protrude at the surface and are in contact with water [43]. The hemoglobin is similar to myoglobin but more complex [44]. There are four heme groups enclosed in the hemoglobin structure. Detailed conformational analysis has shown that hemoglobin is build up from 2 2myoglobin-like subunits, a2 and b2 [45, 46]. Casein is present in several animal and vegetable sources. Commercially, however, casein is primarily obtained from milk that contains about 3% of this protein. The polymer is isolated either by acid coagulation or with the help of enzymes obtained from animal stomachs. It is very heteroge neous. The molecular weight of a large portion of bovine casein is between 75,000 and 100,000. It consists of two components, a and b. Casein belongs to groups of proteins that are identified as phosphoproteins because the hydroxyl residues of the hydroxy amino acids are esterified with phosphoric acid. One other group of proteins that has so far not been fully identified is glycoprotein. This group of proteins contains a prosthetic group that is either a carbohydrate or a derivative of a carbohydrate. Glycoproteins are found in mucous secretions. Very special proteins are called enzymes. These are biological catalysts. Their primary function is to increase the rate of reactions in organisms and they are found in all living systems. Many enzymes, like pepsin or trypsin, are relatively simple proteins. Others are conjugated proteins containing prosthetic groups often known as coenzymes. Because of their extreme importance to biochemists, enzymes and their actions are being investigated extensively. The full structures of several enzymes have been determined. One such enzyme is lysozyme. Lysozyme enzymes occur in many species of plants and animals and the chemical behavior may differ. The enzyme found in egg white has a peptide chain consisting of two sections, approximately equal in size. The two sections are separated by a deep cleft. This enzyme performs its function by binding the substrates within this cleft with hydrogen bonds. The substrate is then hydrolyzed with the aid of glutamine (35th amino acid) and aspertine (52nd amino acid). Egg lysozymes primary structure contains 129 amino acid residues. The polymer is a single polypeptide chain that is cross linked at four places by disulfide bonds [47]. In addition, it was demonstrated [72] that the secondary structure of an enzymic protein is essential to protein’s catalytic activity. Also, it was shown that this structure remains intact in neat organic solvents [72]. The molecules, however, are denatured in water–organic solvent mixtures. The a-helix of lysozyme, for instance, when the enzyme is crystalline or dissolved in neat acetonitrile, 35% of it is an a-helix, but in pure water that value is 23%. In a 60:30 mixture by volume of acetonitrile and water, it is reduced to 13% [72]. Some of the uncertainty about the transition state of the reaction of some enzymes, like b-phosphoglucomutase-catalyzed transfer of a phosphoryl group to a substrate in sugar metabolism, was resolved recently. Allan and Dunaway demonstrated that by means of 19F nuclear magnetic resonance that the transition state involved a bipyramidal ox phosphorane intermediate [72].

اخر الاخبار

اخبار العتبة العباسية المقدسة

العتبة العباسية المقدسة تختتم فعاليات حفل التكليف المركزي الثامن بمشاركة أكثر من 6 آلاف تلميذة

من الخيام إلى الفتوى.. عرض مسرحي ضمن فعاليات اليوم الثاني لحفل التكليف

ضمن فعاليات اليوم الثاني من حفل التكليف المركزي الثامن تلميذات مدارس كربلاء يرددن نشيد التكليف

عرض فيلم عن مشروع الورود الفاطمية ضمن فعاليات اليوم الثاني من حفل التكليف المركزي الثامن

المزيد

الآخبار الصحية

عوامل تضعف القدرات الإدراكية لدى الإنسان

طريقة جديدة لتجديد خلايا الدماغ

دراسة بريطانية: الأطعمة النباتية عالية الجودة تقلل خطر فشل القلب

7 أطعمة يومية "تسمم" جسمك بالبلاستيك دون أن تشعر

المزيد

الآخبار التكنلوجية

اكتشاف أثري في أوريغون الأمريكية قد يعيد كتابة تاريخ البشرية

اكتشاف كائن بحري مدرع بلسان "حديدي" في بحر اليابان

نظام كوكبي "مقلوب" يحير علماء الفلك

بسبب الذكاء الاصطناعي.. هذه الوظائف "ستختفي" بعد أشهر قليلة ؟!

المزيد

مواضيع ذات صلة

Proteins

Polyisoprene

Lignin

Derivatives of Cellulose

Regenerated Cellulose

Cellulose

Starch

Hemicelluloses

Dendrimers and Hyperbranched Polymers

Poly (arylene ether) s and Poly (arylene ether ketone) s

Double-Stranded Polymers

Cardo Polymers