Q.1- a) – What are sugar acids? Give examples of such acids and state their biological importance.
Answer- Sugar acids are formed by the oxidation of –
1) Aldehyde group (C1) to form Aldonic acid, or
2) Primary Alcoholic group (C5) in an aldohexose to form uronic acid or
3) Both groups to form Saccharic acid.
Details of Reactions-
1) Oxidation of Aldehyde group- Under mild conditions, in the presence of Hypobromous acid, the aldehyde group is oxidized to form Aldonic acid. Thus, Glucose is oxidized to Gluconic acid, Mannose to form Mannonic acid and Galactose to form Galactonic acid. Formation of Gluconic acid by the activity of Glucose oxidase is the basis for the Quantitative estimation of urinary and blood Glucose.
2) Oxidation of Primary Alcoholic acid- Under special conditions when the aldehyde group is protected, and the molecule is oxidized at the primary alcoholic group the product is a Uronic acid. Thus Glucose is oxidized to form Glucuronic acid, Galactose to form Galacturonic acid and Mannose is oxidized to Mannuronic acid. Glucuronic acid is used in the body for conjugation reactions to convert the toxic water insoluble compounds in to nontoxic water soluble forms, which can be easily excreted in urine. Glucuronic acid and its epimer Iduronic acid are used for the synthesis of heteropolysaccharides.
3) Oxidation of both Aldehyde and Primary Alcoholic group-Under strong acidic conditions (Nitric acid and heat) the first and the last carbons are simultaneously oxidized to form dicarboxylic acids, known as Saccharic acids. Glucose is thus oxidized to form Gluco Saccharic acid, Mannose to Mannaric acid and Galactose to Mucic Acid .The mucic acid forms insoluble crystals and is the basis for a test for identification of Galactose.
b) What are Glycosides? Discuss the clinical significance of Glycosides
Answer- Acetal or ketal derivatives formed when a monosaccharide reacts with an alcohol are called glycosides. They are formed by the reaction of the hydroxyl group of anomeric carbon (hemiacetal or hemiketal) of monosaccharide with hydroxy group of second molecule with the loss of an equivalent of water.
The second molecule may be-
1) Another sugar (Glycon)- e.g. formation of disaccharides and polysaccharides.
2) Non Carbohydrate (Aglycon)- such as Methanol, Glycerol, Sterol, steroids etc.
In naming of glycosides, the “ose” suffix of the sugar name is replaced by “oside”, and the alcohol group name is placed first. For example, D-glucose reacts with methanol in an acid-catalyzed process: the anomeric carbon atom reacts with the hydroxyl group of methanol to form two products, methyl α -D-glucopyranoside and methyl β -D-glucopyranoside. These two glucopyranosides differ in the configuration at the anomeric carbon atom. The new bond formed between the anomeric carbon atom of glucose and the hydroxyl oxygen atom of methanol is called a glycosidic bond specifically, an O-glycosidic bond
The anomeric carbon atom of a sugar can be linked to the nitrogen atom of an amine to form an N-glycosidic bond. Nucleosides are adducts between sugars such as ribose and amines such as adenine (the linkage between them is N-Glycosidic linkage).
Examples of Glycosides- Glycosides are present in many drugs, spices and in the constituents of animal tissues. Glycosides comprise several important classes of compounds such as hormones, sweeteners, alkaloids, flavonoids, antibiotics, etc. The glycosidic residue can be crucial for their activity or can only improve pharmacokinetic parameters.
1) Cardiac Glycosides
Cardiac glycosides all contain steroids as aglycone or genin component in combination with sugar molecules. These include derivatives of digitalis and strophanthus such as oubain.
2) Other glycosides such as streptomycin are used as antibiotics. Phloridzin is another glycoside which is obtained from the root and bark of apple tree. It blocks the transport of sugar across the mucosal cells of small intestine and also renal tubular epithelium. It displaces Na+ from the binding site of “carrier protein” and prevents the binding of sugar molecule and produces Glycosuria.
3) Glycosides of vitamins, both hydrophilic and lipophylic often occur in nature. Glycosylated vitamins have an advantage over the respective aglycone in their better solubility in water (especially the lipophylic ones), stability against UV-light, heat and oxidation, reduction of the bitter taste and odor (e.g., thiamine), and resistance to an enzymatic action. Some of the vitamin glycoconjugates have altered or improved Pharmacokinetic properties.
c) Discuss the structure and significance of Cellulose
Cellulose- Cellulose is the chief constituent of plant cell walls. It is the most abundant of all carbohydrates .It is insoluble in water, gives no color with iodine and consists of β -D-glucopyranose units linked by β 1 →4 bonds to form long, straight chains strengthened by cross-linking hydrogen bonds. Mammals lack any enzyme that hydrolyzes the β 1→ 4 bonds, and so cannot digest cellulose. It is an important source of “bulk” in the diet, and the major component of dietary fiber. Microorganisms in the gut of ruminants and other herbivores can hydrolyze the linkage and ferment the products to short-chain fatty acids as a major energy source. There is some bacterial metabolism of cellulose in the human colon.
Figure- showing the structure of cellulose.
Cellulose yields Glucose upon complete hydrolysis. Partial hydrolysis yields cellobiose.
Products obtained from Cellulose-
- Microcrystalline cellulose : used as binder-disintegrant in tablets
- Methylcellulose: suspending agent and bulk laxative
- Oxidized cellulose: hemostat
- Sodium carboxymethyl cellulose: laxative
- Cellulose acetate: rayon; photographic film; plastics
- Cellulose acetate phthalate: enteric coating
- Nitrocellulose: explosives; collodion (pyroxylin)
Q.2-a) What are storage polysaccharides? Give a brief description of each of them.
Answer- Glycogen, starch and Inulin are storage polysaccharides.
1) Glycogen- Glycogen is a readily mobilized storage form of glucose. It is a very large, branched polymer of glucose residues (Figure) that can be broken down to yield glucose molecules when energy is needed. Most of the glucose residues in glycogen are linked by α-1,4-glycosidic bonds. Branches at about every tenth residue are created by α–1,6-glycosidic bonds. It is the storage polysaccharide in animals and is sometimes called animal starch, but it is more branched than amylopectin present in starch.
Figure- showing the structure of glycogen.
It is hydrolyzed by both α and β-amylases and by glycogen phosphorylase. The complete hydrolysis yields glucose. Glycogen on reaction with iodine gives a red-violet color.
Glycogen is stored in muscle and liver. The concentration of glycogen is higher in the liver than in muscle (10% versus 2% by weight), but more glycogen is stored in skeletal muscle overall because of its much greater mass. Glycogen is present in the cytosol in the form of granules ranging in diameter from 10 to 40 nm. In the liver, glycogen synthesis and degradation are regulated to maintain blood-glucose levels as required to meet the needs of the organism as a whole. In contrast, in muscle, these processes are regulated to meet the energy needs of the muscle itself.
Glycogen is not as reduced as fatty acids are and consequently not as energy rich. But still animals store energy as glycogen? All excess fuel is converted is not converted into fatty acids. Glycogen is an important fuel reserve for several reasons.
The controlled breakdown of glycogen and release of glucose increase the amount of glucose that is available between meals. Hence, glycogen serves as a buffer to maintain blood-glucose levels. Glycogen’s role in maintaining blood glucose levels is especially important because glucose is virtually the only fuel used by the brain, except during prolonged starvation. Moreover, the glucose from glycogen is readily mobilized and is therefore a good source of energy for sudden, strenuous activity. Unlike fatty acids, the released glucose can provide energy in the absence of oxygen and can thus supply energy for anaerobic activity.
2) Starch- It is a polymer of glucose, found in roots, rhizomes, seeds, stems, tubers and corms of plants, as microscopic granules having characteristic shapes and sizes. Most animals, including humans, depend on these plant starches for nourishment. The intact granules are insoluble in cold water, but grinding or swelling them in warm water causes them to burst. The released starch consists of two fractions.
About 20% is a water soluble material called amylose. The majority of the starch is a much higher molecular weight substance, consisting of nearly a million glucose units, and called amylopectin.
(a) Amylose is a linear polymer of α-D-glucose, linked together by α 1→4 glycosidic linkages. It is soluble in water, reacts with iodine to give a blue color and the molecular weight of Amylose ranges between 50, 000 – 200, 000.
Figure- showing the structure of Amylose
(b) Amylopectin is a highly branched polymer, insoluble in water, reacts with iodine to give a reddish violet color. The molecular weight ranges between 70, 000 – 1 000, 000. Branches are composed of 25-30 glucose units linked by α 1→4 glycosidic linkage in the chain and by α 1→6 glycosidic linkage at the branch point.
Figure- showing the structure of Amylopectin
Hydrolysis: Hydrolysis of starch with hot dilute acids or by enzymes gives dextrins of varying complexity, maltose and finally D-glucose
3) Inulin- Inulin is a polysaccharide of fructose (and hence a fructosan) found in tubers and roots of dahlias, artichokes, and dandelions. It is readily soluble in water and but it is not hydrolyzed by intestinal enzymes. It has a lower molecular weight than starch and colors yellow with iodine.It is used to determine the glomerular filtration rate, Inulin is of particular use as it is not secreted or reabsorbed in any appreciable amount at the nephron allowing GFR to be calculated, rather than total renal filtration.
b) Give a brief description of structure of proteins. Support your answer with suitable diagrams
Proteins perform complex physical and catalytic functions by positioning specific chemical groups in a precise three-dimensional arrangement. The polypeptide containing these groups must adopt a conformation that is both functionally efficient and physically strong. There are different levels of structural organization: Primary, Secondary, Tertiary and Quaternary.
1) Primary structure- Primary structure denotes the number and sequence of amino acids in the protein. The sequence of amino acids is guided by the genetic information present on the DNA. A single nucleotide change in the DNA can bring about alteration in the amino acid sequence with the resultant loss of partial or complete loss of functional capacity of the protein. Example- a single nucleotide change in the genetic information for the synthesis of Beta globin chain of Hemoglobin results in the misincorporation of valine instead of glutamic acid in sickle cell anemia causing gross alterations in the oxygen carrying capacity of hemoglobin.
2) Secondary structure- Secondary structure is formed by the folding of short contiguous segments of polypeptide into geometrically ordered units. The following secondary structures are commonly found in proteins
a) Alphahelix- The polypeptide backbone of an helix is twisted by an equal amount about each alpha carbon .A complete turn of the helix contains an average of 3.6 aminoacyl residues, and the distance it rises per turn (its pitch) is 0.54 nm (Figure-)The R groups of each aminoacyl residue in an helix face outward .Proteins contain only L-amino acids, for which a right-handed helix is by far the more stable, and only right-handed helices are present in proteins. The stability of an helix arises primarily from hydrogen bonds formed between the oxygen of the peptide bond carbonyl and the hydrogen atom of the peptide bond nitrogen of the fourth residue down the polypeptide chain. The ability to form the maximum number of hydrogen bonds, supplemented by van der Waals interactions in the core of this tightly packed structure, provides the thermodynamic driving force for the formation of an helix. Since the peptide bond nitrogen of proline lacks a hydrogen atom to contribute to a hydrogen bond, proline can only be stably accommodated within the first turn of an helix. When present elsewhere, proline disrupts the conformation of the helix, producing a bend. Because of its small size, glycine also often induces bends in helices. Charged amino acids , branched amino acids and the amino acids with a bulky side chain like Tryptophan are also not involved in the formation of alpha helix. Haemoglobin, myoglobin and alpha keratin proteins have most of their structure organized in the form of alpha helix.
b) Beta pleated sheets- The second (hence “beta”) recognizable regular secondary structure in proteins is the sheet. The amino acid residues of a sheet, when viewed edge-on, form a zigzag or pleated pattern in which the R groups of adjacent residues point in opposite directions. Unlike the compact backbone of the helix, the peptide backbone of the sheet is highly extended. But like the helix, sheets derive much of their stability from hydrogen bonds between the carbonyl oxygens and amide hydrogens of peptide bonds. However, in contrast to the helix, these bonds are formed with adjacent segments of sheet (Figure). Interacting sheets can be arranged either to form a parallel sheet, in which the adjacent segments of the polypeptide chain proceed in the same direction amino to carboxyl, or an antiparallel sheet, in which they proceed in opposite directions (Figure ). Either configuration permits the maximum number of hydrogen bonds between segments, or strands, of the sheet. Most sheets are not perfectly flat but tend to have a right-handed twist. Clusters of twisted strands of sheet form the core of many globular proteins.
c) Beta bends- Turns and bends refer to short segments of amino acids that join two units of secondary structure, such as two adjacent strands of an antiparallel sheet. A turn involves four aminoacyl residues, in which the first residue is hydrogen-bonded to the fourth, resulting in a tight 180-degree turn. Proline and glycine often are present in turns. The other amino acids are charged amino acids.
d) Loops and coils- Roughly half of the residues in a “typical” globular protein reside in helices and sheets and half in loops, turns, bends, and other extended conformational features. Loops are regions that contain residues beyond the minimum number necessary to connect adjacent regions of secondary structure. Irregular in conformation, loops nevertheless serve key biologic roles. For many enzymes, the loops that bridge domains responsible for binding substrates often contain aminoacyl residues that participate in catalysis. While loops lack apparent structural regularity, they exist in a specific conformation stabilized through hydrogen bonding, salt bridges, and hydrophobic interactions with other portions of the protein. However, not all portions of proteins are necessarily ordered. Proteins may contain “disordered” regions, often at the extreme amino or carboxyl terminal, characterized by high conformational flexibility. Coils are also there as part of structural components but they are longer than the loops and connect the adjacent secondary structures.
e) Super secondary structures- Beta – alpha –beta, Beta meanders and Greek key are the super secondary structures. Globular proteins are constructed by combining secondary structural elements These form primarily the core region and are connected by loop regions at the surface of the protein. Super secondary structures are usually formed by packing side chains from adjacent structural elements close to each other.
3) Tertiary structure- The term “tertiary structure” refers to the entire three-dimensional conformation of a polypeptide. It indicates, in three-dimensional space, how secondary structural features—helices, sheets, bends, turns, and loops—assemble to form domains and how these domains relate spatially to one another. A domain is a section of protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand. Other domains may anchor a protein to a membrane or interact with a regulatory molecule that modulates its function.
4) Quaternary structure- Quaternary structure defines the polypeptide composition of a protein and, for an oligomeric protein, the spatial relationships between its subunits or protomers. Monomeric proteins consist of a single polypeptide chain. Dimeric proteins contain two polypeptide chains. Homodimers contain two copies of the same polypeptide chain, while in a heterodimer the polypeptides differ.
Examples- Immuno globulins are composed of 4 polypeptide chains, two light chain and two heavy chains , the enzyme Lactate dehydrogenase(LDH) has two types of polypeptide chains arranged in the form of a tetramer, CPK(Creatine phosphokinase) enzyme has two polypeptide chains in its structure.
Forces stabilizing tertiary structure
Higher orders of protein structure are stabilized primarily—and often exclusively—by noncovalent interactions. Principal among these are hydrophobic interactions that drive most hydrophobic amino acid side chains into the interior of the protein, shielding them from water. Other significant contributors include hydrogen bonds and salt bridges between the carboxylates of aspartic and glutamic acid and the oppositely charged side chains of protonated lysyl, argininyl, and histidyl residues. While individually weak relative to a typical covalent bond of 80–120 kcal/mol, collectively these numerous interactions confer a high degree of stability to the biologically functional conformation of a protein.
Some proteins contain covalent disulfide (S—S) bonds that link the sulfhydryl groups of cysteinyl residues. Formation of disulfide bonds involves oxidation of the cysteinyl sulfhydryl groups and requires oxygen. Intrapolypeptide disulfide bonds further enhance the stability of the folded conformation of a peptide, while interpolypeptide disulfide bonds stabilize the quaternary structure of certain oligomeric proteins.
Figure- showing the levels of Protein structure
Q.3- Write short note on each of the followings-
a) Biologically important peptides-
The peptides of biological importance are as follows-
i) Glutathione-It is a tripeptide containing Glutamic acid, cysteine and Glycine. It participates in biological oxidation and reduction reactions.
ii) Carnosine- Dipeptide of β- Alanine and Histidine, present in muscles
iii) Anserine-is methyl Carnosine.
iv) Bradykinin- It is a nano peptide(contains 9 amino acids) , has a smooth muscle relaxant effect.
v) Oxytocin and vasopressin-Nano peptide hormones
vi) Angiotensins- Angiotensin I (10 amino acids)is formed from Angiotensinogen by the action of Renin. Angiotensin II (8 amino acids) is formed from I by splitting of 2 amino acids, which is a potent vaso constrictor. It results in the formation of Angiotensin III which has 7 amino acids.
vii) Gastrin, Secretin and Pancreozymin- are gastro intestinal peptide hormones which affect secretion of bile and other digestive enzymes.
viii) β- Corticotrophin (ACTH), and β MSH are also peptide hormones
ix) Peptide Antibiotics- Penicillin, Gramicidin, Polymyxin, Bacitracins, Actinomycin, and Chloramphenicol are all peptide antibiotics.
x) Toxic peptides-Microcystine and Nodularin are lethal in large dosage.
xi) Anticancer peptides- Busulfan and cyclophosphamide
xii) Brain peptides-Dynorphin is a peptide containing 13 amino acids while met- enkephalin and Leuenkephalin(both pentapeptides) are brain peptides that reduce intestinal motility.
b) Conjugated Proteins
Conjugated proteins are simple proteins with a non protein prosthetic group. They can be classified as follows-
1) Glycoproteins- proteins with carbohydrate as the prosthetic group. The linkage may be O-glycosidic linkage (with –OH group of serine and threonine or it can be N- Glycosidic linkage with amid group of Asparagine or Glutamine. When the carbohydrate content is more than 10%, they are called Mucoproteins.
2) Lipoproteins -with lipid as the prosthetic group, examples are Chylomicron, VLDL, LDL, and HDL. The help in lipid transport in the aquatic plasma.
3) Nucleoproteins- proteins attached to nucleic acids e.g Histones attached to DNA.
4) Chromo proteins- proteins with colored prosthetic group. e.g. Hemoglobin, Myoglobin, Visual purple and Flavoproteins etc.
5) Phosphoproteins- Proteins with phosphoric acid as the prosthetic group, e.g. Ovovitellin of egg and Casein of milk are the examples of phosphoproteins.
6) Metalloproteins- Proteins with Metal as the prosthetic group, e.g. Carbonic anhydrase (Zinc), Carboxypeptidase (Zinc) ,Superoxide dismutase (Zinc and copper), Xanthine Oxidase(Molybdenum) and Aconitase (Iron).
7) Haemoproteins- proteins with haem as the prosthetic group, e.g. Haemoglobin, Myoglobin, Tryptophan pyrolase, Catalase and peroxidase etc.
c) Isoelectric pH
The Isoelectric p H is That p H at which the form of a molecule has an equal number of positive and negative charges and thus is electrically neutral. The isoelectric pH, also called the pI, is the pH midway between pKa values on either side of the isoelectric species. Similar considerations apply to all polyprotic acids (eg, proteins), regardless of the number of dissociating groups present. In the clinical laboratory, knowledge of the pI guides selection of conditions for electrophoretic separations. For example, electrophoresis at pH 7.0 will separate two molecules with pI values of 6.0 and 8.0, because at pH 7.0 the molecule with a pI of 6.0 will have a net positive charge, and that with pI of 8.0 a net negative charge. Similar considerations apply to understanding chromatographic separations on ionic supports .
d) Derived amino acids
Derived amino acids are also called modified amino acids, are classified in to two categories-
i) Derived amino acids found in proteins- examples include- Hydroxy Proline and Hydroxy Lysine, found in collagen. They are modified after translation. Gamma carboxylation of glutamic acid residues for clotting process and methylation or acetylation of histones to alter the gene expression are also examples of derived amino acids.
ii) Derived amino acids not seen in proteins—examples include- Ornithine, Citrulline, Argino succinic acid , Homocysteine and GABA. They are intermediary compounds of various metabolic pathways but are not found in proteins.
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