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Note: Attempt both the section A and B. Section A is compulsory. Draw neat diagram(s) with proper
labeling wherever necessary.
Section A 12X02= 24
(Attempt ALL questions in this section. Each question carries two marks.)
Carbohydrates - Stereochemistry
D/L system used for penultimate carbon
1. most oxidized carbon at top
2. continue carbon chain to bottom
3. non-hydrogen substituent on right=D
Trivial names indicate all other stereocenters
Mutarotation
Cyclic acetals are in equilibrium with open-chain forms
This equilibrium allows a and b forms to interconvert
This interconversion can result in a change in the specific rotation
Physical Properties
Chemical Properties
A. Glycoside (a type of acetal) Formation
B. Methyl ether formation
C. Reduction
D. Oxidation
1. Cyclic Structures of Monosaccharides (Acetal and Hemiacetal Formation)
All monosaccharides with at least five carbon atoms exist predominantly as cyclic hemiacetals and
hemiketals. A Haworth structure can be used to depict the a and b anomers of a monosaccharide.
Anomers are stereoisomers that differ in the 3-D arrangement of groups at the anomeric carbon of an
acetal, ketal, hemiacetal, or hemiketal group.
Glycoside Formation: Cyclic monosaccharide hemiacetals and hemiketals react with alcohols to form
acetals and ketals, referred to as glycosides.
Carbonyl reduction reactions affect the aldehyde or ketone functionality (NaBH4, H2/Pt...)
Oxidation - I
Oxidation by Cu(II) or Ag(I) - a test for reducing sugars
The oxidation of a carbonyl group on a monosaccharide. Since all monosaccharides are in equilibrium
with their cyclic form, they are all reducing sugars.
Benedicts reagent is commonly used to test for the presence of reducing sugars:
Reducing sugar + Cu2+ oxidized compound + Cu2O
(blue) (Orange red ppt)
Oxidation - II
Nitric Acid - oxidizes aldehydes and primary alcohols to carboxylic acids
Esterfication The OH groups of monosaccharides can behave as alcohols and react with acids
(especially phosphoric acid) to form esters.
3. Give an account of HMP pathway and it significances?
Ans: The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose
monophosphate shunt) is a process that generates NADPH and pentoses (5-carbon sugars). There are
two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and
the second is the non-oxidative synthesis of 5-carbon sugars. This pathway is an alternative
to glycolysis. While it does involve oxidation of glucose, its primary role is anabolic rather than
catabolic. For most organisms, it takes place in the cytosol; in plants, most steps take place in plastids.
Significance:
The primary results of the Pathway are:
The generation of reducing equivalents, in the form of NADPH, used in reductive biosynthesis
reactions within cells. (e.g. fatty acid synthesis)
Production of ribose-5-phosphate (R5P), used in the synthesis of nucleotides and nucleic acids.
Production of erythrose-4-phosphate (E4P), used in the synthesis of aromatic amino acids.
Aromatic amino acids, in turn, are precursors for many biosynthetic pathways, notably including the
lignin in wood.
Dietary pentose sugars derived from the digestion of nucleic acids may be metabolized through the
pentose phosphate pathway, and the carbon skeletons of dietary carbohydrates may be converted into
glycolytic/gluconeogenic intermediates.
In mammals, the PPP occurs exclusively in the cytoplasm, and is found to be most active in the liver,
mammary gland and adrenal cortex in the human. The PPP is one of the three main ways the body
creates molecules with reducing power, accounting for approximately 60% of NADPH production in
humans.
One of the uses of NADPH in the cell is to prevent oxidative stress. It
reduces glutathione via glutathione reductase, which converts reactive H2O2 into H2O by glutathione
peroxidase. If absent, the H2O2 would be converted to hydroxyl free radicals by Fenton chemistry,
which can attack the cell. Erythrocytes, for example, generate a large amount of NADPH through the
pentose phosphate pathway to use in the reduction of glutathione.
Hydrogen peroxide is also generated for phagocytes in a process often referred to as a respiratory
burst.[2]
4. Classify the protein with suitable example? Give in details about the ammonia formation?
Ans: Proteins have wide structural and functional diversity. It is difficult to classify these on the basis of
a single property or a characteristic. However, following are some common basis of classifying them.
Shape and structure
Products of hydrolysis
Biological functions
Classification on the Basis of Shape and Size
On the basis of their composition, proteins get different shapes and size which give an indication of their
various functions. These can be broadly put into two classes on the basis of their overall shape. These
are as follows:
Globular proteins: These contain compactly folded coils of polypeptide chains giving them shape of
spheroids or ellipsoids. Examples of this type are albumins, globulins, histones, protamines etc.
Fibrous proteins: This class of proteins looks like fibres or threads. These are insoluble in water and
aqueous solutions of acids and bases. These have high mechanical strength. Keratins in hair, actins and
myosin in muscles and collagen are examples of this type of protein.
Classification on the Basis of Products of Hydrolysis
On the basis of the products obtained on hydrolysis, proteins can be classified into three categories viz.,
simple proteins, conjugated proteins and derived proteins.
Simple proteins: Simple proteins are those which are made of amino acid units, each joined by a
peptide bond. Upon hydrolysis they yield only a mixture of amino acids. Following are some of the
types of simple proteins.
Types of Simple Proteins with their Examples
Conjugated Proteins: Conjugated proteins are composed of simple proteins combined with non protein
substances. The non protein substance is called prosthetic group or cofactor. Following are some of
the types of conjugated proteins.
Types of Conjugated Proteins and their Examples
Derived Proteins: These are not naturally occurring proteins and are obtained from simple proteins or
conjugated proteins by the action of enzymes and chemical agents, heat, mechanical shaking, UV or X-
rays. It includes the following types:
1. Primary e.g., myosin, fibrin
2. Secondary e.g., peptones, peptides, proteoses etc.
Classification on the Basis of Biological Functions
The involvement of proteins in different functions also makes it a basis for their classification. The
different classes along with the functions performed and examples are summaries in Table
Types of Proteins on the Basis of Functions Performed
S.No. Type Function Example
1. Enzymes Catalytic activity Kinases,
dehydrogenases
2. Storage proteins Store amino acids Myoglobin, ferritin
3. Regulatory proteins Coordinate body activities Insulin, glucagons
4. Structural proteins Give support and structure Keratin, collagen
5. Defensive/Protective Protect against diseases Immunoglobulins,
proteins antibodies
6. Transport proteins Facilitate import of Haemoglobin
nutrients into cells or
releases of toxic products
into surrounding medium
7. Contractile and Participate in contractile Actin, myosin
Mobile proteins processes e.g. movement of
muscles
Ammonia formation
Oxidative Deamination Reaction
Introduction:
Deamination is also an oxidative reaction that occurs under aerobic conditions in all tissues but
especially the liver. During oxidative deamination, an amino acid is converted into the corresponding
keto acid by the removal of the amine functional group as ammonia and the amine functional group is
replaced by the ketone group. The ammonia eventually goes into the urea cycle.
Oxidative deamination occurs primarily on glutamic acid because glutamic acid was the end product of
many transamination reactions.
The glutamate dehydrogenase is allosterically controlled by ATP and ADP. ATP acts as an inhibitor
whereas ADP is an activator.
Urea Cycle
Urea is the major end product of nitrogen metabolism in humans and mammals. Ammonia, the product
of oxidative deamination reactions, is toxic in even small amounts and must be removed from the body.
The urea cycle or the ornithine cycle describes the conversion reactions of ammonia into urea. Since
these reactions occur in the liver, the urea is then transported to the kidneys where it is excreted. The
overall urea formation reaction is:
One amine group comes from oxidative deamination of glutamic acid while the other amine group
comes from aspartic acid. Aspartic acid is regenerated from fumaric acid produced by the urea cycle.
The fumaric acid first undergoes reactions through a portion of the citric acid cycle to produce
oxaloacetic acid which is then changed by transamination into aspartic acid.
High ammonia levels are toxic to humans. A complete block of any step in the urea cycle is fatal since
there is no known alternative pathway for the synthesis of urea. Inherited disorders from defective
enzymes may cause a partial block in some of the reactions and results in hyperammonemia which can
lead to mental retardation. Extensive ammonia accumulation leads to extensive liver damage and death.
Liver cirrhosis caused by alcoholism creates an interference in the enzymes which produce carbamyl
phosphate in the first step on the cycle.
4. Define essential fatty acids with suitable examples? Discuss the metabolic disorders of lipids?
Ans: Essential Fatty acids
Essential fatty acids, or EFAs, are fatty acids that humans and other animals must ingest because the
body requires them for good health but cannot synthesize them. The term "essential fatty acid" refers to
fatty acids required for biological processes but does not include the fats that only act as fuel.
Only two fatty acids are known to be essential for humans: alpha-linolenic acid (an omega-3 fatty acid)
and linoleic acid (an omega-6 fatty acid). Some other fatty acids are sometimes classified as
"conditionally essential," meaning that they can become essential under some developmental or disease
conditions; examples include docosahexaenoic acid (an omega-3 fatty acid) and gamma-linolenic acid
(an omega-6 fatty acid).
The basic mechanism by which enzymes catalyze chemical reactions begins with the binding of the
substrate (or substrates) to the active site on the enzyme. The active site is the specific region of the
enzyme which combines with the substrate. The binding of the substrate to the enzyme causes changes
in the distribution of electrons in the chemical bonds of the substrate and ultimately causes the reactions
that lead to the formation of products. The products are released from the enzyme surface to regenerate
the enzyme for another reaction cycle.
The active site has a unique geometric shape that is complementary to the geometric shape of a
substrate molecule, similar to the fit of puzzle pieces. This means that enzymes specifically react with
only one or a very few similar compounds.
The specific action of an enzyme with a single substrate can be explained using a Lock and Keyanalogy
first postulated in 1894 by Emil Fischer. In this analogy, the lock is the enzyme and the key is the
substrate. Only the correctly sized key (substrate) fits into the key hole (active site) of the lock
(enzyme).
Smaller keys, larger keys, or incorrectly positioned teeth on keys (incorrectly shaped or sized substrate
molecules) do not fit into the lock (enzyme). Only the correctly shaped key opens a particular lock. This
is illustrated in graphic on the left.
Not all experimental evidence can be adequately explained by using the so-called rigid enzyme model
assumed by the lock and key theory. For this reason, a modification called the induced-fit theory has
been proposed by Koshland.
The induced-fit theory assumes that the substrate plays a role in determining the final shape of the
enzyme and that the enzyme is partially flexible. This explains why certain compounds can bind to the
enzyme but do not react because the enzyme has been distorted too much. Other molecules may be too
small to induce the proper alignment and therefore cannot react. Only the proper substrate is capable of
inducing the proper alignment of the active site.
Enzymes can act in several ways, all of which lower G (Gibbs energy):[34]
Lowering the activation energy by creating an environment in which the transition state is
stabilized (e.g. straining the shape of a substrateby binding the transition-state conformation of
the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition
state form, thereby reducing the amount of energy required to complete the transition).
Enzymes are highly specific both in binding to chiral substrates and in catalyzing stereo-specific
reactions
- Enzymes are themselves are chiral, L-amino acids
active centers = active site is asymmetric/ stereo selective
Enzymes lower the free energy of the transition state (G) by stabilizing the transition state.
Types of Catalytic Mechanisms
1. Acid-base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Proximity and orientation effects
5. Preferential binding of the transition state
Acid-Base Catalysis occurs by Proton Transfer General acid catalysis: Proton transfer from
an acid lowers the free energy of a reactions transition state
Example, keto-enol tautomerization (a)
Enhanced by proton donation (b) or proton abstraction (c) (general base catalyzed)
The ability of enzymes to arrange several catalytic groups around their substrates makes
concerted acid-base catalysis a common enzymatic mechanism
Covalent Catalysis Usually Requires a Nucleophile
Covalent Catalysis accelerates reaction rates through the transient formation of a catalyst-
substrate covalent bond
Usually, nucleophilic group on enzyme attacks an electrophilic group on the substrate
= nucleophilic catalysis
Example: decarboxylation of acetoacetate
o Stages of Covalent Catalysis
1. Nucleophilic attack of enzyme on substrate
2. Withdrawal of electrons
3. Elimination of catalysts by reversion of step 1
Metal Ion Cofactors Act as Catalysts
1/3 of known enzymes require metal ions for catalysis
Metalloenzymes contain tightly bound metal ion
(Fe2+, Fe3+, Cu2+, Mn2+, Co2+), Na+, K+, or Ca2+ play structural rather than catalytic roles
Mg2+, Zn2+ may be either structural or catalytic
Metal ions participate in the catalytic process:
1. By binding to substrate to orient them properly for reaction
2. By mediating oxidation-reduction reactions through reversible changes in the metal
ions oxidation state
3. By electrostatically stabilizing or shielding negative charges
Often: Metal ion acts similar to a proton, or polarizes water to generate OH
Catalysis can occur through proximity and orientation effects
Enzymes are much more efficient catalysts than organic model compounds
Due to proximity and orientation effects Reactants come together with proper spatial
relationship
Example: p-nitrophenylacetate intramolecular reaction is 24 times faster
Enzymes are usually much bigger than their substrates
By oriented binding and immobilization of the substrate, enzymes facilitate catalysis by four
ways
1. bring substrates close to catalytic residues
2. Binding of substrate in proper orientation (up to 102-fold)
3. Stabilization of transition state by electrostatic interactions
4. freezing out of translational and rotational mobility of the substrate (up to 107-fold)
Enzymes catalyze reactions by preferentially binding the transition state
An enzyme may binds the transition state of the reaction with greater affinity than its substrate
or products This together with the previously discussed factors accounts for the high rate of catalysis
For example, if enzyme binds the transition state
EC
Enzyme Reaction Use
number
Asparaginase 3.5.1.1 L-Asparagine H2O L-aspartate + NH3 Leukaemia
Collagenase 3.4.24.3 Collagen hydrolysis Skin ulcers
Glutaminase 3.5.1.2 L-Glutamine H2O L-glutamate + NH3 Leukaemia
Hyaluronidasea 3.2.1.35 Hyaluronate hydrolysis Heart attack
Lysozyme 3.2.1.17 Bacterial cell wall hydrolysis Antibiotic
Cyanide
Rhodanaseb 2.8.1.1 S2O32- + CN- SO32- + SCN-
poisoning
Ribonuclease 3.1.26.4 RNA hydrolysis Antiviral
Penicillin
-Lactamase 3.5.2.6 Penicillin penicilloate
allergy
Streptokinasec 3.4.22.10 Plasminogen plasmin Blood clots
Trypsin 3.4.21.4 Protein hydrolysis Inflammation
Uricased 1.7.3.3 Urate + O2 allantoin Gout
Urokinasee 3.4.21.31 Plasminogen plasmin Blood clots
a
Hyaluronoglucosaminidase
b
thiosulphate sulfurtransferase
c
streptococcal cysteine proteinase
d
urate oxidase
e
plasminogen activator
7. Give an account of chemistry, sources, function and deficiency disease of vitamin C and
vitamin A.
Vitamin C
The ascorbic acid molecule contains four hydroxyl groups in positions 2, 3, 5 and 6; the -OH group in
position 3 is acidic (pKa,3=4.2), the hydroxyl in position 2 has pKa,2=11.6, while those in position 5 and
6 behave as a secondary and primary alcoholic residue respectively.
The next figure illustrates the tautomeric equilibrium (see Fig. 1) where the C1=O and C3-OH groups
interchange with the shift of the double bond.
Vitamin C is very sensitive to even slight heating, to the light, and to the action of oxidizing agents and
metal ions.Vitamin C is readily oxidized, especially in aqueous solutions, by reacting with atmospheric
oxygen, and behaves as a two-electron donor:
Sources: The richest natural sources are fruits and vegetables, and of those, the Kakadu plum and
the camu camu fruit contain the highest concentration of the vitamin. It is also present in some cuts of
meat, especially liver.
Scurvy is an avitaminosis resulting from lack of vitamin C, since without this vitamin, the
synthesised collagen is too unstable to perform its function. Scurvy leads to the formation of brown
spots on the skin, spongy gums, and bleeding from all mucous membranes. The spots are most abundant
on the thighs and legs, and a person with the ailment looks pale, feels depressed, and is partially
immobilized. In advanced scurvy there are open, suppurating wounds and loss of teeth and, eventually,
death. The human body can store only a certain amount of vitamin C, and so the body stores are
depleted if fresh supplies are not consumed. It has been shown that smokers who have diets poor in
vitamin C are at a higher risk of lung-borne diseases than those smokers who have higher concentrations
of vitamin C in the blood.
Vitamin A
Chemistry
In foods of animal origin, the major form of vitamin A is an ester, primarily retinyl palmitate, which is
converted to retinol (chemically analcohol) in the small intestine. The retinol form functions as a storage
form of the vitamin, and can be converted to and from its visually active aldehyde form, retinal. The
associated acid (retinoic acid), a metabolite that can be irreversibly synthesized from vitamin A, has
only partial vitamin A activity, and does not function in the retina for the visual cycle. Retinoic acid is
used for growth and cellular differentiation.
All forms of vitamin A have a beta-ionone ring to which an isoprenoid chain is attached, called a retinyl
group. Both structural features are essential for vitamin activity. The orange pigment of carrots beta-
carotene can be represented as two connected retinyl groups, which are used in the body to contribute
to vitamin A levels. Alpha-carotene and gamma-carotene also have a single retinyl group, which give
them some vitamin activity. None of the other carotenes have vitamin activity. The carotenoid beta-
cryptoxanthinpossesses an ionone group and has vitamin activity in humans.
Retinol, the form of vitamin A absorbed when eating animal food sources, is a yellow, fat-soluble
substance. Since the pure alcohol form is unstable, the vitamin is found in tissues in a form of retinyl
ester. It is also commercially produced and administered as esters such as retinyl
acetate or palmitate.
Sources
Vitamin A is found naturally in many foods: Cod liver oil, liver , dandelion greens , carrot ,
broccoli leaf, sweet potato, butter, kale, spinach, pumpkin, collard greens, Cheddar cheese, cantaloupe
melon, egg, apricot, papaya, mango, pea, broccoli, milk, tomatoes
Deficiency
A deficiency is impaired vision, particularly in reduced light night blindness. Persistent deficiency
gives rise to a series of changes, the most devastating of which occur in the eyes. Some other ocular
changes are referred to asxerophthalmia. First there is dryness of the conjunctiva (xerosis) as the normal
lacrimal and mucus-secreting epithelium is replaced by a keratinized epithelium. This is followed by the
build-up of keratin debris in small opaque plaques (Bitot's spots) and, eventually, erosion of the
roughened corneal surface with softening and destruction of the cornea (keratomalacia) and leading to
total blindness.
Other changes include impaired immunity (increased risk of ear infections, urinary tract infections,
Meningococcal disease), hyperkeratosis (white lumps at hair follicles), keratosis pilaris and squamous
metaplasia of the epithelium lining the upper respiratory passages and urinary bladder to a keratinized
epithelium. With relations to dentistry, a deficiency in Vitamin A leads to enamel hypoplasia.
Adequate supply, but not excess vitamin A, is especially important for pregnant and breastfeeding
women for normal fetal development and in breastmilk. Deficiencies cannot be compensated
by postnatal supplementation. Excess vitamin A, which is most common with high dose vitamin
supplements, can cause birth defects and therefore should not exceed recommended daily values.
Vitamin A metabolic inhibition as a result of alcohol consumption during pregnancy is the elucidated
mechanism for fetal alcohol syndrome and is characterized by teratogenicity closely matching maternal
vitamin A deficiency.
Each vitamin is typically used in multiple reactions, and, therefore, most have multiple functions.