Assignment Code: BBCCT-101 / TMA / 2021 -2022

Course Code: BBCCT-101

Assignment Name: Molecules of Life

Year: 2021 - 2022

Verification Status: Verified by Professor

Answer all the questions given below. All Questions carry equal marks.

Q1. A) Write a brief note cellular and chemical foundation of life. (5+5) 10

Ans) The cellular basis of life means that all living organisms are made up of cells. Organisms are made of one or more cells, which need a supply of energy and molecules to carry out life processes.

Cells are made of many complex molecules called macromolecules, which include proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.

From the above discussion, we conclude that carbon is the chief building block present in the structure of all biomolecules and hence form the chemical basis of life. Therefore, carbon is the element which forms the chemical basis of life.

Q1. B) Explain the tetrahedral geometry of water molecule.

Ans) In a tetrahedral molecular geometry, a central atom is located at the centre with four substituents that are located at the corners of a tetrahedron. The bond angles are cos−1(−1⁄3) = 109.4712206...° ≈ 109.5° when all four substituents are the same, as in methane (CH

4)[1][2] as well as its heavier analogues. Methane and other perfectly symmetrical tetrahedral molecules belong to point group Td, but most tetrahedral molecules have lower symmetry. Tetrahedral molecules can be chiral.

Water molecule has distorted tetrahedral geometry. O atom has 2 lone pairs and 2 bond pairs of electrons. O atom is sp3 hybridised which results in a tetrahedral geometry. Due to lone-pair, lone-pair bond-pair and bond-pair bond-pair repulsions, the H−O−H bond angle is slightly lower than tetrahedral bond angle of 108degrees.

Q2. A) Define the following terms: pH, Buffer solution and pKa. (5+5) 10

Ans) The ionization products of water have an important role to define the pH of any solution. The pH is defined as the negative logarithm of the hydrogen ion (concentration in moles/litre)and can be represented by the following expression:

Buffer Solution: A buffer is an aqueous solution that resists a change in pH when small Quantities of an acid or a base  are added to it. The property of resistance is Called buffer action. Most commonly used buffers are made up of a conjugate acid base pair. Acidic buffer is a mixture of a weak  acid and its conjugate base  e.g., acetate buffer system. Alkaline buffer contains a weak base and its salt. If hydrogen ions are added to the buffer solution, they are neutralized by the base and similarly on addition of hydroxyl ions they will be neutralized by the acid. As a result of the seneutralization reactions, the pH of buffer solution, remains unchanged. In general, an acid is a proton donor, and a base is a proton acceptor. An acid and its corresponding base are called conjugate acid-base pair. For example, acetic acid is a weak acid, which dissociates into a proton and acetate ions and vice versa in an aqueous solution as follows.

Q2. B) Explain the classification of amino acids based on R-group.

Ans) There are several ways to classify amino acids, but the simplest way of Classification is based on structure and general chemical properties of their side chains or R groups. Amino acids are grouped into five main classes based on the polarity, size and shape of R-groups present in their side chains.

1. Non-polaraliphatic R groups: Glycine, Alanine, Proline, Valine, Leucine, Isoleucine and Methionine amino acids belong to this group. These amino acids have aliphatic side chains which are non-ionizable and hydrophobic in nature. Glycine is the simplest of twenty amino acids; its smallest side chain makes little involvement to the hydrophobic interactions. In a protein, it provides minimum steric hindrance and allows flexibility. Alanine is considered to be the parent of all other amino acids except glycine. All of them can be  derived by replacing one or two H atoms of the methyl group bonded to the -carbon atom. The side chains of  then on polar aliphatic amino acids stabilize protein structure by hydrophobic interactions. It is different from other standard amino acids structurally because its secondary amino (imino) group is formed by ring closure between the R group and the amino nitrogen. It is the only cyclic amino acid. The structure of proline confers rigidity to the peptide chain in proteins.

2) Aromatic R groups: Phenylalanine, Tyrosine and Tryptophan amino acids have bulky, aromatic group as side chains. They belong to this category and have phenyl, phenolic and in dole rings respectively as their R-groups. The hydroxyl group of tyrosine can form hydrogen bonds with water. These amino acids are responsible for UV absorption of proteins at 280nm.

3) Polar uncharged R groups: Serine, Threonine, Cysteine, Asparagine and Glutamine amino acids belongs to this group. These amino acids have polar and ionizable groups in their side chains such as Serine (hydroxyl,-OH),Threonine(hydroxyl,-OH),Cysteine(sulphydryl,-SH), Asparagine(amide,-CO-NH2) and Glutamine(amide,-CO-NH2).The polar functional groups of these amino acids participate in hydrogen bonding with water.

4) Positively charged R groups: Lysine, Histidine and Arginine are positively charged amino acids, as they contain basic groups in their side chains. The side chains groups of Histidine, Lysine and Arginine are called imidazole, amino and guanidinium respectively. ThepI of histidine is near physiological pH, hence it works as biological buffers in proteins. All basic proteins are rich in these amino acids in their sequences. These amino acids mostly occur on the protein surface to interact with water molecules.

5) Negatively charged R groups: As partate and Glutamate amino acids have acidic group(carboxylic,-COOH) in their side chains. All acidic proteins are rich in these amino acids in their sequences. These amino acids mostly occur on the protein surface to interact with water molecules. In proteins these side chain form strong ionic bond with basic amino acids ,which stabilize the protein structures.

Q3. A) Describe the importance of non-standard amino acids and draw their structures. (5+5) 10

Ans) Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the function or regulation of a protein. Non-standard amino acids which one cannot find in proteins are lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Non-standard amino acids are considered to be intermediaries that are present in the metabolic pathway of standard amino acids.

Non-standard amino acids being an essential molecule in biochemistry, have some key functions that help humans to produce different things which act as useful products in their daily lives.

Some of the important functions of non-standard amino acids are as follow:

Non-standard amino acids that are produced in industries are considered to have some important functions that can be very useful. The first commercial production of amino acids was in the year 1908. At that time, a flavouring agent, monosodium glutamate, was prepared using a type of large seaweed. Glycine and cysteine can also do the work as a food additive, and some mixtures of amino acids are also used as flavour enhancers in some food industries. This is considered to be another important function of amino acids that is useful to humans.

Diagrams of Non-Standard Amini Acids:

Q3. B) With the help of neatly labelled diagrams explain the tertiary and quaternary structure of proteins.

Ans) Tertiary: As the secondary structure becomes established due to the primary structure, a polypeptide folds and refolds upon itself to assume a complex three-dimensional shape called the protein tertiary structure. Tertiary structure is the overall shape of a polypeptide. Tertiary structure results from the interactions between the side chains (R groups) of the various amino acids. This three-dimensional structure is due to intramolecular interactions between the side groups along the polypeptide chain. Its domain typically contains 300 – 400 amino acids, and it adopts a stable tertiary structure when it is isolated from their parent protein. As a polypeptide folds into its functional shape, amino acids that have hydrophobic side chains tend to end up clustered at the core of the protein so that they are out of contact with water. Covalent bonds called disulfide bridges can also affect the shape of a protein. Disulfide Bridges form where two amino acids containing sulfhydryl groups on their side chains are brought close together by how the protein is folding. For some proteins, such as ribonuclease, the tertiary structure is the final structure of a functional protein. Other proteins are composed of two or more polypeptides and adopt a quaternary structure. Tertiary Structure of Protein is shown below:

Quaternary: While all proteins contain primary, secondary and tertiary structures, quaternary structures are reserved for proteins composed of two or more polypeptide chains. Proteins that have quaternary structures contain more than one polypeptide and each adopt a tertiary structure and then assemble with each other via intermolecular interactions. The quaternary structure of a protein is the overall structure that is the result of the addition of these polypeptide subunits. The individual polypeptides are called protein subunits, which means different polypeptides folded separately. Subunits may be identical polypeptides, or they may be different. When proteins consist of more than one polypeptide chain, they are said to have quaternary structure and are also known as multimeric proteins, meaning proteins consisting of many parts. Quaternary structures can also define as when more than one protein come together to create either a dimer, trimer, tetramer, etc. Hemoglobin is an example of a quaternary structure that is composed of two alpha subunits and two b

eta subunits.

Q4. A) What is glycosidic bond? Explain different types of glycosidic bonds with suitable example? (5+5) 10

Ans) A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide (or a molecule derived from a saccharide) and the hydroxyl group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside.

 There are two types of glycosidic bonds - 1,4 alpha and 1,4 beta glycosidic bonds. 1,4 alpha glycosidic bonds are formed when the OH on the carbon-1 is below the glucose ring; while 1,4 beta glycosidic bonds are formed when the OH is above the plane, when two alpha D-glucose molecules join together a more commonly occurring isomer of glucose compared to the L-glucose, form a glycosidic linkage, the term is known as a α-1,4-glycosidic bond.

In maltose, for example, two d-glucose residues are joined by a glycosidic linkage between the α-anomeric form of C-1 on one sugar and the hydroxyl oxygen atom on C-4 of the adjacent sugar. Such a linkage is called an α-1,4-glycosidic bond.

Q4. B) Explain amino sugars with the help of their structures. (5+5) 10

Ans) In organic chemistry, an amino sugar (or more technically a 2-amino-2-deoxysugar) is a sugar molecule in which a hydroxyl group has been replaced with an amine group. More than 60 amino sugars are known, with one of the most abundant being N-Acetyl-d-glucosamine, which is the main component of chitin.

Derivatives of amine containing sugars, such as N-acetylglucosamine and sialic acid, whose nitrogens are part of more complex functional groups rather than formally being amines, are also considered amino sugars. Aminoglycosides are a class of antimicrobial compounds that inhibit bacterial protein synthesis. These compounds are conjugates of amino sugars and aminocyclitols.

Q5. Write a detailed note on plant and animal storage polysaccharides with suitable diagrams and examples.

Ans) Organisms store energy in the form of polysaccharides instead of Monosaccharides as they have lower osmotic pressure. Starch and glycogen Fall into this category of functions. While starch serves as energy reserve in plants; glycogen is the storage polysaccharide in animals and microbial cells.

It is the principal energy reserve in plants and stored as granules in the Chloroplast of the plant cell. It  is found in almost every kind of plant cell,  but Grain seeds, tubers and unripe fruits are especially rich in it. It is Starch is a Glucanasit  is a  homopolymer of  D glucose and consists of two types of polymers:- amylose which constitutes 10% to 30% and amylopectin forming remaining 70% to 90% of starch.

Amylose is linear polymer of several thousand to half a million -D glucose Units joined by 1- 4 glycosidic bond Fig.7.2a as shown above. Each glucose residue is Angled with respect to the preceding glucose due to (1-4) linkage in amylose resulting in formation of coil or helical structure as in a telephone wire. Amylopectin also consists of linear chains of -D glucose units joined by (1-4) glycoside bond; however, they branch out at every 24-30 glucose Residues by forming (1- 6) glycosidic bonds Fig.7.2b as shown below which prevents Formation  of coil.

Q6. A) Explain the classification of glycoconjugates with suitable examples. (5+5) 10

Ans) Glycoconjugates are divided into three broad classes:

1. Proteoglycans

Proteoglycans are proteins that are heavily glycosylated. The basic proteoglycan unit consists of a "core protein" with one or more covalently attached glycosaminoglycan (GAG) chain(s).The point of attachment is a serine (Ser) residue to which the glycosaminoglycan is joined through a tetrasaccharide bridge (e.g., chondroitin sulfate-GlcA-Gal-Gal-Xyl-PROTEIN). The Ser residue is generally in the sequence -Ser-Gly-X-Gly- (where X can be any amino acid residue but proline), although not every protein with this sequence has an attached glycosaminoglycan. The chains are long, linear carbohydrate polymers that are negatively charged under physiological conditions due to the occurrence of sulfate and uronic acid groups. Proteoglycans occur in connective tissue.

Examples of proteoglycans are versican (a large chondroitin sulfate proteoglycan), perlecan, neurocan, aggrecan, brevican, fibromodulin, and lumican.

2. Glycoproteins

Glycoproteins are molecules that comprise protein and carbohydrate chains that are involved in many physiological functions including immunity. Many viruses have glycoproteins that help them enter bodily cells but can also serve to be important therapeutic or preventative targets. Glycoproteins are proteins containing glycans attached to amino acid side chains. Glycans are oligosaccharide chains; which are saccharide polymers, that can attach to either lipids (glycolipids) or amino acids (glycoproteins). Typically, these bonds are formed through a process called glycosylation.

Glycoproteins function in the structure, reproduction, immune system, hormones, and protection of cells and organisms. Glycoproteins are found on the surface of the lipid bilayer of cell membranes. Hormones may be glycoproteins.

Examples include human chorionic gonadotropin (HCG) and erythropoietin (EPO).

Glycosylation occurs on a majority of proteins post-translationally with most RER synthesized proteins undergoing glycosylation. There are different forms of glycosylation that attach specific glycans to proteins and lipids.

3. Glycolipids and lipopolysaccharides

Glycolipids are biomolecular structures in the phospholipid bilayer of the cell membrane whose carbohydrate component extends to the outside of the cell. Glycolipids are essential in providing stability of the plasma membrane. Furthermore, they are also associated with cell-to-cell interactions, e.g., cell adhesion to form a tissue. They also facilitate cellular recognition, which is important in immunologic functions.

An example of a glycolipid is a glycosphingolipid. It is comprised of a carbohydrate and a sphingolipid linked together by a glycosidic bond. Hydrolysis of the glycosphingolipid, thus, yields sugar, fatty acid, and sphingosine. The glycosphingolipids are part of the cell membrane and are involved in cell-cell interactions.

Example of glycolipid is a glyceroglycolipid. It is comprised of a glycerol backbone and at least one fatty acid. It includes the galactolipids and sulfolipids.

Lipopolysaccharides (LPS) are large molecules consisting of a lipid and a polysaccharide composed of O-antigen, outer core and inner core joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria. The term lipooligosaccharide ("LOS") is used to refer to a low-molecular-weight form of bacterial lipopolysaccharides.

Example: Lipopolysaccharide (LPS) is the endotoxin portion of the gram-negative bacterial cell wall. It is one of the most abundant proinflammatory stimuli in the gastrointestinal tract and has been seen in high levels in clinical NEC.LPS impairs intestinal barrier function by causing inhibition of intestinal restitution and by promoting the release of signaling molecules such as NO and IFN-γ from enterocytes.

Q6. B) Write note blood group antigens.

Ans) The antigens expressed on the red blood cell determine an individual's blood group. The main two blood groups are called ABO (with blood types A, B, AB, and O) and Rh (with Rh D-positive or Rh D-negative blood types).

The functions of many of the blood group antigens are not known, and if they are missing from the red blood cell membrane, there is no ill effect. This suggests that if the blood group antigens used to have a function, e.g., one particular blood group antigen made red blood cells more resistant to invasion from a parasite, it is no longer relevant today. But the presence or absence of red blood cell antigens becomes extremely important when blood from different people mixes, e.g., when a patient receives a blood transfusion from a blood bank. This also happens when a mother becomes pregnant because during labor, a small amount of fetal blood enters her circulation. In these circumstances, exposure to the foreign antigens on the red blood cells can trigger immune reactions.

Q7. A) Enlist the functions of biological membranes? (5+5) 10

Ans) The main components of biological membranes are proteins, lipids, and carbohydrates in variable proportions. Carbohydrates account for less than 10% of the mass of most membranes and are generally bound either to the lipid or protein components.

Biological membranes have three primary functions:

(1) they keep toxic substances out of the cell;

(2) they contain receptors and channels that allow specific molecules, such as ions, nutrients, wastes, and metabolic products, that mediate cellular and extracellular activities to pass between organelles and between the cell and the outside environment; and

(3) they separate vital but incompatible metabolic processes conducted within organelles.

Membranes consist largely of a lipid bilayer, which is a double layer of phospholipid, cholesterol, and glycolipid molecules that contains chains of fatty acids and determines whether a membrane is formed into long flat sheets or round vesicles. Lipids give cell membranes a fluid character, with a consistency approaching that of a light oil. The fatty-acid chains allow many small, fat-soluble molecules, such as oxygen, to permeate the membrane, but they repel large, water-soluble molecules, such as sugar, and electrically charged ions, such as calcium.

Q7. B) Explain the importance of sphingolipids in biological membranes.

Ans) Sphingolipids are also important constituent of some biological membranes. Like glycerophospholipids, they also have a polar head and non-polar tails. However, they differ from    glycerophospholipids and galactolipids as they do not have glycerol. Instead, they contain along chain amino alcohol, sphingosine. Sphingosine is part of ceramide, which is the parent molecule of sphingolipids.

Sphingolipids are structural components in the plasma membranes of eukaryotic cells. Their metabolism produces bioactive signalling molecules that modulate fundamental cellular processes. The segregation of sphingolipids into distinct membrane domains is likely essential for cellular function. Sphingolipids are highly bioactive compounds that participate in the regulation of cell growth, differentiation, diverse cell functions, and apoptosis. They are present in both plant and animal foods in appreciable amounts, but little is known about their nutritional significance.

Sphingolipids are also important constituent of some biological Membranes and are derived from ceramide. They do not have glycerol, instead, they contain along chain amino alcohol, sphingosine which is part of ceramide.

Q8. Write a detailed note on classification of vitamins with relevant examples. 10

Ans) This topic is about Vitamins – classification and functions. It is a known fact that we require energy in order to perform different activities. We get these energies from the food we eat. Apart from the normal food that we take, our body requires a certain number of compounds in small amounts for the proper functioning and deficiency of these compounds may cause diseases. These compounds are known as vitamins.

Vitamins are chemical compounds that are required in small amounts with our regular diet in order to carry out certain biological functions and for the maintenance of our growth.

Classification of Vitamins

Vitamins are generally classified as water-soluble vitamins and fat-soluble vitamins.

1. Fat-Soluble Vitamins

Vitamin A, D, E and K are fat-soluble. These are stored in adipose tissues and hence are called fat-soluble vitamins.

2. Water-Soluble Vitamins

Vitamins in B-group and vitamin C are water-soluble and cannot be stored in our bodies as they pass with the water in urine. These vitamins must be supplied to our bodies with regular diets.

Vitamins and minerals are substances that are found in foods we eat. Your body needs them to work properly, so you grow and stay healthy. When it comes to vitamins, each one has a special role to play. For example:

Vitamin D in milk helps your bones.

Vitamin A in carrots helps you see at night.

Vitamin C in oranges helps your body heal if you get a cut.

B vitamins in whole grains help your body make energy from food.

Q9. A) Describe the constituents of nucleic acids with suitable structures. (5+5) 10

Ans) A nucleic acid is a polymeric macromolecule made up of repeated units of monomeric ‘nucleotides’ composed of a nitrogenous heterocyclic base which is either a purine or a pyrimidine, a pentose (five carbon) sugar (either ribose or 2′-deoxyribose), and one to three phosphate groups.

Nucleic acid isolation may be required from human cells of different types or free circulating NA. When pathogens are of interest, viruses, bacteria, protozoans, and fungi must be considered. Multiplex testing may depend on simultaneous isolation of NA from some or all of these sources. Many techniques are available, requiring a considered choice of commercial products or a combination of techniques for any given application. Many NA preparation kits from companies specialize in making the process as simple as possible. NA isolation solutions are constantly improving to meet the complex needs of an evolving diagnostic world.

The structure of deoxyribonucleic acid

Deoxyribonucleic acid (DNA) is one of the most important molecules in living cells. It encodes the instruction manual for life. Genome is the complete set of DNA molecules within the organism, so in humans this would be the DNA present in the 23 pairs of chromosomes in the nucleus plus the relatively small mitochondrial genome. Humans have a diploid genome, inheriting one set of chromosomes from each parent. A complete and functioning diploid genome is required for normal development and to maintain life.

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary

Q9. B) With the help of a neatly labelled diagram explain Griffith’s transformation experiment

Ans) Griffith's experiment, reported in 1928 by Frederick Griffith, was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation.

Griffith's famous 1928 experiment showed us that bacteria can distinctly change their function and form through transformation. Transformation is the process which describes one thing changing into another. In his experiment, Griffin injected two types of strep to cocci pneumoniae, Type III-S and Type II-R, into mice.

In the experiment they observed that:

Stage1- Living ‘S’ strain causes death in mouse.

Stage2- Living ‘R’ strain causes no-death in mouse.

Stage3- Heat killed ‘S’, strain cannot cause death in mouse.

Stage4- Mixture containing both heat killed ‘S’, strain and live ‘R’, strain  will

Cause death in mouths.

Hence, they concluded that in stage 4, some substance causing virulence in

‘S’, strain is transferred into ‘R’, strain and is responsible virulence.

Q10. A) Draw the structure of t-RNA and explain its important characteristic features. (5+5) 10

Ans)

Transfer RNA or tRNA is also known as “adapter molecule”. It binds to an Amino acid and transfer it from the cytosol to a growing polypeptide chain at the site of protein synthesis. It has sites for amino acid attachment and anticodon region for codon recognition that binds to a specific sequence on the mRNA chain through hydrogen bonding as can be seen the figure below.

The key features of tRNA are:

1. It is the smallest RNA amongst three major categories of RNA i.e., mRNA,

2. rRNA and tRNA having 73 to 93 nucleotide residues.

3. Comprises around 15% of the total RNA in the cell.

4. Sedimentation coefficient is 4S.

5. Contain certain unusual bases for example dihydrouridine (D), pseudouridine, and extensive intra-chain base pairing resulting into various loops.

6. There is at least one tRNA for each amino acid.

The secondary structure is a characteristic “cloverleaf” structure

Figure shows while tertiary structure looks like an inverted Lor 7

Q10. B) Give a detailed note on effect of temperature and pH on DNA structure.

Ans) Exposure to extremes of temperature (above 80 degrees C) or pH (acids or alkali) Leads to disruption of hydrogen bonds in the DNA duplex. pH below 2 .3 or above 10 disrupts the base-pairing potential and thus the DNA duplex is denatured. Alkali is preferred over acid as a denaturating agent because it does not hydrolyze the glycosidic linkage between sugar and purine bases. The denaturation or unwinding of DNA double helix due to heating is known as Melting of DNA. Melting temperature or Tm is the temperature at which half of the helical structure is lost. It is the midpoint of a temperature range over which the strands of a given DNA molecule separate. Tm of a DNA depends on Its base composition. DNA rich in G-C pairs melts at a higher temperature than The DNA rich in A-T pairs. Can you explain why? Because, G-C pairs have Three hydrogen bonds and are strongly bonded, as compared to A-T pairs Which have two hydrogen bonds.

The melting curve of DNA is sigmoidal. It has been estimated that under normal conditions, increase in 1% G:C in a DNA causes an increase of 0.4 o C in its melting temperature. Tm is also influenced by the salt Concentration of the solution. Every tenfold increase in monovalent cations (Na+, K+, etc) increases Tm by16.6 degrees C.