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UNIT SPECIFICS
Through this unit, we have discussed the following aspects:
● The Molecules of Life- Biomolecules
● Understanding that macromolecules like proteins and nucleic acids are polymers of
monomers with distinct chemical properties
● Carbohydrates as a fuel of living organisms
● Nucleic acids as the carrier of genetic information
● Lipids and Fats as store-house of energy
The practical applications of the topics are discussed for generating further curiosity and creativity as well as improving problem solving capacity.
Besides giving a large number of multiple choice questions as well as questions of short and long answer types marked in two categories following lower and higher order of Bloom’s taxonomy , assignments through a number of numerical problems, a list of references and suggested readings are given in the unit so that one can go through them for practice. It is important to note that for getting more information on various topics of interest some QR codes have been provided in different sections which can be scanned for relevant supportive knowledge.
After the related practical, based on the content, there is a “Know More ” section. This section has been carefully designed so that the supplementary information provided in this part becomes beneficial for the users of the book. This section mainly highlights the initial activity, examples of some interesting facts, analogy, history of the development of the subject focusing the salient observations and finding, timelines starting from the development of the concerned topics up to the recent time, applications of the subject matter for our day-to-day real life or/and industrial applications on variety of aspects, case study related to environmental, sustainability, social and ethical issues whichever applicable, and finally inquisitiveness and curiosity topics of the unit.
Biomolecules
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RATIONALE
To convey that all forms of life has the same building blocks and yet the manifestations are as
diverse as one can imagine. Molecules of life. In this context discuss monomeric units and polymeric structures. Discuss about sugars, starch and cellulose. Amino acids and proteins. Nucleotides and DNA/RNA. Two carbon units and lipids.
It is crucial for engineering students to comprehend the fundamentals of engineering and the introduction of biological concepts in order to interact well on finding solutions to issues relating
to biosystems. Learning this will help to apply engineering principles for analysing biological systems and develop energy‐saving technologies that work in harmony with biosystems.
PREREQUISITES
Biology: Biomolecules (Class XI)
Chemistry: Biomolecules (Class XII)
UNIT OUTCOMES
List of outcomes of this unit is as follows:
U4-O1: Describe the role of biomolecules in the biosystem
U4-O2: List the four major classes of macromolecules and distinguish between monomers and
polymers
U4-O3: Discuss structure, location and function of Glucose, Cellulose and Starch
Explain classification of carbohydrates on basis of hydrolysis
U4-O4: Differentiate DNA and RNA and discuss stability of DNA and RNA
U4-O5: Describe structure and functions of lipids and fats
Unit- Outcomes
EXPECTED MAPPING WITH COURSE OUTCOMES (1- Weak Correlation; 2- Medium correlation; 3- Strong Correla tion) CO-1 CO-2 CO-3 CO-4 CO- U4‐O1 2 3 1 1 1 U4‐O2 1 3 1 1 1 U4‐O3 1 3 1 2 2 U4‐O4 1 3 3 1 1 U4‐O5 1 3 1 2 2
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4.2 STRUCTURAL ORGANIZATION OF COMPLEX BIOMOLECULES
In the first phase, precursors are transformed into metabolites, which are basic organic chemicals that act as intermediaries in the biogenesis of several building block sets, such as glycerol, sugar complex carbohydrates, amino acids, nucleotides, and fatty acids. These building ingredients are joined covalently to form macromolecules, including proteins, polysaccharides, and polynucleotides (DNA and RNA). The next stage of structural organization, supramolecular complexes, is produced by interactions between macromolecules. Various members of one or more macromolecule classes combine to create particular assemblies that perform crucial subcellular tasks. Chromosomes, multifunctional enzyme complexes, ribosomes, and cytoskeletal components are examples of supramolecular assemblies. Before going into these complex structures, we shall have an in-depth view of these monomer molecules and then the polymeric structures of these monomers.
4.2.1 Monomers & Polymers
Polymers are compounds consisting of several smaller monomeric subunits that are bonded covalently. Condensation is a chemical process that binds interacting biological molecules. The removal of water creates a molecule of water for each chemical link, wherein -H and -OH atoms are extracted from opposite sides, forming a bond between the two molecules. In contrast to condensation, hydrolysis releases smaller molecules by rupturing the polymer's bond(s) (often individual monomers). To break the connection, a water molecule is needed. Doing so adds -H and -OH to either side.
Fig. 4. 2 Condensation reaction Fig. 4. 3 Hydrolysis reaction
(Images created using BioRender® software)
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4.3 PROTEINS
4.3.1 Amino acids
Amino acids are the building blocks that form polypeptides and, ultimately, proteins. Consequently, they are fundamental components of our bodies and vital for physiological functions such as protein synthesis, tissue repair, and nutrient absorption. As demonstrated in Fig. (4.4). The fundamental structure of amino acids is the same for all of them and consists of a core carbon atom coupled to:
1) An amine group (NH 2 ) 2) A carboxylic acid group (COOH)
3) A hydrogen atom (H) 4) A variable side chain (R)
Fig. 4. 4 Empirical structure of amino acids Source: wikimedia.org (Creative Common License)
Proteins include 22 different amino acids, although only 20 of them are listed in the human genetic code. Pyrrolysine and selenocysteine are two uncommon amino acids that are found in nature. Because they are less common in nature than the other amino acids, they are known as rare amino acids. While Pyrrolysine (Pyl) is found in methanogenic archaea, Selenocysteine (Sec) is prevalent in bacteria and eukaryotes.
Classification of Amino acids on basis of Polarity - The structure of the variable side chain varies for each kind of amino acid. According to their exact positions within the polypeptide chain, these side chains will have varied chemical characteristics (e.g., charged, non-polar, etc.), causing the protein to fold and function differently.Amino acids are grouped into five categories based on their polarity: (Fig 4.5).
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Non-Essential Amino acids : Of the total of twenty amino acids, eleven are considered non- essential amino acids since the body may produce them on its own. Alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine are among the non-essential amino acids. Conditional Amino acids : Because the body cannot synthesize enough arginine and histidine during particular physiological times of growth, such as pregnancy, teenage growth, or recovery from trauma, these amino acids may be regarded as conditionally necessary.
Stereochemistry of Amino Acids - All other amino acids included in protein structures are chiral in nature except for glycine, the most basic amino acid. All naturally occurring chiral amino acids are S, except for Cys, which is R, according to modern stereochemistry assignments using the Cahn-Ingold-Prelog priority criteria, which are widely used in chemistry. L-amino acids make up almost all proteins known to exist in plants and animals. However, D-amino acids are found in the cell walls of some bacteria, and some antibiotics (such as actinomycin D and gramicidin) include various levels of D-leucine, D-phenylalanine, and D-valine.
Fig. 4. 6 Stereochemistry of Amino acids (Source: Created with ChemDraw software)
4.3.2 Peptide Bond Formation and Primary Protein Structure
The carboxylic acid of the upstream amino acid and the amine functional group of the downstream amino acid combine to produce an amide linkage, which is how a protein's main sequence is joined together by a dehydration synthesis (loss of water). The opposite reaction, called hydrolysis, requires the inclusion of a water molecule to break the amide bond and separate the two amino acids. It should be noted that the ribosome acts as the enzyme that conducts the dehydration synthesis processes necessary to construct protein molecules. In contrast, a class of enzymes called proteases is essential for protein breakdown. The amide linkage between amino acids inside protein structures is a peptide bond. More amino acids will be added to the carboxylic acid terminal of the developing protein. As a result, the amine and carboxylic acid tails are always produced in a particular order throughout the synthesis of proteins. The carboxylic acid tail of the previous amino acid is always where new amino acids are introduced, never the amine. The ribosome controls the directionality of N- to C- synthesis, which is how proteins are synthesized.
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Fig. 4. 7 Formation of the Peptide Bond Source: wikimedia.org (Creative Common License)
Proteins are significant molecules that consist of several amino acid residues connected in a very specific manner. Proteins come in various sizes, with the longest one known to exist having 33,423 amino acids named Titin. Peptides are macromolecules containing less than 50 amino acids, one of the smallest known human proteins, thymosin, only has 44 amino acids. Based on the protein's environment, a protein's folding pattern is determined by the kind and order of the amino acids in its main sequence (i.e., if it is inside the cell, it is likely surrounded by water in a very polar environment, whereas if the protein is embedded in the plasma membrane, it will be surrounded by very nonpolar hydrocarbon tails). Many alternative protein combinations may be employed to produce unique protein structures since a vast selection of amino acids can be inserted at each place inside the protein. Consider a tripeptide created from this pool of amino acids as an illustration. Twenty distinct alternatives may be used at each location. This means that there are a total of 20^3 tripeptides that might result, which is equal to 8,000 potential combinations. Think about the potential uses for a 40-amino-acid short peptide. 20^40 possibilities, or a staggering 1. X 10^52 possible sequence alternatives, would be available. Since the nature of the amino acid side chains influences how the protein interacts with other residues within the protein and its environment, each of these alternatives would result in a different overall protein shape.
The characteristics of the amino acids that make up a protein's 3-dimensional structure aid in protein folding. Protein form equals protein function. Hence the protein must have this 3-D structure to function. Hydrophobic amino acids are frequently located on the interior of protein structures for proteins found within the watery surroundings of cells. In contrast, hydrophilic amino acids, which love water, are found on the surface, where they may form hydrogen bonds and interact with the water molecules. Because it is the sole R-group that associates with the amine functional group in the main chain to generate a cyclic structure, proline is special. Proline adopts the cis conformation inside the backbone rather than the trans conformation due to this cyclization. Since the protein's structure has changed, prolines are frequently seen at locations where bends or directional changes take place. As the first amino acid for practically all of the many thousands of proteins known to exist in nature, methionine is special. Cysteine can be oxidized with other
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4.4 CARBOHYDRATES
Carbohydrates are represented by the chemical formula (CH 2 O)n ,where n is the number of carbon atoms in the molecule. Carbon, hydrogen, and oxygen are arranged in the molecules of carbohydrates in a 1:2:1 ratio. Thus, the definition of the word "carbohydrate" is explained by the fact that it is composed of carbon ("carbo") and water ("hydrate"). Ketones or polyhydroxy aldehydes can be referred to as carbohydrates. Monosaccharides, disaccharides, and polysaccharides are the three subcategories of carbohydrates.
4.4.1 Monosaccharides
Monosaccharides, commonly referred to as simple sugars, are the most basic kind of carbohydrates. They have the general formula Cn (H 2 O)n and cannot be further hydrolyzed. The monosaccharides are divided into distinct categories based on the functional group and the number of carbon atoms. They are divided into two categories based on functional groups: aldoses and ketoses.
Aldoses: When the functional group in monosaccharides is an aldehyde, they are known as aldoses, e.g. glyceraldehyde, and glucose.
Ketoses: When a functional group is a keto group, they are called ketoses e.g,. dihydroxyacetone, and fructose.
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Fig. 4. 10 Monosaccharides (Source: Created with ChemDraw software)
The monosaccharides are classified as trioses (3C), tetroses (4C), pentoses (5C), hexoses (6C), and heptoses (7C) based on the number of carbon atoms. When naming monosaccharides, these terms are used with functional groups. For example, fructose is a ketohexose, whereas glucose is an aldohexose.
Monosaccharides can take the form of a linear chain or a ring-shaped molecule. In aqueous solutions, they are often found in ring shapes. When glucose is in a ring shape, the hydroxyl group (OH) can be arranged in one of two ways around the anomeric carbon (carbon 1 becomes asymmetric during ring formation). When the hydroxyl group is found below carbon atom number 1, it is said to be in the alpha position (α), and when it is located above the plane, it is said to be in the beta position (β).
Fig. 4. 11 Stereochemistry of glucose (Source: Created with ChemDraw software)
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Fig. 4. 15 β‐glycosidic linkage in Maltose (β‐glucose & β‐galactose binds via β‐glycosidic linkage to form Maltose) (Source: Created with ChemDraw software)
1,6-glycosidic bond - A covalent link between the -OH group on carbon 1 of one sugar and the -OH
group on carbon 6 of another sugar is known as a 1,6-glycosidic bond. The polysaccharide branches due to this linkage.
Fig. 4. 16 1,6‐glycosidic bond in amylopectin (Source: Created with ChemDraw software)
The oligo-saccharides are further split into disaccharides, trisaccharides, etc., depending on the number of monosaccharide units present. A disaccharide comprises two monosaccharide units, which can be the same or different, and is kept together by a glycosidic bond. Distinct features include crystalline nature, water-solubility, and sweetness to taste. Examples of disaccharides include lactose, maltose, and sucrose, typically found in nature and everyday diets. The monomers of lactose are glucose and galactose. They naturally occur in milk. Maltose, often known as malt sugar, is a disaccharide formed when two molecules of glucose undergo a condensation reaction in which a water molecule is lost. Yet another prevalent disaccharide is sucrose, or table sugar, made of fructose and glucose.
Two forms of disaccharides exist:
a. Reducing sugars: If the carbonyl group in the sugars is not involved in the glycosidic linkage, then they retain their reducing property; such sugars are called reducing sugars, i.e., having a free aldehyde or ketogroup end, e.g., maltose, lactose.
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b. Non-reducing sugars: If the carbonyl group in the sugars is involved in the glycosidic linkage, then they are not available for reduction. Such sugars are callednon-reducing sugars, i.e. have NO free aldehyde or ketogroup end, e.g., sucrose, trehalose.
4.4.3 Polysaccharides
Polysaccharides are high-molecular-weight polymers comprising monosaccharide molecules (up to a million). They typically have no taste (non-sugars) and combine with water to form colloids. There are two different kinds of polysaccharides: homopolysaccharides and heteropolysaccharides. A homopolysaccharide is a polysaccharide that includes the same type of monosaccharide. Glycogen, Cellulose, and Starch are examples of essential homopolysaccharides. A heteropolysaccharide is a polysaccharidethat includes different types of monosaccharides. Hyaluronic acid and Heparin are examples of homopolysaccharides.
Table 4. 1 Classification of carbohydrates
Disaccharides Polysaccharides Carbohydrates Maltose Sucrose Lactose Starch Cellulose Glycogen Linkages α-1,4- glycosidic linkages
α-1,2- glycosidic linkages
β-1,4- glycosidic linkages
α-1,4- glycosidic linkages & α-1,6- glycosidic linkages
β-1,4- glycosidic linkages
α-1,4- glycosidic linkages & α-1,6- glycosidic linkages
Monomers Glucose Glucose & Fructose
Glucose & Galactose
α-Glucose β-Glucose α-Glucose
Fig. 4. 17 Difference in the arrangement of glucose monomers in different polysaccharides Source: wikimedia.org (Creative Common License)
Cellulose - A straight, ribbon-shaped polymer of glucose molecules called cellulose with the C1, and
C4 carbons of the glucopyranose rings form glycosidic connections to connect the individual
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Fig. 4. 20 Starch in plants (Images created using BioRender® software)
Fig. 4. 21 Structure of Starch Source: wikimedia.org (Creative Common License)
4.5 NUCLEIC ACIDS
Large macromolecules called nucleic acids are necessary for all organisms and viruses to function. The templates for the proteins that cells produce are contained in nucleic acids, which are information molecules. The preservation and expression of genetic data is a crucial role of nucleic acids. Additionally, because reproducing cells convey the blueprints to their progeny, they serve as the genetic material in cells. Deoxyribonucleic acid (DNA) and ribonucleic acid are the two primary forms of nucleic acids (RNA). Nucleotides are the monomers that make up DNA and RNA. A nucleic acid, such as DNA or RNA, is created when the nucleotides combine. Each nucleotide has a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group, whereas nucleosides only have a nitrogenous base and a five-carbon carbohydrate group. Consequently, a nucleoside with one or more phosphate groups attached is what is known as a nucleotide. The nitrogenous base may be either a purine or a pyrimidine. Purines are two-ring structures that
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include inosine (I), adenine (A), and guanine (G) whereas pyrimidines are one-ring structures that include uracil (U), cytosine (C), and thymine (T) (Fig. 4.22). Both purine and pyrimidine nitrogenous bases are made from amino acids. Nucleotide's nitrogenous bases are each joined to sugar molecules that have one or more phosphate groups linked to them. Adenine (A), Thymine (T), Guanine (G), and Cytosine (C) are the bases that are employed in DNA. Thymine (T) is replaced by the nucleotide Uracil (U) in RNA.
Fig. 4. 22 Nucleic acids (Images created using BioRender® software)
4.5.1 DNA
All living things have genetic material called DNA. Eukaryotic cells have it in their nuclei, chloroplasts, and mitochondria. DNA is not contained within a nucleus in prokaryotes. The information that cells require to produce proteins is encoded by deoxyribonucleic acid. A DNA double helix consists of two right-handed spiral chains of a polynucleotide. Hydrophilic and hydrophobic interactions between the molecules that make up DNA and the water in a cell cause DNA to twist. The replication of DNA and the synthesis of proteins in our cells are significantly dependent on the double-helical structure of DNA. Both strands are antiparallel to each other which means that if one strand is in 3’ to 5’ direction then the other will be oriented in 5’ to 3’ direction. The strands are held together by hydrogen bonds between base pairs. Only specific kinds of base pairing take place. The only possible pairings for A and G are T and C. This is referred to as the base complementary rule. Or, to put it another way, the DNA strands are complementary to one another. If one strand has the sequence 5′-AATTGGCC-3′, the complementary strand would have the sequence 3′-TTAACCGG-5′. The base pairs are stabilized by forming two hydrogen bonds
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Fig. 4. 24 Transfer RNA (tRNA) Source: wikimedia.org (Creative Common License) A tRNA joined by an amino acid is known as an aminoacyl-tRNA. The kind of amino acid present in a tRNA is determined by the mRNA codon, a sequence of three nucleotides that codes for an amino acid. The mRNA codon's complementary anticodon, which specifies which amino acid to carry, is located on the anticodon arm of the tRNA. By removing cytochrome c from the body, tRNAs also control apoptosis.
Ribosomal RNA (rRNA) - Ribosomes are necessary for protein synthesis and are made up of rRNA and ribosomal proteins. There are two ribosomal subunits: a large and a small one. A prokaryotic 70S ribosome comprises the small 30S and large 50S ribosomal subunits. The 40S and 60S subunits combine to generate an 80S ribosome in eukaryotes. (Note: Here S is the svedberg unit corresponding to the sedimentation coefficient. It does not comply with the associative property of addition.) The ribosomes have three sites for binding aminoacyl-tRNAs and combining amino acids to form polypeptides: the exit (E), peptidyl (P), and acceptor (A) sites.
MicroRNA (miRNA) - Small, single-stranded, non-coding RNA molecules called miRNA attach to target mRNA to block the creation of proteins by one of two different processes. Primary miRNA (pri-miRNA), which joins the effector complex RNA-induced silencing complex (RISC), is cleaved twice to produce mature miRNA. The miRNA acts as a guide by base-pairing with the target mRNA to inhibit its production. In other words, microRNAs help regulate gene expression in cells.
4.5.3 Linkages in DNA & RNA
Phosphodiester Bonds - Phosphodiester bonds stabilize DNA and RNA. It is the phosphate group's bond with the sugar. The nucleotide polymers DNA and RNA are created by joining two distinct nucleotides via a diester bond (between phosphoric acid and two sugar molecules).
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Fig. 4. 25 Phosphodiester bond in a strand of a polynucleotide (Source: Created with ChemDraw software) A phosphodiester bond is the link between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, such as ribose in RNA and deoxyribose in DNA. With two pentoses that have five carbons apiece and are connected by two ester bonds, the phosphate group produces strong covalent bonds.
Hydrogen Bonds - The positive hydrogen end of a polar N-H bond joins with a pair of electrons on either nitrogen or carbonyl oxygen to create a hydrogen bond. Another crucial characteristic of these "complementary" base pairs is that a purine base (adenine or guanidine) invariably links to a pyrimidine base (cytosine or thymine). This implies that the separation between the two strands is always controlled and the same (three rings and hydrogen bonds). A-T binds together in two hydrogen bonds, while the C-G pair makes three. The two DNA strands are held together by hydrogen bonds formed between complementary nucleotides. Chemical bonding does not apply to hydrogen bonds as they are susceptible to disruption. As a result, the DNA strands can split apart for replication and transcription of DNA to RNA (copying DNA to DNA).
