<h5 id="31-carbohydrates">3.1 Carbohydrates</h5> <ul> <li>Starch, glycogen, cellulose, chitin, and dextran are all polysaccharides with different functions.</li> <li>Starch is a storage carbohydrate in plants, composed of amylose and amylopectin. Glycogen is similar but found in animals.</li> <li>Cellulose is the most abundant extracellular structural polysaccharide, providing rigidity and strength to plant cell walls.</li> <li>Chitin is a structural component in invertebrates and fungi, with a similar structure to cellulose but with acetamido groups.</li> <li>Dextran has a wide range of molecular weights and is used for various purposes, including medical applications.</li> <li>Agar is a gelatinous heteropolysaccharide used for bacterial and plant tissue cultures and as a support for electrophoretic separation of nucleic acids.</li> </ul> <p>======</p> <h5 id="32-fatty-acids-and-lipids">3.2 Fatty Acids and Lipids</h5> <ul> <li>The text provides information about different types of lipids.</li> <li>Simple lipids include: <ul> <li>Triacylglycerols: Esters of glycerol and fatty acids, essential for energy storage.</li> <li>Waxes: Formed by esterification of fatty acids with a high molecular weight monohydric alcohol, serving as protective coatings.</li> </ul> </li> <li>Compound lipids include: <ul> <li>Phospholipids: Amphipathic molecules with hydrophobic fatty acid tails and hydrophilic phosphate group heads, primarily found in cell membranes.</li> <li>Steroids: Hydrophobic molecules with a four-fused ring structure, including cholesterol, which regulates membrane fluidity and is a precursor for steroid hormones.</li> </ul> </li> <li>Phospholipids form micelles and do not spontaneously mix with water.</li> <li>Cholesterol, a steroid, is synthesized primarily by the liver and is the key precursor for steroid hormones.</li> </ul> <p>======</p> <h5 id="33-amino-acids">3.3 Amino Acids</h5> <ul> <li>Amino acids are classified into various groups based on the properties of their R groups. These groups include:</li> </ul> <ol> <li>Polar, uncharged R groups: Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), and Glutamine (Gln).</li> <li>Aromatic R groups: Phenylalanine (Phe), Tryptophan (Trp), and Tyrosine (Tyr).</li> <li>Non-polar aliphatic amino acids: Glycine (Gly), Valine (Val), Alanine (Ala), Proline (Pro), Leucine (Leu), Isoleucine (Ile), and Methionine (Met).</li> <li>Positively charged (basic) R groups: Lysine (Lys), Arginine (Arg), and Histidine (His).</li> <li>Negatively charged (acidic) R groups: Aspartate (Asp) and Glutamate (Glu).</li> </ol> <ul> <li>The numbering of carbon in amino acids is done using Greek letters, with the additional carbons attached to the a-carbon in an R group designated as beta, gamma, delta, epsilon, and so on.</li> <li>At physiological pH (pH = 7), the a-COOH group and a-NH2 group of amino acids are ionized (deprotonated) in solutions to form -COO- (bearing negative charge) and the -NH3+ (bearing a positive charge), respectively, resulting in a dipolar state called zwitterion.</li> <li>Some amino acids are non-standard amino acids, which occur naturally in cells but do not take part in protein synthesis. Examples include 4-hydroxyproline, 5-hydroxylysine, selenocysteine, and γ-carboxyglutamic acid.</li> <li>Amino acids that are not part of proteins are widely present in various plants, animals, and microbes, known as non-protein amino acids. Examples include L-ornithine, L-citrulline, β-alanine, creatine, and γ-aminobutyrate.</li> </ul> <p>======</p> <h5 id="34-protein-structure">3.4 Protein Structure</h5> <ul> <li>Proteins are essential macromolecules in all cells, made up of 20 naturally occurring amino acids.</li> <li>The sequence and composition of amino acids determine the protein’s structure.</li> <li>There are four levels of protein structure: primary, secondary, tertiary, and quaternary.</li> <li>Primary structure is the linear sequence of amino acids linked by peptide bonds.</li> <li>Secondary structure involves specific residual patterns, while tertiary structure includes 3D folding of polypeptides.</li> <li>Quaternary structure is the complex of two or more polypeptide subunits.</li> <li>Proteins play crucial roles in various cellular processes, such as catalysis, transport, immunity, and signaling.</li> </ul> <p>======</p> <h5 id="341-primary-structure-of-proteins">3.4.1 Primary structure of proteins</h5> <ul> <li>The primary structure of proteins is the linear sequence of amino acids linked by peptide bonds.</li> <li>A peptide bond is formed by the coupling of the alpha-carboxyl group of one amino acid to the alpha-amino group of another.</li> <li>The equilibrium of this reaction lies on the side of hydrolysis, making the biosynthesis of peptide bonds require an input of free energy.</li> <li>Polypeptides are named based on the number of amino acids they contain, such as a dipeptide (2), tripeptide (3), and so on.</li> <li>The flexibility of the polypeptide backbone comes from the rotation of two bonds adjacent to the peptide bond, leading to various orientations and many possible ways proteins can fold.</li> </ul> <p>======</p> <h5 id="342-secondary-structure-of-proteins">3.4.2 Secondary structure of proteins</h5> <ul> <li>The secondary structure of proteins pertains to the folding of the polypeptide chain.</li> <li>In 1951, Linus Pauling and Robert Corey proposed two main types of periodic structures: a) Alpha-helix (a-helix) b) Beta-pleated sheet (β-pleated sheet)</li> <li>The a-helix is a rod-like structure with the polypeptide chain coiled around it.</li> <li>The β-pleated sheet is formed by alignment of extended polypeptide chains alongside each other, which can be either parallel or anti-parallel.</li> <li>These secondary structures are crucial in understanding protein conformation and function.</li> </ul> <p>======</p> <h5 id="alpha-helix">$\alpha$ Helix</h5> <ul> <li>The polypeptide chain with planar peptide bonds can form a helical structure, known as an α-helix, by twisting about the Ca−N and the Ca−C bonds.</li> <li>The hydrogen bonds between NH and CO groups of the main chain stabilize the helix, with CO group of each amino acid forming hydrogen bonds with the NH group of the amino acid four residues ahead in the sequence.</li> <li>The α-helix can be right-handed (clockwise) or left-handed (counterclockwise), but all known polypeptides contain right-handed α-helices due to less clash between side chains and the backbone.</li> <li>The occurrence of a helical content in proteins ranges widely, with examples like ferritin having 75% of its amino acid residues form a helix.</li> <li>The α-helices provide mechanical strength to the stiff bundles of fibers, as seen in myosin and tropomyosin of muscles and keratin of hair.</li> </ul> <p>======</p> <h5 id="beta-pleated-sheet">$\beta$ Pleated sheet</h5> <ul> <li>The second type of periodic structure suggested by Pauling and Corey is the $\beta$ pleated sheet.</li> <li>Unlike $\alpha$-helix, $\beta$ pleated sheet involves hydrogen bonds between groups from residues distant from each other in the linear sequence.</li> <li>In $\beta$ sheets, two or more strands widely separated in the protein sequence are arranged side by side, with hydrogen bonds between the strands.</li> <li>Based on the orientation of the strands, $\beta$ sheets are of two types: parallel and anti-parallel $\beta$ sheets.</li> <li>Parallel $\beta$ sheets are less twisted as compared to anti-parallel. The branched amino acids such as valine and isoleucine can fit more easily in $\beta$ sheet structure than in a tightly coiled $\alpha$ helix.</li> </ul> <p>======</p> <h5 id="343-tertiary-structure-of-protein">3.4.3 Tertiary structure of protein</h5> <ul> <li>The tertiary structure of a protein refers to the overall three-dimensional arrangement of all residues in a protein.</li> <li>It includes larger range aspects of amino acid sequences, including interactions between amino acids that are far apart in the polypeptide chain.</li> <li>The formation of additional bonds, such as disulfide, hydrogen, hydrophobic, and ionic bonds, contributes to the tertiary structure.</li> <li>Disulfide bonds, formed by oxidation of a pair of cysteine residues, make the protein globular in shape.</li> <li>The polar R groups of amino acid residues are located on the outer side, while the non-polar R groups are located in the interior to form hydrophobic interactions.</li> <li>The three-dimensional structure of more than one thousand proteins has been revealed by x-ray crystallography and nuclear magnetic resonance (NMR) techniques.</li> </ul> <p>======</p> <h5 id="344-quaternary-structure-of-protein">3.4.4 Quaternary structure of protein</h5> <ul> <li>Proteins can consist of more than one polypeptide subunit, which can be identical or different in their primary structure.</li> <li>These subunits associate specifically to form a comparatively larger and complex molecule, known as quaternary structure.</li> <li>Quaternary structure is the spatial arrangement of the protein subunits, stabilized by hydrogen bonds, electrostatic interactions, ionic bonds, and disulfide bridges.</li> <li>The number of subunits can vary, leading to different types of quaternary structures such as dimer, trimer, etc.</li> <li>Identical protein subunits form homodimers, homotrimers, etc., while non-identical subunits form heterodimers, heterotrimers, etc. An example is the quaternary structure of haemoglobin.</li> </ul> <p>======</p> <h5 id="35-nucleic-acids">3.5 NUCLEIC ACIDS</h5> <ul> <li>Nucleic acids are found in cell organelles like the nucleus, mitochondria, and chloroplasts, associated with histone proteins in the nucleus.</li> <li>The two types of nucleic acids are DNA and RNA, with DNA acting as genetic material and RNA serving as genetic material in some viruses.</li> <li>Nucleotides, the building blocks of nucleic acids, consist of a nitrogenous base, sugar, and phosphate, with sugar types being 2’-deoxy-D-ribose in DNA and D-ribose in RNA.</li> <li>Nitrogenous bases are of two types: purines (adenine and guanine) and pyrimidines (cytosine, thymine in DNA, and uracil in RNA).</li> <li>Nucleotides are created by linking a base, sugar, and phosphate together, while nucleosides are formed by linking only a base and sugar; DNA nucleotides are indicated with a ’d’ prefix.</li> </ul> <p>======</p> <h5 id="351-polynucleotide-chain">3.5.1 Polynucleotide chain</h5> <ul> <li> <p>A polynucleotide chain is formed by the covalent linking of nucleotides, with the 3’hydroxyl ($-\mathrm{OH}$) group of one nucleotide unit esterified to the $-\mathrm{OH}$ group of the phosphate attached to the 5’ carbon atom of the next nucleotide.</p> </li> <li> <p>The two strands of the DNA double helix are oriented antiparallel, with their 3’ and 5’ phosphodiester bonds running in opposite directions.</p> </li> <li> <p>The Watson-Crick structure of DNA, also known as B-DNA, consists of two polynucleotide chains of DNA wound around the same axis to form a right-handed double helix, with the bases of both strands stacked inside the core.</p> </li> <li> <p>Adenine (A) on one strand forms two hydrogen bonds with thymine (T) on the other, and guanine (G) on one strand forms three hydrogen bonds with cytosine (C) on the other.</p> </li> <li> <p>Heating or exposure to acid or alkali can disrupt the hydrogen bonds between the base pairs, leading to denaturation or melting of the DNA, while cooling can allow the strands to reassociate or anneal.</p> </li> </ul> <p>======</p> <h5 id="352-types-of-rna">3.5.2 Types of RNA</h5> <ul> <li>RNA, or ribonucleic acid, is a nucleic acid present in the cells of all living organisms.</li> <li>There are three main types of RNA: mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA).</li> <li>mRNA plays a crucial role in protein synthesis, carrying genetic information from the DNA to the ribosomes.</li> <li>tRNA is responsible for bringing the necessary amino acids to the ribosomes during protein synthesis.</li> <li>rRNA is a component of ribosomes, assisting in the process of protein synthesis by translating mRNA into proteins.</li> </ul> <p>======</p> <h5 id="messenger-rna-mrna">Messenger RNA (mRNA)</h5> <ul> <li>Messenger RNA (mRNA) is a single strand linear polyribonucleotide chain that carries genetic information from DNA to ribosomes.</li> <li>It has untranslated regions (UTR) at both ends, with the 5’ end containing a guanylate that is methylated at its N-7 in eukaryotic mRNA, a process known as capping.</li> <li>The coding region of mRNA is located between the initiation codon and the stop codon.</li> <li>At the 3’ end of mRNA, there is another UTR, followed by the addition of several adenylate residues, a process called polyadenylation.</li> <li>Fig 3.34 provides a schematic representation of a typical prokaryotic mRNA.</li> </ul> <p>======</p> <h5 id="ribosomal-rna-rrna">Ribosomal RNA (rRNA)</h5> <ul> <li>Ribosomal RNA (rRNA) is a significant component of ribosomes.</li> <li>In prokaryotic ribosomes (70S), the smaller subunit (30S) contains 16S rRNA, while the larger subunit (50S) contains 23S and 5S rRNAs.</li> <li>Eukaryotic ribosomes (80S) have a different composition: the smaller subunit (40S) includes 18S rRNA, and the larger subunit (60S) contains 28S, 5.8S, and 5S rRNAs.</li> <li>The S value represents the sedimentation coefficient, which provides information about the size and shape of the ribosomal subunits.</li> <li>The differences in rRNA composition and sedimentation coefficients reflect the distinctions between prokaryotic and eukaryotic ribosomes.</li> </ul> <p>======</p> <h5 id="transfer-rna-trna">Transfer RNA (tRNA)</h5> <ul> <li>Transfer RNA (tRNA) are small RNA molecules that play a crucial role in protein synthesis by transporting amino acids to ribosomes.</li> <li>The structure of a tRNA molecule consists of a single ribopolynucleotide chain folded into four arms.</li> <li>The acceptor arm has a CCA sequence at the 3’OH end, which serves as the amino acid binding site.</li> <li>The anticodon arm contains the anticodon, a set of three bases that recognizes and binds to a specific codon of mRNA during translation.</li> <li>The tRNA structure also includes the D-arm and the TψC-arm, which are important for proper folding and function of the tRNA molecule.</li> </ul> <p>======</p>