CM38 - Reference Book PDF - DNA Molecular Structure

7-7 DNA and the Importance of Molecular Structure Biomolecules - plays an important role in the structure and function of deoxyribonucleic acid or DNA (the molecule that stores the genetic code) Deoxyribonucleic acid - everything depends on your genetic makeup - all physical traits ar...

7-7 DNA and the Importance of Molecular Structure Biomolecules - plays an important role in the structure and function of deoxyribonucleic acid or DNA (the molecule that stores the genetic code) Deoxyribonucleic acid - everything depends on your genetic makeup - all physical traits are determined by the composition of approximately 1m of tightly coiled DNA that makes up 23 double-stranded chromosomes in the nucleus of each cell - deoxyribose units in the backbone chain are joined through phosphate diester linkages. - Phosphoric acid is H3PO4 then by replacing two H atoms with two CH3 groups, it turns into phosphate diester, O=P (OH3) Nucleotides of DNA - DNA is a polymer (a molecule composed of many small, repeating units bonded together) - the phosphate groups and the deoxyribose sugar groups form the backbone of the DNA - the nitrogenous base carries the genetic code - Each repeating unit in DNA is called a nucleotide and it has three connected parts – one sugar unit, one phosphate group (phosphoric acid unit), and a cyclic compound known as a nitrogen base - in DNA, the sugar is always deoxyribose and the base is one of four bases – adenine (A), thymine (T), guanine (G), or cytosine (C), and their single-letter abbreviation often refers to them - the phosphate units join nucleotides into a polynucleotide chain that has a backbone of alternating deoxyribose and phosphate units in a long strand with the various nitrogenous bases extending out from the sugar-phosphate backbone - the order of the nucleotides along the DNA strand carries the genetic code from one generation to the next The Double Helix: Watson-Crick Model - in the early 1950s, Erwin Chargaff measured the quantities of nitrogen bases in DNA samples from a broad range of organism - he found out that any given organism shows that; - (1) the base composition is the same in all cells of the organism and is characteristic of that organism - (2) the quantities of adenine and thymine are equally similar to the quantities of guanine and cytosine - (3) the sum of the quantities of adenine plus guanine equals the sum of the quantities of cytosine plus thymine - the American biologist James D. Watson and the British physicist Francis H. C. Crick proposed the double helix structure for DNA in 1953  - Watson-Crick structure shows two polynucleotide DNA strands winding around each other to form a double helix - Watson and Crick proposed the double helix structure due to how hydrogen bonding could stabilize the DNA - hydrogen bonds form between specific base pairs lying opposite to each other in the two polynucleotide strands - A-T and G-C are hydrogen-bonded to each other forming complementary base pairs (each base in one strand hydrogen bonds to its complementary base in the other strand) resulting in stacking one above the other in the interior of the double helix Francis H. C. Crick & James D. Watson - working in the Cavendish Laboratory at Cambridge, England - Watson and Crick built a scale of the model of the double-helical structure - They compared the model to a 3D jigsaw puzzle - Watson, Crick, and Maurice Wilkins received the 1962 Nobel Prize in Physiology or Medicine Double-stranded DNA - shows the deoxyribose-phosphate backbone of each strand as phosphate groups (orange and red) linking five-membered rings of deoxyribose joined to bases - hydrogen bonds connect the complementary bases (blue): two between adenine and thymine and three for guanine and cytosine implying that the bases occur in pairs - using X-ray crystallography, Rosalind Franklin and Maurice Wilkins found the relative positions of atoms in the DNA as well as the concept of A-T and G-C base pairs The Genetic Code and DNA Replication - the DNA sequence of base pairs in the nucleus of a cell represents a genetic code that controls the inherited characteristics of the next generation as well as most of the life processes of an organism - the total sequence of base pairs in a plant or animal cell is called the genome - in humans, the double-stranded DNA forms 46 chromosomes (23 chromosome pairs)  - the gene that accounts for a particular hereditary trait is usually located in the same position on the same chromosome - each gene is a unique sequence of nitrogen bases that codes for the synthesis of a single protein within the body - the gene can be “read” by chemical processes involving RNA (ribonucleic acid which is a structure closely related to DNA) and used to control the synthesis of a protein molecule - the protein plays its role in the growth and functioning of an individual - each organism (except the virus) begins life as a single-cell - each single strand from each parent forms the double-stranded DNA DNA replication - when the original DNA helix unwinds, each half is a template on which nucleotides from the cell environment assemble to produce a complementary strand - each new double strand is an exact replica of the original - DNA strands are accurately copied with a low chance of error - replication is the process of copying a DNA molecule and it takes place as enzymes that help in breaking hydrogen bonds between strands unzipping the DNA helix - this process is called semiconservative because, in each of two new cells, each chromosome consists of one DNA strand from the parent cell and one newly made strand 10-7 Biopolymers: Polysaccharides and Proteins Biopolymers - naturally occurring polymers - an integral part of living things - helps in creating and understanding synthetic polymers - cellulose and starch made in plants by condensation polymerization reactions resemble synthetic polymers because their monomer molecules–glucose–are all alike - proteins differ from synthetic polymers because they include many different monomers - the occurrence of different monomers along the protein polymer chain is regular and it results in proteins being extremely complex condensation copolymers. Monosaccharides to Polysaccharides - nature makes an abundance of compounds with the general formula Cx(H2O)y where x and y are whole numbers - Examples: glucose (C6H12O6) - these compounds are known as sugars, carbohydrates, mono-, di-, or polysaccharides and they are derived from the Latin word saccharum which means sugar because they taste sweet. - the simplest carbohydrates such as glucose are called monosaccharides or simple sugars (because they only contain a single saccharide molecule)  - disaccharides consist of two monosaccharide units joined together such as sucrose (table sugar, glucose, and fructose linked) or maltose (two glucose units linked) - polysaccharides are polymers that contain many monosaccharide units, up to several thousand - the monomer units of disaccharides and polysaccharides are joined by a C-O-C structure called glycosidic linkage between carbons 1 and 4 or 1 and 6 adjacent monosaccharide units Glycosidic linkage - is formed by a condensation reaction similar to how synthetic polymers are formed - water molecule is released during the formation of each glycosidic bond from the reaction between the -OH groups of the monosaccharide monomers - joins two monosaccharide units - polysaccharides contain many saccharide monomers via glycosidic linkages - starches and cellulose are the most abundant natural polysaccharides - D-glucose is the monomer in each of these polymers which contains as many as 5000 glucose units Polysaccharides: Starches and Glycogen - plant starch is stored in protein-covered granules until glucose is needed for the synthesis of new molecules or energy production - if these granules rupture via high temperature, they yield amylose and amylopectin - natural starches contain 75% amylopectin and 25% amylose both of which are polymers of glucose units joined by glycosidic linkages - amylose is a condensation polymer with an average of about 200 glucose monomers per molecule arranged in a straight chain - amylopectin has about 1000 glucose monomers arranged into branched chains and these branched chains of glucose units give amylopectin properties different from unbranched amylose - the main difference between amylose and amylopectin is their water solubility - family of enzymes called amylases helps in breaking down starch into a mixture of small branched-chain polysaccharides called dextrins and ultimately into glucose - dextrins are used as food additives and in mucilage, paste, and finishes of food paper and fabrics - in animals, glycogen serves the same function as starch does in plants  - glycogen is stored in the liver and muscle tissues and provides glucose for instant energy until the process of fat metabolism can take over and serve as the energy source - chains of D-glucose units in glycogen are more highly branched than those in amylopectin - amylose turns blue-black when tested with an iodine solution and amylopectin turns red - animals store energy as fats rather than carbohydrates because fats have more energy per gram Cellulose, a Polysaccharide - cellulose is the most abundant organic compound on Earth and it is found in the woody part of trees and supporting material in plants and leave - cotton is the purest natural form of cellulose - cellulose is also composed of D-glucose monomer units similar to amylose - about 280 glucose units are bonded together to form a chain - chains lie parallel to each other held by hydrogen bonds - cellulose and amylose are both made of glucose, but they are different. In cellulose, the glucose pieces link in an alternating pattern, like flipping every other block, which makes it strong and hard for our bodies to break down. In amylose, all the glucose pieces connect the same way, like a row of blocks facing the same direction, which makes it easier for us to digest. This is why we can eat and digest foods with starch (like bread) but not foods with cellulose (like wood). - however, termites, a few species of cockroaches, and ruminant mammals such as cows, sheep, goats, and camels do have the proper internal chemistry for this purpose. Because cellulose is so abundant, it would be advantageous if humans could use it, as well as starch, for food. Amino Acids and Proteins - amino acids contain a carboxylic acid group and an amine group - proteins are polymers of amino acids - there are 20 naturally occurring amino acids where proteins have the same formula: - they are described as s α-amino acids because the amine (-NH2) is attached to the alpha-carbon (the first carbon attached next to carboxylic acid or -COOH group - amino acids differ because they have different R-group - each amino acid has a three-letter abbreviation for its name - essential amino acids must be part of the human diet - histidine is essential to juveniles but not adults - other amino acids can be synthesized by the body - growing children require arginine in their diet  - like nylon, proteins are polyamides - the amide bond in a protein is formed by a condensation polymerization reaction between the amine group of one amino acid and the carboxylic acid group of another - amide linkage in proteins is called peptide linkage or peptide bond - a relatively small amino acid polymer (up to about 50 amino acids) is called a polypeptide - proteins contain hundreds to thousands of amino acids bonded together - any two amino acids can react to form two different dipeptides, depending on which amine and acid groups react with each amino acid. - polypeptide chains are named by starting at the ONH2 end and naming each amino acid (with a “yl” ending) until the COOH group is reached. - all proteins, no matter how large, have a peptide backbone of amino acid units covalently bonded to each other through peptide linkages. - as the number of amino acids in the chain increases, the number of variations quickly increases to a degree of complexity not usually found in synthetic polymers. Primary, Secondary, and Tertiary Protein Structure Primary Structure - the 3D shape of the protein and its function is determined by primary structure (the sequence of amino acids along the polymer chain)  - even one amino acid out of place can create dramatic changes in the shape of a protein, which can lead to serious medical conditions. - Sickle-cell anemia occurs when a mutation replaces the sixth amino acid, glutamic acid, in hemoglobin with valine, causing the hemoglobin molecules to clump together and form fibers that distort red blood cells into a sickle shape, impairing their function Secondary Structure - regular, recurring structural patterns held in place by hydrogen bonding. - two major types of secondary protein structure: the alpha-helix (α-helix) and the beta-pleated sheet (β-pleated sheet). Alpha-helix - Hydrogen bonds hold a protein chain in a spiral (helix) structure. - It occurs within a single protein chain. - hydrogen bonds form between the hydrogen of an N-H bond in one peptide linkage and the oxygen of a C=O bond four amino acids away, creating a coiled structure with the R groups extending outward. - Wool is primarily the protein keratin, which has an alpha helix secondary structure. Beta-pleated sheet - Hydrogen bonds hold adjacent protein chains in a puckered (pleated) sheet. - involves two or more adjacent sections of protein chains; the two adjacent sections may be in separate molecules or within the same molecule where a protein chain folds so that different sections of the chain are parallel - hydrogen bonds form between the backbones of adjacent protein chains, creating a zigzag pattern with R groups alternating above and below the sheet. - the rigid planar structure of the peptide bond, due to its partial double-bond character, restricts rotation and results in the pleated sheet formation with bends occurring only at the carbon atoms attached to the R groups. - Fibroin, the principal protein in silk, is largely beta-pleated sheets. Tertiary Protein Structure - the overall three-dimensional arrangement that accounts for all the twists and turns and folding of a protein - the twists and turns of the tertiary structure result in a protein molecule of maximum stability - determined by interactions among the side chains that are strategically placed along the backbone of the chain and these interactions include non covalent forces of attraction and covalent bonding - proteins can be divided into two broad categories: fibrous proteins and globular proteins—that reflect differences in their tertiary structures.  - The hydrogen bonding, hydrophobic interactions, and electrostatic attractions bring the groups closer together. Metal ions, such as Fe2+ in hemoglobin, are incorporated into a protein by the donation of lone pair electrons from oxygen or nitrogen atoms in side chain groups to form coordinate covalent bonds to the metal ions. By loss of H, the OSH groups in nearby cysteine units are oxidized to form disulfide, OSOSO, and covalent bonds that cross-link regions of the peptide backbone. The number and proximity of disulfide bonds help to limit the flexibility of a protein. Fibrous proteins - hair, muscle fibers, and fingernails have little tertiary structure and are rod-like, with the coils or sheets of protein aligned into parallel bundles, making for tough, water-insoluble materials. Globular proteins - are highly folded, with hydrophilic (water-loving) side chains on the outside, making these proteins water-soluble. Hemoglobin and chymotrypsin are globular proteins, as are most enzymes. Because of the complexity and the variety of properties provided by the different R groups and associated molecules or ions, proteins can perform widely diverse functions in the body. Consider some of them: