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Chem 4343Lecture Topic : Nucleic AcidsIntroductionThere are three major types of biological macromolecules in mammalian systems:Carbohydrates, Nucleic acids and Proteins . While often they are treated separately indifferent segments of a course in fact, the principles governing the organization of three-dimensional structure are common to all of them. We will begin with the monomer units.monosaccharide -- for carbohydrate nucleotide -- for nucleic acids amino acid -- forproteins We will describe the features of representative monomers, and see how themonomers join to form a polymer. The three-dimensional structure of each type ofmacromolecule will then be considered at several levels of organization. We will investigatemacromolecular interactions and how structural complementarity plays a role in them. Thestories for proteins, monosaccharides and nucleotides are just variations on the same theme.So you'll need to learn only one pattern, then apply that pattern to the other systems. Wewill conclude this section of the course with a consideration of denaturation and renaturation-- the forces involved in loss of a macromolecule's native structure (that is, its normal 3-dimensional structure), and how that structure, once lost, can be regained.Concept I - monomer characteristics and primary structureTHE MONOMER UNITS OF BIOLOGICAL MACROMOLECULES HAVE HEADSAND TAILS. WHEN THEY POLYMERIZE IN A HEAD-TO-TAIL FASHION, THERESULTING POLYMERS ALSO HAVE HEADS AND TAILS.These macromolecules are polar [polar: having different ends] because they areformed by head to tail condensation of polar monomers. Nucleotides polymerize to yieldnucleic acids. Nucleotides consist of three parts. Phosphate. Monosaccharide. Ribose (inribonucleotides) Deoxyribose, which lacks a 2' -OH (in deoxyribonucleotides) Thepresence or absence of the 2' -OH has structural significance that will be discussed later. Abase. There are four dominant bases; here are three of them: adenine (purine) cytosine(pyrimidine) guanine (purine) The fourth base is (a pyrimidine) uracil (in ribonucleotides)or thymine (in deoxyribonucleotides) Be aware that uracil and thymine are very similar; theydiffer only by a methyl group. You need to know which are purines and which arepyrimidines, and whether it is the purines or the pyrimidines that have one ring. The reasonsfor knowing these points relate to the way purines and pyrimidines interact in nucleic acids,which we'll cover shortly. Nucleotides polymerize by eliminating water to form estersbetween the 5'-phosphate and the 3' -OH of another nucleotide. A 3'->5' phosphodiesterbond is thereby formed. The product has ends with different properties. An end with a free5' group (likely with phosphate attached); this is called the 5' end. An end with a free 3'group; this is called the 3' end.Let's look at the conventions for writing sequences of nucleotides in nucleic acids.Bases are abbreviated by their initials: A, C, G and U or T. U is normally found only inRNA, and T is normally found only in DNA. So the presence of U vs. T distinguishesbetween RNA and DNA in a written sequence. Sequences are written with the 5' end to theleft and the 3' end to the right unless specifically designated otherwise. Phosphate groupsare usually not shown unless the writer wants to draw attention to them. The followingrepresentations are all equivalent. uracil adenine cytosine guanine | | | | P-ribose-P-ribose-P-ribose-P-ribose-OH 5' 3' 5' 3' 5' 3' 5' 3'pUpApCpGUACG3' GCAU 5' (Note that in the last line the sequence is written in reverse order , but the ends are appropriately designated.)Branches are possible in RNA but not in DNA. RNA has a 2' -OH, at whichbranching could occur, while DNA does not. Branching is very unusual; it is known tooccur only during RNA modification [the "lariat"], but not in any finished RNA species.The sequence of monomer units in a macromolecule is called the PRIMARY STRUCTUREof that macromolecule. Each specific macromolecule has a unique primary structure. Thisconcludes our consideration of the relationship between the structures of biologicalpolymers and their monomer subunits.Concept II - The three-dimensional shapes of these macromolecules in solution and the forces responsible for these shapes : secondary structureTHE REGULAR REPEAT OF MONOMER UNITS HAVING THE SAME SIZE ANDTHE SAME BOND ANGLES LEADS TO HELICAL (SPIRAL) POLYMERS. IFTHESE HELICES CAN BE STABILIZED BY SUITABLE INTRA- ORINTERMOLECULAR INTERACTIONS, THEY WILL PERSIST IN SOLUTION, ANDWILL BE AVAILABLE AS ELEMENTS OF MORE COMPLICATEDMACROMOLECULAR STRUCTURES.Biopolymers consisting of regularly repeating units tend to form helices. Thefundamental reason for this is that the bond angles of the constituent atoms are never 180degrees, so linear molecules are not likely; rather, a gentle curve should be expected alongthe length of the macromolecule. Just what is a helix? A helical structure consists ofrepeating units that lie on the wall of a cylinder such that the structure is superimposableupon itself if moved along the cylinder axis. A helix looks like a spiral or a screw. A zig-zagis a degenerate helix. Helices can be right-handed or left handed. The difference between thetwo is that: Right-handed helices or screws advance (move away) if turnedclockwise.Examples: standard screw, bolt, jar lid.Left-handed helices or screws advance(move away) if turned counterclockwise.Example: some automobile lug nuts. Helicalorganization is an example of secondary structure. These helical conformations ofmacromolecules persist in solution only if they are stabilized. What might carry out thisstabilization? Stable biological helices are usually maintained by hydrogen bonds.Helices in nucleic acids involve single chains of nucleic acids that tend to fromhelices stabilized by base stacking. The purine and pyrimidine bases of the nucleic acids arearomatic rings. These rings tend to stack like pancakes, but slightly offset so as to followthe helix. The stacks of bases are in turn stabilized by hydrophobic interactions and by vander Waals forces between the pi-clouds of electrons above and below the aromatic rings. Inthese helices the bases are oriented inward, toward the helix axis, and the sugar phosphatesare oriented outward, away from the helix axis. Two lengths of nucleic acid chain can form adouble helix stabilized by Base stacking Hydrogen bonds. Purines and


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ST. EDWARDS CHEM 4343 - Nucleic Acids

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