CHEMISTRY REPORT ON

CEMICAL AND CHEMICAL PROCESS IN FORENSIC STUDIES

BY: SHREYA SHARMA XIITH B

ST. THOMAS ENGLISH MEDIUM SCHOOL

INTRODUCTION TO NUCLEIC ACID

Nucleic acids are biological molecules essential for known forms of life on Earth. They include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids are the most important biological macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information. Molecular composition and size Nucleic acids can vary in size, but are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known. Wellstudied biological nucleic acid molecules range in size from 21 nucleotides (small interfering RNA) to large chromosomes (human chromosome 1 is a single molecule that contains 247 million base pairs In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form.

Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components: a purine or pyrimidine nucleobase (sometimes termed nitrogenous base or simply base), a pentose sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides - DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring.

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides linked in a chain through phosphodiester bonds. In biological systems, they serve as information-carrying molecules or, in the case of some RNA molecules, catalysts. This brief review will focus on aspects of structure of particular importance in manipulating DNA. Bases, Nucleosides and Nucleotides Nucleotides are the building blocks of all nucleic acids. Nucleotides have a distinctive structure composed of three components covalently bound together:

a nitrogen-containing "base" - either a pyrimidine (one ring) or purine (two rings)

a 5-carbon sugar - ribose or deoxyribose a phosphate group

The combination of a base and sugar is called a nucleoside. Nucleotides also exist in activated forms containing two or three phosphates, called nucleotide diphosphates or triphosphates. If the sugar in a nucleotide is deoxyribose, the nucleotide is called a deoxynucleotide; if the sugar is ribose, the term ribonucleotide is used.

The structure of a nucleotide is depicted below. The structure on the left - deoxyguanosine - depicts the base, sugar and phosphate moieties. In comparison, the structure on the right has an extra hydroxyl group on the 2' carbon of ribose, making it a ribonucleotide - riboguanosine or just guanosine.

In the right-hand figure, note also the 5' and 3' carbons on ribose (or deoxyribose) - understanding this concept and nomenclature is critical to understanding polarity of nucleic acids, as discussed below. The 5' carbon has an attached phosphate group, while the 3' carbon has a hydroxyl group. There are five common bases, and four are generally represented in either DNA or RNA. Those bases and their corresponding nucleosides are described in the following table:

Abbr. Base A Adenine

Nucleoside deoxyadenosine

Nucleic Acid DNA

adenosine deoxyguanosine G Guanine guanosine deoxycytidine C Cytosine cytidine T U Thymine Uracil deoxythymidine (thymidine) uridine

RNA DNA RNA DNA RNA DNA RNA

Another useful way to categorize nucleotide bases is as purines (A and G) versus pyrimidines(C, T and U). Although committing this to memory is often difficult, the importance is that in double-stranded nucleic acids, base pairs are always formed between a purine and a pyrimidine. Nucleic Acids DNA and RNA are synthesized in cells by DNA polymerases and RNA polymerases. Short fragments of nucleic acids also are commonly produced without enzymes by oligonucleotide synthesizers. In all cases, the process involves forming phosphodiester bonds between the 3' carbon of one nucleotide and the 5' carbon of another nucleotide. This leads to formation of the so-called "sugar-phosphate backbone", from which the bases project.

A key feature of all nucleic acids is that they have two distinctive ends: the 5' (5-prime) and 3' (3-prime) ends. This terminology refers to the 5' and 3' carbons on the sugar. For both DNA (shown above) and RNA, the 5' end bears a phosphate, and the 3' end a hydroxyl group. Another important concept in nucleic acid structure is that DNA and RNA polymerases add nucleotides to the 3' end of the previously incorporated base.Another way to put this is that nucleic acids are synthesized in a 5' to 3' direction. Base Pairing and Double Stranded Nucleic Acids Most DNA exists in the famous form of a double helix, in which two linear strands of DNA are wound around one another. The major force promoting formation of this helix is complementary base pairing: A's form hydrogen bonds with T's (or U's in RNA), and G's form hydrogen bonds with C's. If we mix two ATGC's together, the following duplex will form:

Examine the figure above and note two very important features:

The two strands of DNA are arranged antiparallel to one another: viewed from left to right the "top" strand is aligned 5' to 3', while the "bottom" strand is aligned 3' to 5'. This is always the case for duplex nucleic acids.

G-C base pairs have 3 hydrogen bonds, whereas A-T base pairs have 2 hydrogen bonds: one consequence of this disparity is that it takes more energy (e.g. a higher temperature) to disrupt GC-rich DNA than AT-rich DNA.

The figures above fail to impart any appreciation of the three-dimensional structure of DNA. This deficiency can be rectified to some extent by viewing and manipulating a 3-D model of duplex DNA.

What about double stranded RNA? RNAs are usually single stranded, but many RNA molecules have secondary structure in which intramolecular loops are formed by complementary base pairing. A simple example of this is shown in the figure to the right, and much more extensive and complex examples are known. Base pairing in RNA follows exactly the same principles as with DNA: the two regions involved in duplex formation are antiparallel to one another, and the base pairs that form are A-U and G-C. Finally, does understanding base-pairing have relevance to

biotechnology per se?Absolutely yes! This simple chemistry is at the heart of nucleic acid hybridization, polymerase chain reaction, antisense technology, mutagenesis, and many other of the techniques commonly applied in biotechnology labs.

DNA and RNA Structure/Function

Introduction: DNA (deoxyribonucleic acid) is the genetic material and is largely found in the chromosomes. RNA (ribonucleic acid) is made up of nucleotides containing sugar ribose. When these two work together, they build the amino acid sequence in a protein. This section is going to look at them individually. DNA Here is the structure of a DNA. As many have heard, or possibly made models of, the DNA is a double helix. This simply means it has two strands that spiral around each other. In the middle of these strands are nucleotides that are bonded by hydrogen bonding. The bonds created are: A with T, and G with C. These are

called complimentary paired bases. This colorful DNA structure image was found at www.biologycorner.com. The function of DNA is to replicate. Its job is to make an exact replica of itself. The fancy scientific term for this process is called: DNA replication. Here is a brief explanation of how DNA replicates. This is pulled straight from our text book, but I found it to be the simplest and most clear.

1. Before replication starts, the two strands of the original DNA are hydrogen-bonded together. 2. An enzyme unwinds and unzips the DNA 3. New complementary DNA nucleotides, which are always in the nucleus, fit into place by the process of complimentary base pairing. These position and are then joined by the enzyme DNA polymerase. 4. To complete replication, an enzyme seals any breaks in the sugarphosphate backbone 5. The two double-helix molecules are identical to each other and the

original DNA. This general overview of DNA replication is from fig.cox.miami.edu. RNA Now for an RNA structure. We now know that DNA is made up of the A,T,G, and, C nucleotides. RNA, on the other hand, is made up of C,G,A, an U nucleotides. RNA is also single stranded. There are also three types of

RNA. Lets explore them. (Below is an RNA image fromwww.jncasr.ac.in)

The first is Ribosomal RNA or rRNA. It is produced in the nucleolus and its main job is to join with proteins made in the cytoplasm to form the subunits of ribosomes.