Nucleic Acids PDF - BSN 1-C 2024-2025

BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED...

BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED NUCLEIC ACID NUCLEIC ACIDS PHOSPHATE Are ploymers of nucleotides Are polar since they are highly ionized oxygen atoms Also known as phosphoric acid. NUCLEOTIDES Are composed of a heterocyclic nitrogenous base, a phosphate group and a pentose group Building blocks (monomers) of nucleic acid chains. NUCLEOSIDE A nucleotide without its phosphate group The combination of sugar and base A compound composed of ribose or deoxyribose and a base. Two kinds of nucleic acids are found in the cells: DNA Deoxyribonucleic Acid Is present in the chromosomes of the nucleic of eukaryotic cells. Double stranded, carrier of genetic information RNA Ribonucleic acid Not found in the chromosomes, but rather, is located elsewhere in the nucleus and even outside the nucleus, in the cytoplasm. Single stranded, an intermediate in the expression NITROGENOUS BASE of genetic information and other diverse roles There are two major groups of nitrogenous bases in nucleic acids: the purines and pyrimidines NUCLEOTIDES GROUPS Both are heterocyclic aromatic amines which makes these BASES molecules basic Found in DNA and RNA. PURINE Purines and pyrimidines, which are components of Has to 2 rings while pyrimidines has 1 ring nucleotides, DNA, and RNA. CYTOSINE, ADENINE, AND GUANINE Are found in both DNA and RNA THYMINE Is found in DNA only URACIL In RNA only. Both DNA and RNA contains four bases: two pyrimidines, and two purines. For DNA, the bases are A, G, C, and T. For RNA, the bases are A, G, C, and U. SUGARS 5 carbon sugar ( pentoses ) Pentoses contains the ribose and deoxyribose The sugar component of RNA is D-ribose In DNA, it is 2 - deoxy-D-ribose PHOSPHATE GROUP Can be esterified at the 3’ and 5’ (’ - prime) to indicate the carbon number A single phosphate group esterified to a pentose forms a phosphoester linkage. If two phosphate groups are esterified at the 3rd and 5th carbon, this is called a 3’,5’ phosphodiester bond. ROBLES BSN 1-C 1ST YEAR  BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED NUCLEIC ACID PRIMARY STRUCTURE The primary structure of DNA is comprised of the nucleotide sequences. Note that it can be divided into two parts: The backbone of the molecule The bases that are the side - chain groups. The backbone in DNA consists of alternating deoxyribose and phosphate groups. The primary structure of RNA is the same except that each sugar is ribose (so an -OH group appears in the 2' position) rather than deoxyribose, and U is present instead of T. DNA REPLICATION STRUCTURE OF DNA Is a double stranded helix. Each strands of helix are in opposite direction of each other ( antiparallel). The strands are held together by the complement base pairing of the nitrogenous bases through H^- SECONDARY STRUCTURE bonds: A-T has two H^- bonds and C-G base pairing The secondary structure involves the helical conformation has three H^- bonds. of the two strands bound together by H^- bonding. In 1953, James Watson and Francis Crick (1926 - 2004) established the three dimensional structure of DNA. DOUBLE HELIX DNA is composed of two strands entwined around each other. In the DNA double helix, the two polynucleotide chains run in opposite directions ( which is called the antiparallel). CHARGAFF’S RULE For each adenine on one chain, a thymine is aligned opposite it on the other chains; each guanine on one chain has a cytosine aligned with it on the other chain. COMPLEMENTARY BASE PAIRS The bases so paired from hydrogen bonds with each other, two for A - T and G - C. ROBLES BSN 1-C 1ST YEAR  BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED NUCLEIC ACID RNA TYPES MESSEMGER RNA (MRNA) Are produced in the process called transcription, they TERTIARY STRUCTURE carry the genetic information from the DNA in the Involves the supercoiling of the DNA around a cluster of nucleus directly to the cytoplasm, where most of the proteins called histones forming the nucleosomes. protein is synthesized. HISTONES Messenger RNA consists of a chain of nucleotides Are comprise of five main types, called H1, H2A, whose sequences is exactly complementary to tat of H2B, H3, and H4. one of the strands of the DNA. All of them contain large numbers of basic amino This type of RNA is not long lived. It is synthesized as acid residues, such as lysine and arginine. needed and then degraded, so its concentration at any given time is rather low. NUCLEOSOMES When the acidic DNA and basic histones attract TRANSER RNA (TRNA) each other by electrostatic (ionic) forces. Containing from 73 to 93 nucleotides per chain, tRNAs are relatively small molecules. There is at least one different tRNA molecule of the 20 amino acids from which the body makes its proteins. The three dimensional tRNA molecules are L-shaped, but they are conventionally represented as a cloverleaf in two. ROBLES BSN 1-C 1ST YEAR  BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED NUCLEIC ACID RIBOSOMAL RNA (RRNA) RIBOSOMES GENES Which are small spherical bodies located in the A gene is a stretch of DNA, containing a few hundred cells but outside the nuclei, contains rRNA. nucleotides, that carries one particular message. They consists of about 35% protein and 65% One DNA molecule may have between 1 million and 100 ribosomal RNA. These large molecules have million bases. molecular weights up to 1 million. EXONS Coding sequences. Short for “ expressed sequences”. INTRONS Noncoding sequences, Short for “intervening sequences”. REPLICATION The DNA in the chromosomes carries out two functions: It reproduces itself It supplies the information necessary to make all the RNA and proteins in the body, including enzymes. Replication begins at a point in the DNA called an origin of replication. In human cells, the average chromosomes has SMALL NUCLEAR RNA (SMRNA) several hundred origins of replication where the copying A recently discovered RNA molecules is smRNA, occurs simultaneously. which is found, as the name implies, in the nucleus REPLICATION FORK of eukaryotic cells. The point on the DNA where replication proceeds. This type of RNA is small, about 100 to 200 The DNA is replicated in a semi-conservative mechanism nucleotides long, but it is neither a tRNA molecule where each of the parent strand is used as a template for nor a small subunit of rRNA. the new strand to allow preservation of the nucleotide In the cell, it is complexed with proteins to form sequences (applying Chargaff’s rules in base pairing). small nuclear ribonucleoprotein particles, snRNPs, also pronounced “snurps”. Their functions is to help with a processing of the initial mRNA transcribed from DNA into a mature form that is ready for export out of the nucleus. This process is often referred to as splicing, and it is an active area of research. MICRO RNA (MIRNA) A very recent discovery is another type of small RNA, miRNA. These RNAs are only 20 - 22 nucleotides long but are important in the timing of an organism’s development. They play important roles in cancer, stress responses, and viral infections. They inhibit translation of mRNA into protein and The pathway begins by uncoiling of the DNA by the DNA promoted the degradation of mRNA. gyrase (also called topoisomerase). Followed by the unwinding by Helicase. SMALL INTERFERING RNA (SIRNA) The process called RNA interference was heralded The unwound DNA is stabilized by single-stranded binding as the breakthrough of the year 2002 by Science proteins, forming the replication fork. magazine. The main enzyme that catalyzes the addition of new Short stretches of RNA (20 - 30 nucleotides long), nucleotides in the growing strand is called DNA polymerase called small interfering RNA, have been found to III. have an enormous control over gene expression. The enzyme reads the template in a 3’ to 5’ direction and This effect serves as a protective mechanisms in synthesizes in a 5’ to 3’ direction (this is often a confusion). many species, with the siRNAs being used to One strand is leading strand where the replication is eliminate expression of undesirable gene, such as continuous, while the other is the lagging strand where the one that causes uncontrolled cell growth or one elongation is discontinuous leading to synthesis of small that came from a virus. fragments. The siRNA degrade specific mRNA molecules to An RNA primer is needed in to begin the DNA synthesis. The control gene activity. primer is added using RNA primase Unlike the leading strand, the RNA primer in lagging strand is used multiple times since the synthesis is discontinuous, the primers are then removed by DNA polymerase I. ROBLES BSN 1-C 1ST YEAR  BIOCHEMISTRY LABI UNIT 2 I CHAPTER 2 I NUCLEIC ACID BSN 1- C I UNIVERSITY OF SAN AGUSTIN I A.Y. 2024 - 2025 I 1ST SEMESTER ISABILLE NICOLE V. ROBLES MAIN TOPIC SUB TOPIC I SUB TOPIC II SUB TOPIC III SUB TOPIC IV IMPORTANT NOTED NUCLEIC ACID The small discontinuous synthesized fragments called Okazaki fragments are then joined together using DNA ligase. SUMMARY ROBLES BSN 1-C 1ST YEAR