Introduction to Nucleic Acids PDF

Introduction to Nucleic Acids Dr. Hilal Eren Gözel I. Okan University DNA is the genetic material Hereditary information is encoded in the chemical language of DNA and reproduced in all the cells of our body. It is the DNA program that directs the development of many...

Introduction to Nucleic Acids Dr. Hilal Eren Gözel I. Okan University DNA is the genetic material Hereditary information is encoded in the chemical language of DNA and reproduced in all the cells of our body. It is the DNA program that directs the development of many different types of traits. How is the DNA structure discovered? By the 1920s, scientists generally agreed that genes reside on chromosomes, and they knew that chromosomes are composed of both DNA and proteins. Which one is the hereditary molecule? Griffith Experiment!! In 1928, Fred Griffith was studying Streptococcus pneumoniae (pneumococcus), a bacterium that causes pneumonia. As antibiotics had not yet been discovered, infection with this organism was usually fatal. Griffith Experiment – Messages from the dead Pneumococci come in two forms: a pathogenic form that causes a lethal infection when injected into animals, and a harmless form that is easily conquered by the animal’s immune system and does not produce an infection. Griffith Experiment – Messages from the dead When the pathogenic pneumococci that had been killed by heating were no longer able to cause infection! Griffith Experiment – Messages from the dead The surprise came when Griffith injected both heat-killed pathogenic bacteria and live harmless bacteria into the same mouse. This combination proved that: not only did the animals die of pneumonia, but Griffith found that their blood was teeming with live bacteria of the pathogenic form. He mentioned that there is a ‘transforming principle’ that causes that phenomenon.  Transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s).  15-year-old Experiment - Avery, MacLeod, and McCarty Experiment What is this transforming principle???? The first strong evidence that genes are made of DNA: The American bacteriologist Oswald Avery and his colleagues Colin MacLeod and Maclyn McCarty, following up on Griffith’s work, discovered that the harmless pneumococcus could be transformed into a pathogenic strain in a culture tube by exposing it to an extract prepared from the pathogenic strain (1944). They successfully purified the “transforming principle” from this soluble extract and to demonstrate that the active ingredient was DNA. How is the DNA structure discovered? Erwin Chargaff analyzed the base composition of DNA from a number of different organisms In 1947, Chargaff reported That DNA composition (number of different nucleotides) varies from one species to the next (evidence of molecular diversity among species) That the number of adenines approximately equaled the number of thymines, and the number of guanines approximately equaled the number of cytosines.  The Search for the Genetic Material: Scientific Inquiry Chargaff Rules: 1. The base composition varies between species, 2. Within each species, the number of A and T bases are equal, and the number of G and C bases are equal. How is the DNA structure discovered? Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure In May 1952, Raymond Gosling a graduate student working under the supervision of Rosalind Franklin took an X-ray diffraction image, labeled as "Photo 51" (a) Rosalind Franklin (b) Franklin’s X-ray diffraction Figure 16.6 a, b Photograph of DNA (6) Antiparallel How is the DNA structure discovered? Franklin had concluded that DNA was composed of two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior The nitrogenous bases are paired in specific combinations: adenine with thymine, and cytosine with guanine (a) Rosalind Franklin (b) Franklin’s X-ray diffraction Figure 16.6 a, b Photograph of DNA How is the DNA structure discovered? When James Watson came to Cambridge University to visit Francis Crick, he saw this photograph. Watson was familiar with the type of X-ray diffraction pattern that helical molecules produce, and an examination of the photo confirmed that DNA was helical in shape and made up from two helices. (a) Rosalind Franklin (b) Franklin’s X-ray diffraction Figure 16.6 a, b Photograph of DNA  How is the DNA structure discovered? In 1953, James Watson and Francis Crick shook the world with an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA https://www.nature.com/articles/171737a0 re 16.1  Components of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group The portion of a nucleotide without the phosphate group is called a nucleoside (nitrogenous base + pentose sugar)  5' end 5'C 3'C Nucleoside Nitrogenous base 5'C Phosphate 3'C group Sugar 5'C (pentose) 3'C (b) Nucleotide 3' end (a) Polynucleotide, or nucleic acid  Nucleotide Monomers Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases: Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group  Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases  The DNA Double Helix A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)  5’ end O OH P Hydrogen bond –O 3’ end O OH O T A O O CH2 O P –O O O– O P O H2C O O Phosphodiester bond G C O O CH2 O P –O O O– O P O H2C O O C G O O CH2 O P O –O O– O P O H2C O O A T O CH2 OH 3’ end O O– P O O (b) Partial chemical structure Figure 16.7b 5’ end  Nucleic Acids The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next. DNA provides directions for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis.  Nucleic Acids In a eukaryotic cell, ribosomes are in the cytoplasm, but DNA resides in the nucleus. Each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (mRNA). Messenger RNA conveys genetic instructions for building proteins from the nucleus to the cytoplasm. The flow of genetic information: DNA  RNA  protein  DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Ribosome via nuclear pore 3 Synthesis of protein Amino Polypeptide acids RNA The primary structure of RNA is generally similar to that of DNA with two exceptions: the sugar component of RNA, ribose, has a hydroxyl group at the 2 position and thymine in DNA is replaced by uracil in RNA.  Sugars Deoxyribose (in DNA) Ribose (in RNA)  Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases RNA Unlike DNA, most cellular RNAs are single-stranded and exhibit a variety of conformations. Differences in the sizes and conformations of the various types of RNA permit them to carry out specific functions in a cell. The simplest secondary structures in single-stranded RNAs are formed by pairing of complementary bases. “Hairpins” are formed by pairing of bases within ≈5–10 nucleotides of each other, and “stem-loops” by pairing of bases that are separated by >10 to several hundred nucleotides. These simple folds can cooperate to form more complicated tertiary structures, one of which is termed a “pseudoknot.” RNA RNA The folded domains of RNA molecules may have catalytic capacities. Such catalytic RNAs are called ribozymes. Although ribozymes usually are associated with proteins that stabilize the ribozyme structure, it is the RNA that acts as a catalyst. Some ribozymes can catalyze splicing, a remarkable process in which an internal RNA sequence is cut and removed, and the two resulting chains then ligated.  RNA World Hypothesis  The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self- replicating RNA molecules proliferated before the evolution of DNA and proteins.  Types of RNA The vast majority of genes carried in a cell’s DNA specify the amino acid sequences of proteins. Some genes code for RNA molecules! Important RNAs for Transcription: Types of RNA *Telomeres are transcribed generating long non-coding RNAs known as TERRA! DNA and RNA References Chapter 417 and 351