Nucleic Acids Biochemistry Chapter 1 PDF
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Uploaded by MeticulousRegionalism
Dr Nadiawati Alias
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Summary
This document provides a detailed overview of nucleic acids, including topics such as DNA and RNA structure, their properties, and functions. It also discusses eukaryotic and prokaryotic genomes, and the central dogma of biology, along with examples and diagrams.
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* By: Dr Nadiawati Alias * * Living cells are highly complex and organized. * Cells possess a gene4c program encoded in a collec4on of genes * Genes ar...
* By: Dr Nadiawati Alias * * Living cells are highly complex and organized. * Cells possess a gene4c program encoded in a collec4on of genes * Genes are more than storage lockers for informa4on: * Cons4tute the blueprints for cellular structures * The informa4on carried by DNA is held in the sequence of pieces of DNA called genes. DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The number or chromosomes varies from species to species. Fruit flies have a total of 8 chromosomes per cell The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes per cell. * *The gene4c informa4on in a genome is held within genes * A gene is a unit of heredity and is a region of DNA that influences a par4cular characteris4c in an organism. * Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the expression of the open reading frame. *Genomic DNA is different between eukaryo>c and prokaryo>c cell. Eukaryotes: Prokaryotes: Plants Bacteria Animals Archea Fungi Protozoa * Bacterial Chromosomes In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid the nucleoid (meaning nucleus-‐like and also known as the nuclear region, nuclear body or chroma>n body) is an irregularly-‐shaped region within the cell where the gene>c material is localized. Nucleoid also is not surrounded by a nuclear membrane or separate cellular compartment bounded by a membrane. The nucleic acid is a circular, double-‐stranded piece of DNA, and mul4ple copies may exist. Their genomes have no introns, less repe44ve sequences then eukaryo4c genomes. * * Bacterial chromosomal DNA – usually circular molecule. * Contains: * origin of replication, * structural gene sequences * some repetitive sequences. * 1. Nucleolus 2. Nucleus 3. Ribosome 4. Vesicle 5. Rough endoplasmic reticulum 6. Golgi apparatus (or "Golgi body") 7. Cytoskeleton 8. Smooth endoplasmic reticulum 9. Mitochondrion 10. Vacuole 11. Cytoplasm 12. Lysosome 13. Centriole http://www.dnai.org/c/index.html * * Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in mitochondria and chloroplasts. * DNA is packed into chroma>ns and sequestered within a membrane-‐enclosed organelle called the nucleus * It contains the cell's gene>c material (DNA molecules complex with a variety of proteins) such as histones, to form chromosomes * The chromosomes of eukaryo>c cells are packages composed of DNA and protein. * This packaging must be highly ordered and compact in order to fit the huge DNA molecules into the cell’s nucleus. * Total length of all DNA in human cell is es4mated at 1-‐2m * But size of the nucleus is only 5 µm in diameter. * * to fit into the nucleus of every cell Assembly of a nucleosome, which is formed when eight separate histone protein subunits attach to the DNA molecule. Six nucleosomes are coiled together and these then stack on top of each other. The end result is a fiber of packed nucleosomes known as chromatin. This structure, is then looped and further packaged using other proteins to give the final "chromosomal" shapes. And a typical cell nucleus is so small that ten thousand could fit on the tip of a needle http://www.dnai.org/c/index.html Two chromatids Nucleosome= composed of double-stranded DNA wrapped around an octamer of histone proteins. Chromatin The combined tight loop of core histones Histone DNA nIt is important to realize that chromosomes are not always present, they form only when cells are dividing. * * In many species, only a small fraction of the total sequence of the genome encodes protein. * For example, only about 1.5% of the human genome consists of protein- coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences * However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression * sRNA, tRNA, rRNA, siRNA etc. * Introns are non-coding sections of a gene, transcribed into precursor mRNA seq but ultimately removed by RNA splicing Exon Intron Exon Exon Intron Exon * *Some non-‐coding DNA sequences play structural roles in chromosomes. *Telomeres and centromeres typically contain few genes, but are important for the func4on and stability of chromosomes *An abundant form of non-‐coding DNA in humans are pseudogenes, which are copies of genes that have lost their protein-‐coding ability (due to muta>on) or no longer expressed in cell. * * Stable, infec4ve par4cles composed of a nucleic acid (DNA or RNA) and protein subunits. * Vary in size, shape and chemical composi4on. * Viral packages-‐protein molecules form a protec4ve shell around the nucleic acid core (capsid). * In more complex viruses (T2, T4), the protein shell is coated with an envelope of glycoproteins and membrane lipids. * Rely on host cells for replica4on * Most viruses exhibit a limited host range – which is the spectrum of host cell types that a virus can infect. * *Many virus can infect only specific types of cells of one host species. *Virus with simple structure may self-‐assemble to make mature virus par4cles. *Viruses cannot exist independently: *Parasi4c-‐ they survive by infec4ng a host cell and pira4ng the metabolic machinery which is used to form new viral par4cles. *Each viral form is usually specific for a type of host cell. *Bacteriophages *Plant viruses-‐tobacco mosaic virus *Animal viruses * *Bacteriophages/ phages *Specific for bacteria *Majority of phages are DNA viruses *Their genome is in the form of DNA *A well-‐studied phage: *X174, which infects E. coli cells. *Plant viruses *Ex: Tobacco mosaic virus (TMV) *Which infects the leaves of the plant *Contains single strand of genomic RNA *Animal Viruses * *Viruses that infect animals *Although viruses infect all cellular life (animals, plants, bacteria), each has their own specific range of viruses that ocen infect only that species. *Some are highly pathogenic in humans (influenza, human papilloma virus, rotavirus, mumps virus, herpes, HIV) * Direct their host cells to synthesize the enzyme to decode their gene4c informa4on. * Is an explanation of the flow of genetic information within a biological system. First stated by Francis Crick at 1956 * *First discovered in 1869 by Miescher. *Found as a precipitate that formed when extracts from nuclei were treated with acid. *Compound contained C, N, O, and high amount of P. *Was an acid compound found in nuclei therefore named nucleic acid. * *1944 Oswald, Avery, Mac Leod and Mc Carty demonstrated that DNA is the molecule that carrier gene4c informa4on. *1953 Watson and Crick proposed the double helix model for the structure of DNA * *Nucleic acids (DNA or RNA)-‐ polymers of nucleo4des linked in a chain through phosphodiester bonds. *serve as informa4on-‐carrying molecules or, in the case of some RNA molecules, catalysts. *Nucleo'de has 3 chemical parts: *An aroma4c and nitrogenous bases -‐either a pyrimidine (one ring) or purine (two rings) *A 5-‐carbon carbohydrate (an aldopentose)-‐ribose or deoxyribose *A phosphate groups. * *Nucleo4des also exist in ac>vated forms containing two or three phosphates, called nucleo4de diphosphates or triphosphates. *If the sugar in a nucleo4de is deoxyribose, the nucleo4de is called a deoxynucleo'de; if the sugar is ribose, the term ribonucleo'de is used. *The bases of nucleo4des are planar, aroma4c, heterocyclic molecules of either purine or pyrimidine. Purine Pyrimidine Purine-‐ form bonds to 5-‐carbon sugar ( a pentose) via N9 atoms. Pyrimidines-‐ form bonds to pentose via N1 atoms. * RNA DNA * *The combination of a base and sugar is called a nucleoside *Nucleosides are similar to nucleotides but have no phosphate groups. *The linking of a nitrogenous base by β-N-glycosidic linkage to 1 carbon of pentose sugar results in nucleoside. Examples of nucleosides: * Notice the named given for purine and pyrimidine * Abbr. Base Nucleoside Nucleic Acid deoxyadenosine DNA A Adenine adenosine RNA deoxyguanosine DNA G Guanine guanosine RNA deoxycytidine DNA C Cytosine cytidine RNA T Thymine deoxythymidine (thymidine) DNA U Uracil uridine RNA * * Two types of 5-‐carbon carbohydrate are found in the nucleic acids. *Ribose occurs in RNA *a monosaccharide containing five carbon atoms, and including an aldehyde func4onal group in its linear form. It has the chemical formula C5H10O5. Β-D-Ribose * *2-‐deoxyribose in DNA *deriva4ve of ribose, lacks an oxygen atom at C2 Β-D-2-Deoxyribose -The differences between D-‐Ribose and D-‐2-‐deoxyribose are-‐ 2'-‐OH vs 2'-‐H -‐This difference affects secondary structure and stability * *Phosphate ester of nucleosides * Other Func>ons of Nucleo>des Nucleoside 5'-‐triphosphates are carriers of energy Bases serve as recogni>on units Cyclic nucleo>des are signal molecules and regulators of cellular metabolism and reproduc>on ATP is central to energy metabolism GTP drives protein synthesis CTP drives lipid synthesis UTP drives carbohydrate metabolism * *DNA and RNA are synthesized in cells by DNA polymerases and RNA polymerases. *In all cases, the process involves forming phosphodiester bonds between the 3' carbon of one nucleo>de and the 5' carbon of another nucleo>de. *The sequence of DNA molecules is always read in the 5’ to 3’ direc'on *This leads to forma>on 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. 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. * Nucleo>de monomers are joined by 3’-‐5’ phosphodiester linkages to form nucleic acid (polynucleo>de) polymers * *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 promo>ng forma>on 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 an'parallel to one another G-‐C base pairs have 3 hydrogen bonds, A-‐T base pairs have 2 hydrogen bonds: higher temperature is needed to disrupt GC-‐rich DNA than AT-‐rich DNA. H bonding of adjacent an4parallel DNA strands form double helix structure * *Distance between the 2 sugar-‐phosphate backbones is always the same, give DNA molecule a regular shape. *Plane of bases are oriented perpendicular to backbone *Hydrophillic sugar phosphate backbone winds around outside of helix *Noncovalent interac4ons between upper and lower surfaces of base-‐pairs (stacking) forms a closely packed hydrophobic interior. *Hydrophobic environment makes H-‐bonding between bases stronger (no compe44on with water) *Cause the sugar-‐phosphate backbone to twist. View down the Double Helix Hydrophobic Interior with base pair Sugar-‐phosphate stacking backbone *Within groves, func>onal groups on the edge of base pairs exposed to exterior *involved in interac>on with proteins. Factors stabilizing DNA double Helix *Hydrophobic interac'ons – burying hydrophobic purine and pyrimidine rings in interior *Stacking interac'ons – van der Waals interac>ons between stacked bases. *Hydrogen Bonding – H-‐bonding between bases *Charge-‐Charge Interac'ons – Electrosta>c repulsions of nega>vely charged phosphate groups are minimized by interac>on with ca>ons (e.g. Mg2+) *RNA *Single stranded molecule *Chemically less stable than DNA *presence of 2’-‐OH makes RNA more suscep4ble to hydroly4c alack (especially form bases) *Prone to degrada4on by Ribonucleases (Rnases) *Has secondary structure. Can form intrachain base pairing (i.e.cruciform structures). *Mul4ple func4ons *Type of RNA *Ribosomal RNA (rRNA) – integral part of ribosomes (very abundant) *Transfer RNA (tRNA) – carries ac>vated amino acids to ribosomes. *Messenger RNA (mRNA) – endcodes sequences of amino acids in proteins. *Cataly'c RNA (Ribozymes) – catalzye cleavage of specific RNA species. *
