Molecules, Genes and Disease - Nucleic Acids: DNA & RNA - PDF

Molecules, Genes and Disease DNA Structure and Chromosome Organization Part one: Nucleotides and nucleic acids  References Human Heredity Chap.8 Marks’ Basic Medical Biochemistry Chap.12,13 (p. 207-230) Medical Biochemistry Chap31 Lippincott’s Illustrated...

Molecules, Genes and Disease DNA Structure and Chromosome Organization Part one: Nucleotides and nucleic acids  References Human Heredity Chap.8 Marks’ Basic Medical Biochemistry Chap.12,13 (p. 207-230) Medical Biochemistry Chap31 Lippincott’s Illustrated Reviews: Biochemistry Chap.29  The Central Dogma of Molecular biology The Central Dogma: is the flow information from DNA to RNA to Protein in all organism. In most of organism the DNA is storage the genetic information with exception of some viruses have RNA serve as the genome. According to the Central Dogma: In mammalian cell : The information flow Retrovirus ex: human immunodeficiency virus(HIV): The information flow:  Nucleic Acids: DNA and RNA Nucleic Acids : are linear polymers of nucleotides‘ polynucleotides’ that required for the storage and expression of genetic information. There are two chemically distinct types of nucleic acids: Deoxyribonucleic acid(DNA): is polymer of deoxyribonucleotides covalently linked by 3’→ 5’ phosphodiester bond carrying the genetic information in all cellular forms of life and some viruses. Ribonucleic acid(RNA): is polymer of ribonucleotides covalently linked by 5’→ 3’ phosphodiester bond that function as an intermediary in the transfer of genetic information from DNA to protein.  Nucleotides: Building blocks of nucleic acids Nucleotides: are basic building block of DNA and RNA: Each nucleotide consists of three components: Nitrogenous base Pentose sugar Phosphate molecule While nucleoside composed of only: Nitrogenous base Pentose sugar  Nucleotides: Building blocks of nucleic acids Nucleotides Components Nitrogenous base : there are two types ✓ There is similarity between the 6-membered rings ✓ These structures are ‘planar’(it can be represented on a flat surface)because of the double bonds, and unsaturated  Nucleotides: Building blocks of nucleic acids Nucleotides Components Nitrogenous base: there are two types 1. Purine: have two- ring structure [Adenine(A) Guanine(G)] 2. Pyrimidine: have one-ring structure Thymine, T, Cytosine, C, and Uracil U. ❖ DNA has A, G,T,C and RNA has A,G,U,C  Nucleotides: Building blocks of nucleic acids Nucleotides Components ✓ Pentose sugar: there are two types ✓ Phosphate group: The phosphate groups are strongly acidic and, it’s a reason for calling DNA and RNA as an acids.  Nucleotides: Building blocks of nucleic acids Nucleotides Structure Nucleotides: are formed by covalent bonding of the phosphate, base, and sugar.  Nucleotides: Building blocks of nucleic acids Nucleotides Nomenclature  Polynucleotides chain: Formation and Characteristics Nucleotides are covalently linked via3'→5‘ phosphodiester bonds to form polynucleotides chains. The resulting chain has polarity: a5'-end(free phosphate)and a 3'-end(free hydroxyl group), resulting in chain with 5'→3'direction. The bases written in the conventional 5'→3'direction: 5'-AGCT-3‘ DNA has two polynucleotides chains and RNA has only one. Each single-strand nucleic acid chain has a polarity.  Key Features of Double Helix DNA Double helix DNA: Watson-Crick Model(1953) According to Watson and Crick model, DNA characterizes by DNA usually exit as double-stranded helix molecule Anti-parallel: DNA is composed of two Polynucleotide chains running in opposite directions, one chain run in 5'→3‘direction,the other in 3'→5‘direction. Base pairing: is highly specific: A in one chain pairs with T in the opposite chain by two hydrogen bonds, and C pairs with G by three bonds. Key Features of Double Helix DNA Key Features of Double Helix DNA Double helix DNA: Watson-Crick Model (1953) ✓ Complementary base pairing: The base pairing of the Model makes the two polynucleotide chains of DNA complementary in base composition: If one strand has the sequence 5′-ACGTC-3′. The opposite strand must be 3′-TGCAG-5′. The double-stranded structure would be written as Chargaff Rule(base ratio):  Key Features of Double Helix DNA Double helix DNA: Watson-Crick Model (1953) ✓ Complementary base pairing and hydrogen bonds formation  Key Features of Double Helix DNA Double helix DNA: Watson-Crick Model (1953) Secondary structure: The two chains are twisted(coiled) around each other in a right-handed to form a double helix(B-Form). ✓ One complete turn is10 base pairs and space between base pairs is 0.34nm. ✓ Creates a major(wide)groove and a minor(narrow)groove. The bases in these grooves exposed and therefore interact with proteins or other molecules.  Key Features of Double Helix DNA Double helix DNA: Watson-Crick Model (1953) Negative charge: The third-OH group on the phosphate is free and dissociates a hydrogen ion at physiologic pH. Therefore, DNA helix has negative charges coating its surface that facilitate the binding of specific proteins(histones and non-histones)  Key Features of Double Helix DNA ✓ DNA Denaturation & Renaturation : the double strands can separate in to single strands by disruption the hydrogen bonds between the paired bases using acidic or alkaline pH or heating. (phosphodiester bond are not broken by such treatment). Complementary DNA strands can reform the double helix under appropriate conditions. ✓ DNA degradation: Phosphodiester bonds (in DNA & RNA) can be cleaved hydrolytically by chemicals , or hydrolyzed enzymatically by nucleases ( deoxyribonucleases ).  Structural forms DNA double helix There are three major structural forms of DNA that all exhibit Watson and Crick complementary base pairing and anti-parallel: A, B and Z forms: A-form: is a right handed double B-form : is the chief or min helix with 11 base pair (bp) per the cells , is a right handed Z- form : is zigzag structure , a left handed turn, which produced form double helix with 10 basepair with 12 basepair (bp) per turn. moderately dehydrating B form. (bp) per turn of helix.  Ribonucleic acid (RNA) RNA: is polymer of ribonucleotides covalently linked by 3'→5 ‘ phosphodiester bonds. RNA: is single strand that has polarity with direction from5'→3‘ and Bases sequence always written from 5'-endto3'-end: 5'-AGCU-3' Phosphodiester bonds: can be cleaved hydrolytically by chemicals, or hydrolyzed enzymatically by nucleases (ribonucleases). Part two: DNA, chromosomes and DNA replication  DNA Condensation A cell's genetic information, in the form of DNA, is stored in the nucleus. The space inside the nucleus is limited and has to contain billions of nucleotides that compose the cell's DNA. Therefore, the DNA has to be highly organized or condensed. There are several levels to the DNA packaging The DNA coils around proteins called histones, forming a beads-on-a-string-like structure. The bead part is called a nucleosome. It is a little like wrapping a very long, thin piece of thread around your fingers, to keep it from unraveling and tangling.  DNA Condensation DNA wraps at several levels, until it is compacted into a chromosome. Specifically, a nucleosome composed of eight histone proteins (a pair of each of four types). A fifth type of histone protein anchors nucleosomes to short “linker” regions of DNA, which then tighten the nucleosomes into fibers 30 nanometers (nm) in diameter. As a result, at any given time, only small sections of the DNA double helix are exposed.  DNA Condensation To further condense the DNA material, nucleosomes are compacted together to form chromatin fibers.The chromatin fibers condense to form chromosome during cell division. DNA Condensation  DNA Condensation Chromatin In the nucleus, the DNA double helix is packaged by special proteins (histones) to form a complex called chromatin. The chromatin undergoes further condensation to form the chromosome. -Chromatin is observable in the interphase nucleus. Chromosomes A compact structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. -Chromosomes are observable during M- phase or nuclear division.  DNA Condensation In a cell in which DNA synthesis (DNA Replication) has occurred all the chromosomes are duplicated and thus each consists of two identical sister chromatids. Remember DNA Replication occurred before mitosis  DNA Replication DNA replication is a biological process that occurs in all living organisms and copies their DNA ;it is the basis for biological inheritance. DNA replication occurs during S phase of the cell cycle. DNA Replication is a semi-conservative process that results in a double-stranded molecule that synthesizes to produce two new double stranded molecules such that each original single strand is paired with one newly made single strand. DNA Replication  DNA Replication Semi-conservative replication would produce two copies that each contained one of the original strands and one new strand  DNA Replication Replication begins at specific sites on DNA molecule called "origins of replication, " Origins are specific sequence of bases Mammalian DNA have many origins  DNA Replication The replication forks: a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together.  DNA Replication Replication fork is where the parental DNA strands hasn't untwist. Replication bubbles allow DNA replication to speed up therefore the untwisted DNA would not be attacked by enzymes while replicating.. DNA replication of the leading and lagging strand: 1-The helicase: unwinds the double-stranded DNA for replication, making a forked structure. 2-The primase: generates short strands of RNA that bind to the single-stranded DNA to initiate DNA synthesis by the DNA polymerase. 3-DNA polymerase III: can work only in the 5' to 3' direction, so it replicates the leading strand continuously. Lagging-strand replication is discontinuous, with short Okazaki fragments being formed and later linked together. DNA Replication  DNA Replication ✓ Leading strand: new strand DNA that synthesized continuously ✓ Legging strand: new strand DNA that synthesized dis- continuously  DNA polymerase and other important enzymes participating in DNA Replication There are many enzymes involved in DNA replication due to the complex nature of the whole process. Here are the main enzymes and their functions in eukaryotic cells, during cell division. DNA helicase DNA polymerase Single strand binding protein Topoisomerase DNA ligase Primase DNA polymerase and other important enzymes participating in DNA Replication DNA polymerase and other important enzymes participating in DNA Replication  DNA polymerase and other important enzymes participating in DNA Replication Three DNA polymerases (I, II, and III) have been purified from E. coli. DNA Polymerase I has functioning in filling the gaps between Okazaki fragments. DNA polymerase II functioning in the DNA repair. DNA polymerase III, catalyzes chain elongation at the growing fork in leading and legging stand. The rate nucleotide additions in Mammals add about 50 bases/second while in bacteria add about 500 bases/second.  Cell Cycle The cell cycle or cell-division cycle is the series of events that take place in a cell leading to its division and duplication of its DNA(DNA replication)to produce two daughter cells. Cell Cycle  Cell Cycle The durations of the phases of a cell cycle: G1, S, G2, and M phases are 11 h, 8 h, 4 h, and 1 h, respectively. Cell Cycle  Cell Cycle Chromosomes are also used as a way of referring to the genetic basis of an organism as either diploid or haploid Many eukaryotic cells have two sets of the chromosomes and are called diploid. Other cells that only contain one set of the chromosomes are called haploid. A human has 46 chromosomes (2n = 46) in diploid cells that involving all somatic cells, and 23 chromosome in haploid cell that involving the gametes (egg and sperm).  Cell Cycle Some haploid & diploid cells divide by mitosis. Each new cell receives one copy of every chromosome that was present in the original cell. Produces 2 new cells that are both genetically identical to the original cell.