DNA Replication 1 PDF

BCH 1211/BCH 1218 Molecular Biology, Oncogenesis and Immunology Week 1:- DNA Replication Dr. Nerina Harborne  BCH 1201/BCH 1208 Molecular Biology “The study of biology at a molecular level.” “Molecular biology chiefly concerns itself with unders...

BCH 1211/BCH 1218 Molecular Biology, Oncogenesis and Immunology Week 1:- DNA Replication Dr. Nerina Harborne  BCH 1201/BCH 1208 Molecular Biology “The study of biology at a molecular level.” “Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.” “The course explores the transfer and expression of genetic information, the mechanisms of regulation of gene expression, and oncogenesis.”  BCH 1201/BCH 1208 Molecular Biology “The study of biology at a molecular level.” “Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and Protein biosynthesis as well as learning how these interactions are regulated.”  The “Central Dogma” of Molecular Biology DNA makes RNA makes Protein  The “Central Dogma” of Molecular Biology Information carried in DNA:- can be copied to more DNA Can be transferred to RNA Can be used to provide the instructions to make protein  The “Central Dogma” of Molecular Biology DNA is REPLICATED to make more DNA DNA is TRANSCRIBED to make RNA RNA is TRANSLATED to make protein  Recap “The Central Dogma” of Molecular Biology This is the most usual flow of information.  Recap “The Central Dogma” of Molecular Biology In some special cases, information can be transferred from RNA to RNA, or from RNA to DNA. These are less common.  Recap “The Central Dogma” of Molecular Biology There are NO KNOWN mechanisms or cases in which information is transferred from protein sequence to nucleic acid sequence.  “The Central Dogma”Recap of Molecular Biology “The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.” Francis Crick (1958, 1970) Crick, F (August 1970). "Central dogma of molecular biology.". Nature 227: 561–3.  Recap Why Should Medical Professionals Learn About Molecular Biology? It “fills the gap” left by other subjects studied.“  Recap Why Should Medical Professionals Learn About Molecular Biology? The use of molecular biology in medicine:- Molecular Medicine Medical therapies arising from molecular biology:- Gene Therapy. Molecular biology plays important role in understanding the structure and function of cells and cellular structures which can be used to targeting new drugs and for the diagnosis of disease. DNA DNA – Double Helix The discovery of the structure of DNA led to the understanding of the function of DNA, and so to the field of Molecular Biology.  The Story of the Double Helix Model published in 1953 (with x-ray diffraction evidence). “A Structure for Deoxyribose Nucleic Acid” J. D. Watson and F. H. C. Crick April 25 1953, Nature 171, 737-738 Specific Base Pairing Structure of DNA suggests function of DNA  DNA Structure ↔ DNA Function 1. DNA is a Double Helix 2. DNA is a Right Handed helix 3. DNA double helix has Known Dimensions 4. DNA double helix has Major and Minor Grooves 5. DNA double helix has a Sugar-Phosphate Backbone 6. Each strand of the DNA double helix has Strong Covalent Bonding 7. DNA double helix has Inbuilt Directionality 8. DNA bases form Complementary Pairs 9. Paired Bases of the DNA double helix are held together by Hydrogen Bonding 10. DNA double helix has a Hydrophobic Interior and Hydrophilic Exterior. DNA is a Double Helix Two strands of the sugar- phosphate backbone of the primary structure are wound around each other. The double nature of the DNA molecule allows information to be carried with it's own back- up copy. The helical coiling provides a basis for condensing, organising and packaging the genetic material.  DNA is a Right-Handed Helix Helices can be right or left handed. (If the thumb of a hand points in the direction of the axis, then the fingers curl in the direction of the helix.) Normal DNA is a Right-Handed helix.  DNA is a Right-Handed Helix Understanding the direction that the DNA helix coils helps to understand how further coiling in the same or opposite direction produces supercoils. Important in unwinding DNA for replication or transcription DNA double helix has Known Dimensions Measured in Ångstrom Units Å – 10-10 m One turn of the helix = pitch of the helix - 34 - 36Å (10 – 10.5 bases) Distance between adjacent bases 3.4Å Fibre Diameter 20Å DNA double helix has Known Dimensions Knowing the dimensions of DNA aids in understanding how it can interact with other molecules – e.g. wind around histones, or be accessed by DNA binding proteins.  Major and Minor Grooves The double helix is asymmetric. 2 grooves - one wide and deep - Major Groove One narrower and shallower - Minor Groove  Major and Minor Grooves When DNA-binding proteins interact with DNA, they can 'read' information about specific DNA sequences from molecular information in the major groove. The minor groove is similar whatever the sequence, so allows non-specific interactions.  Sugar-Phosphate Backbone Two strands of the sugar- phosphate backbone of the primary structure are wound around each other.  Sugar-Phosphate Backbone The 'simple' repeating nature of the sugar- phosphate backbone provides a stable format into which the information carried by the base sequence can be 'written'.  Covalent Bonding David L. Nelson and Michael M. Cox LEHNINGER PRINCIPLES OF BIOCHEMISTRY Fifth Edition The sugars and phosphate © 2008 W. H. Freeman & Co. groups are linked by strong phosphodiester bonds. Bases are attached to the backbone by glycosidic bonds. These are formed enzymatically. This strong bonding makes DNA a very stable molecule. This stability allows it to safely carry genetic information, vital for the life of the cell. The DNA double helix has in-built directionality. The direction of the sugar-phosphate backbone runs in opposite directions on the two strands. Each strand has a free 5' and 3' end. 5'G-T-C-A3' 3'C-A-G-T5' The DNA double helix has in-built directionality. The direction in which the sequence of bases is read on each DNA strand is vitally important for maintaining the integrity of the information carried in DNA - the sequential arrangement of bases. Complementary Base Pairing The molecular shapes of the bases only allow specific pairs to occur without distorting the helix. These pairs are: adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine) Complementary Base Pairing Complementary base pairing allows the mechanisms of DNA replication and transcription to take place, vital for its function as the genetic material.  Hydrogen Bonding G – C forms 3 hydrogen bonds. A-T forms 2 hydrogen bonds.  G – C forms A single hydrogen 3 hydrogen bonds. bond is weak, A-T forms multiple hydrogen 2 hydrogen bonds. bonds are strong. This means that the two strands of the double helix can be 'unzipped' – separated for replication or transcription. A-T rich regions separate more easily than G-C rich regions.  Hydrophobic Interior and Hydrophilic Exterior. A-T and G-C base pairs have similar molecular dimensions. Allow the double helix of the backbone to maintain a regular shape. Bases are 'stacked', maintaining hydrophobic interactions with each other. The sugar-phosphate backbone is hydrophilic, allowing interactions with molecules in surrounding solution.  Hydrophobic Interior and Hydrophilic Exterior. The properties of DNA in solution are important for DNA function, and DNA packaging. Also important in the laboratory manipulation of DNA for genetic engineering etc. (We will soon isolate DNA in our Molecular Biology practical, by taking advantage of its solubility characteristics. BCH 1201/BCH 1208 Molecular Biology and Molecular Immunology DNA Replication 1  DNA Contains Information Information necessary to make copies of itself Information necessary to construct an entire organism.  DNA Contains Information Information necessary to make copies of itself DNA makes copies of itself DNA replication DNA synthesis  DNA Replication Process by which a copy of a DNA molecule is made. Through base-pairing, each strand of the DNA double helix carries all the information necessary to make a new copy of the other strand.  Why is DNA Replicated? When a cell divides, each new cell must carry an accurate copy of the genetic instructions of the organism. DNA Replication = DNA Synthesis Takes place during the 'S' (Synthesis) stage of the cell cycle.  How is DNA Replicated? From Alberts et.al, Molecular Biology of the Cell Garland Science Each strand of the DNA double helix acts as a template for its own replication. Template = Acts as a pattern that is copied. Semi-Conservative From Alberts et.al, Molecular Biology of the Cell Garland Science Replication Each DNA double helix carries one original strand and one new strand. The DNA is semi (half) conserved (remains the same) The whole length of the (long!) DNA molecule is copied in this way.  Replication Fork From Alberts et.al, Molecular Biology of the Cell Garland Science When DNA strands separate to allow replication, a 'forked' structure is formed:- The Replication Fork New DNA strands are synthesised in a 5' to 3' direction. Replication Fork - Detailed From Alberts et.al, Molecular Biology of the Cell Garland Science  Direction of DNA Replication Circular (bacterial) From Alberts et.al, Molecular Biology of the Cell Garland Science DNA:- Replication starts at Origin of Replication A Replication Bubble forms Replication forks move in both directions:- Bidirectional Replication  Direction of DNA Replication Linear DNA (as in chromosomes) Each DNA molecule has many Origins of Replication Multiple Replication Bubbles form Replication Forks move in both directions until they merge to produce the duplicate strands Bidirectional Replication  To Find Out More In the library (open shelves) Voet and Voet (1995) Stryer (1988) Lehninger (1982)  To Find Out More I use:- Molecular Biology of the Cell 5th ed. - 2008 Alberts et. al. Garland Science Molecular Biology of the Gene th th 5 ed. - 2004 or 7 ed. - 2013 Watson et.al. Pearson  To Find Out More Internet and Computer Resources?