Molecular Structure of DNA and RNA PDF

Molecular Structure of DNA and RNA Biol 3301 Class 12 © McGraw Hill ©Scott Camazine/123RF 1  Transition to Molecular Genetics There is a point to all of this: Life is possible due to the proper...

Molecular Structure of DNA and RNA Biol 3301 Class 12 © McGraw Hill ©Scott Camazine/123RF 1  Transition to Molecular Genetics There is a point to all of this: Life is possible due to the proper interactions and functions of molecules. This is biology/genetics at the molecular level. Chemical and physical principles are important for understanding structure and functions of molecules. The details are quite detailed and complex. Many new “players.” When you learn about a new molecule, a key question to ask is “Is it DNA, RNA, or protein?” © McGraw Hill 2  DNA RNA Protein The Central Dogma of Biology © McGraw Hill 3 © McGraw Hill 4  Identification of THE Genetic Material: Requirements To fulfill its role, the genetic material must meet several criteria Information: It must contain the information necessary to make an entire organism Transmission: It must be passed from parent to offspring Replication: It must be copied in order to be passed from parent to offspring Variation: It must be capable of changes to account for the known phenotypic variation in each species © McGraw Hill 5  Frederick Griffith Experiments with Streptococcus pneumoniae Griffith studied a bacterium (pneumococci) now known as Streptococcus pneumoniae S. pneumoniae comes in two strains Type S  Smooth Secrete a polysaccharide capsule Protects bacterium from the immune system of animals Produce smooth colonies on solid media Type R  Rough Unable to secrete a capsule Produce colonies with a rough appearance © McGraw Hill 6  Griffith’s Experiments on Genetic Transformation 1 In 1928, Griffith conducted experiments using two strains of S. pneumoniae: type S and type R 1. Inject mouse with live type S bacteria Mouse died & type S bacteria recovered from the mouse’s blood 2. Inject mouse with live type R bacteria Mouse survived & no living bacteria isolated from the mouse’s blood © McGraw Hill 7  Griffith’s Experiments on Genetic Transformation 2 3. Inject mouse with heat-killed type S bacteria Mouse survived & no living bacteria isolated from the mouse’s blood 4. Inject mouse with live type R + heat-killed type S cells Mouse died & type S bacteria recovered from the mouse’s blood © McGraw Hill 8  Griffith’s Experiments on Genetic Transformation 3 (a) Live type S (b) Live type R Access the text alternative for slide images. © McGraw Hill 9  Griffith’s Experiments on Genetic Transformation 4 (c) Dead type S (d) Live type R + dead type S Access the text alternative for slide images. © McGraw Hill 10  Transforming Principle Griffith concluded that something from the dead type S bacteria was transforming type R bacteria into type S He called this process transformation The substance that allowed this to happen was termed the transforming principle Griffith did not know what type of substance it was © McGraw Hill 11  The Experiments of Avery, MacLeod and McCarty: Background and Rationale Avery, MacLeod and McCarty realized that Griffith’s observations could be used to identify the genetic material They carried out their experiments in the 1940s At that time, it was known that DNA, RNA, proteins and carbohydrates are the major constituents of living cells © McGraw Hill 12  The Experiments of Avery, MacLeod and McCarty They prepared cell extracts from type S cells and purified each type of macromolecule Only the extract that contained purified DNA was able to convert type R bacteria into type S Treatment of the DNA extract with RNase or protease did not eliminate transformation; treatment with DNase did © McGraw Hill 13  The Experiments of Avery, MacLeod and McCarty 3 Access the text alternative for slide images. © McGraw Hill 14  Evidence Provided by Hershey and Chase Hershey and Chase provided evidence that DNA is the genetic material of T2 phage Used radioisotopes to distinguish DNA from proteins P labels DNA specifically 32 S labels proteins specifically 35 Radiolabeled phages were used to infect non-radioactive Escherichia coli cells © McGraw Hill 15  Evidence Provided by Hershey and Chase 2 After allowing sufficient time for infection to proceed, the residual phage particles were sheared off the cells (using a blender) Most of the 32P had entered the bacterial cells (DNA) Most of the 35S remained outside the cells (protein) Indicates that DNA is the genetic material Fred Waring demonstrating his blender © McGraw Hill 16 © McGraw Hill 17  Overview of DNA and RNA Structure DNA (deoxyribonucleic acid), and its molecular cousin RNA (ribonucleic acid), are known as nucleic acids First identified by Friedrich Miescher in 1869 in waste surgical bandages Named the substance “nuclein” Material from the nucleus of a cell Later research showed that DNA (and RNA) release H+ in water and therefore are acids Became named “nucleic acids” © McGraw Hill 18  Overview of DNA and RNA Structure DNA and RNA are large macromolecules with several levels of complexity Nucleotides form the repeating unit of nucleic acids Nucleotides are linked to form a linear strand of RNA or DNA In DNA, two strands can interact to form a double helix The 3-D structure of DNA results from folding and bending of the double helix. Interaction of DNA with proteins produces chromosomes within living cells © McGraw Hill 19  Nucleotides Single strand Double helix Three-dimensional structure © McGraw Hill 20  Nucleotide Structure The nucleotide is the repeating structural unit of DNA and RNA A nucleotide has three components A phosphate group A pentose sugar Ribose in RNA Deoxyribose in DNA A nitrogenous (nitrogen-containing) base © McGraw Hill 21  The Components of Nucleotides Access the text alternative for slide images. © McGraw Hill 22  (a) Repeating unit of (b) Repeating unit of ribonucleic deoxyribonucleic acid (DNA) acid (RNA) © McGraw Hill 23  Structure of a DNA Strand In a DNA strand, nucleotides are linked together by covalent bonds (called ester bonds) A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of an adjacent nucleotide; this is called a phosphodiester linkage A DNA strand has 5’ to 3’directionality In a strand, all sugar molecules are oriented in the same direction The phosphates and sugar molecules form the backbone of the nucleic acid strand The bases project from the backbone © McGraw Hill 24  Nucleotides are Linked (Polymerized) in Strands Access the text alternative for slide images. © McGraw Hill 25  Discovery of the Double Helix In 1953, James Watson and Francis Crick elucidated the double helical structure of DNA The scientific framework for their breakthrough was provided by other scientists including Linus Pauling (helices) Rosalind Franklin and Maurice Wilkins (X-ray diffraction) Erwin Chargaff (nucleotide ratios, complementation) © McGraw Hill 26  Rosalind Franklin Performed X-ray Diffraction of DNA Fibers 1 Working in the same laboratory as Maurice Wilkins, Rosalind Franklin used X-ray diffraction to study wet fibers of DNA A diffraction pattern is interpreted (using mathematical theory) to provide information concerning the structure of a molecule © McGraw Hill 27  Rosalind Franklin Performed X-ray Diffraction of DNA Fibers 2 (b) X-ray diffraction of wet DNA fibers © McGraw Hill 28  Rosalind Franklin Performed X-ray Diffraction of DNA Fibers 3 Franklin made marked advances in X-ray diffraction techniques with DNA The diffraction pattern she obtained suggested several structural features of DNA Helical More than one strand 10 base pairs per complete turn These findings were instrumental in solving the structure of DNA; her results were shared with Watson and Crick, presumably without her knowledge © McGraw Hill 29  Erwin Chargaff’s Experiment Chargaff pioneered many of the biochemical techniques for the isolation, purification and measurement of nucleic acids from living cells It was known that DNA contained the four bases: A, G, C and T Chargaff analyzed the base composition of DNA isolated from many different species © McGraw Hill 30  The Data Base Content in the DNA from a variety of Organisms* Percentage of Base Content (Based on Molarity) Organism Adenine Thymine Guanine Cytosine E. coli 26.0 23.9 24.9 25.2 S. pneumoniae 29.8 31.6 20.5 18.0 Yeast 31.7 32.6 18.3 17.4 Turtle red blood cells 28.7 27.9 22.0 21.3 Salmon sperm 29.7 29.1 20.8 20.4 Chicken red blood cells 28.0 28.4 22.0 21.6 Human liver cells 30.3 30.3 19.5 19.9 * When the base compositions from different tissues within the same species were measured, similar results were obtained. These data were compiled from several sources. See E. Chargaff and J. Davidson, Eds. (1995), The Nucleic Acids. Academic Press, New York. © McGraw Hill 31  Interpreting the Data Hundreds of measurements were made, and the compelling observation was that Percent of adenine = percent of thymine Percent of cytosine = percent of guanine This observation became known as Chargaff’s rule It was a crucial piece of evidence that Watson and Crick used to elucidate the structure of DNA © McGraw Hill 32  Watson and Crick: How Many Experiments Did They Perform? © McGraw Hill 33  Watson and Crick Watson and Crick set out to solve the structure of DNA They tried to build ball-and-stick models that incorporated all known experimental observations Sugar-phosphate backbone on the outside Bases projecting toward each other They first considered a structure in which bases form H bonds with identical bases in the opposite strand, but later realized this was incorrect For example, A to A, T to T, C to C, and G to G © McGraw Hill 34  Watson and Crick Watson & Crick later realized that the hydrogen bonding of A to T was structurally similar to that of C to G, prompting further modeling with AT and CG interactions between the two DNA strands Their final double helical model was consistent with all known data about DNA structure Watson, Crick and Maurice Wilkins were awarded the Nobel Prize in 1962 Rosalind Franklin died in 1958, and Nobel prizes are not awarded posthumously © McGraw Hill 35  Structure of the DNA Double Helix Two strands are twisted together around a common axis There are 10 base pairs (bp) and 3.4 nm per complete turn of the helix The two strands are antiparallel One runs in the 5’ to 3’ direction and the other 3’ to 5’ The helix is right-handed As it spirals away from you, the helix turns in a clockwise direction © McGraw Hill 36  Structure of the DNA Double Helix Key Features Two strands of DNA form a right-handed double helix. The bases in opposite strands hydrogen bond according to the AT/GC rule. The 2 strands are antiparallel with regard to their 5’ to 3’ directionality. There are ~10.0 nucleotides in each strand per complete 360° turn of the helix. © McGraw Hill 37  Stabilization of the Double Helix The double-helical structure of DNA is stabilized by: Hydrogen bonding between complementary bases A bonded to T by two hydrogen bonds C bonded to G by three hydrogen bonds Base stacking Within the DNA, the bases are oriented so that the flattened regions are facing each other © McGraw Hill 38  Stabilization of the Double Helix 2 © McGraw Hill 39  Grooves on the DNA double helix There are two asymmetrical grooves on the outside of the helix Major groove Minor groove Certain proteins can bind within these grooves They can thus interact with a particular sequence of bases © McGraw Hill 40  Grooves on the DNA double helix (a) Ball-and-stick model of DNA (b) Space-filling model of DNA © McGraw Hill 41  RNA Structure The primary structure of an RNA strand is much like that of a DNA strand, with a couple of exceptions: RNA uses Uracil as a base, instead of Thymine RNA uses Ribose with 2’ OH, instead of Deoxyribose RNA strands are typically several hundred to several thousand nucleotides in length In RNA synthesis, only one of the two strands of DNA is used as a template © McGraw Hill 42  9.7 RNA Structure 2 Access the text alternative for slide images. © McGraw Hill 43  Structure of RNA Molecules 1 Although usually single-stranded, RNA molecules can form short double-stranded regions This secondary structure is due to complementary base- pairing A to U and C to G Allows short regions to form a double helix RNA double helices typically Are right-handed Have 11 to 12 base pairs per turn Different types of RNA secondary structures are possible © McGraw Hill 44  Structure of RNA Molecules 2 (a) Bulge loop (b) Internal loop (c) Multibranched loop (d) Stem loop © McGraw Hill 45  Structure of a Transfer RNA Many factors contribute to the tertiary structure of RNA Base-pairing and base stacking within the RNA itself Interactions with ions, small molecules and large proteins (a) Ribbon Model Access the text alternative for slide images. © McGraw Hill 46