DNA Structure and Replication
Nucleic Acids Function: genetic material stores information genes blueprint for building proteins DNA RNA proteins transfers information blueprint for new cells blueprint for next generation DNA proteins
Nucleic Acids Examples: Structure: RNA (ribonucleic acid) single helix DNA (deoxyribonucleic acid) double helix Structure: monomers = nucleotides DNA RNA
RNA & DNA RNA DNA single nucleotide chain double nucleotide chain N bases bond in pairs across chains spiraled in a double helix double helix 1st proposed as structure of DNA in 1953 by James Watson & Francis Crick
DNA Function series of bases encodes information like the letters that make up words in a book stored information is passed from parent to offspring need to copy accurately! stored information = genes genetic information All other biomolecules we spoke about served physical or chemical functions. DNA & RNA are information storage molecules. DNA well-suited for an information storage molecule: chemically stable stores information in the varying sequence of nucleotides (the genetic code) its coded sequence can be copied exactly by the synthesis of complementary strands; easily unzipped & re-zipped without damage (weak H bonds) damage to one strand can be repaired by addition of bases that match the complementary strand
Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group Nitrogen base I’m the A,T,C,G or U part! DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis. Are nucleic acids charged molecules?
Nucleotides 2 types of nucleotides Differ in nitrogen bases purines double ring N base adenine (A) guanine (G) pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)
DNA Structure - Nucleic polymer Backbone sugar to PO4 bond phosphodiester bond (a type of covalent bond) new base added to sugar of previous base polymer grows in one direction N bases hang off the sugar-phosphate backbone
DNA Structure – Paired nucleotides Nucleotides bond between DNA strands H bonds The base pairing ules: purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds The 2 strands are complementary. One becomes the template of the other & each can be a template to recreate the whole molecule.
DNA molecule Double helix H bonds between bases join the 2 strands A :: T C :: G H bonds = biology’s weak bond • easy to unzip double helix for replication and then re-zip for storage • easy to unzip to “read” gene and then re-zip for storage
Building the polymer
Copying DNA Replication 2 strands of DNA helix are complementary have one, can build other have one, can rebuild the whole when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system?
DNA replication “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” James Watson Francis Crick 1953 The greatest understatement in biology!
Rosalind Franklin (1920-1958) Rosalind’s X-Ray diffraction pictures helped Watson and Crick develop their theory A chemist by training, Franklin had made original and essential contributions to the understanding of the structure of graphite and other carbon compounds even before her appointment to King's College. Unfortunately, her reputation did not precede her. James Watson's unflattering portrayal of Franklin in his account of the discovery of DNA's structure, entitled "The Double Helix," depicts Franklin as an underling of Maurice Wilkins, when in fact Wilkins and Franklin were peers in the Randall laboratory. And it was Franklin alone whom Randall had given the task of elucidating DNA's structure. The technique with which Rosalind Franklin set out to do this is called X-ray crystallography. With this technique, the locations of atoms in any crystal can be precisely mapped by looking at the image of the crystal under an X-ray beam. By the early 1950s, scientists were just learning how to use this technique to study biological molecules. Rosalind Franklin applied her chemist's expertise to the unwieldy DNA molecule. After complicated analysis, she discovered (and was the first to state) that the sugar-phosphate backbone of DNA lies on the outside of the molecule. She also elucidated the basic helical structure of the molecule. After Randall presented Franklin's data and her unpublished conclusions at a routine seminar, her work was provided - without Randall's knowledge - to her competitors at Cambridge University, Watson and Crick. The scientists used her data and that of other scientists to build their ultimately correct and detailed description of DNA's structure in 1953. Franklin was not bitter, but pleased, and set out to publish a corroborating report of the Watson-Crick model. Her career was eventually cut short by illness. It is a tremendous shame that Franklin did not receive due credit for her essential role in this discovery, either during her lifetime or after her untimely death at age 37 due to cancer.
Interesting note… Ratio of A-T::G-C affects stability of DNA molecule 2 H bonds vs. 3 H bonds biotech procedures more G-C = need higher T° to separate strands high T° organisms many G-C parasites many A-T (don’t know why) At the foundation of biology is chemistry!!
Another interesting note… ATP Adenosine triphosphate modified nucleotide adenine (AMP) + Pi + Pi + +
HELIXHELIX
DNA REPLICATION Preparing for Mitosis
DNA REPLICATION DNA IS COPIED DURING the S-phase of INTERPHASE PREPARATION FOR CELL DIVISION (when each daughter cell gets a complete set of DNA)
SEPARATION Helicase is the enzyme that splits the 2 strands of DNA (Scissors) THE POINT OF SEPARATION IS CALLED THE REPLICATION FORK
SEPARATION Helicase will separate the strands of dna in multiple places along the molecule so that separation occurs quickly Multiple Replication bubbles form along the entire dna molecule
PREPARATION WITHIN EACH REPLICATION BUBBLE, primase, The second enzyme, primes the dna for replication.
EXTENDING THE STRANDS DNA POLYMERASE MOVEs ALONG THE OPEN CHAINS AND adds COMPLEMENTARY NUCLEOTIDES to build a new strand of DNA
BUILDING DNA STRANDS The 2 ends of a strand of DNA are different and antiparallel - one end is 5 prime (5’), other is 3 prime (3’), complementary to opposite ends Dna polymerase can ONLY add nucleotides to the 3’ end, never to the 5’ end.
EXTENSION The leading strand is the strand that is made by adding nucleotides to the 3’ end as the replication fork opens up The lagging strand is the strand that has to somehow build a dna strand in the 5’ direction
PROBLEM!!! How does DNA build a lagging strand that is extending in the 5’ direction?
ANSWER!!: Okazaki fragments are partial segments of DNA that form as the replication fork exposes more of the DNA
FINALIZING THE NEW STRANDS The final enzyme, Ligase, “lags” behind and reforms the phosphate & Sugar backbone, “gluing” the okazaki fragments together
TWO STRANDS NOW THERE ARE TWO double STRANDS of DNA EACH STRAND contains HALF OF THE ORIGINAL STRAND EACH Daughter STRAND IS IDENTICAL TO THE ORIGINAL, parent, STRAND
Unzipped by: Helicase
Unzipped by: Helicase Primed by: Primase Unzipped by: Helicase New base pairs added by: DNA Polymerase Primed by: Primase
Unzipped by: Helicase Primed by: Primase Finalized by: Ligase Unzipped by: Helicase New base pairs added by: DNA Polymerase Primed by: Primase Finalized by: Ligase
MOVIES http://www.johnkyrk.com/DNAreplication.html http://www.pbs.org/wgbh/aso/tryit/dna/# http://www.ncc.gmu.edu/dna/repanim.htm http://sites.fas.harvard.edu/~biotext/animation s/replication1.swf http://www.hhmi.org/biointeractive/dna- replication-advanced-detail