DNA & RNA- Nucleic Acids and Protein Synthesis

DNA & RNA- Nucleic Acids and Protein Synthesis IB Biology Ch. 16: Campbell

Objectives • Describe the history behind the discovery of DNA and its function • Outline the structure of a nucleotide • Describe the structure of the DNA molecule • Describe the process of DNA replication including the various enzymes and that it is a semi-conservative process.

Discovery of DNA • In 1868, Friedrich Meischerfirst isolated deoxyribonucleic acid from cells in pus and from fish sperm. • No one knew DNA’s function.

Fredrick Griffith- 1928 • First suggestion that about what genes are made of. • Worked with: 1) Two strains of Pneumococcus bacteria: Smooth strain (S) Virulent (harmful) Rough strain (R) Non-Virulent 2) Mice-were injected with these strains of bacteria and watched to see if the survived. 3) Four separate experiments were done: -injected with rough strain (Lived) -injected with smooth strain (Died) -injected with smooth strain that was heat killed (Lived) -injected with rough strain & heat killed smooth (????)

Mixture of heat-killed S cells and living R cells EXPERIMENT Living R cells (control) Living S cells (control) Heat-killed S cells (control) RESULTS Mouse dies Mouse healthy Mouse healthy Mouse dies Living S cells

Griffith’s Conclusion • Somehow the heat killed smooth bacteria changed the rough cells to a virulent form. • These genetically converted strains were called “Transformations” • Something (a chemical) must have been transferred from the dead bacteria to the living cells which caused the transformation • Griffith called this chemical a “Transformation Principle”

Next Breakthrough came from the use of Viruses • Viruses provided some of the earliest evidence that genes are made of DNA • Molecular biology studies how DNA serves as the molecular basis of heredity • Are only composed of DNA and a protein shell. T2 Bacteriophage- a typical virus

Phage reproductive cycle Phage attaches to bacterial cell. Phage injects DNA. Phage DNA directs host cell to make more phage DNA and protein parts. New phages assemble. Cell lyses and releases new phages. Figure 10.1C

Photo of T2 Viruses Fig. 16-3 Phage head Tail sheath Tail fiber DNA 100 nm Bacterial cell

Hershey-Chase Experiment- 1952 • In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2 • To determine the source of genetic material in the phage, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection • **They concluded that DNA provides the genetic information of a virus.

Fig. 16-4-1 EXPERIMENT Radioactive protein Phage Bacterial cell DNA Batch 1: radioactive sulfur (35S) Radioactive DNA Batch 2: radioactive phosphorus (32P)

Fig. 16-4-2 EXPERIMENT Empty protein shell Radioactive protein Phage Bacterial cell DNA Batch 1: radioactive sulfur (35S) Phage DNA Radioactive DNA Batch 2: radioactive phosphorus (32P)

Fig. 16-4-3 EXPERIMENT Empty protein shell Radioactivity (phage protein) in liquid Radioactive protein Phage Bacterial cell DNA Batch 1: radioactive sulfur (35S) Phage DNA Centrifuge Pellet (bacterial cells and contents) Radioactive DNA Batch 2: radioactive phosphorus (32P) Centrifuge Radioactivity (phage DNA) in pellet Pellet

Video Clip of Hershey-Chase • http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html#

Erwin Chargaff- 1950 Already known- DNA is a polymer of nucleotides- nitrogen base, pentose sugar, and a phosphate group. Chargaff noticed a ratio of the bases: 30.3% Adenine 30.3% Thymine 19.5% Guanine 19.9% Cytosine

Chargaff’s Rules: The amount of A = T, and the amount of C = G.

Who Discovered the Shape of DNA? • James Watson and Francis Crick (1954). They established the structure as a double helix - like a ladder that is twisted. The two sides of the ladder are held together by hydrogen bonds.

How did they get to their conclusions? • They built many models, always perplexed at how it fit together, until one day, when they wandered into the office of a fellow scientist, Dr. Rosalind Franklin.

Rosalind Franklin used x-ray diffraction techniques to produce images of DNA molecules • She concluded: • DNA exists as a long, thin molecule of uniform diameter • The structure is highly repetitive • DNA is helical X-ray Diffraction

Along with Dr. Maurice Wilkins, she had taken x-ray crystallography photos of DNA. They saw her photos and realized the great secret- that DNA was coiled like a spring. They then made their model and won the Nobel Prize in 1962. Franklin’s famous photo of DNA

So, What is DNA?Deoxyribonucleic Acid • blueprint of life (has the instructions for making an organism) • codes for your genes • made of repeating subunits called nucleotides • shape is the double helix (twisted ladder)

I. Structure of DNA- 3 parts: • Sugar- Deoxyribose • Phosphate Group • Nitrogen bases The sugar and phosphates make up the "backbone" of the DNA molecule. Nucleotide

DNA and RNA are polymers of Nucleotides DNA is a nucleic acid, made of long chains of nucleotides- Sugar, phosphate, nitrogen base. Phosphate group Nitrogenous base Nitrogenous base(A, G, C, or T) Sugar Phosphategroup Nucleotide Thymine (T) Sugar(deoxyribose) DNA nucleotide** Figure 10.2A Polynucleotide Sugar-phosphate backbone

Nitrogen bases Bases come in two types: a. Purines (adenine and guanine- A&G) b. Pyrimidines (thymine and cytosine- T&C).

DNA Maintains a Uniform Diameter • See pg. 310

Base Pairing- Chargaff’s Rules • Watson and Crick reasoned that the pairing was more specific, dictated by the base structures • They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) • The Watson-Crick model explains Chargaff’s rules: Adenine pairs to Thymine (A-T)Guanine pairs to Cytosine (G-C)**Very important- remember this!!!!

DNA Bonding The two sides of the helix are held together by Hydrogen bonds (weak) The sides of the DNA, the sugar and phosphate, are held together with covalent bonds (strong).

Simple Diagram of DNA-Think of it like a ladder, the bases being the rungs.

Each strand of the double helix is oriented in the opposite direction • The ends are referred to as the 3’ and 5’ ends. 5 end 3 end P P P P P P P P 3 end 5 end Figure 10.5B

Summary: • Chargaff ratio of nucleotide bases (A=T; C=G) • Watson & Crick (Wilkins, Franklin) • The Double Helix • √ nucleotides: nitrogenous base (thymine, adenine, cytosine, guanine); sugar deoxyribose; phosphate group

Putting it all together: here are some images of what the DNA double helix looks like:

DNA Replication and Repair • The relationship between structure and function is manifest in the double helix • Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material

The Basic Principle: Base Pairing to a Template Strand • Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication • In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

Fig. 16-9-1 A T C G T A A T C G (a) Parent molecule

Fig. 16-9-2 A T T A C G G C A T A T T A T A C C G G (b) Separation of strands (a) Parent molecule

Fig. 16-9-3 A T A T A T A T C G C G C G C G A T A T A A T T T A T A T T A A C C G C G C G G (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand (b) Separation of strands (a) Parent molecule

Three Proposed Models of DNA Replication

Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand • Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new)

DNA Replication: A Closer Look • The copying of DNA is remarkable in its speed and accuracy • More than a dozen enzymes and other proteins participate in DNA replication

DNA replication depends on specific base pairing • In DNA replication, the strands separate • Enzymes use each strand as a template to assemble the new strands Nucleosomes Parental moleculeof DNA Both parental strands serveas templates Two identical daughtermolecules of DNA

Anti-parallel Structure of DNA

Antiparallel nature • 5’ end corresponds to the Phosphate end • 3’ end corresponds to the –OH sugar • Replication runs in BOTH directions • In the original, one strand runs 5’ to 3’ while the other runs 3’ to 5’ • ** The new DNA strand forms and grows in the 5’  3’ direction only • So, nucleotides are added on the 3’ end of the original strand.

Building New Strands of DNA 5’ end 3’ end 5’ end

Building New Strands of DNA • Each nucleotide is a triphosphate: (GTP, TTP, CTP, and ATP) • Nucleotides only add to the 3’ end of the original strand (never on the 5’ end) • Two phosphates are released (exergonic) and the energy released drives the polymerization process.

Getting Started • Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” • A eukaryotic chromosome may have hundreds or even thousands of origins of replication • Replication proceeds in both directions from each origin, until the entire molecule is copied

Fig. 16-12b Origin of replication Double-stranded DNA molecule Parental (template) strand Daughter (new) strand 0.25 µm Replication fork Bubble Two daughter DNA molecules (b) Origins of replication in eukaryotes

Fig. 16-12 Origin of replication Parental (template) strand Daughter (new) strand Replication fork Double- stranded DNA molecule Replication bubble 0.5 µm Two daughter DNA molecules (a) Origins of replication in E. coli Origin of replication Double-stranded DNA molecule Parental (template) strand Daughter (new) strand 0.25 µm Replication fork Bubble Two daughter DNA molecules (b) Origins of replication in eukaryotes

Getting Started- Enzymes • At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating • Topoisomerasecorrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands • Helicasesare enzymes that untwist the double helix at the replication forks • Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template

Fig. 16-13 Primase Single-strand binding proteins 3 Topoisomerase 5 3 RNA primer 5 5 3 Helicase

DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end • The initial nucleotide strand is a short RNA primer

DNA & RNA- Nucleic Acids and Protein Synthesis