DNA Structure - Biology 22 Spring 2022 PDF

Biology 22: Spring 2022 DNA Structure  Two Core Ideas of Biology The Cell Theory The Central Dogma of Molecular Biology So how do cells divide? How do cells...

Biology 22: Spring 2022 DNA Structure  Two Core Ideas of Biology The Cell Theory The Central Dogma of Molecular Biology So how do cells divide? How do cells know what to do? Note: in prokaryotes, all of this occurs in the cytoplasm. We will talk about where each step occurs in eukaryotes. The History of DNA  The Morgan Experiment The first solid evidence associating a specific gene with a specific chromosome came from Thomas Hunt Morgan, an embryologist Morgan’s experiments with fruit flies provided convincing evidence that chromosomes are the location of Mendel’s heritable factors Several characteristics make fruit flies a convenient organism for genetic studies: They produce many offspring A generation can be bred every two weeks They have only four pairs of chromosomes  Questions, Questions But, there were several questions still unanswered. 1. What part of the chromosome is the actual genetic material that is used to inherit factors? (What do you remember made up a chromosome?) 2. What does DNA look like? 3. How does DNA work? Question 1: What Part of the Chromosome is the Source of Genetic Information?  Proteins or DNA? After Morgan’s discovery that genes are located on chromosomes, the two components of chromosomes, protein and DNA, became candidates for genetics material. (Also potentially RNA) Proof of the role of DNA in heredity was the first discovered by studying bacteria and the viruses that infect them.  Griffith: Change in Phenotype The discovery of the genetic role of DNA began with research by Frederick Griffith in 1928 Griffith worked with two strains of a bacterium, one pathogenic and one harmless When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic He called this phenomenon transformation, now defined as a change in genotype and phenotype due to assimilation of foreign genetic material. The Griffith Experiment (1928)  What Causes the Change? But there are several components to genetic material: DNA, RNA, and protein. Which of these caused transformation to occur? The Avery, MacLeod, and McCarty Experiment (1944) Heat killed, homogenized, and filtered Nonvirulent bacteria  Bacteriophages and DNA More evidence for DNA as the genetic material came from studies of viruses that infect bacteria Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research A virus is DNA (sometimes RNA) enclosed by a protective coat, often simply protein (will go into detail at the end of term)  Hershey and Chase: Work with Bacteriophages So there was some thought that DNA was the main genetic material. However, there was questions about whether protein hidden in DNA could still be carrying the information for inheritance. Alfred Hershey and Martha Chase understood that viruses carried DNA and protein. They wanted to see what part of the virus entered into the cell when infecting the cell. The Hershey and Chase Experiment (1952) Only DNA goes into the cell. Therefore, DNA must be the genetic material that carries the information for inheritance. Answer 1: DNA is the Part of the Chromosome that is the Source of Genetic Information. Question 2: What Does DNA Look Like?  Chargaff: DNA Composition It was known that DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next This evidence of diversity made DNA a more credible candidate for the genetic material  The Chargaff Experiments Based upon several different experiments, Chargaff determined that: - The base composition of DNA varies between species - In any species the number of A and T bases are equal and the number of G and C bases are equal - The basis for these rules was not understood until the discovery of the double helix  The Chargaff Experiments After Chargaff’s results, the challenge was to determine how its structure accounts for its role in heredity The Franklin and Wilkins Experiments (1947) Maurice Wilkins and Rosalind Franklin were using a technique called X-ray crystallography to study molecular structure Franklin produced a picture of the DNA molecule using this technique Franklin also determined that the two outer sugar- phosphate formed the backbones, with the nitrogenous bases paired in the molecules interior  The Watson and Crick Conclusion (1953) Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA Watson built a model in which the backbones were antiparallel (their subunits run in opposite directions) At first, Watson and Crick thought the bases paired like with like (A with A, and so on) but such pairings did not result in a uniform width Instead, pairing a purine with a pyrimidine resulted in a uniform width consistent with the X-ray data Watson and Crick Experiment  Watson and Crick and Chargaff 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: in any organism the amount of A =T, and the amount of G = C Final DNA Structure Answer 2: DNA is a Double Helix Side Note: RNA  The Fraenkel-Conrat Experiment (1956) RNA also carries genetic information in RNA viruses. Again, we’ll cover at the end of term but the experiment was: Thefactfactor.com Question 3: How does DNA Work? Recall Macromolecules In Biol 21? DNA in 3D  DNA Is 2 Strands of Nucleic Acids Phosphate group Bases Phosphate group Phosphodiester bond Bases Phosphodiester bond Deoxyribose sugar Deoxyribose sugar Bases DNA Can Be Thought of as a Ladder The Rungs of DNA: 4 Bases A nucleotide (A) (G) (T) (C) A way to remember: “All Girls are Pure” Purines and Pyrmidines Nucleotides (Monomers)  Hydrogen Bonds Between Bases Purines and pyrimidines pair with each other via hydrogen bonds. A pairs with T G pairs with C Just remember straight letters stick together & round letters stick together Hydrogen Bonds Between Bases There are 2 hydrogen bonds formed between A and T There are 3 hydrogen bonds formed between G and C (a way to remember: G and C are round, so they have space to make more hydrogen bonds) 2 Strands of Nucleic Acids that Bond Together 3 H- bonds 2 H- bonds 3 H- bonds 3 H- bonds 2 H- bonds  DNA is Made of Two Complementary Strands By seeing one strand’s base sequence, you should be able to figure out the other (aka complementary) strand’s base sequence. Complementary Strands This is the basis of DNA replication DNA Strands are Anti-Parallel These complementary strands run antiparallel to one another (See 3’ to 5’ vs 5’ to 3’?)  DNA Sequence 5’ = phosphate group side 3’ = not phosphate side 3’ = not phosphate side 5’ = phosphate group side Writing Out the DNA Sequence 5’ = phosphate group side A gene is a sequence of nucleotides. 3’ = not phosphate side  Major Groove and Minor Groove See how one side has a bigger indent?  Major Groove and Minor Groove What are some benefits with having a major/minor groove? (Recall in what situations shape = important)  Major Groove and Minor Groove The distance for 1 full rotation of DNA = ~ 3.4 nm  Answer 3:DNA Works as Antiparallel, Complementary Strands with Specific Orientation (more to come…)  DNA Isolation DNA can be isolated by lysing cells. Which membranes need to be broken down to extract DNA?  DNA Precipitation DNA can be precipitated out of solution using ethanol or any. To precipitate out means to transform a dissolved substance into a solid. Wikipedia.com  DNA Charge/Polarity Ethanol precipitation takes advantage of the fact that DNA is strongly negatively charged because it has the phosphate backbone. (so it DNA polar or nonpolar?) https://cnx.org/  DNA Isolation Since the cell is mostly water and DNA is hydrophilic, DNA is found “dissolved” in water. The water molecules surround the DNA. Laage et al., 2017  DNA Isolation If you add enough ethanol to a lysis, the DNA stops interacting with the water and precipitates out. (For those interested in the chemistry, we use ice-cold ethanol because you are going from a liquid (higher energy) to a solid (lower energy) state. Ice cold = lower energy so helps the DNA get to the lower energy state faster!)