This unit begins several lessons all directed at understanding the chemical/molecular basis for the the Mendelian genetics you studied in the last unit. We will study the structure of the genetic material, DNA, how it makes duplicate copies of itself during cell division, and how the DNA is ultimately translated in to the organisms phenotype in terms of the protein synthesis that it directs. This material is the foundation for the revolution in genetic engineering over the past few decades that has had profound implications for your medical care, food supply, and our understanding of basic biological process most importantly that of evolution.
Learning Objectives: the successful student will be able to ...
- briefly describe the early experiments of Griffith, Avery et al, and Hershey and Chase that identified DNA has the genetic material.
- describe the contributions of Chargaff, Watson & Crick, and Franklin to our understanding of the structure of the DNA molecule and its relationship to its function as the genetic material.
- describe and identify the components of a nucleotide and their arrangement in the DNA molecule.
- describe the double helix, antiparallel (5'-3' vs 3'-5') nature of the DNA molecule and explain how this structure is related to the semi-conservative mode of replication of DNA.
- describe the experiments and their significance of the Meselson & Stahl experiments.
- describe the sequence of events in the replication process of DNA. In particular, be able to explain the role of DNA helicase, Topoisomerases, DNA polymerase, Primase, Ligase, and Telomerase.
- explain the differences in DNA replication in the leading and lagging strands of DNA and explain how this relates to the antiparallel nature of the DNA molecule.
- describe and explain the significance of the Beadle & Tatum experiments with Neurospora and the "one gene, one enzyme hypothesis.
- explain why the genetic code is based on "triplets" or codons of DNA bases and be able to read the genetic code tables to predict the amino acid sequence of a peptide.
- explain the two stage process of gene expression and the events that take place during transcription and translation.
- compare the similarities and differences between DNA and ribosomal, transfer, and messenger RNAs and describe the functions of the three types of RNA during translation.
- describe the events that take place on the ribosomes during translation.
- explain the nature of nonconding sequences of DNA (entrons) and coding sequences (exons) in eukaryote genes and other forms of post transcriptional modification of mRNA.
- name and describe the various types of mutations including point, deletion, frame shift, and transposons.
Lesson One: The Early Experiments.
Although most students today learn early on that DNA is the molecule that represents our genetic material, this was not always the case. An intense debate took place between scientists that thought large complicated proteins must be the genetic material versus those that championed DNA. Three critical experiments led to the conclusion that DNA must be the stuff of our genes. You need to be able not only to describe these experiments, but understand their fundamental significance as well.
Frederick Griffith and Transformation. Understand that Griffith's experiment did not clarify the question about the nature of the genetic material. What it did do was open an experimental door that others used to answer these questions. Often experiments such as Griffith's are the critical breakthrough that leads to important discoveries. Go to Kimball's pages to read about these experiments on transformation in bacteria.
Avery, McLeod, and McCarthy. These scientist did what scientist are trained to do; they recognized the significance of Griffith's work and applied it to a new question. Their simple concept (not so simple to actually do) lead to the the first solid evidence that DNA was the genetic material. Kimball has a brief description and more complete information can be found here and here.
Hershey and Chase. If one set of experiments stands out as the defining evidence that DNA is the genetic material it is the work of Alfred Hershey and Martha Chase. Their experiments represent the final chapter in the protein vs DNA debate. It is also an elegant example of how a complex question is often best answered by a clever but simple experiment. Kimball has a brief description and more information is found at the blog of Linus Pauling (ironically one of the strongest proponents of the "genes are proteins" hypothesis).
Here is a clever video summary of the Hershey-Chase experiment from Youtube.
Homework, Due .
Run the first two animations at this site (Avery's experiment and the Hershey-Chase experiment). You don't have to submit any work. However, be sure you can describe in some detail both these experiments and answer the following questions.
- Why was the virus used by Hershey and Chase the ideal organism to address the question about the protein vs DNA nature of the gene?
- E.coli bacteria usually reproduce asexually when one cell divides into two (fission). Why does this mode of reproduction make the results of the Avery experiments much easier to evaluate? Remember, the bacteria used were isolated from colonies started with a single bacterial cell.
Lesson Two. The Structure of DNA.
The important experiments you studied in lesson one demonstrated that DNA was the genetic material. Keep in mind that these experiments did not reveal the structure of the molecule or how genes functioned. These questions were left to another group of scientists. You need to know the significance of their work as well.
DNA is a long polymer constructed of thousands of monomers called nucleotides. These in turn are composed of a five-carbon sugar linked to a phosphate group and to one of several nitrogen containing bases (nitrogenous base). Go to Kimball for details. These pages also mention RNA. Don't spend to much time with this molecule; we study it soon enough. Be sure you can recognize a nucleotide when you see one and distinguish the sugar from the phosphate group from the base. Know the names of the base but you don't need to recognize each of them individually. You can view some simple but nice diagrams of these molecules here.
Keep in mind that these molecules not only are the building blocks of DNA (and RNA) but play other vital functions in cells. You have already met ATP (a triphosphate nucleotide) and cAMP ( a monophosphate nucleotide) that often functions as an intracellular messenger helping to regulate cell metabolism and gene expression.
Go to the animation site of John Kyrk and select the DNA structure program. This is a fairly involved animation and you may have to go through it a few times. Look for the following information.
- The spacial relationship among the components of each nucleotide.
- How each nucleotide is connected to its adjacent nucleotides.
- The base pairing of the four different nucleotides in the double helical DNA molecule.
- Why DNA is said to be composed of two "antiparallel" strands.
Homework, Due 19 March.
Go to this Jmol site by Eric Martz and run tutorials "A" and "C" on DNA structure. Then answer questions 11-13, 15, 16, 19, and 20. Warning! This tutorial is challenging. It expects you to take your time exploring these molecules and discovering the answers for yourself. Don't expect to go through this quickly. Email the answers to me.
Lesson Three: DNA Replication.
Recall that one of the three tenets of the "Cell Theory" is that all cells come from other living cells. This carries with it the assumption that the genetic material of the original cell is passed on to the new daughter cells as accurate copies of DNA. This is no small challenge considering the fact that DNA is a very large and delicate molecule.
At the time there were three competing hypotheses to explain how the DNA molecule makes copies of itself during cell division; the "conservative" hypothesis, the "semi-conservative" hypothesis, and the "dispersive" hypothesis. The classic experiments of Meselson and Stahl clarified this point and demonstrated that DNA replication is "semi-conservative" meaning that the DNA splits into two mirror image halves each of which is used as a template to build the new half of the molecule.
Go here for a simple animation of the Meselson and Stahl experiments. Be sure you understand how the banding pattern of the nitrogen isotopes from the centrifuge allowed the scientists to determine the mode of DNA replication in the first and subsequent generations of cell division. Here is another animation of the same experiment.
Homework, Due . Write a brief statement answer each of the following questions and email me your work using your FBA account.
- Why were isotopes of nitrogen the ideal "marker" for the Meselson and Stahl experiments?
- Why did the results from the first generation of cell division rule out the "conservative" hypothesis?
- Why were addition generations required to distinguish between the "semi-conservative" and the "dispersive" hypotheses?
