It took a while for biologists to figure out that genetic information was carried on DNA.

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1 DNA Finally, we want to understand how all of the things we've talked about (genes, alleles, meiosis, etc.) come together at the molecular level. Ultimately, what is an allele? What is a gene? How does an allele do its work? It took a while for biologists to figure out that genetic information was carried on DNA. See 10.1 if interested - demonstrates how biologists did this. We already took a brief look at DNA. [OVERHEAD, not in text, but see 10.2A, p. 184] Each nucleotide consists of: A sugar A phosphate group A nitrogenous base The phosphate and sugar forms the backbone, of the DNA (gives it its structure). DNA uses four different nitrogenous bases: A = adenine, T = thymine, C = cytosine, G = guanine [OVERHEAD, similar to fig. 10.2B, p. 185] RNA uses the same, except it uses U = uracil instead of T. RNA also has a slightly different sugar (ribose instead of deoxyribose) [OVERHEAD, fig. 10.2C, p. 185]. The actual structure of DNA was finally pieced together by Watson and Crick with lots of help from Rosalind Franklin [OVERHEAD, fig A & B] (she provided X-ray information that showed DNA to be a double helix). Watson and Crick won the Nobel Prize for this in 1962 (Franklin died in 1958). They postulated a double helix, with the strand held together by hydrogen bonds going from a base pair on one strand to a base pair on the other strand. Also deduced that C only bonds with G, and A only with T G and C both form three bonds, A and T both form two bonds. A and G are twice as big as C or T, To keep a consistent size, and to allow for the differences in the number of bonds, we must pair C w/ G, and A w/ T [OVERHEAD, fig. 10.3D, p. 187] See section 10.3 for some more history if interested.

2 DNA duplication. One of the requirements of DNA was that it could replicate (make copies of itself). Otherwise, how can you pass on genetic information? Watson and Crick showed how this is possible. Since A can only pair with T, and G only with C, we have only one way in which we can make a complimentary strand. Essentially, DNA unzips. An enzyme comes along, and for each A, puts in a T for the new strand. For each T, puts in an A, for C, puts in G, and for G puts in C. Details: [OVERHEAD, fig. 10.4A & B, p. 188] An enzyme called DNA polymerase duplicates DNA. Part of the DNA double helix will unwind and form a bubble. DNA polymerase moves into the bubble, and begins to replicate DNA. [OVERHEAD, fig. 10.5A, p. 189] To speed things up, numerous bubbles form at the same time and grow towards each other to make the final replicated strand. Mammals can pair up to 50 nucleotides / second (bacteria up to 500!). Now we know where our duplicated chromosomes come from (i.e., our chromatids). This is only half the story, though. We still need to figure out how we go from DNA to a protein. DNA protein. There are several steps involved. First, that part of the DNA that is our allele must be transcribed into RNA. The information on the RNA must then be translated into our protein. [OVERHEAD, fig. 10.6A, p. 190] [OVERHEAD, fig. 10.7, p. 191] We also need to figure out how we go from four different bases (A,T,C,G) to 20 different amino acids. Obviously, it can't be one to one (we'd only get four different amino acids)

3 It can't be two to one (we'd only get 16 different amino acids) It is three to one (we could actually get a lot more (64) than 20, but there's a lot of redundancy built in to the system). This redundancy helps prevent mutations being carried over into proteins (more later). This explains the overhead, where we see that each group of three bases will code for an amino acid. The genetic code: [OVERHEAD, fig. 10.8A, p. 192] Shows which triplets (= codons) in our RNA code for which amino acids. This table was first deciphered by using artificial RNA with just one type of base (UUUUUUUUUUU...), so this will give us the amino acid that's coded for by UUU. The rest of the table was deciphered in a similar way. As mentioned, the code may be redundant, but each codon (triplet) codes for only one amino acid NOT vice versa Transcription: Several triplets can code for the same amino acid. But each triplet codes for one (and only one) amino acid [OVERHEAD, fig A & B, p. 193] RNA is made in pretty much the same way that DNA is duplicated. BUT: Only one strand is made U substitutes for T. The strands of DNA separate to let RNA polymerase (not DNA polymerase) access. After the RNA strand is made, DNA closes up again. RNA manufacture is started at a section of DNA called a promoter (a special sequence of bases (nucleotides). RNA manufacture stops at another special sequence of bases called the terminator

4 The RNA made in this way is called messenger RNA (mrna). It takes the message (information) from DNA to a place where it can be converted into proteins. Our messenger RNA then gets cleaned up a bit more (details in text if you're interested) trna Transfer RNA is yet another kind of RNA. Essentially it's a piece of RNA with an anticodon on one end (that will fit into our triplets), and the appropriate amino acid on the other end. [OVERHEAD, fig A, p. 195] These trna molecules will connect to the mrna For each triplet, there will be one type of trna. It will fit into the appropriate triplet, and then drag along the right amino acid. Going from mrna proteins: or, putting all this together are the ribosomes! Ribosomes are made up of mostly proteins and bits and pieces of rrna (ribosomal RNA). rrna is a third kind of RNA, and is an important part off ribosomes. Ribosomes are made up of two pieces, a smaller piece, and a bigger piece. Essentially, a ribosome will work a little like an assembly line. It has two (actually three) slots (called a P site and an A site (and E)). One trna will fit into one of the slots (it'll have the appropriate anticodon for the first triplet). The next slot will be filled with the appropriate trna for the next triplet. An enzyme will then take the amino acids attached to each of the trna molecules and combine them. [OVERHEAD, fig A - C, p. 196] Some more details: The start of our mrna molecule has a special sequence of nucleotides which helps it bind to the smaller subunit of the ribosome [OVERHEAD, fig B, p. 197] A trna will then bind to the start codon, a special triplet that says start here. This makes sure translation starts in the right place.

5 This trna molecule generally also has the amino acid methionine attached. Once this trna binds to the start codon, the larger subunit binds to everything Now we need to add more amino acids. Three steps to making polypeptides [OVERHEAD, fig , p. 197]: (see also figure 10.15, p. 198 for a summary) 1) Codon recognition - the next triplet (codon) is recognized. The appropriate trna is found, and placed into the A site of our ribosome (which is right next to the P site) 2) A peptide bond is formed between the polypeptide attached to the trna that's in the P slot and the amino acid that's attached to the trna that's in the A slot. 3) The trna in the P slot now leaves (moves to the "E" slot and leaves), and the one in the A slot moves into the P slot. the process starts over. This process continues until a stop codon tells the ribosome to stop. The final polypeptide is released from the ribosome, which splits apart into its two subunits. (Note that several ribosomes can attach to one mrna at the same time [OVERHEAD, not in book]) Mutations: A single change in one nucleotide (say, T changes to A), can cause a huge change in the resulting protein. ote that due to the redundancy in the genetic code, a lot of mutations wont do anything at all. But sometimes a mutation can have profound effects. [OVERHEAD, fig A, p. 199] mutations can be due to: Base substitutions Deletions Additions Examples of each of these are in [OVERHEAD, fig B, p. 199]

6 Mutations can be caused by: Chemicals or radiation, or sometimes just mistakes in copying There are enzymes which try to correct mistakes, but sometimes they'll get it wrong. Incidentally, many mutations don't so anything, some are harmful, a few are actually beneficial (hint of evolution, here). Some examples of using this information (we're skipping over several sections here): Viruses [OVERHEAD, fig , p. 201]: A virus is a short piece of DNA or RNA, surrounded by a protein coat, and possible a membrane Some RNA viruses are the ones that cause flu, measles, mumps, the common cold, polio, AIDS. Some DNA viruses cause hepatitis, chicken pox, herpes infections. The virus can attach to a cell (bacteria, body cell, etc.). Once this happens, the virus will release it's genetic material into the cell. The genetic material is wrapped in a protein coat to further protect it. In the case of RNA, a complimentary strand is then made using enzymes from the virus. This becomes mrna that the cell than uses as if it were its own mrna. This mrna usually makes more viral proteins, but also make new RNA for new viruses. The new viral RNA gets packed into the viral proteins, and released back outside the cell. Lots of new viruses can be made in this way. The host cell is basically hijacked by the viral genetic material. The damage caused by viruses is often a factor of which cells a virus will attack: Polio attacks nerve cells which can not divide again (once destroyed, your body can't replace them). A cold virus attacks cells along the respiratory tract which

7 can rapidly divide again. AIDS virus (HIV) [OVERHEAD, fig A & B, p. 203]: This will actually incorporate itself into the host cell's DNA. HIV includes a special enzyme that will convert RNA DNA (it's called reverse transcriptase, and some AIDS medicines work by disabling reverse transcriptase). The virus' RNA is converted into DNA. A complimentary strand is added. This short piece of double stranded DNA then merges with the host DNA. The virus then becomes a provirus: a virus that is now part of the host's DNA. This provirus will occasionally be transcribed, and the process follows the usual pattern, except that in this case the stuff being made is new viruses and the necessary proteins. HIV attacks cells of the immune system. We suspect many other viruses may have made their home in our genetic material. Some may be duplicated when our cells divide and even passed on from one generation to the next. Finally, just a few quick comments about other things: Viruses attack not just animals, but also: Plants (some serious diseases of agricultural plants are viruses) Bacteria (can even be used to treat some bacterial diseases!). Bacteria can pass genetic information to each other (sometimes between different species). They use plasmids, short sequences of DNA. One reason why bacteria with resistance to antibiotics can spread so fast. But humans can also hijack this process place genes into plasmids and then give these to bacteria so that they make useful things (like insulin). Read sections & if interested.

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