Chapter 13 DNA
What were Chargaff's rules? How did they contribute to deciphering the structure of DNA? (figure 13.8 helps here)
1. The base composition of nucleotides in DNA varies between species. 2. The amount of Adenine equals the amount of Thymine, and the amount of Guanine equals the amount of Cytosine. Naturally, this knowledge helped lead to the discovery that Adenine binds to thymine and guanine to cytosine.
Describe the structure of a nucleotide.
A nucleotide consists of deoxyribose, a nitrogenous base, and a phosphate.
How are purines different from pyrimidines.
Adenine and Guanine are purines, while Thymine and cytosines are Pyrimidines. Purines have a single ring structure, while pyrimidines have a double ring structure.
Summarize the evidence that Watson and Crick used to figure out the structure of DNA.
Chargaffs rules, combined with the image that showed the size and shape of DNA. The base pairs connecting the way we know they do know is the only way that the shape and size they saw could be possible.
How can DNA and proteins be used as "tape measures" of evolution?
DNA is inherited, and naturally can be used to establish genetic relationships between individuals. Moreover, DNA from different species will be more similar if they are more closely related. Studying DNA can help us discover the relationships between different groups of animals.
Study Figure 13.23. Briefly describe Histones Nucleosomes DNA looping at the 30 nm and 300 nm level.
DNA is packed in chromatins, which are DNA protein complexes. Histones are the basic protein that allow for the first level of DNA packing. Nucleosomes are the basic unit for DNA packing, small beads of DNA linked by strings of linker DNA. Histone tails and linker DNA interact to pack DNA into a fiber of 30 nm. This fiber loops into looped domains, which are 300 nm, and are attached to chromosomes.
Explain how synthesis on the leading strand is different from that on the lagging strand (see figure 13.16). Include a description of Okazaki fragments.
DNA is the leading strand is synthesized continuously, while in the lagging strand it's synthesizes in a series of segments. These segments are called Okazaki fragments.
Explain the roles that nucleic acids play in living things. As you do, distinguish between the roles of RNA and those of DNA.
DNA serves as a way to store and pass down genetic information, while RNA allows for DNA instructions to be read and performed.
What was Rosalind Franklin's contribution to the discovery of DNA's structure? Why didn't she get a Nobel prize (as did Watson, Crick, and Wilkins)? If you're interested, there are many books and websites about Franklin...
Franklin took an image of DNA using X-ray diffraction, and Watson recognized that the shape of the image must have been caused by a double helix shape. She didn't get a noble prize because she was dead when it was awarded.
Summarize the Hershey Chase experiment (illustrated in figure 13.4): why was it important?
Hershey and Chase took two groups of viruses, in one they marked the proteins with radiation, in the other they marked the DNA. They found that the viral protein remained separate from the bacteria, but the viral DNA was incorporated into the bacteria. Thus, the viruses genetic information had to be carried by the DNA.
Compare and contrast heterochromatin with euchromatin.
Heterochromatin is a type of interphase chromatin, that's more compact than Euchromotin, and can't be read by the cellular machinery.
What are the base pairing rules in DNA? In RNA?
In DNA: Guanine-Cytosine Adenine-Thymine In RNA: Guanine-Cytosine Adenine-Uracil
What is transformation? How did it contribute to our discovering the significance of DNA?
It's a change in genotype and phenotype when a cell assimilates external DNA. Transformation was discovered by accident, and later on scientists like Oswald Avery figured out that DNA caused transformation. Clearly DNA effected phenotype.
Why is DNA replication correctly described as semiconservative. How was the semiconservative model of replication proved to be correct (
It's semiconservative because the original DNA strands end up separate from each other, but they still exist as whole individual strands that aren't split up between other strands. This was proven by Meselson and Stahl's, who added radioactive isotopes of Nitrogen to DNA, by taking the bacteria they are using them and putting them into environments where they had to incorporate said isotopes when making DNA. They found that when duplicated the first time around, and put in a fluid medium to separate DNA by different densities caused by the isotopes, the DNA was all together, ruling out the conservative model. This is because the new DNA's consist of two double helixes, each with an original strand and a copy strand. They found that when duplicated the second time around, there were two bands of different densities, ruling out the dispersive model which says that the strands get both original and copy DNA.
Why is DNA referred to as a "double helix?
It's shaped as such, two strands of DNA wrap around each other. It's two helixes together.
Why is DNA so important?
It's the store for all of an organisms genetic information. It's what makes them what they are.
Describe the parts involved in replication of DNA replication (use figures 13.12-13.17): Origin of replication Replication fork Replication bubble Key enzymes and what they do (DNA helicase, single strand binding proteins, topoisomerase, DNA polymerase, DNA primase, DNA ligase)
Origin of replication: specific nucleotide sequences that certain proteins recognize. These proteins start replication. Replication bubble: this is the region where DNA is being replicated, and is opened by the aforementioned proteins. Replication fork: The two strands of DNA are separated, the area where this occurs in the bubble is called the replication fork. Key enzymes and what they do DNA helicase: These enzymes untwist the DNA at the replication forks, so as to separate the strands. single strand binding proteins: They bind to a strand and keep it from reconnecting to its partner. topoisomerase: The untwisting of DNA causing strain in DNA ahead of the bubble and yet to be untwisted. topoisomerase relieves the train by breaking, swiveling, and rejoining this DNA. DNA primase: The separated strands are then copied, but the enzymes that do the copying process can't actually initiate it. Instead DNA primes does this by creating a primer, which is a short strand of RNA, copied from the DNA. The other enzymes can start copying by starting from this RNA primer. DNA polymerase: They add nucleotides to create the new DNA. DNA ligase: It connects the strands after this is all done.
How are the ends of DNA molecules replicated? Why is this a problem for mortal, multicellular eukaryotes like you and me? What are telomeres? Telomerase?
The ends of DNA molecules are not replicated because DNA polymerase can only add nucleotides to the 5' end of DNA strands. In order to keep genes at the end from just eroding, we have telomeres. These are segments of DNA at the ends that don't code for anything. They act as a buffer, just eroding away to protect the important DNA. However, eventually however all your telomeres will erode, causing DNA damage. This is believed to be linked to aging. Telomerase is an enzyme that repairs telomeres, but its only found in germ cells that produce gametes, and some cancer cells, not normal somatic cells.
DNA and RNA are information storing molecules. How do they do this? Which part of the molecule stores the information?
The nitrogenous bases store the information.
Use figure 13.7 and the text to describe the Watson-Crick model of DNA (nucleotide structure, overall shape, base pairing rules, sugar-phosphate bonds, anti-parallel structure, purines/pyrimidines, etc.).
The sugau-phospate backbones of DNA are on the outside, the nitrogenous bases are on the outside. The strands are oriented in opposite directions hence antiparallel. Adenine binds to thymine and guanine to cytosine.
Use the text and Figure 13.10 to explain, on a big picture level, how DNA replication works.
The two halves of a DNA molecule separate, and the separate strands each receive another half that is complementary to them. When this happens again you end up with four DNA molecules. Two of them have an original strand and a copy, but two of them have only copies, because during the second duplication the copy strands are separated and get their own copies.
What does it mean to say that the two strands of DNA are antiparallel in orientation?
Their subunits go in opposite directions, hence, antiparallel.
Why, from an evolutionary perspective, are mutations important?
They allow for adaption to an environment to occur.
Why was protein, at one point in the history of science, considered to be a stronger candidate than DNA for being the genetic material?
They are widely varied and have many specific functions, which seems like it would be important for genetic information.
Describe, in general terms, how DNA is proofread and repaired. Cover mismatch repair, nucleases, and nucleotide excision repair.
While DNA is replicating DNA polymerase checks for mismatched nucleotides, and when it's found a mismatch it removes the wrong base and replaces it with the right one. Mismatch repair: Sometimes a mismatch might get past polymerase. In this case other enzymes perform what's called mismatch repair, which is similar to polymerase does, just afterwards. Nucleases: these enzymes cut out damaged DNA, and fill in the gap based on the other strand. Nucleotide excision repair: This is a system for DNA repair. First, when damage is detected, nuclease come in and cuts out the section. Then DNA polymerase fills in the gap, and DNA ligase reconnects the two strands.