Seven Mammals for AP Biology
Mar 8th
The file required to complete the “Making Phylogenetic Tree using the Computer” assignment – Seven Mammals.
Chart of Primates Split from Human Lineage (MYA)
Mar 8th
Table of Millions of Years Ago (MYA) that each primate split from the human lineage.
Data from Richard Dawkins’ An Ancestors Tale (2004)
A Biology Reminder
Mar 5th
Today, Friday, your Unit 1 Project Guide was due with the question, variables, hypothesis, materials, and procedures completed for both the Human Evolution and the T. rex project. If you did not complete this, I suggest getting this done and turned in as soon as possible – it can even be emailed (swanbiology [at] gmail [dot] com). Obviously, this is in addition to the table we were working on in class today for the Human Evolution project that was also due today. (If you missed what this should look like, I have included an example.)
Finally, if you are behind, or want to get ahead, I would utilize the resources I posted previously to start typing out all the parts to your mini-science fair board.
Classification of Mammals by DNA Sequence
Mar 5th
Much like I introduced using DNA sequence to classify organisms with my Biology class, we have made those some steps in AP Biology. However, this is leading out of our discussion of evolution and into our look at the diversity of organisms.
While far more inclusive of the three Domains than we will be, the phylogenetic tree above examines the relatedness of organisms in much the same way that we will be. However, another key component to this tree is the use of the simple bar to represent the size of the organisms genome – kind of interesting.
The work that we began in class, and that is due on Monday can be found here in both Microsoft Word and Adobe PDF format. Please select the one you wish to use and complete the table and tree as homework. This will provide the foundation for the work that we will be beginning in class on Monday and continuing through Wednesday.
Science Fair Projects and Grades
Mar 4th
Please take a little time to check your grades to ensure that all necessary work has been submitted. If you have any questions about your grade please see me in class or send me an email.
Below you will find a list of all science fair topics and questions that we will be working from for the rest of the semester. We will be discussing the next steps very soon in class, but I recommend that you start thinking about your variables, hypothesis and procedures as they relate to your question. Once again, if you have any questions, send me an email.
The “Central Dogma”
Mar 4th
The use of “Dogma” in relation to the “Central Dogma” has often been questioned, even by Francis Crick,who first used the term (Wikipedia), for many years. However, it is still used and provides a general term for the processes related to the process of DNA replication, transcription, and translation.
At the right we can see each of these processes explained in a very simple manner, and containing much of the information that is important for you to understand for both the class and the projects we are doing in class. Lets look at each step to help you better understand this important concept in biology.
(Although there are special cases where other processes occur, I am going to describe the most basic and common.)
- Takes place in the nucleus of eukaryotic cells.
- The entire strand of DNA is replicated by a number of special enzymes and proteins.
- The new strand of DNA is identical to the original – the two new strands (daughter strands) contain one parent strand (template) from the original DNA strand and one new strand.
- Important for cell division.
- Animation.
- Takes place in the nucleus of eukaryotic cells.
- A section of the DNA molecule, a gene, is used to synthesize (make) a messenger RNA molecule (mRNA).
- mRNA is a single strand nucleic acid and the base thymine is replaces by uracil. Therefore, all the adenine bases on the DNA code for uracil in mRNA.
- mRNA is able to leave the nucleus to move on to the next phase.
- Animation.
- Takes place at a ribosome in the cytoplasm outside the nucleus.
- The final step of protein synthesis.
- tRNA molecules that carry an amino acid to add to the polypeptide (growing protein) match up to the appropriate section of mRNA to determine both order and length of amino acids.
- At the end of the phase a complete protein is built.
- Animation.
I would definitely check out each of the animations for each part of the “Central Dogma” – I believe that these will be a big help to understand how these take place. In addition, it would be helpful to try out Learn.Genetics in order to perform each of these processes on your own through an interactive “simulation.”
Primates of Importance
Mar 3rd
While I feel that all our primate cousins are of some importance, there are only eighteen that we are going to look at from the long list in our BLAST results. The scientific names of the primates we will be adding to our tables are as follows:
Homo sapiens- Homo sapiens neanderthalensis
- Pan troglodytes
- Pan paniscus
- Gorilla gorilla
- Hylobates lar
- Macaca fascicularis
- Trachypithecus obscurus
- Macaca mulatta
- Presbytis melalophos
- Semnopithecus entellus
- Nasalis larvatus
- Papio hamadryas
- Colobus guereza
- Chlorocebus tantalus
- Chlorocebus sabaeus
- Macaca sylvanus
- Pongo pygmaeus
Based on these names you will have to look-up the common name of each of these primates for your table (enter scientific name in Google) and use the data from the BLAST to get the BLAST Identity and BLAST Percent Identity. From the BLAST Percent Identity you can easily solve for the BLAST Percent Difference by subtracting the Percent Identity from 100%. These four items will make the bulk of the chart, we will discuss the last two columns in class.
Phylogeny and Genomes
Mar 1st
We have touched on both phylogeny and genomes in class. In fact, we have connected the two when helping to determine how related one individual is to another individual. One thing that people tend to get confused is the belief that the large size of a genome means an organism is more sophisticated – or as some people mistake, more like humans. First, humans do not have the largest set of genes, Asian rice is much longer). Second, it is important to avoid thinking that just because an organism does not have human-like qualities that it is not sophisticated or advanced. Consider organisms like cockroaches. These have been around much longer than humans, survive extreme conditions that kill humans, and will continue to be around after we are gone. That is pretty sophisticated. Just something to think about.
Lets consider these ideas when looking at the two phylogenetic trees below. Both look at the three domains: archaea, bacteria, and eukaryote and representative species of each that have had their genomes sequenced. The other interesting fact is that the bar next to the species name diagrams the size of the organisms genome.
The tree on the left is how we have traditionally looked at them and the one on the right is done in a circular format.
(To see full-size, right click on image and “Save Link As…”)
Trees from Interactive Tree of Life (iTOL) and Letunic and Bork (2006) Bioinformatics 23(1):127-8
Procedures and A Small Problem
Feb 26th
In class we learned a very quick lesson about writing procedures: THEY NEED TO VERY SPECIFIC. Based on our simple “Write the Instructions for Drawing a Smiling Stick Man” assignment, it was very clear that saying “Draw a circle”, “Draw a line for the body”, and “Add a mouth” are not specific or clear for someone to complete if they are unfamiliar with the procedure already. As we move forward working on our science fair projects this is something to continually keep in mind. A good way to think about it is to imagine that you are giving instructions for a task over the phone to someone how has never done the task you are describing. Be very specific in each step and include every possible detail necessary to complete the task.
We also learned another important lesson today: even the best plans can run into problems. It took over an hour after class was over to figure out why things weren’t working like before. And just as I was about to get really upset and start scrambling to completely modify our project I found a tiny mistake. Let me explain.
When I had previously done the experiment I had put in the accession number in the NCBI search box as described and got the same “error” that we saw in class – the sequence was removed. However, I recalled that when I put the accession number for the human mitochondrial NADH dehydrogenase subunit 5 (NADH5) in the BLAST query (search) everything came up like it should. So, I knew something was wrong when we weren’t getting anything to come up in class.
After recreating the steps for a couple different accession numbers, I thought I would repeat the procedures step by step as written. The first two times were met with the same results. Then I looked closely at Step 10c. The step describes that the “Entrez Query” should contain “595:605 [slen]“. Here was my problem. On the printed copy the “l” (“L”) in “[slen]” looked a lot like an “i” and that is what I had typed each time. After changing the “i” for an “l” (“L”) everything worked perfectly. (Run the query yourself – just have patience, it takes a little time to run the search.) Hooray!
Because things have worked out as I thought they should, we will be able to move forward as planned. But it is important to realize that there are times when things aren’t going right, but if you keep at it and remain persistent it will work out in the end. Like it did with our project.
Once again, if you have missed anything over the past couple of days, check this page first.
AP Lab #8 Data and More
Feb 26th
We have finished the lab and hopefully people are already working on their some of the analysis questions for their write-up. The remaining data can all be found on our Google Doc. Please realize that this is simply the class copy, you will need to copy and paste the data in your own Doc for submission. Don’t forget, the lab is to be completed in Google Wave or any other digital format and is due on Wednesday of next week, 3 March, at 23:59 (eleven fifty-nine).
Because this is second semester and we should all be growing as learners, I will no be excepting late work after Friday, 5 March. However, please realize that each day your work is late it will be one full grade lower. (If your lab would have been an “A” on Wednesday, it would be a “B” on Thursday and a “C” on Friday. After Friday, it is a zero.)