Honors Biology schedule and homework for April 24-28, updated April 23 @ Noonish PDT.
NOTE: It is not realistic to expect that your first exposure to a concept will result in understanding....just like learning a new language. Do not allow yourself to become frustrated. With effort and repetition, you will gain the clarity your brain so desires.
yeast_lab_data_in_bubbles_per_minute.doc Thank you to the first period Owens for helping me format the table.
* Monday - Viruses. Download and read this...a few times. 2732.introduction_to_viruses.doc
* Tuesday - Viruses and their replication. Yest Lab Due.
* Wednesday - Group study session.
* Thursday - Test #3 (Fungi, protists, viruses, etc. see notes below)
* Friday - TBD
The test: As we move through organismal biology, we are revisiting concepts from earlier units. For example, the yeasts provide us with a wonderful opportunity to review glycolysis and cellular respiration; Protists help us to recall the evolution of eukaryotic cells; fungi remind us of the importance of decomposers in ecosystems; and so on.
WHAT ARE "PROTISTS?" - The term "protist" has traditionally been used for eukaryotic organism that are not plants animals and fungi. In 1969 Whittaker divided these diverse organisms into 3 groups based on their mode of nutrition: The plant-lke protits....ALGAE; the animal-like protists...PROTOZOANS; and the Fungus-like protists....slime molds and water molds. These get their energy via photosynthesis, ingestion, and absorption, respectively. It was a reasonable and well thought out system, and it became widely accepted very quickly. Then along comes DNA analysis, and we learn that mode of nutrition can be superficial. We find that some protozoans have chloroplasts (the Euglenas), and the water molds are more closely related to some phytoplankton (Diatoms) than they are to fungi. Thus, "Kingdom Protista" is not a valid kingdom at all. Yet the name persists.
Most protists are microscopic and unicellular. The most notable examples are the multicellular algae (which, by the way, were members of the plant kingdom when I was in college). The evolutionary history of single celled eukaryotes is a very controversial topic among the scientists who are working on it. We are 99% certain that the mitochondria and chloroplasts are descended from bacteria. However, and this is the big controversy, the origin of the nucleus (and linear DNA, and chromosomes, etc), as well as the other components of the endomembrane system is not known. What we do know is that about 1.8 billion years ago, some eukaryotic cells were kind enough to allow themselves to be fossilized (that means a cell wall). In his recent book, The Vital Question, Nick Lane proposes (he's channeling other scientists) that ALL of the eukaryotic life on this planet can be traced back to ONE CELL about 2 billion years old. The problem is that Mr. Lane and his muses simply do not have evidence. Furthermore, Lane and his sources do not even mention the information side of things, only energy metabolism. I don't like speculation presented as fact. But who am I to criticize? What do I know? Like I said, it's controversial.
The Yeast Lab: In case you haven't figured it out yet, lab report grades/points are more valuable than homework points. This will be a full blown lab report with the question, the hypothesis, Materials and Procedures, data, graph, analysis...the works. I'll collect it Tuesday of next week, but I'll scan (and comment on) your early drafts through Thursday of this week, but not after.
The Yeasts: Most fungi are filamentous (hyphae and mycelium). With very few exceptions, the yeasts are unicellular. A common yeast that can cause infections in humans can grow in both unicellular and filamentous forms (polymorphic). Yet for the most part, we consider yeasts to be unicellular. As you recall from our study of cellular respiration, yeasts can continue to grow in the absence of oxygen. Pyruvate (3C) is converted to ethyl alcohol (2C) and CO2. The alcohol concentration in the yeast environment will reach a certain level that is inhibitory to the yeast, and the yeast will shut down. This is called end-product inhibition. Over the course of human history, yeast strains have been selected with higher and higher levels of alcohol tolerance. The yeast that grows naturally on the skin of fruits like grapes and apples will typically be inhibited when the ethanol concentration reaches about 6%. Through artificial selection, humans have "bred" yeasts that have alcohol tolerances of 15-20%. If you think about it, you will understand the reason for this. Nowadays, with the popularity of alcohol for fuel, yeasts have been engineered to tolerate alcohol concentrations of 25% or more. This is advantageous for the distillation process.
The lab this week: Here's the deal: The packets of dry yeast you buy at the grocery store of ascospores of Saccharomyces cerivisae, the common bread yeast. Spores are resistant structures (in this case they are resistant to desiccation or drying out). How quickly will they break dormancy (wake up) and start dividing as vegetative cells? Should we wake the up a day before the lab? Would they prefer to be "fed" glucose or sucrose, or does it make any difference? Can we assume that the rate at which they respire will determine how "happy" they are? Can they use other sugars, like fructose, lactose, galactose, etc?
As you know, whether through aerobic or anaerobic fermentation, carbon dioxide gas will be given off, and we can measure the rate as we did with the decomposition of hydrogen peroxide by the catalase enzyem in potatoes. In aerobic fermentation, we would get 6 CO2 molecules per 6-carbon sugar, but only 2 via anaerobic. So might we then expect the rate of gas coming out to be faster before the oxygen is gone? Can we measure "bubbles per minute" and graph it? What will our independent and dependent variables be, and what variables must we control? Be ready to answer these and other questions on Monday.
As we often do, we will come together as one and use the 4 classes as 4 replicates.
Fungal Life Cycle drawings. Draw, label, and color-code the life cycles of Zygomycetes, Ascomycetes, and Basidiomycetes (3 drawings, 20 pts). Your drawings should very clearly show the stages that are haploid, hetero- or diplo-karyotic, and diploid. Plasmogamy and Karyogamy should also be noted. What you will notice if you pay attention is that the sexual life cycles of fungi become increasingly important (vs asexual reproduction) as we move from Zygo to Asco to Basidio. In fact, sex is rare in Zygos, and the opposite is true in the Basidios. Ascos are somewhere in the middle. Each drawing should be done on a separate sheet of plain white paper that is 8.5 X 11 in. You will see that meiosis is identified by that name, but fertilization is not. That is because fungi don't produce sperm and egg. What happens is that the filamentous strands (hyphae) fuse (Plasmogamy) and the haplod nuclei from the compatible "mating types" remain isolated from one another for a certain period of time. The fusion of the compatible nuclei happens later in an event called karyognamy. Where to find them? Google "life cycle of ____" for each of the 3.
This week's test: We're at the point where concepts are overlapping. For example, in ecology we learn about symbiosis, which we called co-evolution in the unit on evolution. You should also recall that water is a product of cellular respiration, and thus cellular respiration contributes to the water cycle. Word to the wise: There may be concepts in the documents and notes from this website that were not covered in class. That doesn't mean that they will not be on the test. Want to survive in college? Don't expect to be spoon-fed.
Sustainability: When natural resources are depleted faster than they are restored or replenished, the practice is not sustainable. This is true of many human activities including food production, harvesting of seafood and trees, and many other human activities.
Population density: Simple concept; The number of individuals of a population per unit area. For example, the number of deer per square mile in Thurston County, or the number of earthworms per square meter in your backyard, or the number of humans per hectare in Seattle (or Beijing). Obviously, critical resources limit population density. So can diseases or predators. We will discuss this on Tuesday.
The Nitrogen Cycle: With the nitrogen cycle you get to review your chemistry (inorganic and organic), learn something about plants, and gain an even better appreciation for the role of bacteria in ecosystems. There are plenty of nitrogen cycles available on the web (make sure to cite your source). The nitrogen cycle is also pictured and discussed in your text on page 642, but I prefer other approaches. You drawing must include 1. nitrogen fixation, 2. nitrification, 3. assimilation, ammonification, and denitrification. Plus, each of these processes must be defined on the back of your drawing. 10 points.
Virtual Field Study: Coral reefs are sensitive ecosystems. Recent studies have sadly determined that much of the Great Barrier Reef north of Australia is dying. Warmer water and pollutants can have significant consequences on these organisms. For this reason, it is important to conduct ongoing field studies in coral reefs around the world to monitor their health as an indicator of the health of larger, interdependent ecosystems. One such study involves a mesophotic coral off the coast of Honduras in the Caribbean Sea. Corals are animals in the same group with jellyfish. They do not progress to the common adult body shape of jellyfish, and remain in what looks like a jellyfish larva called a polyp. Like jellies, corals can extend their tentacles to capture prey....making them predators. Corals live in reef communities constructed of calcium carbonate in what amounts to huge apartment complexes. Mesophotic corals have co-evolved with single-celled algae. The algae live in the "jelly" layer of the coral's body (mesoglea), and the two species live in an obligate (no other option) mutualistic relationship. The corals provide a safe home for the algae, and the algae provide the corals with food from photosynthesis. Because light penetration is limited in the oceans (limited to the photic zone), so are the mesophotic corals. We will take a virual tour of a MCE (mesophotic coral ecosystem), and collect data to determine the relationship between coral population density and depth.
Niche, and the competitive exclusion principle. Every organism has its niche (rhymes with witch or quiche, depending on your preference). Niche is the sum of all interactions with the biotic and abiotic components of the ecosystem. The Fundamental Niche is the potential for any organism, but there is competition for resources in every ecosystem, so no organism actually achieves its fundamental niche. The niche an organism is left with is its Realized Niche....you could even say it's real niche. Since competition prevents organisms from realizing their fundamental niche, we refer to the "compromise" as the competitive exclusion principle.
Biomes and ecosystem types: Because these concepts are human constructs (not discoveries), different sources will present different versions of what we might call any given ecosystem. Biomes typically refer to terrestrial ecosystem types (tropical rain forests, deserts, tundra, temperate grasslands, savannas, etc)..... Section 25.1 (7 pages including pictures). Aquatic ecosystems might be lakes and rivers (freshwater), or marine. (Section 25.2, 4 pages) Estuaries are ecosystems where rivers meet the ocean (or Puget Sound).
Trophic cascades: Apex predators have a profound effect on all other trophic levels. There is a really cool video embedded in this article/link. https://www.theguardian.com/environment/georgemonbiot/2014/dec/12/how-whale-poo-is-connected-to-climate-and-our-lives
Soil Community Lab: There will be no lab report for this activity. Consider it as one might consider a field trip. We found producers, consumers, and decomposers, yet most of the soil community eluded us.
Lab Report: Title; Introduction ; Results and Observation; Analysis and conclusion. Your introduction should provide the reader with a succinct background on gram positive and gram negative bacteria, as well as a succinct background on the two modes of action of the various antibiotics we used. There should also be a question or objective addressing what we expect to learn from the lab. The Results and observations should include the bar graph we discussed with the zone of inhibition (which relates directly to antibiotic efficiency) as the dependent variable (y axis) and the 4 combinations of G+/CWSI; G+/PSI; G-/CWSI; G-/PSI as the 4 bars on your histogram. Include also observations that appear to contradict the trends that will be evident in the bar graph (so that this too can be referenced in the analysis). The Analysis/Conclusion should address the obvious trends in the data, and offer deductive reasoning to offer possibilities regarding how these trends might be explained. Be careful not to draw conclusions that are too broad based on such a limited data set. In fact, it is important that you make the reader aware of these limitations. Try to think about all that you have learned about biology this year and see if you can come up with some overarching themes. I've given you more than enough information here. I will not write your reports for you. I will look for thought on your part, and as always, if you find information from outside sources, you must cite it. I prefer parenthetical citations even if you have full citations at the end. sample_data_analyses.doc
The 2 videos and .doc below will help you with background information for analyzing our data from the G+/-: Antibiotic mode of action lab report. See also notes below.
Notes for the week:
This lab involves two experimental variables (G+/G- bacteria; CWSI/PSI antibiotics). To understand the concepts behind the lab, you must do the reading and watch the videos for Monday and Tuesday. Otherwise you may not have a clue what we're doing. Because there is no printed protocols for this lab, it is imperative that you keep detailed notes about everything you do and observe. I will provide you with more background information in class, and it is incumbent on you to make sure you get it. Be responsible.
ECOLOGY...THE STUDY OF ECOSYSTEMS: It may seem like a sudden course change to move into ecology right now, but since we'll be discussing the role of various groups of organisms in their ecosystems, it makes sense to me that we familiarize ourselves on the different roles organisms can play within their ecosystems. If you think about it, we were introduced to bacteria because they were the first cells to emerge from the primordial soup. In ecology, you will see the very significant role of bacteria.
History of life on earth assignment: The document is writable history_of_life_on_earth.doc , but I see a lot of people out there with copies that lost formatting in translation to google docs or whatever. So here's a .pdf version: history_of_life_on_earth-14.pdf What you need to do is fill in the significant biological events for each of the designated periods. First appearance of significant groups, like land plants, seed plants, flowering plants, fish, amphibians, reptiles, mammals, birds, insects, etc. Tiny little drawings would help. Don't forget to indicate the 5 major extinctions with a red horizontal line. The back of the sheet should include the linear timeline. You can use your text or some online source....make sure you indicate any source that is not from class or your text.
Timeline: From radiometric dating, scientists have determined that the earth formed 4.56 billion years ago. There is evidence that for the next 500 million years, the young planet was being bombarded by giant asteroids, smallish planets, and lots and lots of comets. This is called the period of great bombardment. Thus scientists speculate that cataclysmic impacts would wipe out any proto-life that may have formed during this time. The bombardment ended about 4 billion years ago, and by 3.8 billion years ago there is compelling evidence of life (chemical signatures of carbon compounds known to be associated only with cellular activity). That's a window of "only" 200 million years. The oldest real fossils date to 3.5 billion years ago.
As we transition from the history and evolution of life on earth, we need to keep a perspective of the original life forms on the planet ... the microbes. Please read the following short exerpt: deep_history_of_life.doc primordial_soup.jpgThe tree of life as represented in 1866 by Ernst Haekel (an "apostle" of Charles Darwin): haeckel1866-1.pdf
The tree of life as represented in the 21st century: tolmmbr2009-3.pdf
A simplified version of the modern tree of life: threedomains.pdf
In the Trees shown above, please note the difference in how the microbes are treated.
Abiogenesis, aka Origin of Life, aka Chemical Evolution: This is not biological evolution, which deals only with changes in life over time. Abiogenesis (origin of the first cells) is different. Unlike biological evolution which is an empirical fact, the origin of the first cells is hypothetical and speculative. Nevertheless, we have some brilliant minds working on it, and some progress has been made, but the obstacles in our understanding always come back to ORGANIZATION. You see, if life self-organized from some sort of primordial soup primordial_soup.jpg , we really can't demonstrate self organization. You should be aware that the other two possibilities are not testable. They are: Panspermia (cells came to earth from outer space >3.8 billion years ago), and Supernatural/Divine intervention (which is not testable and for which there is no evidence). In the 1920s, Oparin (Russia) and Haldane (England) both hypothesized that the early earth would have had a very chemically rich atmosphere with lots of energy. They also hypothesized that there would not be NO OXYGEN in this atmosphere (thus a "reducing" atmosphere) because it's too reactive and must be continuously replenished by photosynthesis. Fast forward to the 1950s at the University of Chicago, where Stanly Miller and Harold Urey developed a rudimentary contraption to test the hypothesis of Oparin and Haldane (see figure 17.9, p 447). What they got from these experiments was exciting: For example, these experiments produced some amino acids, nitrogenous bases, and aldehyde sugars. But that leaves a Grand Canyon-sized chasm in understanding how these pieces could have self-assembled. Especially problematic is the evolution of the universal genetic code.
Archived downloads and links
Test 1 Break
More Hardy-Weinberg problems: http://www.k-state.edu/parasitology/biology198/hardwein.html
End of first semester:
Contrasting mitosis and meiosis: 6:45 https://www.youtube.com/watch?v=jjEcHra3484
Meiosis video: 5:30 https://www.youtube.com/watch?v=nMEyeKQClqI
Contrasting mitosis and meiosis: 6:45 https://www.youtube.com/watch?v=jjEcHra3484
Meiosis video: 5:30 https://www.youtube.com/watch?v=nMEyeKQClqI
Videos related to gene expression:
The Crash Course guy covers it all in his own annoying (to me) way, 14 minutes https://www.youtube.com/watch?v=itsb2SqR-R0
Transcription, 2 minutes https://www.youtube.com/watch?v=SMtWvDbfHLo
Translation, 3 minutes https://www.youtube.com/watch?v=TfYf_rPWUdY
Mutations, 6 minutes https://www.youtube.com/watch?v=xYOK-yzUWSI
Test 4 break
I made this crossword puzzle for you: cell_puzzle.pdf
DNA Replication: https://www.youtube.com/watch?v=wcOZHK5bRLs
DNA from Bozeman: https://www.youtube.com/watch?v=q6PP-C4udkA
Inner life of the cell: Harvard biologists made a bunch of computer-animated videos that are incredible. This is some seriously cool stuff. I'll show some short exerts in class as we come to that particular structure/function. You can check it out as you like....it's amazing: https://www.youtube.com/results?search_query=inner+life+of+a+cell
Khan Academy cells: https://www.youtube.com/watch?v=Hmwvj9X4GNY
Features of cells: https://www.youtube.com/watch?v=1Z9pqST72is
Test 3 break:
This is an excellent video overview of cellular respiration: https://www.youtube.com/watch?v=XIJvVCA9RPs
Photosynthesis video from the same production company: https://www.youtube.com/watch?v=QSFUHB8VnD0
Mr. Anderson's photosynthesis video: https://www.youtube.com/watch?v=g78utcLQrJ4
Photosynthesis video game, tutorial, and quiz from Bioman: http://www.biomanbio.com/
Ted Ed's Calvin Cycle video: https://www.youtube.com/watch?v=0UzMaoaXKaM
Test 2 break
This 12 minute video will help you understand the concept and terminology of enzymes. http://www.youtube.com/watch?v=ok9esggzN18
Test 1 break
Water: Hank https://www.youtube.com/watch?v=HVT3Y3_gHGg
ABOUT TEST CORRECTIONS: Because of issues in the past, I'm tightening up my test correction policy. I reserved the right to disregard all submitted test corrections if I find that a student is purposefully attempting to submit phony test corrections. For full credit, please follow these guidelines: ONLY HAND WRITTEN CORRECTIONS WILL BE ACCEPTED FOR CREDIT.
1. Do not: Restate the question and/or answer options as written on the test.
2. Do not: Share your personal reflections on what you were thinking (or not thinking) while you were taking the test.
3. Do not: Say the same thing over and over again.
4. DO: Identify the concept that the question deals with. Use 1/2 page to address that concept using words, labeled diagrams, etc. test_correction_format.doc
5. ALL TEST CORRECTIONS MUST BE HAND WRITTEN/DRAWN, AND LEGIBLE.