Characteristics of the Major Animal Phyla

Bios,

After our discussion after the mock test I thought that I would post the hastily written notes from the board with a few additions. So here is a description of selected (meaning not all) Phyla and Classes of Kingdom Animalia.

Kingdom Animalia: Animals are multicellular eukaryotes that obtain their food by ingestion.

Phylum Porifera (the sponges): No symmetry, no true tissues, filter feeders, and sessile. Mostly marine freshwater. The simplest form of animal life.

Phylum Cnidaria: Radial symmetry, tissues, mouth, simple gut, and nerve net. Free-living form is the medusa and sessile form the medusa.
Class Scyphozoa – Marine free-living, jelly fish.
Class Anthozoa – Marine sessile, sea anemone and corals.

Phylum Platyhelminthes: Ribbon-like soft bodied animals with bilateral symmetry, simple organs, central nervous system, cephalization, free-living and parasitic. Examples - flatworms, tapeworms, and flukes.

Phylum Annelida: Soft segmented bodies with bilateral symmetry, cephalization, closed circulatory system, free-living, marine, freshwater, and soil. Some parasitic. Examples - earthworms and leeches.

Phylum Mollusca: Soft bodies with bilateral or asymmetry, muscular foot and most have a shell. Most are marine but many live in freshwater and on land. Examples – snails, slugs, clams, oysters, squid, and octopus.
Class Polyplacophora (many/plate/bearer) – bilateral symmetry, eight shell plates, marine, foot for locomotion. Example - chiton
Class Gastropoda (stomach/foot) – asymmetric body with spiral shell tough the shell may be absent, foot for locomotion. Examples – snails, slugs.
Class Cephalopoda (head/foot) – marine, foot modified into tentacles, big eyes. Examples – squid and octopus.
Class Bivalvia (two/shells)– marine and freshwater, two shells, filter feeder. Example - clams, oysters, mussels

Phylum Arthropoda: Two out of three organisms on Earth are arthropods and they are found in every ecosystem! Jointed appendages, exoskeleton, segmented body, compound eye (in most), and many other well developed sensory organs.
Class Arachnida – simple eyes (8), no antennae, two body segments (head and cephalothorax), eight legs. Examples – spiders, ticks, scorpions, and mites.
Class Crustacea – compound eyes, two pair of antennae, multiple body segments, multiple legs, mostly marine. Examples – lobsters, crabs, shrimp, copepods, barnacles.
Class Diplopoda – multiple segments each with two pair of legs, herbivore. Example – millipedes.
Class Chilopoda - multiple segments each with one pair of legs, carnivore. Example – centipedes.
Class Insecta – compound eyes, three segments (head, thorax, abdomen), usually with two pair of wings, six legs, terrestrial, complete and incomplete metamorphosis. Examples – flies, bees, dragonflies, wasps.

Phylum Echinodermata: Radial symmetry, sessile or sedentary, endoskeleton, marine. Examples – starfish, sea urchins, sea cucumbers, sand dollars.

Phylum Chordata: Identified by these structures present during embryo stage - notocord, dorsal nerve cord, gill slits.
Subphylum Vertebrata: Animals with backbones.
Class Agnatha – jawless, skeleton of cartilage, notochord, marine and freshwater. Example – lamprey.
Class Chondrichthyes – Marine, skeleton of cartilage, jaws, paired fins, streamlined bodies, internal fertilization, oviparous and ovoviviparous, cloaca. Examples – sharks, rays.
Class Osteichthyes – Freshwater and marine, skeleton of bone, jaws, paired fins, operculum, swim bladder, great majority have external fertilization, oviparous, cloaca. Examples – trout, tuna, goldfish, koi.
Class Amphibia – four legs, scaleless skin, terrestrial (but needs water to reproduce), ectotherm (cold blooded), oviparous, jelly-like egg, cloaca, lungs, metamorphosis. Examples – salamanders, frogs, newts, toads.
Class Reptilia – four legs, scaly skin, primarily terrestrial, ectotherm, lays eggs on land, leathery shelled egg, oviparous cloaca. Examples – lizards, snakes, turtles, crocodiles.
Class Aves – Feathers, forelimbs modified into wings, acute vision, endothermic (warm blooded), internal fertilization, hard shelled eggs, cloaca. Examples – robin, penguin, bald eagle.
Class Mammalia – Hair, endothermic (warm blooded), mammary glands, internal fertilization, most viviparous (some oviparous), large brain, differentiated teeth. Examples – human, bear, kangaroo, platypus, shrew, blue whale.

Have fun with this. It could help on a few questions. Be sure to write, I will be monitoring the blog.

Mr. Baker

Photosynthesis Animations

Bios,

Here are a few links to photosynthesis animations that may help you remember how it works.

Light Reactions:
http://www.stolaf.edu/people/giannini/flashanimat/metabolism/photosynthesis.swf
http://www.cnr.vt.edu/DENDRO/forestbiology/photosynthesis.swf
http://www.youtube.com/watch?v=eY1ReqiYwYs
http://bcs.whfreeman.com/thelifewire/content/chp08/0802002.html

Dark Reactions:
http://bcs.whfreeman.com/thelifewire/content/chp08/0802003.html
http://www.metacafe.com/watch/yt-mHU27qYJNU0/the_calvin_cycle_or_dark_reactions_photosynthesis/

By the way, follow this lnk to a good site that reviews many topics covered in class.
http://bcs.whfreeman.com/thelifewire/

Feel free to post questions to me as comments to this blog.

Mr. Baker

Comments on AP Labs

Bios,

Some of you have expressed an interest in reviewing labs we did not perform in class. I have found a web site that has very good summaries of every lab with a self-quiz section. Check this out - http://www.phschool.com/science/biology_place/labbench/ . I think you will find it helpful.

If you look over the labs you will see that we have done labs 1, 2, 3, 7, and 8. We did a couple of others that are not AP Labs and because many of you take biotechnology, I did not do lab 6. Of the labs on the Pearson web site be certain to go through 4, 5, and 12. All have been on past exams and each do a good job reinforcing concepts we covered in class. However, this web site is easy to use and you should go through them all for review purposes.

In class tomorrow we will be looking at the immune response and Saturday is the mock exam.

Mr. Baker

Human Chimp Homology

Bios,

The next few posts are presented to help you prepare for the AP exam. This first post addresses the homologies between humans and chimps. Recall that homologies are traits that are derived from the same ancestral form - they have a shared ancestry.

First of all, here is a brief timeline:
40 mya - primates diversify
15 mya - the great apes (Hominidae) diverge from the lesser apes
10 mya - the chimp human line diverges from the gorilla line
7 mya - the line that leads to humans diverges from chimps
4.4 mya - hominin bipedalism

Second, many of the human/chimp homologies relate to their arboreal origin.
Forward facing eyes
Stereo vision
Grasping hands, opposable thumb
Sensitive, dexterous fingers with nails rather than claws
Fully rotating shoulder
Extended care of young

Last, homologies not related to arboreal living
DNA sequence similarity (approximately 98%)
Chromosome banding similarity
Evidence for chimp chromosome #s 12 and 13 fusing to form human chromosome #2

More later,

Mr. Baker

Hey there,

You may already have heard of this story, but it's a great example of biology, medicine, public health, and public policy coming together to attack a problem that faces a large population. In this case there is an apparent outbreak of flu in Mexico with isolated clusters of cases in the United States. It's a developing story. If you worked for the CDC, how would you manage this problem?

http://www.nytimes.com/2009/04/27/world/27flu.html

--Ken

The Link to the Web Lecture on Animals

Bios,

Here is the link to the Animal Diversity web lecture.

http://www.wiziq.com/tutorial/96-An-Introduction-to-Animal-Diversity

On Monday we will be reviewing the last FRQs. Please bring questions and comments to class. It will help our discussion.

Mr. Baker

The Shop is Open

Bios,

You have a test over chapters 22-25 tomorrow and I will be available all day for questions. Just write your question(s) as a comment to this post.

Mr. Baker

TQT Time

Bios,

Submit your TQTs based on the chapters 19 and 21 notes as comments to this post.

Mr. Baker

Notes for Chapters 19 and 21

Bios,

Here are the notes I promised you in class. Sorry about the formatting but Blogger's text editing is a bit clunky. It may be best to copy and paste the text into a word document so you can edit the formatting. Have your book in hand as you read through the notes. I want your TQT for this week to come from this material. I will write a post for your TQT on Wednesday and please write your TQT as a comment to that post.

Mr. Baker

Chapter 19 – Cancer

1. Proto-oncogene – normally codes for a cell growth or division regulating protein. If it mutates, it may result in a change in the control of cell growth an division and cause the cell to rapidly divide and become a tumor.
2. The mutated proto-oncogene is now an oncogene.
3. There are three means to cause a proto-oncogene to become an oncogene.
a. Translocation to a new chromosomal region and promoter
b. Gene duplication
c. Point mutation of the DNA code
4. Another family of genes that are implicated in cancer is the tumor-suppressor genes. These genes have many functions such as DNA repair, cause cell death, and contact inhibition.
5. See your text for the function of the ras and p53 genes.
6. See your text (pp 359-361) for an explanation of how multiple mutations are implicated in tumor development and specific examples.

Chapter 21 – The Genetic Basis of Development

1. Embryonic development involves
a. Cell division
b. Differentiation
c. Morphogenesis
2. Model organisms
3. Differential Gene Expression
a. All cells have the same genes. The cells of a zygote are totipotent. They have not differentiated and can become any part of an organism.
i. Carrot cloning
ii. Frog embryo – from early cells, normal tadpole. From intestinal cells, only 2%. Conclusion, nuclei change as cells differentiate.
iii. Sheep clone accomplished with transplantation of the nucleus of an udder cell into a de-nucleated egg cell.
1. cultured udder cell in nutrient poor medium
2. cell went into G0 phase
3. then inserted into egg cell
4. one of several hundred survived and became Dolly
b. As a cell differentiates it expresses specific proteins.
i. These proteins regulate development and function
ii. In muscle cells it is due to a regulatory protein myoD that is is a transcription factor.
c. How does it start?
i. Maternal signals from the egg such as mRNA. These are called cytoplasmic determinants.
ii. Induced by signals from other cells
4. There is a pattern to Development
a. The pattern formation is the result of positional information given through molecular signals that tell a cell where it is relative to the body axes.
b. As your book states on page 397. “In Drosophila, cytoplasmic determinants that are present in the unfertilized egg provide positional information for the placement of the two axes even before fertilization. After fertilization, positional information operating on a finer and finer scale establishes a specific number of correctly oriented segments and finally triggers the formation of each segment’s characteristic structures.” These “cytoplasmic determinants” are mRNA that were produced by the egg during its development.
c. Read the section – “Gradients of maternal molecules in the early embryo control axis formation” on page 399 to understand how the concentration of the bicoid gene mRNA at the end of an egg determines where the body segments go.
d. Homeotic genes direct the identity of body parts.
i. The development and placement of body parts requires the identification of body regions. The genes that regulate this are the homeotic genes.
ii. For example, in Drosophila homeotic genes of the thorax direct the production of proteins that cause leg development.
e. The Hox (homeobox) genes.
i. All homeotic genes have an identical sequence 180 nucleotides long called the homeobox. Genes with this region are therefore called Hox genes.
ii. Most homeobox genes are associated with development and Hox genes are found in other animals.

Moving On

Bios,

Now that we have finished our study of genetics we will now take on evolution. Theodosius Dobzhansky who made many important contributions to our understanding of evolutionary genetics said, "Nothing in biology makes sense except in the light of evolution." Evolution is the idea that unifies biology and maybe makes it a science rather than stamp collecting.

But now that I have piqued your interest I must temper it a bit. While you should begin to read chapter 22 on, we will finish the Drosophila experiment first. On Monday you will be introduced to the chi-square test and Tuesday you will be given time to write up your report. By Wednesday we will begin our study of evolution in class.

Also, there will be a twist to your TQT. I will be posting notes from chapter 21 and from those notes you will base this week's TQT. While reading the notes be sure to consult your text. You will find that the notes follow the text.

Mr. Baker

This Week

Bios,

The purpose of this post is to give you a preview to this week in AP Biology. Tomorrow your FRQs are due and I will be lecturing (with animation support) on the trp and lac operons on E. coli. Tuesday we will count fruit flies. I was at school today and many have emerged from their pupae and by Tuesday there should be many more. Wednesday I will lecture with animation on gene expression in eukaryotes and chapter 21. Thursday, let's have a test review and a test on Friday.

See you tomorrow,

Mr. Baker

TQT Time

Bios,

Please submit your TQTQs for this week as a response to this post. Look ahead in your text and look at the LAC operon in bacteria and gene expression in eukaryotes for inspiration. A test looms, I just am not sure when.

Mr. Baker

URL for the Central Dogma Animation

Bios,

You asked for the URL to the central dogma animation so here it is - http://207.207.4.198/pub/flash/26/transmenu_s.swf

Also TQT is on the horizon.

Mr. Baker

Your Flies

Bios,

Just an update on your flies. Most of the vials look great with many larvae and pupae. I expect adults to emerge any time now. There were some vials that did not produce - oh well, we should still be able to have plenty of data. On to chi-square tests!

Get some rest as the mid-winter break comes to a close. I hope you used this time to read your text because a test looms. If I do not submit another post before then, see you Monday.

Mr. Baker

Finally, TQT - for Monday

Bios,

I have finally found the time for the TQT post. Please write your TQTs as a comment to this post.


What sex is this fly?

Considering the class content, let me take a minute to review what you should , in general terms, know by now.
1. Offspring obtain genes from their parents by inheriting chromosomes.
2. Like begets like - sort of.
3. Meiosis; know the stages and what role it plays in life cycles.
4. What meiosis has to do with the origin of genetic variation.
5. Mendel's principles and how they lead to predicting probabilities.
6. Exceptions to simple Mendelian transmission.
7. Mendelian inheritance in humans and pedigree analysis.
8. Genes and chromosomes; TH morgan and his "Fly Lab", Morgan traced a gene to the behavior of a chromosome.
9. Linked genes, how they alter Mendelian expectations, crossing over produces recombinants, and using recombinants to map genes.
10. Chromosomal errors.
That takes us through chapter 15. I am planning to test chapters 13-21 on or around February 27. Get to reading.

The Stuff of Life

I just wanted to post a book I heard about on Science Friday. It's a genetics comic book that looks like it goes into pretty good detail. If you need a visual way to study genetics for the AP exam, it might help.

http://us.macmillan.com/thestuffoflife

DJ

More interesting times in Oklahoma

Just wanted to share a great news article we had here in Oklahoma. A pair of conjoined twins were separated! I believe these girls are thoraco-omphalopagus conjoined twins. I got to see their heart catherization on my cardiology rotation. Fascinating!
Here's the article:
http://www.oumedcenter.com/body.cfm?id=2601
and pictures:
http://www.oumedcenter.com/body.cfm?ID=2602

TQT Time and What is Up for Tomorrow

Bios,

Again, I encourage you to post comments to the posts of the other authors. It could start interesting conversations.

Now to school - Tomorrow is TQT and you should send them as comments to this post. We will begin tomorrow with a few comments on FRQ-12 then we will see if you have questions regarding FRQ-13. After, we will take a look at the fruit flies. I will demonstrate how to anesthetize the flies and show you how to sex and distinguish the phenotypes. Finally, you will have an opportunity to work with and observe the flies. If we have time we will discuss how the experiment will be conducted.

Be reading the text. You should be through chapter 14 and beginning 15. Read, Read, Read. Trust your intelligence and keep pushing. The AP test is on May 11.

Mr. Baker

Medicine!

Hi!
I'm Ken, another former Mr. Baker student. I took his AP biology class in 1999-2000, and I can honestly say that without Mr. Baker's class, there's a good chance I would not have ended up in the biosciences. You're lucky to be where you are! I remember drawing diagrams of helicase unzipping a coil of DNA, and that's still pretty much the model I have in my head.

After high school I went to the University of Washington, double-majored in Computer Science and Molecular Biology (and minored in math for good measure). At the same time, I shot pictures for UW's student newspaper, which is where I learned I needed a career where I was intimately involved with all types of people every single day. So I went to medical school! I'm in my fourth and final year at Columbia in New York, where I've confirmed that medicine is exactly the right career for me. And it opens doors to do anything from solely practicing clinical medicine, to answering the unanswered questions of life (and that's what biology is, anyway), to teaching next year's doctors.

There are many, many, many questions yet to be answered in medicine and in biology. Science gives us the tools to answer these questions. The most popular article on the New York Times' website right now is about a possible link between coffee drinking and lowered dementia risk (http://www.nytimes.com/2009/01/24/health/research/24coffee.html). The research is preliminary (they allude to why in the NYT article) and there is a lot of work to be done to either prove or disprove this hypothesis. Are you going to be the one that solves this? If you're really interested, you can dig up the actual article - an abstract, or summary, is at http://www.ncbi.nlm.nih.gov/pubmed/19158424

Goodbye Chapter 14

Bios,

Tomorrow, we will be wrapping-up chapter 14. I will focus on reading pedigrees and you should read pages 252-258. Pay particular attention to learning the particular examples of human genetic disorders, fetal testing, and neo-natal testing. I will not discuss these directly and will rely on you to ask questions.

Later this week we will dive into chapter 15 and begin to understand the relationship between chromosomes and genes and how the chromosome theory of inheritance was first formed. To supplement this learning we will begin the Drosophila genetics lab. It is great fun seeing Mendel's ratios in action!

Be sure to ask the blog co-authors questions when they submit a post. They are an excellent information resource.

Mr. Baker

Applied Sciences: Medicine

Hello!
My name is Samara Mohamed. I'm also a former student of Mr. Baker, who took general biology in 1994, genetics in 1997, and was formally introduced to the wonderful world of genetics bench work by Mr. Baker in 1997.

I went to Seattle University, and Majored in Biology and Chemistry with a minor in Physics. I did continue to do research in college: various collegiate projects and even a 2 summer internship with the Merck pharmecutical company in their vaccine department. However, I felt a greater need for human connection which led me to medicine.

I went to Midwestern University--Arizona College of Osteopathic Medicine. Osteopathic medicine is a parallel track to allopathic medicine with a focus on holistic treatment of the patient and includes additional manipulation treatment. I graduated in 2002 and started a Pediatric Residency at the Oklahoma State University Medical Center in Tulsa, OK. I'm currently 6 months from finishing my residency and will be deployed by the US Army for general practice. Since the military paid for my medical school bills, I will repay them with 4 years of Active Duty service. I do plan on pursuing a sub-specialty in Pediatrics in the near future--possibly Adolescent medicine, palliative care, emergency medicine or interventional cardiology.

I like to think of medicine as applied science. I have been amazed at how helpful basic chemistry, genetics, and newtonian physics have contributed to my understanding of the human body. It's been invaluable to have good research background to decipher the mounds of research that comes out daily.

I don't have any cool articles to post at the moment, but I'll try to post some as I come across any.

Cells, Molecules, Neurons & Synapses

Hi everyone,

My name is DJ Brasier. I took Mr. Baker's freshman biology class back in 1994, and my senior year he taught an advanced class in genetics instead of the AP biology that you all are taking. In college, I majored in biology with an emphasis on cellular and molecular processes.

I went to graduate school at Univ. of California, San Diego in Neurosciences where my dissertation focused on how the synaptic connections between neurons change as your brain learns. Aside from my dissertation work, I've done molecular neurobiology research on protein structure and function. Currently, I'm working as a postdoctoral fellow at UC - San Francisco. I've had to reacquaint myself with the details of genetics that I learned in Mr. Baker's genetics class in my current research using fruit fly genetics as a tool to look at synaptic function.

The research that I do is basic science: which means that instead of working on curing a particular disease like Alzheimer's, I am working to understand the basic biological processes that go on in all of our neurons. That isn't to say that my work doesn't have relevance for diseases. In fact, problems with synaptic function are known to contribute to almost every known neurological disease from epilepsy to Parkinson's to schizophrenia. I believe that we need a much more complete understanding of the basic biological processes in order to know how healthy as well us unhealthy brains function and to provide more intelligent treatments.

I'm going to steal Jonathan's idea and post a couple of interesting articles. The first is from Scientific American and it shows how modern brain imaging equipment can be used first to watch brain activity and the coordination of different brain areas as a subject (in this case a monkey) makes a decision. Then, after the task becomes familiar, the imaging is used to see how the pattern of brain activity is different than it was when the subject was first learning the task.

http://www.sciam.com/article.cfm?id=decision-making-in-brain

The second article discusses a rare neurological phenomenon called synesthesia, when sensory input from one of the senses (such as vision) activates the area of the brain that normally processes information from a different sense. In this case visual input activates the auditory region of the brain, so people with this experience "hearing" a visual stimulus. Only in the last few years has it even become accepted that this actually happens and it's not just people speaking metaphorically. I think the most interesting thing about this is that essentially no one has the first clue how this is happening or what goes on genetically or developmentally to cause this.

http://news.bbc.co.uk/2/hi/health/7545888.stm

Happy reading!

DJ

No TQT This Week

Hey Bios,

Because I have been getting many good questions in class this week I have cancelled TQT for this week. Please complete your FRQ-12 by Friday. On Friday I will be distributing FRQ-13. This is a genetics problem set that extends simple Mendelian genetics. Read the remainder of chapter 14 to get acquainted with this material.

Also, two more former students have accepted my invitation to join the blog. Ken Michelson is studying medicine at NYU (right Ken?)and DJ Braiser is working on a post-doc project at the University of California San Francisco. So feel free to ask these guys about life after high school and in particular studying science.

Tomorrow, the remainder of chapter 14.

Mr. Baker

What to Read For Your FRQ This Week

The information needed to understand the FRQ for this week can be found in chapter 14 on pages 239-247. Take time to learn the vocabulary and Mendel's laws of segregation and independent assortment. Becoming familiar with terms such as P generation, true-breeding, allele, and others is essential in order to understand the genetics problems. Next week you will receive questions that cover the second part of chapter 14. I will be monitoring the blog this weekend so if you have questions be sure to write and remember that you can help each other. Finally, welcome Jonathan Richardson to the blog, read his post, and ask him questions.

Mr. Baker

An Interlude for Ecology

Hi Everyone,

I just wanted to quickly introduce myself and post links to a couple of articles that you all might be interested in. My name is Jonathan Richardson and I was a student in Mr. Baker's AP Biology class back in 1999-2000. We certainly didn't have a blog back then, so it's been interesting to see how this one has started and been used by Mr. Baker and you guys. Anyway, I'm currently a graduate student at the Yale School of Forestry and Environmental Sciences here in New Haven, Connecticut. My dissertation research deals mainly with the intersection of population ecology and evolution, both topics that you will cover soon enough (at which point I will probably be of more use to your class). Specifically, I study amphibian populations (spotted salamanders and wood frogs native to the eastern US and even into Alaska) and how landscape structure (as in intact forest habitat vs. habitats with barriers to these guys moving to other areas) can alter the long-term persistence of populations. Hopefully my own research will more interesting to you and germane to your studies once Mr. Baker starts to talk about ecology and evolution. In the meantime, I just wanted to introduce myself and I'll also attach links to 2 very interesting articles.

The first is from the Seattle Times in 2005, and discusses the reintroduction of wolves to the Greater Yellowstone ecosystem. When wolves were hunted to extinction, their prey no longer needed to worry about being killed, so they (elk, in this article) consumed more of the vegetation, which in turn led to a dramatic shift in the tree species regenerating and forest ecology. The wolves were reintroduced in 1995, so now ecologists have a fantastic opportunity to see how things change when the top predator is returned to the ecosystem. One of my good friends is currently tranquilizing wolves from a helicopter as a student at the University of Wyoming as part of this project. Ecologists get to do some amazing things in amazing places!

The second article is from this week's New York Times Science Tuesday section (a great read every week!). It discusses a phenomenon called artificial selection. This is analogous to the natural selection Charles Darwin described, however the selective force here is introduced by humans (hence the term "artificial"). A quick example of this is fishing - if you only catch and keep the large fish and throw the small one back, you are "selecting against" big fish and selecting for small fish within the population (it sounds counterintuitive at first), and the size of fish within that population will decrease. Dog breeding is also an extreme form of artificial selection (from wolves originally?).

Anyway, take a look if you have some time. Hopefully they will get you excited for the evolution and ecology sections of Mr. Bakers class - definitely my favorite! Have a great weekend.

Jonathan

http://community.seattletimes.nwsource.com/archive/?date=20050211&slug=fearfactor11

http://www.nytimes.com/2009/01/13/science/13fish.html

Three Question Thursday for 1-15-09

It is that time again! Send me your TQTQs as a comment to this post. As before, I will try to answer as many as I can.

Mr. Baker

Walking Through Chapter 13

Hey Bios, tonight's post will be a walk through chapter 13. So grab your book and come along.

First of all, be sure to work on understanding the bold typed words. The bold typed words in chapter13-15 are central to your understanding genetics because they will be used freely and regularly. If you will look at my comment to Ana in the previous post you will see that I am questioning taking time to prepare vocabulary cards. I would like your opinion on this.

The chapter has three main sections; An Introduction to Heredity, The Role of Meiosis in Sexual Life Cycles, and Origins of Genetic Variation. The first section points out that understanding meiosis is really the first step in understanding genetics because genetics (heredity) is transmitted through gametes and meiosis makes gametes. It also discusses asexual and sexual reproduction in terms of the amount of variation passed to the next generation. See figure 13.1, this is a hydra budding. It is a type of asexual reproduction. A hydra is like a tiny sea anenome, notice the tentacles. Many simple animals have the ability to reproduce asexually.

Now we move to the second section, The Role of Meiosis in Sexual Life Cycles, on page 229 there is a description of how a human karyotype is made. Spend some time examining figure 13.3 and 13.4. Notice how the 2n and n stages alternate and whenever gametes come together (fuse) there is new genetic variation. Now the chapter moves on to meiosis. Study figure 13.6 and if you do not understand it, ask me questions. Notice that there is two divisions and at metaphase I the chromosome twins pair up rather than line up as in mitosis. Meiosis I is the reduction division because there is only one set of chromosomes in each cell when it is complete. Meiosis II is just about separation the chromatids and it results in four cells.

The final section is about how meiosis creates genetic variation. First, independent assortment is the "shuffling" of chromosomes at metaphase I. With 4 chromosomes there are (4) combinations and the 46 chromosomes of humans results in well, an astronomical number (see text)! Now that's variation. Second is crossing over the process in which homologous (twin) chromosomes exchange parts (See figure 13.9). This introduces additional shuffling. So with just independent assortment and crossing over there exists tens of millions if not more possible genetic variants in the gametes of one human. This leads us to the last source of variation - random fertilization. Think of it this way, if any gamete has an equal chance of meeting all the others, imagine the potential number of new genetic variants! And this does not even account for mutation! That is a lot of shuffling? Comments?

That's it for now. I will be up for just 1/2 hour more but will be looking for your comments. Gotta go get Kingston's bone ready for the morning and prep the coffee maker.

Mr. Baker

Read Ahead

Please feel free to read ahead. Read chapters 13 and 14 and do not try to understand everything. I suspect that you will understand some of it and the rest I will explain in class. But read, get in the habit. Find the time, set it aside and read an hour a day. You will know more, feel better about your effort, and biology will become interesting - really.

An unabashed lover of biology,
Mr. Baker

Morning Cup O' Joe

Ok, here is the reminder to study for the test. The test requires you to recall the content of all six chapters so cuddle up with your book and study. Here is a brief list of topics study.

1. The difference between a prokaryote and eukaryote.
2. The parts of plant and animal cells and their functions.
3. The structure and function of the cell membrane.
4. Diffusion and osmosis.
5. Active transport mechanisms.
6. Cellular respiration - glycolysis, Krebs cycle, and electron transport chain.
7. Alcoholic fermentation.
8. Photosynthesis - light reactions and Calvin cycle.
9. C3, C4, and CAM plants - know the difference.
10. Cell signaling - G-protein-linked receptors, tyrosine-kinase, and phosphorylation cascade.
11. Cell cycle - mitosis and control of cell cycle.

This is just to get you going. Study, trust your intelligence, and I will be monitoring the blog today so if you have a question, post a comment to this post.

When you get to class, the test will be up front ready for you to pick up and start. Just put your things away and get going. There are 50 multiple-choice questions.

Mr. Baker

Getting Ready for the Test

Be sure to read the questions posted by your classmates and the responses as you get ready for the test. Remember, you are welcome to answer each others questions. It would be a good way to prepare for the test. Also, as you re-read the chapters and chapter summaries, if questions pop up send it as a comment to this post.

Mr. Baker

Morning Cup O' Java - aka TQT Time

Ca asked -
1. What caused the decline of "maturation promoting factor" (M-phase) at the end of the mitosis cycle?
Answer - The M-phase promoting factor, the complexing of B-cyclin and Cdk-1, signals the cell to move to metaphase and initiate the anaphase-promoting complex (APC). Once activated the APC will signal the separation of sister chromatids and the destruction of B-cyclins thus "turning off" the M-phase promoting factor.

2. A protein is released by a certain body to stimulate other cells to divide. At which point would cells stop dividing?
Answer - I don't know much about this but what I know is, a cell is signaled to grow and divide when growth factors are released from other cells. When this signal is turned off cells cease growing a dividing. This is an area of active research.

3. What are the differences between density-dependent inhibition and anchorage dependence?
Answer - Both are related to the growth and division of cells but are different in that density-dependent inhibition is about the restraint of cell division and anchorage dependence is about stimulating cell division. As the number of cells increases and thus the density, a point is reached where the cells no longer divide. This is density-dependent inhibition. In anchorage dependence cells do not divide unless they are on some sort of substrate (surface). This was originally discovered when researchers notice that when cultured cells were suspended in a liquid medium they greatly slowed or stopped their division. But when placed on a solid medium the same cells freely divided (until density-dependent inhibition).

Tahira, your questions make me smile. I am not sure how to answer them but I like 'em.


Hong-An asked -
1. In many online science website, mitosis has a prometaphase. Does that mean that the distinction between prophase and metaphase stage is very broad?
Answer - Really, the entire cell cycle is a continuous process not a series of steps. We teach it as steps to aid understanding and the introduction of intermediate steps such a prometaphase introduces emphasis on what is happening. So regarding prophase, prometaphase, and metaphase; prophase is when the chromosomes are condensing and the nuclear membrane disintegrates, prometaphase is when further condensation happens and microtubules begin to attach to the kinetochore, and metaphase is when the chromosomes have lined-up at the equator of the cell.

2. In pictures they always show four chromosomes. Is this to simplify?
Answer - You bet. The mechanics of mitosis is the same no matter the number of chromosomes. It is just easier and hopefully clearer if we sketch 4 chromosomes rather than 46 (humans), 68 (coastal cutthroat trout), or 114 (lilly).

That took two cups of coffee and I am sufficiently caffinated but it is Saturday and I will have more. BTW - did you know that coffee has its origins in Ethiopia? I learned that when the family visited the Lucy exhibit at the Pacific Science Center over winter break.

More Later Ta-Ta,

Mr. Baker

Su-more TQTQ Answers

Anna asked the following three questions -
One of the chapter quizzes (11) had the following Question:
Lipid soluble signal molecules, such as testosterone, cross the plasma membranes of all cells but affect only their target cells because?
The answer:
Intracellular receptors are present only in target cells.
Could you please explain this?
Typically, lipid signal molecules such as testosterone will bind to a receptor molecule within the cytoplasm. This molecule, now activated will then turn on gene(s).

In chapter 10 there is the talk about photosystems I and II. Can a thylakoid membrane function without one of these? Well, the thylakoid membrane is where the proteins of photosystem I and II are embedded. So the membrane can be seen as scaffolding for the photosystems. They are both part of the photosynthetic structure called a chloroplast.

What exactly is Pyruvate? Recall that cellular respiration is composed of three main steps; glycolysis, Kreb's cycle, and electron transport chain. Glucose, the food molecule, is first processed in series of reactions called glycolysis which occurs in the cytoplasm. During this process glucose is transformed into two, three-carbon molecules called pyruvate. It is pyruvate with the help of a transport protein that enters the mitochondrion for further processing. The goal of glycolysis, Kreb's cycle, and electron transport chain is to harvest the energy and transfer it to form ATP. It is ATP that can be used for work in the cell.

From Keely, this is interesting -
Since genetic disorders come from mutation in chromosomes in gametes why doesn't the body find a way to destroy mutated gametes? Like how the body destroys mutated cells during mitosis. Answer - It does seem that just as defective cells are destroyed but the immune system the same should hold true for gametes. So why not? Until release, gametes are protected by cells that in effect guard them. The cells keep away the macrophages that may destroy them.

That's all for now. I see a couple of interesting questions from Ca. I will get to those tomorrow.

Mr. Baker

And More TQTQ 1-8-09 Responses

Zena asked - What is meristem? Meristem is a type of cell in plants that has not differentiated. This means that the cells have not become a specific type of cell. Because of this they can become many types of cell. So when you see that we are looking at apical meristem in the onion root tip this tells us that the tissue is likely rapidly dividing and can become vascular tissue, epidermis, root hairs, root cap, and others.

Zena also asked - Does an ameoba have cell division? Yes, they do what is called binary fission. During this process the nucleus does replicate its DNA and divides it equally. This is how you get more ameobas.

Wendy asked - Is it a conicidence that the cell cycle and one day are 24 hours in duration? The answer for the cells we were looking at, yes. Remember, there is a great range of cell cycle times. For example a nerve cell never divides, whereas a bacterial cell can divide in as few as 15 minutes. So the time for cell cycle completion depends on the type of cell you are looking at.

Going to the lab now, more later.

Mr. Baker

Some More Responses to TQTQ 1-8-09

I have a few minutes here and with my cup of coffee in hand here goes -

Inwoo asked - Without centrioles, how do plant cells split? It is interesting that though animal cells have centrioles, plant cells do not. So clearly the organization of the spindle does not require centrioles. But I read Inwoo's question as asking about chromatid splitting during anaphase. The movement of chromatids is due to the action of kinetochore motor proteins "walkimg" along a kinetochore microtubule, dragging its chromatid along.

Gotta go,

Jon

Some Responses to TQTQ for 1-8-09

Hey thanks for the great questions. I have only enough time for a few answers now but tune in later for more.

Cintia asked why cancer cells lose their density dependent inhibition and anchorage dependence. Briefly, this is due to multiple gene mutations in the original tumor cell. Cancer likely is the result of more than one mutation and if those mutations involve genes that regulate the cell cycle, density dependent inhibition, and anchorage dependence; you have a tumor that can metastasize.

Which leads us to a question by Inwoo, what is metastasis? This is the spreading of cancer cells throughout the body. Rather than being encapsulated and a benign tumor, a metastatic tumor is malignant and spreads, this is one of the reasons they are so deadly.

Inwoo also asked why human chromosomes are purple. The answer is they are not. The chromosomes you saw in class were stained (probably with aceto orcin stain) which causes them to be purpleish-pink and easily visible.

More later,

Mr. Baker

Three Question Thursday Time

Write your TQTQ for 1-8-09 here. Just click on comments and submit your questions. I will respond to some of them and each week post a new TQTQ request.

Peace,
Mr. Baker

Snow is Pretty - Particularly in the Mountains

As you know by now, we are two hours late today. This means a short class period and no lab. Instead, we will review mitosis and meiosis and familiarize everyone with the blog.

See you in class,
Mr. Baker

Prepare for the Lab Monday

Monday through Thursday we will conduct the mitosis and meiosis lab. It would be best if you would review mitosis and look ahead to meiosis. Mitosis is covered in chapter 12 while meiosis is found in chapter 13.



Though chapter 13 is not included in the next exam, pairing the learning of mitosis and meiosis allows you to compare and contrast each. Meiosis is the type of cell division that reduces the chromosome complement by 1/2 and is done by gametes (sex cells / sperm and eggs).

Test is Looming

The chapter 7-12 exam will be this Friday. It will be all multiple choice with 40 to 50 questions. If you have questions about the chapters reply with a comment to this posting and I will answer as soon as I can.

Mr. Baker