Videos to Guide You Through Ch. 2 and 3

The videos to the right are supplemental lectures that will assist you with Chapters 2 and 3 in Campbell and Reese.  Chapter 2 should be a review of Chemistry.  Take note of anything that is particularly confusing (or is brand new) and prepare to ask clarifying questions when we get back to school.
Chapter 3 is not required summer work, but I highly suggest that you get some exposure to this material before we plunge head first into Organic Chemistry.

Blast

Gene files:
http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/

BLAST Homepage:
http://blast.ncbi.nlm.nih.gov/Blast.cgi

Entrez Gene Website
http://www.ncbi.nlm.nih.gov/gene

Trees in Paradise

Listen to this.  It's awesome.
http://www.kqed.org/a/forum/R201405260930#disqus_thread

Now You are Less Dumb

https://www.youtube.com/watch?v=zWSe2qezhm4&app=desktop

Science Fair Ideas

http://www.sciencebuddies.org/science-fair-projects/project_ideas.shtml

Q 10

So, this equation is on the given equations for the test, yet it was not part of any of our labs.  Watch this video and familiarize your self with Q 10.  Feel free to post questions.
http://www.bozemanscience.com/q10-the-temperature-coefficient

Video to Watch this AM

Happy Mother's Day!
https://www.youtube.com/watch?v=tFNJLs-Ql0o

Signal Transduction
http://www.bozemanscience.com/038-signal-transduction-pathways

Bozeman Science Homepage

This is the entire Bozeman collection, organized by the three "Big Ideas" in AP Bio.
http://www.bozemanscience.com/ap-biology/

Watch a few of the Science Practices today
Watch this one today:
http://www.bozemanscience.com/032-signal-transmission-and-gene-expression

Practice Problems and Other Resources (draft)

Hardy Weinberg
http://www.indiana.edu/~l111/handouts/hardy.htm
(the bottom links you to the solutions)

Population Growth
http://netclass.landmark-cs.org/ClassDocuments/5036/loggrowth_answers.pdf
http://www.westonk12-ct.org/file.cfm?resourceid=16123&filename=ExamView_-_pop_growth_practice.pdf

Okay, I made a song.

I will sing it for you tomorrow.
It goes to the Adam's Family theme song https://www.youtube.com/watch?v=_YFk4b6yeX4

Here are the lyrics

Verse One:

The data fit (clap clap)
The data fit (clap clap)

When data we collected
Match the unexpected
Our hypothesis is rejected
We don't reject the null.

A chi square that is smaller
Shouldn't make you holler
The null is still the baller
We don't reject the null.

Critical value (clap clap)
Critical value (clap clap)

When data we collected
Match the unexpected
Our hypothesis is rejected
We don't reject the null.





If you can learn this song, then you know, that if the data doesn't fit, (high chi) we reject the null.

Chi Square

Sorry for the confusion (it's my fault):

Chi square is a way to measure "goodness of fit" between data based on expected values and data obtained through experiment or calculations ("observed").

How do we know our "expected values?"  We use tools like Punnet squares and Hardy Weinberg to give us our expected values.  Sometimes our expected values are simply an even distribution (like in the fruit fly behavior example)

What is the null hypothesis?  The null hypothesis states that there is no significant difference between the expected and the experimentally derived ("observed") data.  In other words, the data "fit."

For example, we think that the coin used in the NFL is unfairly weighted to land on "heads."  Our "expected" data is 50/50 heads tails (even though we actually think the coin is rigged).  Our null hypothesis is that there will be no difference between the NFL coin and any other coin.

The experimental, or "alternate" hypothesis should describe a situation when the data do not "fit."
(one of the major sources of confusion was the practice problem we did today in class had a hypothesis that predicted a "fit."  Do you see why this would jumble up the null with the hypothesis?)
Our alternate hypothesis is that the NFL coin will disproportionately land on "heads."

If the data "fit" nothing significant is happening.  The coin is not rigged.

If the data don't "fit" then we need to call the NFL commissioner because the coin is rigged.

Again, we use chi-square to determine the fit.  We need to use the Critical Values Table

When the calculated chi-square value exceeds the critical value in the table for a 0.05 p value, then we can reject the null hypothesis.  Which means, in the NFL case, the coin is rigged.

If the calculated chi-square is less than the critical value, then we do not reject the null hypothesis, because the data "fit."  Which means the coin was not rigged and we are paranoid football fans.

Finals Schedule

SPRING SEMESTER FINALS SCHEDULE

JUNE 3-6, 2014

Tuesday, June 3, 2014

Period		Time		4 minute passing time before period 4
1		9:00 – 11:00	(120)
Lunch		11:00 – 12:56		Instructional Minutes
4		1:00 –   3:00	(120)	244

Wednesday, June 4, 2014

Period		Time		4 minute passing time before period 6
7		9:00 – 11:00	(120)
Lunch		11:00 – 12:56		Instructional Minutes
6		1:00 –   3:00	(120)	244

Thursday, June 5, 2014

Period		Time		4 minute passing time before period 2
3		9:00 – 11:00	(120)
Lunch		11:00 – 12:56		Instructional Minutes
2		1:00 –   3:00	(120)	244

Friday, June 6, 2014

Period		Time		4 minute passing time before period 1, 2, 3, 4, 5, 6, and 7
5		8:18 – 10:18	(120)
Break		10:18 – 10:31
1		10:35 – 10:48	(  13)
2		10:52 – 11:05	(  13)
3		11:09 – 11:22	(  13)
4		11:26 – 11:39	(  13)
5		11:43 – 11:56	(  13)
6		12:00 – 12:13	(  13)	Total Instructional Minutes
7		12:17 – 12:30	(  13)	239

Some Ecology Videos and Helpful Links

Practice with these Climate Graphs:
http://www.geoknow.net/pages/climategraphs.html

Eutrophication
https://www.youtube.com/watch?v=ahOmeTOIrRg

r and K Selection
http://www.bio.miami.edu/tom/courses/bil160/bil160goods/16_rKselection.html

Demography and Life Histories
http://www.uic.edu/classes/bios/bios101/Demography/sld001.htm

A really cray cray video about DDT (don't miss)
https://www.youtube.com/watch?v=-UiCSvQvVys

How DDT affects a marine food chain:


DDT in fat tissue and human breast milk (DDE = DDT - hydrogen)

Watch these before class tomorrow:

Positive and Negative Feedback Loops
http://www.bozemanscience.com/positive-and-negative-feedback-loops/

And for a specific example of feed back involving hormones in the body...
https://www.youtube.com/watch?v=WVrlHH14q3o

And the reproductive system!!!  YAY!!!
https://www.youtube.com/watch?v=_7rsH2loIY8

Experimental Design

Design an experiment to test how fruit flies respond to various environmental stimuli, for example,  the presence of a piece of banana in various stages of ripeness, cotton soaked in various molarities of sucrose, cotton soaked in various toxic substances, various colors of light etc.  You will take data by observing the flies in a choice chamber as shown below.




List the following:
Your hypothesis:
Your null hypothesis:
Your independent variable:
Your dependent variable:
Constants:
The control trial:


Imagine you conducted the experiment with a banana and got the following data:

Perform a Chi-square analysis of the above data using this chart:

The Synapse and the Neuromuscular Junction

The synapse (We will go over this today as a class)
https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/neuronal-synapses--chemical

This is a good time to review cellular respiration!
http://www.youtube.com/watch?v=00jbG_cfGuQ

The motor neuron:
https://www.khanacademy.org/science/health-and-medicine/musculoskeletal%20system/Introduction%20to%20muscles/v/motor-neurons

The neuromuscular junction:
https://www.khanacademy.org/science/health-and-medicine/musculoskeletal%20system/Introduction%20to%20muscles/v/neuromuscular-junction

Crash Course:  The Muscular System
http://www.youtube.com/watch?v=jqy0i1KXUO4&index=32&list=PL3EED4C1D684D3ADF

The Nervous System

Use this site to continue your studying of the nervous system.
http://people.eku.edu/ritchisong/301notes2.htm

Weekend Homework- Nervous System

Crash Course- The Nervous System
https://www.youtube.com/watch?v=x4PPZCLnVkA

Here is the main page for the Khan videos on the nervous system:
https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/anatomy-of-a-neuron

The questions will be posted in batches- the first batch Saturday morning and the second batch Sunday morning.

Video #1- “Anatomy of a Neuron”

1. What is the function of the neuron?
2. Draw and label a typical neuron.
3. Describe the various parts of the neuron (soma, dendrite, axon, axon terminal, axon hillock, Schwann cells (myelin sheath), and nodes of Ranvier)
4. How do neurons connect to each other?

Video #2 and #3- "The Sodium Potassium Pump" and "Correction to Na-K Pump Video"

1. What is an action potential?
2. What is a voltage potential?  Or, what is voltage in general?  What is the difference between the outside and inside of the neuron in MV?
3. What is the role of sodium-potassium pumps?  Where are they located?  How do they get the energy to “pump?”
4. What does ATP-ase do?  Why does the Na-K pump need to use energy from ATP?
5. How many and what kinds of ions are pumped in each “pump?” Where are they pumped?  So, how does Khan use this to explain why there is a voltage potential across the membrane?  How does he correct himself in the third video? (In other words, what is the main reason for the voltage potential?)
6. How is a voltage potential like a concentration gradient?

Video #4- “Electrotonic and Action Potential.” This is one of the most useful Khan videos of all time!!!

1.     Why does sodium flow through the membrane (two reasons)

2.     Describe the spread of an electrotonic potential.

3.     What are voltage-gated ion channels and how do they work?

4.     What is the relationship between the electrotonic potential and the opening and closing of the ion channels?  How is this dynamic responsible for the propagation of the signal?

5.     Define action potential.

Video #5- “Saltatory Conduction in Neurons.”

1.     How is the structure of the neuron related to its function?  ***One of the main questions in the AP Biology curriculum***

2.     How does the stimulus spread from the dendrite to the axon hillock?

3.     What is the threshold voltage that is required to open the voltage-gated sodium channels?  How does this explain how we can be touched, but not feel it?

4.     Does the voltage go up or down when the voltage gated ion channels are triggered?  Does this mean the voltage difference is greater or less?

5.     Why do we insulate wires?  How does this relate to the axon? Why is it not a perfect analogy?  Why can’t we surround the  axon completely with Schwann cells?

6.     What are the pros and cons of electrotonic potentials and action potentials?

7.     Sometimes teachers say that the signal “jumps from node to node?”  Why is that inaccurate?

8.     Define saltatory conduction.

Prepare for your quiz!

Re-watch the Crash Course (two posts ago) and finish up the Khan Academy Videos below:

Helper T Cells:
https://www.khanacademy.org/science/biology/immunology/v/helper-t-cells

Killah T Cells:
https://www.khanacademy.org/science/biology/immunology/v/cytotoxic-t-cells



Also, for those of you thinking one month ahead- here is the info on the AP test. Including a practice test and last year's short answer questions.
http://apcentral.collegeboard.com/apc/members/exam/exam_information/1996.html

Immune System Homework for Tuesday Night

Review the immune system with this video by Mr. Anderson (note the castle analogy!)
https://www.youtube.com/watch?v=z3M0vU3Dv8E

Watch the following videos from Khan Academy and take notes in preparation for a quiz on the immune system on Friday.

B Cells
https://www.khanacademy.org/science/biology/immunology/v/b-lymphocytes--b-cells

APC and MHC
https://www.khanacademy.org/science/biology/immunology/v/professional-antigen-presenting-cells--apc--and-mhc-ii-complexes

As requested by Mel:  (So, motherhood calls, so will add some tomorrow in the early AM.  This will get you through the first video.  Just take good notes on the second video and you'll be okay!!!)
1) What is the relationship between the MHC, antigens and antibodies?
2)  Describe the structure of an antibody.  What do antibodies do? (This is at the end)
3)  How can there be so many different variable groups on membrane bound antibodies, I mean HOW?!
4)  What is clonal selection?
5)  Contrast plasma cells and memory cells.
6)  How does the B cell response explain why you don't get sick from the same virus twice?

Get ahead:

Helper T Cells
https://www.khanacademy.org/science/biology/immunology/v/helper-t-cells

Killer T Cells
https://www.khanacademy.org/science/biology/immunology/v/cytotoxic-t-cells

Immune System Homework (Must be done by class on Tuesday 4/8)

The immune system is one of the few systems that you need to know for the AP test.
Watch the three videos below:

Watch the Crash Course video for an overview.
https://www.youtube.com/watch?v=CeVtPDjJBPU&list=PL3EED4C1D684D3ADF&index=33

Then, take notes on the following Khan Academy Videos and bring them to class tomorrow.
https://www.khanacademy.org/science/biology/immunology/v/role-of-phagocytes-in-innate-or-nonspecific-immunity
https://www.khanacademy.org/science/biology/immunology/v/types-of-immune-responses--innate-and-adaptive---humoral-vs--cell-mediated

Want to get ahead?  Take notes on the following videos.

https://www.khanacademy.org/science/biology/immunology/v/b-lymphocytes--b-cells

https://www.khanacademy.org/science/biology/immunology/v/professional-antigen-presenting-cells--apc--and-mhc-ii-complexes

Study Guide and Short Answers on the Plant Test MOVED TO MONDAY

One of the short answers will One of the short answers will be on the Went experiment on page 826 seen below:

Be SURE you know which side is undergoing more cell division.

The second Short Answer will directly relate to the Transpiration Lab we did in class.

Study Guide for the Multiple Choice:

Focused Study Guide on Plant Structure and Function

1. What would happen if the mycorrhizae were removed from a plant?
2. What are apical meristems?  What hormone is produced there and what effect does this hormone have?
3. What are some examples of active transport?
4. What are the functions of proton pumps?
5. What are the characteristics of land plants’ earliest ancestor?
6. What factors contribute to the movement of water up the xylem?
7. How can water potential be affected?
8. How does water move in response to solutes and pressure?
9. What are the factors that affect transpiration rates?
10. How (and where) do plants exchange gasses with the environment?
11. What is the sequence of events in the alternation of generations in an angiosperm?
12. What is the sequence of events in angiosperm reproduction, specifically?
13. Know how to label a diagram of alternation of generations.
14. What parts of a plant are affected by auxins?
15. How does auxin result in plant growth according to the acid-growth hypothesis?
16. What are the steps of a signal-transduction pathway?

There will be questions that you can't study for, but will require critical thinking and graph reading- don't freak out.

Plant Kingdom Spring Break Homework.

You are responsible for the information contained within the following videos.  Our test is the Friday after Spring Break.
General Plant Video (Bozeman)
http://www.youtube.com/watch?v=X4L3r_XJW0I
Plant Structure and Function (Bozeman)
http://www.youtube.com/watch?v=zHp_voyo7MY
Plant Resource Acquisition and Transport (Bozeman)  This is very important for the AP exam.
http://www.youtube.com/watch?v=bsY8j8f54I0
Water Potential (Bozeman)
http://www.youtube.com/watch?v=nDZud2g1RVY
Photosynthesis (Bozeman)  This is important to review so you know how structure relates to function.
http://www.youtube.com/watch?v=g78utcLQrJ4
Photosynthesis (Hank, my boyfriend)
http://www.youtube.com/watch?v=sQK3Yr4Sc_k&list=PL3EED4C1D684D3ADF
Plant Reproduction (Hank)
http://www.youtube.com/watch?v=ExaQ8shhkw8&list=PL3EED4C1D684D3ADF

You can also take the practice test in your yellow AP Bio review book.

Tiktaalik

http://tiktaalik.uchicago.edu/meetTik.html

Short Answer

Creationists often argue that the slow accumulation of mutations would take far longer, than the 3.4 billion year history of life.  Use what you learned from Crash Course Video #17 to refute this argument.

Points will be given for: 1) explaining Hox genes (regulatory genes) and how they function, 2) Experimental evidence for how Hox genes function (butt eyeball), 3) experimental evidence for the evolutionary development of animals (bird teeth, cave fish eyes, snake legs)

Pages 445-447 Hox genes

371 Maternal effect genes

701 figure 34.6 is expression of Hox in vertebrates.

http://www.youtube.com/watch?v=9sjwlxQ_6LI&index=18&list=PL3EED4C1D684D3ADF

A Bunch of Videos to Watch

http://www.youtube.com/playlist?list=PL3EED4C1D684D3ADF

Videos that are relevant to our unit "The Evolutionary History of Biological Diversity" include
#16, #17, #19, #21, #22, #23, #24, #36, #37.

Chapter 32, 33 and 34 Study Guide

Chapter 32: An Overview of Animal Diversity

1. Instead of cell walls, animals have______________.
2. Copy figure 32.2 (p. 655) into your notes and define the following vocabulary: cleavage, blastula, blastocoel, gastrulation, gastrula, endoderm, ectoderm, archenteron, blastopore.
3. Review homeoboxes and hox genes from chapter 21.
4. What happened in the Cambrian Explosion? (p. 657)
5. Draw a picture (like a stick figure) and label the following: anterior, posterior, dorsal, ventral.
6. Draw some pictures to represent radial symmetry, bilateral symmetry and cephalization.(p658-659)
7. Using figure 32.8, compare and contrast acoelomates, pseudocoelomates, and coelomates. (p.660)
8. Define the four different types of cleavage (p.660-661)
9. Explain how protostomes and deuterostomes are different. (p. 661)
10. Familiarize yourself with the animal phylogentic trees from pages 662 and 663.

Chapter 33 Introduction to Invertebrates

Read this chapter for its coolness factor.  Especially look at the pictures.  If you have interest in Marine Biology, read this chapter a little more closely.

Describe what makes these groups unique and list at least one representative from the following:

Porifera

Cnidaria

                Hydrozoa

                Scyphozoan

                Cubozoa

                Anthozoa

Lophotrocozoa

                Platyhelminthes

                Rotifera

                Ectoprocta

                Brachiopoda

                Mollusca

                Annelida

Ecdysozoa

                Nematoda

                Arthropods (know about trilobites!)

Deuterostomia

                Echinodermata

                Chordata

Chapter 34 The Origin and Evolution of Vertebrates

1. What is a “derived character?”
2. What are the characteristics of chordates? (p.697-699) Include definition of all related bold-faced words.
3. Study figure 34.2 (p. 698) and list the major evolutionary changes that caused branches in the tree. 
4. On page 701, there is a figure 34.6.  The book asks you to “make connections” to chapter 21.  Explain your connection.
5. Define oviparous, ovoviviparous and viviparous (p. 707)
6. How are the chondrichthyans different from the osteichthyans? (p. 705-707)
7. Explain why Tiktaalik was such an important discovery. (p.710)
8. Define the sub structures in an amniotic egg. (p714)
9. Define endothermic and ectothermic (p. 715)
10. What defines a mammal?
11. Explain the evolution of the “ear drum.” (Fig 34.37 p.721)
12. What were major evolutionary changes that led to modern humans (729-733)

Thomas and Karla- You were fabulous in the play.