First lab day!!!

I started you off with daily questions to get you thinking - but as a CLASS we didn't answer them.  I asked you to work within your group to see if you could start to do this on your own.  I have told you before and will tell you again and again, Get comfortable with being a little confused. IT'S OK!!!  Don't SETTLE (our motto for this year) for being confused though - work it out!!!!  

Collaborate with each other and see what happens!!!  Here were the questions and answers.

Wednesday August 29^th

The fact that we sweat when it is hot outside could be an example of two different characteristics of life.  Which two and why?
Homeostasis - because we are trying to maintain a constant body temperature.
Respond to Stimuli because we are responding to our environment.

Determine which choice best answers the following question. (Be prepared to tell me what is wrong with the others)

Which characteristic is share by all prokaryotic and eukaryotic organisms?

A.  Need for a source of energy(Correct answer because this is metabolism)

B.  Ability to make their own food
All organisms don't make their OWN food, but all organisms to go through metabolism.

C.  Ability to reproduce asexually
Not all organisms reproduce asexually, but all organisms DO have the capability of reproducing.

D.  Need for oxygen for respiration
Not all organisms need OXYGEN for repiration, but all organisms do go through different forms of metabolism.

E.  Have Feelings
Not all organisms have feelings - but all organisms DO respond to stimuli in some form.

I also had you working through your first lab, see a future blog post about this and we will discuss what happened tomorrow!!
Great job today with your first lab.  It was a little chaotic, but sometimes labs get that way.  As long as we are focusing on our goal, a LITTLE chaoes never hurt anyone ;)
Great job today with your first lab.  It was a little chaotic, but sometimes labs get that way.  As long as we are focusing on our goal, a LITTLE chaoes never hurt anyone ;)

Finishing characteristics of life notes

Tuesday August 28^th

All living organisms can be classified as prokaryotic or Eukaryotic.  These names tell you the type of Cell that make them up.  Of these two types, bacteria are considered Prokaryotic

An organism’s ability to maintain a constant internal environment in an ever-changing external environment is known as Homeostasis

Give me one example of this. Maintaining a constant body temperature, blood glucose level, blood oxygen level.  As well as MANY more!!!  ANY time our bodies start adjusting to a changing cellular environment to keep a constant internal environment is an example of homeostasis.

After the daily question we continued throught the notes on the characteristics of life including metabolism, reproduction, repsonse to stimuli and growth.  I hope that over the next three days we will be able to actually LOOK at some of these characteristics in real life!

Here were some of the slide we looked at.

How do we maintain a constant body temperature?!?!

Plants responding to their environment

First Part of Characteristics of Life Notes

Today was your first set of notes!  We started the class with the following daily questions:

In order to be considered alive - all living organisms must contain at least one Cell.

Within that (cell) all living organisms contain a molecule of DNA which codes for everything about the organism.

True or False:  If something moves then it is alive. Why or why not?
FALSE:  Just because something moves (like my car) does not mean it's alive and just because something DOESN'T move (Like a tree) does not mean it ISN'T alive.

I then let you guys see the "Movie Trailer" to this section.  Here it is again for you to see.  There were some good questions in here to keep in mind as we go through these notes.

We then started into the characteristics of life notes.  Please check Edline if you missed any of these.

We got through the slides dealing with cellular organization and some of the examples of homeostasis. Tomorrow we will continue through these notes with the hopes of doing our first activity on Wednesday and Thursday this week!

What's coming this week!

This week we will be answering the following question 

We saw on Friday that biology is the study of life - so...... what does it mean to be "Alive"  All the "creatures" shown on the slide above are alive and there are SEVEN things that ALL of them have in common.  By the end of this week I hope that we will be able to discuss, differentiate and categorize different characteristics of life and give specific examples of how we can determine if something is living or not.

First Set of Daily Questions and getting into the "routine" of things!

Today I started the class with our first set of daily questions.  This is how just about EVERY class period will go.  When you enter class, start writing down the daily questions in your notebook and looking for the answers.  I already received the question "Do we have to write down the question?" YES!!!  While today's may not have seemed necessary, other days it will be crucial.  Most Friday's we will have a Daily Question Quiz (DQQ) that are based off of these, you will not be able to actually USE your notes, but that is what you want to use to study for them.  By only having answers written down without questions, you will not know what you are studying!!  This will make more sense as the year progresses.

Here were today's Daily Questions:

Friday August 24

How many times can you use a hall pass in a nine-week period? THREE (This includes if you let me know before class that you need to stop at your locker or go the restroom before class.  If you are back in class after the bell rings - that was a hall pass usage.  After you have used your three hall passes those would be considered tardies)

What parts of the class can you use them?

 First or last 5 minutes of class.  

Biology is the study of what? Life.  The term "-ology" means "The study of" and the prefix "Bio" means "life" (For instance - a BIOgraphy is a story of someone's LIFE)

Tell me one characteristic that you think defines “life”

*** I had you guys brain storm this together and you came up with a lot of these on your own.  I was very pleased with how you worked through this and look forward to doing this more often with daily questions (having at least one that you discuss together and answer on a note card)

The correct answers are:

cellular organization(All organisms contain at least one cell), homeostasis (The ability to maintain a constant internal environment), metabolism(taking in nutrition and releasing waste), responsiveness, reproduction, heredity(all living organisms contain DNA), and growth.

We will be looking at this in more detail on Monday and will probably have this as a daily question again.

In the discussion of metabolism I was able to give you the first "real world" example about Morning breath.  Here is a clip that discusses what I did about morning breath really being the result of Bacteria Metabolizing in your mouth.  So morning breath is sort of "bacteria farts"

Welcome Back!!!

      Here we are at the beginning of another school year!!  Today I showed you guys a welcome back video that introduced a little about what to expect and what I will be expecting of you.  I have great expectations for this year!!  I then had you tell me a little about yourself as both a person and a student.  This is INCREDIBLY important to me and I am very grateful for your participation in that "getting to know you" survey.  Tomorrow we will start the class off with Daily Questions to get us into the "routine"of how this class works!

If you missed the video - here it is!!

Change in Dates

We are HERE - Time for finals !!!

     If you decided to do the write up as your final - just a reminder that is due on Friday.  If you are doing the write up only as a discussion on evolution and natural selection it is now due on THURSDAY (not tomorrow as originally stated)!!!
     You received a review packet yesterday in class and continued to work through it today.  Please take time looking at each section using it as a reminder of what we have learned so far.  I also put last years bio 1 final on edline for your referance.  Take a look at this to help you prepare for  yours!!

Flashy Fish Simulation

Today I showed you the following link that goes through different scenarios that would affect the rates of evolution in a population.  http://www.pbs.org/wgbh/evolution/educators/lessons/lesson4/act2.html

A little background on the guppies.  MALE guppies are the ones that are usually "pretty" or "Flashy" as they are trying to impress the females who are usually very "drab".  There needs to be a balance though between being flashy to impress the ladies - but not TOOO flashy that all the predators are able to see you and therefore eat you. We ran through a couple scenarios for many generations to see what happened to the population.  What we found was that in certain scenarios, the types of predators did not affect the population at all.  Other times the brightest fish died off and only the drab survived.  I encourage you to run through these scenarios and look at the results and the analysis which speaks of why

Survival of The Sickest and Why Elephants Have Big Ears

So far we have continued through the notes on Evolution/natural selection.  I printed out the major forms of micro and macroevolution for you to give us some time to start into a project.  I mentioned in class today that if I can get REAL creative, I will have your final be a paper based off the chapter I assigned you and how you can relate all that we have learned this semester with your chapter.  The two books the chapters are taken from are below.

You have also received a "packet".... oh dreaded packet..... with questions based on this chapter.  I encourage you to work through this at your own pace as this will mostly likely take the place of a test on this topic.  I really would like you to work on showing how everything we have learned this semester molds so perfectly together!!!   I will give you a detailed rubric to the project as soon as I get it typed!!!!

Evolution and Natural Selection

This week we started in to our LAST chapter :) :) :) on Evolution and Natural Selection.  The daily questions we received Tuesday, Wednesday and Today are below.  I know that you covered basics of evolution and natural selection last year but this year we will be applying our understanding of Genetics and gene expression to get a better understanding of how exactly allele frequencies change over time.
Tuesday:
1.  Which population of organisms would be in greatest danger of becoming extinct?
***A population of organisms having few variations living in an unstable environment.
*Having little variation is not a good thing when a major environmental change occurs.


2.  In order for a new species to develop, there must be a change in the
**Genetic makeup of a population.  (This can be DUE to a change in the temperature or migration patterns, but ultimately it comes down to a change in the allele frequencies of a population)


3.  Which statement is NOT part of the concept of natural selection?
A.  Individuals that possess the most favorable variations will have the best chance of reproducing.
B.  Variation occurs among individuals in a population
C. More individuals are produced than will survive
D.  Genes of an individual adapt to a changing environment***GENES do not adapt - individuals adapt and populations adapt - but genes do not.  They may "change" due to random mutations though.

** 2  - a decrease in the advantage of having white fur.  Since over a 10 year period the presence of ANY white rabbits was eliminated, that most likely means that having white fur was no longer a good thing.
Which statement best describes a current understanding of natural selection?
A.  Natural Selection influences the frequency of an adaptation in a population.

We then started into the notes on Evolution and natural selection.  Please check edline for these

Wednesday May 2^nd

The scientist who traveled to the Galapagos island’s was……… Charles Darwin

He specifically looked at what type of organisms? Finches (along with many other interesting creatures!!)

True or False:  All Mutations are Bad FALSE!!!  Mutations simply mean a change in DNA  This can sometimes have an advantage, sometimes be bad, or other times have no affect on the phenotype.  For instance, i showed you the clip about a child that was born with 6 fully functional fingers and toes (see Below)

True or False:  Not all mutations are passed on to our offspring. TRUE - Only mutations that occur in germ line cells (those that will go through meiosis to become our gametes) will be passed on to our offpsring.

Thursday May 3^rd

*What did Darwin notice about the finches and what did that lead him to believe about the “evolution” of them? He noticed that their beak shapes directly corresponded to the type of food they ate.  What he theorized was that the finches has migrated from the main land of South America and overtime adapted to different food sources.  He called this "Descent with modification"

*With our understanding of genetics, these different “variations” are known as what? Alleles

*What do you think caused these different variations? Mutations

*What two types of variations do you believe would provide an “advantage” to a species?  Any allele that would allow them to survive (eat and not be eaten) and reproduce.

Today we continued with the notes and will next move into some chapters from the book Survival of the Sickest.

Tests back and.... "Our Deepest Fear" Life lesson ;~)

Today I gave you your tests back.  You guys did pretty well on this.  Second period had an 89% average score and 8th period had an 80% average - Both GREAT averages for such a complex topic so don't be too discouraged if you did not do as well as you had hoped.  Since the next chapter springs RIGHT from this I felt is was worth the time going over each question with you to make sure that you understood how our genes effect our traits and how CHANGES in those genes ultimately lead to new characteristics.... Sometimes good, sometimes bad.... sometimes with no great effect.

 As I often do on tests/quizes, I provided you wil the following sections of a writing by Marianne Williamson called "Our Deepest Fear."  You guys got one of my "life lesson lectures" about how I see this tendancy in a LOT of you to downplay your own potential because that is "easy."   It really is much easier to say.... "Oh.... don't ask me... I'm not smart, I'm not strong enough, I'm not fast enough.... etc" because that gets you out of actually living up to your potential!!!!  It much scarier to think about what you are capable of doing!!!  So if you remember NOTHING more about this class - I hope you remember that "you'r playing small" serves NO ONE!!!

Here were some Passages

Last Minute Study Stuff

Here are a couple slides that may help you remember transcription and translation

Also - you have all the songs as well ;)

And then the more "Formal" description

Review Game Link

Guess some of you want to look at the game eh?!?! Here ya go!!!!

http://jeopardylabs.com/play/miss-evrards-honors-biology-review-games

Mutations Wrap Up

There were a couple of you that still needed to present your slides so I had you do that.  We started class with the following daily questions though.  This is a good wrap up for mutations and how they affect not only the RNA sequence, but consequently the protein itself.

Wednesday April 25^th

In a frameshift mutation, which would cause more harm to the protein the addition on 1 nucleotide or the addition of 6 nucleotides?Why?

Adding just one - when adding nucleotides in sets of three you are just adding another amino acid instead of moving everything down (unless of course you add three in the middle of a codon)

*Mutations such as missense and nonsense would occur during which of these processes?

** During DNA Replication or Transcription.  These types of mutations are changes in the actual DNA or RNA sequence - therefore it could only happen when DNA or RNA is MADE.  So during DNA replication if the DNA Polymerase doesn't do a good job of "proof-reading" that will change the DNA which then during transcription will be coded into mRNA with that same mistake. 

*Mutations such as translocation and nondisjunction would occur during which of those?

Meiosis - these are when crossing-over goes "Wrong" or when chromosomes do not fully separate from each other. 

A couple last things then that I discussed.  First, we have talked about mutations that have no effect (silent mutations) and those that cause LARGE changes in the protein shape that are harmful; but a key thing to understand is that some mutations are actually advantageous!!  We will talk more about this in the next chapter and you will see how this all just flows together.  If no mutations ever occurred then there would only really be two sets of genes that ALL of us had (from the first male/female).  The word Mutation often times gets a bad wrap when really ANY change in the DNA is a mutation.  So different alleles are just different "mutations" which ultimately give us the variety in traits that we have today.

Tomorrow will be our formal review - I have almost finished typing it up so feel free to check it out tonight but here is a run down of the content that we have covered this chapter.

*DNA Structure

*DNA Replication

*Transcription

*Translation

*Mutations

What does this all MEAN?!?!?!

All right.  So we have made it through what DNA is and how we get from that crazy "snotty" stuff to our actual characteristics.  We then looked at what happens when this "instruction manual" gets messed up.  NOW...... if there are all these genes in EVERY single cell in our body..... WHY aren't all these proteins being made in every cell?!?!  Remember, that comes down to cellular environment.  Only certain genes are actually expressed (meaning they go through transcription and translation) in any given cell.  What the human genome project did was look at EVERY SINGLE chromosome and determine the genes that are found on them.  Here is a quick link to the image that is found in the back of the room.

https://public.ornl.gov/site/gallery/highres/GenomePoster2009.pdf 

The best way to see this is to actually zoom in on each chromosome and you will see what genetic disorders are associated with that region of the chromosome.  BUT...... not every cell in the body would be affected by these since they are not being expressed in all cells.

I take NO responsibility for THIS one!!!

So you guys have been through a lot of Biology "songs" that i have so kindly found and played for you... over..... and over... and over.........

BUT - THIS time - YOU gave me a song.  Thanks 8th period for this Gem!?!?!?! (I can't think of any better word than that.......)

Again.... I take NO responsibility for this one..... I am pretty sure you should get some kind of award if you make it through the whole song!!! ;~)

Presentation of Mutation slides!!!

Today I had you present your slides describing your specific mutation.  Here are a couple examples!!

Overall I liked what I saw!!  Check Edline and I will put together an overall mutations powerpoint with the details that I really wanted you to take away from this project!!  We will finish that up tomorrow and start our review.  I am still looking to have the test on Friday with our formal review on Thursday!!

Finishing Mutations

Today I gave you some time to finish up your slides on mutations.  Tomorrow you will present them and I will make sure to let you know of any missed information from these slides.  We will be wrapping this up and will have the test on this chapter by Friday.

Remember I told you about how different amino acids have different chemical properties and that is what determines how they will fold on top of each other.  Here are some picks about how changing one amino acid can completely change the overall structure of the protein it codes for and recall that protein function is directly related to its structure

Each Pin represents a different Amino Acid 

The chemical makeup of these Amino Acids determines how the protein will fold on itself

When properly folded  the protein can function

Changing just ONE amino Acid could cause
a different "fold" and this can drastically
change the structure and function of this particular
protein.

Happy DNA Day!!!!

Today was National DNA day.  This day is celebrated every April to commemorate the discovery the structure of DNA in 1953 as well as the completion of the Human Genome Project in 2003.

Red Velvet DNA Cupcakes - YUMMM!!!

DNA Day Brownies!! Good Stuff - Thanks Guys :)

Today we took our Daily Question Quiz and after feasting on some sweets (well at least 2nd period did) you continued to work on your Mutations slides. We will finish these up and present them on Monday!!!

Want to extract your own DNA?

Just found this video podcast that shows you a real quick and easy way to extract your own DNA - Check it out!!!

Introduction to Mutations

Now that we have gone through translation in a lot of detail.  Lets see what happens when something goes WRONG (in ANY of the processes we have learned about this chapter - DNA Replication, Transcription or Translation).  To introduce this topic I had you guys predict the outcomes with the following Daily Questions.

Thursday April 19^th

Using your codon chart – translate the following mRNA sequence

AUG CCA UAC CGC CGG UUU

   Met – Pro – Tyr – Arg – Arg - Phe

What would happen if the following letter changed?

AUG CCG UAC CGC CGG UUU

Met – Pro – Tyr- Arg – Arg – Phe

 The amino acid sequence remained the same – “Silent” mutation.

AUG CCA UAC CGC CAG UUU

Met – Pro – Tyr – Arg – Gin – Phe

“Missense” mutation

AUG CCA UAG CGC CGG UUU

Met – Pro - STOP

“NonSense” mutation

I then had you start working on a project where each of you got a different type of mutation.  You will be making a couple slides describing your mutation, what its effect is on the mRNA and ultimately what effect it has on the amino acid sequence

Wrapping up Translation

Today we did not have any daily questions as we moved right into some activities to wrap up transcription and translation.  We will be moving into mutations next but many of you already got a dose of this when you"messed up" your DNA models or read the mRNA wrong during translation!  Some of you got pretty frustrated at first because it wasn't a simple "Look in your notes and find the answer"  You actually had to APPLY what i've taught you about transcription and translation. The ONE area that i will admit would cause confusion was with Introns and Exons.  An area that i did not go into is a process known as RNA splicing.  If you take Bio 2 (or my hopeful genetics/immunology class) you will get into much more detail.)  Here is a little information about gene structure and the  Human Genome Project.

Translation Models

Today I had you guys use pre-made mRNA strands to go through translation.  You "read" the mRNA in sets of 3 base pairs (codons) that each code for an amino acid.  When you then added the amino acid you were acting as the tRNA that is found in the cells cytoplasm.  Translation started at the AUG - Codon (which codes for the amino acid Methionine) and continued until you reached a Stop codon.  There were no daily questions today so that we could get right into the activity.  Here are some pics!

Adding Amino Acids using the Codon Chart

Reading the mRNA sequence three bases at a time (codons)

The Amino acids will be bonded together by peptide bonds creating a "polypeptide chain" of amino acids

This shows how the amino acid is "transfered" to the mRNA molecule by a tRNA molecule (represented by the green paper) with the complementary "anti codon"  once the Amino acids is "dropped off" the tRNA will then leave and pick up another amino acids.

Transcription and Translation PBS Video

We had a hard time viewing this today in class, hopefully you will have a better time viewing it here.

Then..... there was another song.......... Just bare with me - they may be corny - but they really do provide a LOT of useful information to remembering the structure of DNA and replication / transcription & translation

Continuing on with Translation

Most of you had to make up your Daily Question quiz from Friday and then we started into some daily questions about Translation.

Monday April 16^th

During translation tRNA “transfers” what organic molecule to the ribosome? Amino Acids

The mRNA is read in sets of 3(Three) base pairs known as codons.  Each of these codes for an Amino Acid

EVERY Gene starts with what mRNA sequence? AUG

What amino acid does that code for? Amino Acids

    When does translation finish? (what part of mRNA) A Stop Codon

After that I went back over the notes we already took on translation and showed a clip that use digital animations to show you how the mRNA leaves the nucleus, enters the ribosomes and tRNA carries in the appropriate Amino Acids to build a protein. (Watch Below)

Blame it on the D d d d d DNA......

Here is the "Blame it on the DNA" song I started today's notes with.  As silly as it may have sounded, if you actually listen to the lyrics it tells a LOT about the structure of DNA, Transcription and translation.  Have fun :)!!!!!

Translation... day one..... brace yourself!!!!

            First we wrapped up our discussion on Transcription.  The daily questions focused on a review of transcription and then an introduction of Translation.

Thursday April 12^th

How does the cell know what DNA to transcribe? (What is located there)

 There is a Promotor Region on the DNA that signals that a gene is about to start.

When the end of the gene is transcribed what happens to the mRNA that has been created?

 It will now leave an head out to the cytoplasm (and eventually to a ribosome)

What then happens to the DNA that coded for this?

 The DNA just gets zipped back up left unchanged.  Sometimes this will be "read" again if the cell needs more of the protein that gene codes for.

What PROCESS will the mRNA now go through?

Translation

We then got through SOME of the notes on Translation.  This is a MUCH more complicated process then transcription so we will be spending longer on this!  

Transcription

Today we moved into the specifics of transcription and used the K'nex models to transcribe a section of DNA.  Today's daily question was as follows.

Wednesday April 11^th

The two main processes in Gene Expression are known as Transcription and Translation.

During the first process RNA is made from DNA

During the second process we make PROTEIN from RNA

Please transcribe the following DNA sequence

ATGCGATCG

UACGCUAC

What enzyme is responsible for unwinding the DNA during transcription?

RNA polymerase

Making mRNA from DNA the mRNA will now leave the nucleus
and head out to cytoplasm to go through translation in the ribosomes

Now for the tough stuff!!

We got through the DNA structure and DNA replication without too much trouble.  NOW to move into the fun stuff!!!  We had a chance to actually LOOK at DNA.. so now what?  What does DNA actually DO!?!!?!  That's what this week will be about.  As with the last section this will include some notes and then follow up activities with the Knex models.  Today's daily questions where as follows:

Tuesday April 10^th

DNA ultimately codes for what type of organic molecule?

 Proteins

What Nucleic acid actually takes the Instructions that DNA provides and MAKES this? RNA (Ribonucleic Acid)

In what organelle will this happen? Ribosomes

We then moved into the first part of notes on RNA and Gene Expression.  Please check out edline for any notes you may be missing!  We got through the overall process of transcription and translation and then made it almost to the end of the detailed slides on transcription.  Please make sure you are up to date with your notes!!

Extracting DNA from Strawberries

Before break I had you guys extract DNA from strawberries.  This was to show you that we have a LOT of DNA and it is found in each cell in our body.  This "snotty" looking molecule does more than just hang out in our cells though and that is what the next chapter is about.   Here are some pics from our lab though

Smashing up the strawberries and adding the DNA Extraction buffer to break through the Cell Membrane and nuclear membrane

Preparing to pour the Strawberry mixture

Adding the Ethanol to separate the DNA 

Not as glamorous as it sounds?!?!  THIS is what DNA looks like when mixed with proteins and jumbled together with hundreds/thousands of other DNA molecules

It wouldn't be a proper "wet lab" without SOMETHING end up on the floor!! (Way to go 2nd period)