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Sunday, November 21, 2010

Apologia Biology, Module 7, Cellular Reproduction and DNA

Quizlet Vocabulary Game, M7 
M7 Recap Blog Post at Sahm-I-Am

(1) p. 197-198, Experiment 7.1, DNA Extraction
Our class did this experiment last year.  (See our results)
Here are instructions if any other blog readers need them, and an instructional video.
►And just for fun, you can try this DNA Extraction Virtual Lab.

This is Applie's video below from when her class did this, and here is her Module 7 post.


(2) p. 198b-200, Protein Synthesis - Part 1: Transcription
"Synthesis" means the making of or production
The point of the next 2 sections is to show how proteins are made from DNA.
Cells synthesize, or make, proteins that result in the traits that DNA gives us.  The cell's genes determine what kinds of protein a cell will make, which determines the job of that particular cell.

A scribe is someone who writes down a copy. You can see the word scribe in transcribe, and script in transcription. Transcription means to copy or transcribe. 
Something called RNA is what helps make the copy of DNA, which is in the nucleus of the cell.   RNA looks like DNA, but it ends up being only a single strand of nucleotide bases. 

The differences between DNA and RNA are:
DNA: has nucleotide base pairs of cytosine & guanine, and adenine & thymine.
►See diagram of DNA strand. (source)
RNA: has individual nucleotide bases of cytosine, guanine, adenine, and uracil, but they are not in any particular order yet.  They will match up to corresponding DNA nucleotides so they will be in the correct order for transcription (copying)
--There are two nucleotides that are different - uracil in RNA, and thymine in DNA.
Uracil in RNA will match up to adenine in DNAAdenine in RNA will match up to thymine in DNA, so U-A, and A-T.
DNA: has deoxyribose (on the "rail" of the "ladder").
RNA: has ribose.
DNA: is twisted in a double helix of paired nucleotides.
RNA: usually in a single strand of joined nucleotides.

►See diagram of DNA and nucleotides.
Only a certain section of DNA will be copied.  As this section of the DNA strand unwinds, individual RNA nucleotides match up to compatible DNA nucleotides and take a "negative snapshot" of the DNA code.  For example, if the DNA has a nucleotide of guanine, an individual nucleotide of RNA cytosine will match to it.  If the DNA has a nucleotide of adenine, an individual nucleotide of RNA uracil will match to it.
Before, the RNA nucleotides were individuals, and not in a strand since they had to match up to the DNA in the correct order.  Now they are a "negative" copy of the DNA, and will be used by the ribosome to make a protein.
This is copying, or transcribing the DNA code.


(3) p. 201- 204, Protein Synthesis - Part 2: Translation

Transcription and Translation.  A polypeptide is a chain of amino acids.  Poly means many.

After the RNA "negative" of the DNA is made, the RNA takes this negative out of the nucleus and into the cytoplasm to a ribosome.  Because of this, it is called messenger RNA, or mRNA
Near the ribosome is a different kind of RNA called transfer RNA, or tRNA.  This tRNA contains a special sequence of three nucleotides called an anticodon.
A special sequence of three nucleotides on mRNA is called a codon.
The codon and anticodon aren't just any three nucleotides, but certain various combinations.

The tRNA is bonded to an amino acid, but only a certain type of amino acid will bond to a certain sequence of three nucleotides in the tRNA.
For example, if the three-nucleotide anticodon is made up of uracil, uracil, and cytosine, the tRNA is bonded to the amino acid lysine.  (p. 202 shows a few more combinations).
A codon on mRNA attracts a specific amino acid.  Then the tRNA links up to the mRNA.

After the tRNA links up to the mRNA, the amino acids on each of the tRNA anticodons bind together to make a protein.
The chain of amino acids that make a protein is called a polypeptide. (poly- means many)
(The first 30 seconds of this video are the same as a video already posted, but good to see it again.)

Learn the difference between mRNA codon and tRNA anticodon, and how a chain of amino acids form a protein.  A stop codon is a special codon that signals the stopping point for translation.
Learn which codon is the starting point for Translation (which 3 letters).

Through studying DNA, a man realizes only God could have created all this!

►To practice what you've learned, go to the DNA Workshop
Click on DNA Workshop Activity, then in the pop-up window on the top right, click on Protein Synthesis.
Follow the directions to first build RNA, then match tRNA anticodons to mRNA codons to build proteins from the amino acids.
If you don't understand this, go back and watch all the above videos, and re-read the textbook.   


(4) p. 205-211a, Mitosis: Eukaryotic Asexual Reproduction

Exp. 7.2, Mitosissince we do not have a microscope, watch/read what is posted here.

Mitosis is the process of cells splitting and multiplying, for repair of cells, or growth of new cells from existing cells.  
This is asexual reproduction.

Mitosis is the growth of new cells, either to replace damaged cells, or for a growing person or unborn baby.
But before Mitosis begins its 4 stages, the DNA that is in the nucleus must duplicate itself into sister chromatids, then coil up into chromasomes.

Exp. 7.2, Mitosis
►Watch this video of Mitosis.  Click Animation.
[If you need to, press your F11 key to make the screen larger. Sometimes clicking F11 while in a different tab works better.]

►After watching the animation, click Tutorials at the bottom.
Below that, 5 Interactive Tutorials are listed:   
Roles of Mitosis, Overview of Mitosis, Cell Cycle, Stages of Mitosis, and Summary.    
Do all except the middle one, the Cell Cycle.  Mastering these is important.

Learn the 4 phases of Mitosis, and briefly what each one does.  You can remember their order by the acronym PMAT.  (Interphase is not a phase of mitosis; it is an 'in-between' phase.)  
After completing the Summary, click on each cell to see descriptions of each cell.
►Fill in this printable Study Sheet for Mitosis.

►This will help you understand what you are drawing & labeling in Fig. 7.6, p. 208 which is also your assignment for today.
If you don't understand this, go back and watch all the above videos, and re-read the textbook.   


(5) p. 211-213a, Diploid and Haploid Cells
--All living things have different numbers of chromosomes.  An onion has 16 chromosomes in each cell; a horse has 64; and a carp has 104.
--Humans have 46 chromosomes in each cell.  The chromosomes are in pairs, so humans have 23 pairs in each cell.
Each pair consists of similar types of chromosomes, and therefore they are called homologous chromosome pairs, or homologous pairs.  Homo- means same, but homologous means similar, but not identical.
Each chromosome is attached to its sister chromatid (its duplicated chromosome) at the centromere, giving them their X shape.  Two sets of these make a pair of similar, homologous chromosomes.  XX.
--The 23rd pair of chromosomes are chromosomes that determine sex.  In a female these are both X chromosomes, or XX, but in a male, they are XY.  So in males, the 23rd pair is not homologous.
►See image of Human Chromosomes

Read carefully.
--When a cell's chromosomes come in pairs, it is called a diploid cell.  XX, XX, etc.
--Cells with chromosomes that do not come in pairs are called haploid cells.  A haploid cell has only one representative of each chromosome pair.  X, X, etc.
Cells can have 23 pairs of chromosomes, or 23 chromosomes, depending on what phase the cell is in.

There is also a diploid number and a haploid number.  This can be rather confusing, but read carefully:
--The diploid number represents the total number of chromosomes in 1 cell or counting both partners in the pair.  In other words, the total number of chromosomes in a diploid cell.  46.
--The haploid number is the number of chromosomes in a haploid cell.  23.  Makes sense, right?
But it is also the number of homologous pairs in a diploid cell.  23.

►►So how can a diploid cell have a haploid number?  A diploid cell has homologous pairs, but a haploid cell does not have any pairs.  So how can this be?
►It's like saying there are 46 people at the party, and 23 couples.  But 23 is also the number of boys.

This is not a haploid cell, but a haploid number.  A haploid number is the number of chromosomes represented by one chromosome from each pair in the organism.  So in a human haploid cell, there is only one chromosome from each pair, equaling 23; in a human diploid cell, one chromosome from each pair will still be 23.
(Thanks to the teachers at Apologia for being willing to email me several times until my brain finally got it!)


(6) p. 213-218a, Meiosis: The Cellular Basis of Sexual Reproduction
The purpose of meiosis is for sexual reproduction.  
It is the process by which a diploid cell forms a haploid cell called a gamete (eggs and sperm are gametes).

►Watch this video of Meiosis.  Click Animation.
[If you need to, press your F11 key to make the screen larger. Sometimes clicking F11 while in a different tab works better.]

--After watching the animation, click Tutorials at the bottom.
--Below that, 5 Interactive Tutorials are listed:   
Homologous Chromosomes, Meiosis I, Meiosis II, Comparing Mitosis and Meiosis, and Summary.
Mastering the first 4 are important.
►Use this comparison printable Study Sheet for Meiosis.  You will be able to fill this in after you complete Comparing Mitosis and Meiosis, but you should do all the first 4 Interactive Tutorials to be able to understand this.
►Watch this video to be able to answer the last question about Recombination.
This is why parents can have children that look so different from one another.
These haploid cells (that were produced by diploid cells) will have only 23 chromosomes (one from each pair), and are the cells that determine sex.  These are called gametes.  Gametes are the eggs and sperm.
After an egg and sperm unite, the resulting cell is called a zygote.  The zygote now is a diploid cell with 46 chromosomes (or 23 homologous chromosome pairs).
The zygote will multiply again and again by mitosis (not meiosis), forming a baby.

After you understand meiosis, here is a fun video to watch.  =)
The DNA first coils up into chromosomes (see image or Fig. 7.4, p. 205).


(7) p. 218-222, Viruses
Learn The Lytic Pathway (or Lytic Cycle) for cells in general, (not just the one for bacteria in Fig. 7.14).
►Read the paragraph on p. 219 that ends in "This process is called the lytic (lih' tik) pathway."
Sorry about the green flashes, etc.  This video must have a virus, hehe!

The virus transcribes and translates.  Transcription and Translation.
This is how the cell reproduces the virus.  The virus cannot reproduce itself.

Tuesday, November 9, 2010

Apologia Biology, Module 6, The Cell

Animal Cell Pizza!
The Secretion Vesicle looks like someone took a bite, haha!  =)
Quizlet Vocabulary Game, M6, part 1
Quizlet Vocabulary Game, M6, part 2
Quizlet Vocabulary Game, M6 
M6 Recap Blog Post at Sahm-I-Am
Read Julie's Tip for learning the vocabulary.

Go to at least one of these links each day to study the organelles you are learning. 
♦ Centre of the Cell  Watch the moving parts of cells.  Click on the white circle connected to an organelle to see the name and function.  Very simple and easy to understand.  Does not include all the organelles, tho.
♦ Cells Alive!  See if you can recognize and name all the organelles.  Read the organelles at the bottom and see if you can find them in the picture.  Hover your mouse over an organelle to see if you are correct.
♦ Virtual 3D Cell  Hover your mouse over the 3D cell.  Click on the organelles you are learning for more information and a closer view.  Some can zoom or rotate.  Some will open for you to see inside. If it says click next, click one of the arrows on the left. ►◄ 

Games, etc:
Cell Quiz
Plant cell
Plant and animal cells
♦ Words to Plant and Animal cell songs.

Look here for examples of Incredible, Edible Cells:
2008, Michelle's class at Applie's Place
2009, Michelle's class at Applie's Place
2010, Michelle's class at Applie's Place
2010, Julie's class at Mindful Ramblings (scroll down.  You can click on the picture to enlarge.)
I also like this cake made from a soccer ball pan and fondant.

(1) p. 161-163, Cellular Functions
There are 11 functions of plant and animal cells listed in this first section of Module 6.  Three of the functions aren't listed as a vocabulary word, but they are in bold print in the text.
Some functions both plant and animal cells perform; other functions are specific to only animal or only plant cells.  

I couldn't find a video that covered this very well, so here is an overview of cells. 


(2) p. 164-166a, Cell Structure... The Cell Wall... The Plasma Membrane
Near the bottom of p. 164, it says, "...cells are small for a reason... the volume of materials in a cell increases with the cube of the radius of the cell."  After a brief introduction, he explains why cells are small and will not keep growing larger and larger.

Plasma Membrane


(3) p. 166-167a, The Cytoplasm

►Watch this short video about the cytoplasm.  Scroll down a bit.

Cytoplasmic Streaming (remember, cyto means cell) is the movement of the cell's cytoplasm, transporting things such as nutrients, proteins, etc.  
You will soon learn about active transport and passive transport.   

Here is cytoplasmic streaming in the chloroplasts in a leaf.  You don't need to watch it all.


(4) p. 167-174, various parts of a cell

This video covers several organelles in the cell, but not in the order they are in your textbook.
p. 167-168, and 171
Endoplasmic Reticulum/ER, Ribosomes, Gogi Body (same as Gogi Apparatus)
Lysosomes, Mitochondrian 

p. 169
Vacuoles and Vesicles

Also listed in your text is the vocabulary word Phagocytosis.
Phago- means to eat or engulf; cyto- or means cell.
This should help you remember what a Phagocytic vacuole is as well.  (The ic on -cytic is the adjective part that means having to do w/ cells)
Read your definitions and study all your diagrams!  =)

p. 172-173
Centrioles and Cytoskeleton
Oddly, I found a strange video that goes over the 2 remaining organelles the above videos didn't cover.

Plant Cell

► Play this Cell Quiz.  Play it several times if you like.


(5) p. 175-176Experiment 6.1, Cell Structure I  
My Class:  Look here at onion cells (the first 3 pics), and on the blank, unlined lab sheet I gave you, draw each magnification.  Label which magnification each picture is. 


(6) p. 176-180, How Substances Travel In and Out of Cells

Before watching these videos, study Figure 6.7, The Construction of the Plasma Membrane.

Remember, lipids are fats, and repel water.
Part of a phospholipid (see image) is attracted to water, and part is repelled by water.  This causes the phospholipids to arrange in such a way as to make up the plasma membrane of a cell.

The Plasma Membrane

Passive Transport and Active Transport.
Active Transport requires energy, called ATP.

Animal Cell
Near the end, see the centrioles. In the Animal Cell Pizza picture at the top of this post, we used pieces of celery to represent the centrioles.

Examples of Passive Transport
►Remember diffusion and osmosis - scroll down and read the part that is below the pictures of eggs.
Remember, osmosis occurs in an attempt to "even up" the concentration or dilution of solutes in the water on both sides of a semi-permeable membrane, such as the membrane of a raw egg or of a cell.

Watch three videos:  

(a) Isotonic solution - a cell is said to be in an isotonic solution when the amount of concentration in the cell is equal to amount of concentration that is in the solution the cell is in.
Your kidneys get rid of excess solutes in the blood to ensure that the bloodstream stays isotonic with your red blood cells.  
Evolution?  I think not.  Or you'd be dead before you "adapted" to everything that is necessary to live!

(b) Hypertonic solution - the amount of concentration in the solution (that the cell is in) is greater than the amount of concentration that is in the cell itself. This causes the cell to lose water because the cell's water is drawn toward the higher concentration that is outside of the cell.
This causes the cell to shrink in on itself or implode (opposite of explode).
This collapse of a walled cell's cytoplasm (remember, cyto means cell) due to a lack of water is called plasmolysis  
This is why when a person drinks ocean water, the water in their cells will move out of the cells by osmosis to the higher concentrated salt water, which can be fatal.

(c) Hypotonic solution - the amount of concentration in the solution (that the cell is in) is less than the amount of concentration that is in the cell itself.  This causes the cell to absorb more water and swell up due to osmosis, and causes the cell to explode.
This rupturing of a cell due to excess internal pressure is called cytolysis.  (remember, cyto means cell)  

(a) Red blood cells in an isotonic environment

(b) Red blood cells in a hypertonic solution causes plasmolysis (the cell implodes and shrivels)

(c) Red blood cells in a hypotonic solution causes cytolosis (the cell explodes)


(7) Experiment 6.2, Cell Structure II  p. 181-182 

My Class:  
We don't have a microscope, so use these links that show a small cut out piece of a leaf, with its layers.
Leaf 1, Leaf 2, Leaf 3

On the blank lab sheet you were given, draw a diagram of a cut view of a leaf.  You may use different parts from either of the diagrams at the links.

►►Label these parts:
xylem, phloem, and vein, | stoma and guard cells, | and the chloroplasts.
•The chloroplasts are not labeled in the above diagrams of the cut leaves.  However, I bet you can find them.  They are green, and they are in the palisade layer.  The little dots are the chlorophyll that is in the chloroplasts.

1-6. On the back of your page or on a separate lab report page with lines, briefly explain (in your own words, not mine that I typed here) what each of those ↑ 6 parts do.
7. Also explain what plasmolysis does.
8. From the videos above, tell what word is the opposite of plasmolysis?

•Xylem (zy' lum) and phloem (flow' um) tubes are together in a vein
•The xylem tubes transport water and minerals (that are taken in by the roots) up throughout the plant.
•The plant makes glucose in the chloroplasts that are in the leaves.  The phloem tubes then transport the glucose down to all parts of the plant.

How to remember which way xylem and phloem flow.

•The stomata (sing. stoma) are openings on leaves that allow carbon dioxide to enter the plant and oxygen to exit the plant, as well as the release of water vapor. 
•Pairs of guard cells on the leaf open and close the stoma to control this process.  They open or close depending on if they are full of water or not.  Remember from p. 169 that turgor pressure from being full of water helps keep a plant rigid.  The same applies to guard cells.

This celery regains turgor pressure as the vacuoles in each of its plant cells fill with water.

Stomata on leaves are usually open during the day during photosynthesis, and closed at night.  Sometimes stomata close during the day if it is too hot and the plant starts losing too much moisture.  At these times, photosynthesis ceases.
►See image of guard cells when they are open and when they are closed.

Remember the video that is posted above of Cytoplasmic Streaming.  (Sometimes putting a leaf in warm bright light will cause the streaming to begin.)
Adding salt water (high concentration of solute) will cause osmosis, and the cells will begin to lose their cytoplasm.  This is called plasmolysis. (animation) When you see a plant wilt, it is beginning to experience plasmolysis, though not from salt water; just from a lack of water.
Watering a plant can reverse plasmolysis, and the plant will once again "stand up" due to turgor pressure.
In this video, you can see the process of plasmolysis begin around 40 seconds.


(8) p. 182-185, How Cells Get their Energy

►An excellent animation of Cellular Respiration.
Click on The Big Picture, then the play icon.
When you watch each of the steps of Cellular Respiration, there are various checkpoints to see what you remember.
This animation combines Step 2 and 3 below↓ into the Krebs Cycle.
These animations are not exactly like Apologia Biology, but it will help you understand the process.

--The purpose of Cellular Respiration is to make energy.  Your cells constantly make energy through a series of steps, divided into stages.  There are four stages of Cellular Respiration, and in each stage there are molecules that react together in a chemical reaction that produce other molecules as products. 
--In a chemical formula, the reactants (the molecules that react together) are on the left of the arrow, and the products (the molecules that are produced from the reaction) are on the right of the → arrow.
--In each stage of cellular respiration, some products from the previous stage (or more than one previous stage) are now used as reactants to make new products in the current stage.

Like factories make ingredients, and a baker might take only some of those ingredients to now bake bread, then you might take only 2 slices of that bread and make a sandwich. But the leftovers are still there in the end.
Watch for which products are used as reactants in the next stage(s), and which products are "saved" to be used in a later stage.

Aerobic cellular respiration is the converting of glucose into a usable form of energy.  This energy is stored as adenosine triphosphate, or ATP.  It is called aerobic cellular respiration because this means of cellular respiration uses oxygen.
The general equation for cellular respiration is:
1 glucose molecule + 6 oxygen molecules (after a very complicated series of steps) will produce → 
6 carbon dioxide molecules, 6 water molecules, and about 36 molecules of ATP (energy).
C6H12O6 + 6O2 → 6CO26H2O + energy
Do you recognize these molecules?  This is the reverse of photosynthesis!
Now we will discuss a little about those very complicated steps.  =)

The first stage of cellular respiration is (1) glycolysis, or the breaking down of glucose. This takes place in the cytoplasm.
The other three stages take place in the mitochondrion.
They are (2) the formation of acetyl coenzyme A, (3) the Krebs cycle, and (4) the electron transport system.

The purpose of cellular respiration is to get energy, but right from the beginning, the first stage uses 2 ATP's as a "push" to get going, the activation energy.  This is like an investment because in the end, about 36 ATP's are finally produced..

Stage 1 Glycolysis 
A monosaccharide molecule goes into the cytoplasm where enzymes catalyze (speed up) a reaction that causes the monosaccharide molecule to lose some hydrogen atoms and convert one molecule of glucose into 2 molecules of pyruvic acid (sometimes called pyruvates) with some hydrogen (H) left in the product as well.  Two ATP's are used to get this process started.  It also produces 2 more ATP's (energy).
C6H12O6 → 2C3H4O3 + 4H + energy
  glucose        pyruvic acid               2ATP's

Stage 2:  The formation of acetyl coenzyme A
The 2 molecules of pyruvic acid head to a mitochondrion.  As they cross into the mitochondrion, the pyruvic acid molecules are broken down, freeing carbon dioxide and hydrogen (which are products in the formula below).  Then something new is introduced.  Two proteins (called coenzyme A) attach to the remains of the pyruvic acid, forming 2 acetyl coenzyme A's.  (The - sign in the formula below does not mean minus.  It means it is attached.)  Two other products of this chemical reaction are carbon dioxide and hydrogen.  This stage is sometimes called the "oxidation of pyruvic acid."
The coenzyme A's are neither used up nor produced.  They simply cycle through the stages of respiration.
No additional ATP is formed in this stage.
2C3H4O3 + 2(coenzyme A) → 2C2H3O-(coenzyme A) + 2CO2 + 2H
pyruvic acid         a protein                        acetyl coenzyme A

Stage 3:  The Krebs Cycle
This is the first stage that uses oxygen.  The 2 molecules of acetyl coenzyme A react with oxygen to make hydrogen, carbon dioxide, and coenzyme A again.  This is actually a summary of a very long, complicated procedure (like this explanation isn't complicated?!?)  =)  Two ATP's are also produced. 
2C2H3O-(coenzyme A) + 3O2 → 6H + 4CO2 + 2(coenzyme A) + energy 
      acetyl coenzyme A                                                               proteins              2ATP's
Stage 4:  The electron transport system
The hydrogen from the previous three stages reacts with oxygen to make water and energy. This stage produces the most energy of all four stages.  Thirty-two ATP's, for a total of 36.
12H + 3O2 → 6H2O + energy
                                          32 ATP's

In each stage, you need to look at the product and see what of that is used in the next stage, and what is not used.
•In stage 1, glycolysis, the products are 2C3H4O3 (pyruvic acid), 4H (hydrogen), and 2ATP's (energy).
The 2C3H4O3 is used as a reactant in the next stage, but the 4H and 2ATP's are not. (so we "save" those in our mind)
•In stage 2, the formation of acetyl coenzyme A, the products are acetyl coenzyme A, 2H and 2CO2 (carbon dioxide).
The acetyl coenzyme A is used as a reactant in the next stage, but the hydrogen and carbon dioxide are not.  (add those to your total so far)
[note here that in stage 2, two coenzyme A's are used, and in stage 3, two coenzyme A's are produced.  The net result is that nothing changed.  Two coenzyme A's will be produced and used over and over again with each full cycle of cellular respiration.]
•In stage 3, the Kreb's cycle, excluding the coenzyme A's, the products are 6H, 4CO2, and 2ATP's.  The 6H (as well as the previously produced 4H and 2H) will now be used as reactants in the last stage, and 3O2 (oxygen molecules) are also added in as reactants in the formula.  The 4CO2 and 2ATP's are not used as reactants in the last stage.
•In stage 4, the electron transport system, all the 12H are used as well as 3 more O2. 6H2O (water molecules) are left, and 32ATP's are produced.

We started with one glucose molecule, and along the way added 3 oxygen molecules, then 3 more.
Here is total what was used, and what is left:
C6H12O6 + 6O2 → 6CO26H2O + energy (36ATP's)
This is cellular respiration, and the formula is the opposite of photosynthesis.
In cellular respiration, we use glucose and oxygen in our bodies.  We get carbon dioxide (which we breathe out as a waste product), water, and energy.  Our catalyst to speed up this process is enzymes.
A plant uses the energy from the sun, carbon dioxide, and water to produce glucose for itself, and gives off its waste product of oxygen.  Remember, the catalyst for plants is chlorophyll.
There is a video on the MMCD, but you really need to study your textbook first, and what I have written here.


(9) p. 186-189 ATP and ADP
Adenosine Triphospate (one adenosine and three phosphates)
Adenosine Diphosphate (one adenosine and two phosphates)

Synthesized means produced.
Making ATP from ADP in the Mitochondrion

►Please watch this very thorough video of How Cells Obtain Energy.