Biology 101, Chapter 7, The 6th Day – Biology History, Cells, Genetics [post 2/3]

We made DNA! =)

Blog Posts for Chapter 7:
• Post 1/3 - Cells
• Post 2/3 - DNA
• Post 3/3 - Genetics

In addition to Biology 101:
• Apologia Biology Exp 7.1, DNA Extraction
Here are instructions if you don't have an Apologia Biology book, and a video.
• Have Your DNA and Eat it Too! (click the pdf links), Our class has done this twice (diff students), so even tho I have 3 new kids, I have 3 who have already done this so we aren't doing it this year.

Other Study Links
• DNA Extraction Virtual Lab.

2. DNA

Four criteria for life:
If something fails to meet even ONE of these, it is not alive.

1. All life forms contain DNA.
2. All life forms can take energy from their surroundings and convert it to usable energy for themselves.
3. All life forms can sense and respond to changes.
4. All life forms reproduce.

DNA - deoxyribonucleic acid, Hear pronunciation.  Click on the little speaker.


Apologia Biology Experiment 7.1, DNA Extraction

My previous biology class did this experiment about 3½ years ago.  (See our results)
If you don't have an Apologia Biology book, here are instructions (with explanations of why), and a video below.  (I always like to look at several sources to get a good idea of how and why to do things.)
(1) Pea DNA Extraction


►And just for fun, you can try this DNA Extraction Virtual Lab.
►Read how another blogger's class did this experiment.  Her posts are always fun to read! =)

Of course this DNA is in clumps, or we would never be able to see anything.
In fact, it takes a powerful microscope to even be able to see the chromosomes, which are long strands of DNA in the nucleus that are coiled up and compacted.  See image. (source)

(2) DNA Structure
Note that A and T are linked together, and C and G are linked together.  These letters represent the names for the nucleuotides in DNA.  In DNA, Adenine always links to Thymine, and Cytosine always links to Guanine.
Apples in a Tree, Car in the Garage.  A-T, C-G




How proteins are made from DNA
All the writing below and three videos make up this section.

Part 1: Transcription of DNA
"Synthesis" means the making of or production.  
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. 

(3) Transcription and Translation Overview
A polypeptide is a chain of amino acids.  Poly means many.



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.
(Apples in a Tree, Car in the Garage.  A-T, C-G)
►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)


►►DNA vs RNA image (source)◄◄ Read below↓

--There are two nucleotides that are different - uracil (in RNA), and thymine (in DNA).
Uracil in RNA will match up to adenine in DNA.  
Adenine in RNA will match up to thymine in DNA, so A-U, and A-T.
(For RNA, remember Apples Under the tree) 

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 (source).
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. 


Part 2: Translation of DNA
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.

Transfer RNA strands will link to a messenger RNA strand on a ribosome in order to make a protein chain.
Here is how:
The tRNA is already bonded to an amino acid, but only a certain type of amino acid will bond to a certain sequence of three nucleotides in the mRNA.
For example, if the anticodon (a three-nucleotide sequence on tRNA) is made up of guanine, adenine, and adenine, the tRNA is bonded to the amino acid leucine.  This anticodon will only link to a portion of mRNA that has a codon with the sequence of cytosine, uracil, and uracil.  
Each codon (3-nucleotide sequence) on mRNA attracts a specific amino acid. 
So then the tRNA links up to the portion of mRNA that will accept the anticodon that is on the tRNA.

After the tRNA links up to the mRNA, the amino acids on each of the subsequent tRNA anticodons bind together one by one to make a protein. 
►The chain of amino acids that make a protein is called a polypeptide. (poly- means many)

(4) From RNA to Protein Synthesis - how proteins are made



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).
(5) Protein Synthesis: Translation Process



And that is how proteins are made from DNA

(6) DNA Double Helix
How one man realizes through studying DNA that only God could have made all this! =)
"Without DNA there is no self-replication, but without self-replication, there is no natural selection. So you can’t use natural selection to explain the origin of DNA without assuming the existence of the very thing you’re trying to explain!"

Two Types of Cell Reproduction:

A) Mitosis - asexual  reproduction of cells

Mitosis is the growth of new cells, either to replace damaged cells like when you have scraped your arm, or for a growing child, or an unborn baby as it grows.

The replicated cells are identical.  Skin cells replicate skin cells; muscle cells replicate muscle cells, etc.

This is asexual (nonsexual) reproduction.

(7) The Cell Cycle and Cancer - how cells multiply by Mitosis

(8) Mitosis:  The Amazing Cell Process that uses Division to Multiply!

(9) How DNA is Packaged  After DNA that is in the nucleus duplicates itself into identical sister chromatids, then it coils up into chromosomes. The X shape you may be familiar with.

(10) Mitosis  He says, "having already replicated..." Because before Mitosis begins, the DNA that is in the nucleus must duplicate itself into identical sister chromatids, then coil up into chromosomes.

(11) Mitosis Animation - also G1, S, and G2 that occur during Interphase.

B) Meiosis - the purpose of meiosis is sexual reproduction. 

-All living things have different numbers of chromosomes.  An onion has 16 chromosomes in each cell; a horse has 64 in each cell; and a carp has 104 in each cell.

--Humans have 46 chromosomes in each cell.  The chromosomes are in pairs, so humans have 23 pairs in each cell. 

Meiosis:  

The cool process of meiosis is why all humans do not look alike.  =)

Each pair of chromosomes determines many different traits (hair color, hair texture, curly, straight, etc, just to name a few).  There are hundreds of genes on each chromosome!  When parents have children, they contribute one chromosome from each pair, which "cross over" with each other to form new combinations.  The results of crossing over are random, and give more possibilities for each trait a child will have.  Since there are many, many kinds of traits, the possibility of having a child who doesn't look exactly like a parent is great.

Things to know:

--When a cell's chromosomes come in pairs, it is called a diploid cell.  XX, XX, etc.

--Cells with chromosomes that are not 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.

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 that is in a pair is attached to its sister chromatid (its duplicated chromosome), 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

Mitosis results in 2  identical diploid daughter cells, 
and meiosis results in 4 genetically different haploid cells.

►►These videos only show a few pairs of chromosomes in the cells, but know that there are 23 pairs, all exchanging information to produce varied traits.

(12) Meiosis - This is why parents can have children who look so different from one another. 

(13) Difference Between Mitosis and Meiosis

Mitosis results in 2 identical diploid daughter cells, 

and meiosis results in 4 genetically different haploid cells.

So what happens to the extra haploid cells?  In females, randomly, one of the gametes (eggs) takes up most of the cytoplasm and organelles.  As a result, what gets produced are 3 tiny gametes and one large gamete called the egg.  Only the large one will function properly, and that is the one that gets successfully fertilized by the male gamete (sperm).  The others, if fertilized, will quickly degenerate and die.

►The haploid sperm cell and haploid egg cell fuse to form a diploid cell with 23 pairs of chromosomes, totaling 46.

►This diploid cell, now called the zygote, will begin to multiply and produce many cells by mitosis, forming a baby.  =)

(14) Phases of Meiosis  2²³ = 8,388,608 possibilities! WOW!

After you understand meiosis, here is a fun video to watch.  =)

The DNA first coils up into chromosomes (see image).

(15) Meiosis Square Dance

Biology 101, Chapter 7, The 6th Day – Biology History, Cells, Genetics [post 1/3]

I really wish we had more time to cover this chapter!  It is huge, with a lot of my favorite things! =)
So there are 3 blog posts total, since they kind of divided themselves up that way.  =)
And since the moms agreed we were too busy to fit in another class, I had the kids to go ahead and be studying up on some stuff during spring break.  They were thrilled, lol.  ; )

But I am adding stuff in, and we do take 4 weeks per chapter instead of 3, so that and the pre-studying will have to do.  =)
I'd advise 6 weeks if you have it.  ; )

Animal Cell Pizza!
The Secretion Vesicle looks like someone took a bite, lol! =)

Blog Posts for Chapter 7:
• Post 1/3 - Cells
• Post 2/3 - DNA
• Post 3/3 - Genetics

In addition to Biology 101:
• Fun Cell Activity (teacher cheat sheet included) 1 point for placement, 1 point for naming the organelle, 1 point for giving the function.
Games like this give a jump start and make studying easier when they get home.
• Animal Cell Pizza and Plant Cell Cake - we will not be doing these this year, but here is the link.
• Google for more edible cell ideas.

Other Study Links
• Animal Cell coloring page
• Plant Cell coloring page
• Plant and Animal Cell Venn diagram (found here) - I made this blank one for our class.
• Comparison of plant and animal cells.  Click on an organelle name to jump to its description.  Use your back arrow to jump back to the cell.
A green square      beside the name of an organelle's description means that the organelle is typically only found in plant cells.  A red square      indicates organelles that are typically in animal cells.
• Interactive Cell - watch the motion of organelles in a cell.  Click the organelle labels to read the name of the organelle.  Read the description in the box on the side.
Not all organelles are pictured, but can you tell if this is a plant cell or an animal cell?  
•Interactive, animated tutorial w/ 6 questions at the end: From Cells to Systems.  Subtitles if needed.
• Really cool - Comparing Cell Size - use the slider below the pic to slowly zoom in.
• Read Potential Effects of Drinking Saltwater
• Another, super cute video about Osmosis, by the Amoeba Sisters! =)  Accompanying worksheet.

1. Cells

a. History

(1) The Wacky History of Cell Theory







b. The Cell

From cells, to tissues, to organs, to systems:

1. Blood cells, skin cells, brain cells, muscle cells... lots of types of cells!  There are hundreds of trillions of cells that make up your entire body, and there are all kinds.
2. Cells make up tissues.  A group of the same type of cell is called tissue.   Muscles cells form muscle tissue.
3. Tissues make up organs.  An important organ is your heart, and is made up of muscle and other tissues.  The brain and lungs are other important organs made up of tissues.
4. Groups of organs make up systems (like the digestive system, skeletal system, respiratory system, etc).

►Interactive, animated tutorial: From Cells to Systems. Turn on the subtitles if needed.
See if you can get all 6 questions right at the end.  You can re-do the tutorial as many times as you like.

►Really cool:  Comparing Cell Size - Use the slider below the picture to slowly zoom in.
Compare the size of a grain of rice to a blood cell!  Also see an atom and a water molecule at the end.
On the way, notice the amoeba, smaller than a grain of salt.
And the paramecium, (pear-uh-ME-see-um) about the size of an extremely tiny sliver of the corner of an amoeba.  When you zoom all the way back out, the paramecium disappears from view, but you can still barely see the amoeba.  Also see adenine - one of the nucleotides that make up DNA.



(2) Cell Structure and Function





(3) Nuclei, Membranes, Ribosomes, Eukaryotes, and Prokaryotes



All cells have a cell membrane (sometimes called a plasma membrane).  Think of a small balloon filled with jelly.  The membrane is the thin covering that keeps the cell together.  This cell membrane is what regulates what is allowed to be absorbed into the cell, and what goes out of the cell.
--Inside eukaryotic cells are many organelles (little organs), and these are also membrane-bound like the cell.  The DNA in eukaryotic cells is enclosed in a membrane-bound organelle called the nucleus.
--Inside prokaryotic cells is DNA, but there are no organelles, therefore no nucleus.  So the DNA can be seen all throughout the cell. 
►►►But with few exceptions, the two kingdoms that also have a cell wall are primarily kingdom Fungi and kingdom Plantae.  These need the added stiffness of a cell wall on the outside of the membrane to keep the plant or mushroom standing upright.  The material for the cell walls of these two kingdoms is quite different from one another, as you could probably guess.

All living things are made up of cells.
Some have many, many cells, and some have only one cell.  These are referred to as multi-cellular or single-cellular organisms.
The three basic kinds of cells are animal cells, plant cells, and bacteria cells.  All cells do not fit neatly into these categories as some are animal-like or plant-like. 
No matter how many cells an organism has, or which of the three basic cells an organism has, all cells are either prokaryotic cells or eukaryotic cells.

►Eukaryotic cells have organelles (or tiny organs) like a nucleus, vacuoles, and other organelles.  The nucleus holds the DNA of eukaryotic cells.
Four of the five kingdoms have eukaryotic cells. (kingdoms Protista, Fungi, Plantae, and Animalia)
►Prokaryotic cells contain no organelles.  The DNA does not have a nucleus to stay in.  Under a microscope, the DNA strands are visible throughout the cell.
Only one of the five kingdoms has prokaryotic cells, and that is kingdom Monera (bacteria).
►SEE the difference

(4) Organelle Overview





(5) Cell Organelles and their Function Animation





(6) Vacuoles-Vesicles - what is the difference?





(7) Parts of a Plant Cell - photosynthesis, xylem and phloem, and did you know that not all plant cells have chloroplasts??







c. Diffusion and Osmosis

(8) Diffusion and Osmosis (clipped bc the osmosis part got confusing) If you want to watch it, I advise doing so after watching the next few videos.





Remember the egg experiment?  That was a demonstration of osmosis.
(9) How Osmosis Works




►Another, super cute video about Osmosis, by the Amoeba Sisters! =)
--Accompanying worksheet.



(10) Osmosis Demo

(11) A Tour of the Cell - a good review

At 11:12, he is WRONG.  Some people teach that mitochondria, which can make their own DNA, were once prokaryotic bacteria that evolved.

d. The Cell Membrane

A whole section on the cell membrane?  YES!  The cell membrane is much more complex than one may realize!  How can fluid and other things flow in and out of a cell?  How can other things be kept out of the cell??  It isn't full of tiny holes as one might imagine.  Oh, no.  It is SOOO much more complex than that!
Only our Creator could have designed such a thing.
For if evolution were to make it by chance??... well... if you took a marker and wrote the ABCs on 26 index cards... how many tries do you think it would take to throw them into the air and the alphabet line up perfectly???  And if organisms needed to evolve to live... um, how could they live before they evolved.  They didn't.
So this section is pretty important.  It's important for us to know how complex God's creation is, so that we know there is absolutely no way evolution (which claims these things were done by chance!) could have done such a thing.

(12) Cell Membrane Introduction


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.




(13) Cell Membrane Overview and Fluid Mosaic Model





(14) Cell Membrane Proteins





(15) Cell Membrane Fluidity





(16) Diffusion and Osmosis in cells (and Active Transport)



► Read Potential Effects of Drinking Saltwater




(17) The Cell Membrane - a quick review

e. Cellular Respiration
How our body converts food into energy.

(18) An excellent Animation of Cellular Respiration - how our body converts food to energy.
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.

--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 (the animation above combines 2 of them), 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. 

The general chemical formula for cellular respiration is:
1 glucose molecule (from food we eat) + 6 oxygen molecules (that we breathe in) will produce  →  6 carbon dioxide molecules (that we breathe out), 6 water molecules, and about 36 molecules of ATP (energy).
     C₆H₁₂O₆ + 6O₂   →   6CO₂ +  6H₂O + energy
Do you recognize these molecules?  This is the reverse of photosynthesis!

--In each stage of cellular respiration, some products from the previous stage (or more than one previous stage) will then be 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 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.

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 (ATP), 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.

►Click if you want to read more about each step.  Scroll down to section 8, How Cells Get their Energy.
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.

Chemistry??

I've had several emails and at least one comment from people asking about chemistry, and I am very sorry, but I do not plan to post videos for chemistry.
However, here are a few links you might be able to use.  Some are for videos.

► Intro to Chemistry videos and AP Chemistry videos
(scroll to the playlist you want and click View Full Playlist)
Here is what a full playlist looks like: Intro to Chemistry: Introductory Unit.  They are not in order, but the videos are numbered.  This one is "Intro to Chemistry: 1.1: Properties of Matter (1/2)."  So that means there is also a 1.1 (2/2).

► Khan Academy Chemistry - videos "roughly covering a first-year high school or college course"

► Periodic Table of Videos - a video for each element.  I think many show the actual element. =)

► Queensland Science Teachers - looks to be simple explanations, like charts and/or bullet statements.  May be good to print out for reference for whatever topic you're on.

►Excellent video on balancing equations!!

► Periodic Table of Elements interactive online games at Jefferson Labs - practice identifying what the numbers and symbols mean on the periodic table, practice balancing equations and more.
Love this!

Here is my Pinterest Chemistry page, in case there might be a thing or two more that looks interesting.  There are a couple of pins to free chemistry curriculum.  Most things pinned here are just chemistry funnies that I found and wanted to save. =)

If kids are having trouble understanding something, it may be that they had missed a basic somewhere.  Videos, etc. can be a good refresher and/or a simple explanation that can help so much.





If I do chemistry this fall, it will be Chemistry 101 (available for purchase at ChristianBook.com), but I will only be doing it with my son and don't plan to have a class.  I didn't take chemistry in highschool, so this will all be new to me!  =)
If the Intro to Chemistry videos above already seem too easy for your student, then Chemistry 101 may not be for you except as a supplement for a more involved Chemistry curriculum.

My son has mild dyslexia as well as dyscalculia (has to do with math. For example, algebra problems or any problems with many steps, i.e. long division, are tedious and take lots of repetition in order to retain -- getting the steps done in order, not skipping steps, etc.), so when I heard that Chemistry 101 did not have math, I knew that even if we don't end up doing it for a full credit, he will enjoy this.


One question I have been asked several times is What will you be doing with Chemistry 101?

If Chemistry 101 is like Biology 101, I would say each DVD segment probably gives the basics, an overview, etc, to get a good idea of the chapter topic.  I would watch the Chemistry 101 DVD, then use what resources I had to delve in further where needed.
There are 19 video segments in Chemistry 101. =)  Biology 101 only had nine.

If you use Chemistry 101 as your base, be prepared to work finding materials to accompany the program.  (See sample assignments.)  The above links can give you a start.
We will be substituting some of the assignments with other things I find.


Besides the above video links, etc., my indefinite plans so far...

I want to get Apologia's elementary Exploring Creation with Chemistry and Physics (sample pages) as well as their high school Chemistry.  I'm sure I will be doing some of their experiments.  =)
Also on my list are John Hudson Tiner's books Exploring the World of Chemistry [also available as pdf download] and Exploring the World of Physics [also available as pdf download].
I also want Physics 101!  We probably will just watch the DVDs sometime. =)
I just really want them all because I just love science and books so much! =)



Just a little extra for beginners.  Watch these videos in order.

1.  How to read an element on the periodic table - protons have a postive charge, and electrons have a negative charge, so there will be the same number of each to cancel each other out.

The protons and neutrons (neutral charge) are together in the nucleus, and added together they make up the atomic weight, that when rounded, is called the mass number.
If the mass number is 15 and there are 7 protons, then there are 8 neutrons.  Also you will know there are 7 electrons to match the number of protons.

2.  Atoms and the Periodic Table - more info about what all those numbers and symbols mean

There is a maximum number of electrons that can fit in each "shell" or "ring" of an atom.  

The first shell will hold 2 electrons, the second will hold up to 8, and so on... When one shell is full, any electrons left goes to the next shell in order, even if there is only 1 left.  So it could be 2, 8, 1, if that's all the electrons there are.  Elements that have 8 electrons in their outermost shell are more stable than those with fewer. The electrons in the outer shell are called valence electrons.

Now practice what you've learned so far.  =)

3.  A Tour of the Periodic Table - the groups, periods, how it is arranged and why.

Atoms whose outer shells aren't full love to link up with other atoms whose number of valence electrons will make both their outer shells full.  Then these linked atoms are called a molecule.  Example H2O.

Atoms whose outer shells (valence shells) are full are more stable.  

4.  A Beginner's Guide to Balancing Equations - after watching, go practice! =)


►The practice links above are from Jefferson Labs.