Mitosisssss

So like actually all we've done the last few classes is mitosis. Basically what it is is cell replication so that cells can divide and make more and more and more! Cells are usually in interphase, where they go through 3 stages: G1, S (DNA replication), and G2 (organelle doubling). Next it goes a little something like this!

Prophase: Chromatin condenses and the nuclear membrane disappears.
Prometaphase: Chromatin starts to move as the spindle gets its crap together (by that I mean it gets fully organized haha).
Metaphase: All the chromatin lines up in the middle.
Anaphase: The chromatin is split apart to the opposite sides of the cell.
Telophase: Two nuclear membranes are formed around the chromatin.
Cytokinesis: The two new cells are pinched apart and free to live their lives!

Real life mitosis that we saw in class!! 

Your Inner Fish Chapter 6

Embryology is the study of embryos, or eggs, before they become fully formed animals.  When eggs are fertilized, they begin to form 3 germ layers, shown above.  These layers form literally everything in the entire body, whether it be a fish body or a human body.  The endoderm develops the digestive system and lungs, the mesoderm skeletal and muscular features, as well as blood, and the ectoderm develops skin an the nervous system.    This development is controlled by the Operator works together with Hox genes to regulate the normal arrangement of organs and the creation of the correct amount, unlike flies with mutated Hox genes growing feet from their head and such.

 However, knowledge about the Operator was nor really acquired until the 90s, and it fell in and out of favor since its discovery, much like Justin Bieber.  Moved around Operators can result in organisms with two sets of organs, and switched germ layers could mean a whole host of developmental differences more the embryo.  Embryology provides insight into the arrangement of many animals that comes from our evolutionary past, and more similarities than differences between man and beast.

Pedigree

I would like to start with my favorite pedigree:

Basically pedigrees are just a family tree with genetic information on them so that traits or diseases can be tracked and predicted.  There's a whole bunch of symbols that mean a lot of things (most referring to incest) and are kind of confusing, but for the most part pedigrees are pretty basic.  Look at the one above, it denotes people with hemophilia, people who are carriers, and family relations.  Pretty simple huh? Then all you have to do is label generations and you're good to go! (Oh also you should probably find out if it is autosomal or sex-linked, that's pretty important too, but you can find that out by seeing how many males have it opposed to how many females have it. In this pedigree hemophilia is sex-linked). Well, that's all there is to it!

I have a test next class, so wish me luck! (I'll sorely need it)   

Break break break!

So, as all teenagers do at 1 AM, I was watching this really cool YouTube video and though it's a little irrelevant at points, the beginning of it has to do with what we're doing in class and it's just really interesting and I figured maybe someone would appreciate it!
http://www.youtube.com/watch?v=BhtgINeaJWg
Enjoy my 50th cousins! (that'll make a lot more sense if you watch the video haha)

When Genetics Get Special

Epistasis: Two different genes work together in harmony to create on phenotype. For example, in labs the genes for melanin production (B for black and b for brown) and deposition (E for deposition and e for no deposition) both help determine what color the lab will be (black, chocolate, or yellow). Black labs are heterozygous or homozygous dominant for both.  Chocolate labs are homozygous recessive for production but heterozygous or homozygous dominant for deposition.  Yellow labs just need to be homozygous recessive for deposition.  With that, you can figure out the genotypes for these dogs and the ratios of breeding and such.

Incomplete dominance: Both alleles in a heterozygous organism may be expressed in the phenotype. Examples include palomino horses and tortoiseshell cats, where having both alleles will make them a new color instead of the color they would be homozygous for either allele (tortoiseshell instead of brown or black)

Codominance: A single gene has more than one dominant allele.  For example, in blood type both types A and B are dominant over type O.  So if you had AO, you would just be type A.  However, if you have both type A and B, you would have type AB blood.  Simple as that.

Sex-linked: A gene is carried only on the x-chromosome, so males are more likely to get the disorder because they only have one X.  An example is colorblindness, which is rare in females but very common in males.  Females are normally only the carriers.

Dihybrids!

So you know that easy peasy Punnett Square thing? Yeah, it gets harder. You can do it with two different traits, for example coat color and walking style.  So you could have a cross between something like CcWW x CCww and have to work it out. There are two ways to do this:
1. Huge, obnoxious Punnett Square: make a large Punnett square with each allele at the top of a column/end of a row, and then do it like you normally would.
2. Make a Punnett square for coat color and one for walking style.  Then multiply together your genotypic or phenotypic ratios (for example, here all of them would have the phenotype for big C, so 4/4, and 3/4 of them would have the genotype CC).  If you wanted to know how many of them had the phenotypes for C and W, then you would do 4/4*4/4 and get 16/16. Okay, bad example.  But still, it's actually pretty simple once you get the hang of it, although it is a lot of work (but what isn't?!)

Mendelian Genetics

Can I call him the mad monk? I mean, I know that's Rasputin but I just like the ring of it.
Anywho, basic Mendelian Genetics involve just a bunch of Punnett Squares, that look like this:

So the mom goes on the top and the dad goes on the side.  Lowercase letters are recessive and uppercase letters are dominant, so you only need one capital letter (dominant allele) to see that trait, but you need two lowercase letters (recessive alleles) to see the recessive trait.  It's actually really simple (I learned it in the 7th grade!). That's all for this exciting post, I promise the next one will be more complicated/exciting!

SNORKS

Today in class we had to take a strand of DNA, transcribe it to mRNA, and then determine what traits our snork would have based on the amino acids that the RNA coded for. We had Snicker Snork, and it came out looking a little...demonic.
But even before we could get to this project, we had to understand protein synthesis, which is how this DNA became visible traits. If you're not quite sure about how that works, here's a quick review.
1 TRANSCRIPTION:
Starting at the promoter (or TATA box in eukaryotes), DNA is unzipped and filled in with RNA polymerase.  This RNA polymerase is single-stranded so it can get out of the nucleus, but it's not quite ready yet.
2 RNA PROCESSING:
This only happens in eukaryotes, but the RNA is fitted with a G cap to protect it and a poly-A tail to stop enzymes in the cytoplasm from digesting any coding nucleotides.
3 TRANSLATION
rRNA in the ribosome. The ribosome reads the mRNA 5'-3' while accepting amino acids from the tRNA, creating a polypeptide chain, and releasing the tRNA. You go ribosome! Also, the tRNA has anticodons which correspond to the codons of mRNA, or groups of 3 nitrogen bases that code for a specific amino acid.
All this out of a little demonic picture. DNA really is pretty cool when you think about it (otherwise it's just confusing!)

ITS GONNA TAKE OVER THE WORLD

So we played around with some E. coli for our lab and added pGLO genes to it.  These genes made it resistant to ampicillin, an antibiotic, and glow under a UV light.  Well, sometimes glow under a UV light.  Since that gene was located behind the arabinose operon, which is inducible, arabinose is needed to be able to code for that protein. Fun, huh? With that sugar, our little bacteria colonies could glow in the dark and not die, so they're gonna take over the world and start a pandemic and wait no, we killed them.  Anyway, they were really cool and I think I get the operon system now! Protein synthesis, that's another story (see awful quiz where I got a 2/10).
But there is so much more on this lab, and it can be found in this huge, comprehensive lab report right here!

Explain! Those! Pictures!

That was supposed to be read in a cheesy game show voice.

The coloration in this flower is due to a mutation in its genes, resulting in its beautiful two colors.  This change in genetics could be due to radiation caused by scientists, or it could be transposons (jumping genes) that worked their way into it's DNA.  Either way, something (from nature to lab experiments) altered this flower's genetics to make it purple and white.

We all have a sonic hedgehog gene that affects the way our limbs grow and how correct they are.  An error with this gene can cause a child to be born with too many fingers, as this baby obviously was.

Survival of the Sickest Chapter 3 CRAP NO

This chapter redefined skin tone and medical conditions that go hand and hand with it and sun exposure
-light skin tone developed in places with limited access to sunlight so they can more easily absorb vitamin D
-speaking of vitamin D, it's super important in helping human survival, from contributing to baby development to cell functions in adults
-cholesterol? yeah, that isn't bad for you like they make it seem, instead it's made and given by the sun, but Northern Europeans and some Africans have too much of it
-folic acid, also absorbed from the sun, is essential to proper cell division and normal body functions
-Asians tend to have the Asian flush when drinking alcohol, as opposed to Europeans who drank alcohol because it was safer than water so they evolved to better break it down
-some diseases may affect certain racial groups more than others because they adapted to different things
Well, here's the actually really fascinating micro-summary of chapter 3. Good night!
SO this post was supposed to be on Your Inner Fish. Shoot. So I read the wrong thing. Oops.
Here's Your Inner Fish.
-the ZPA, which can be affected by Vitamin A, keeps the pinky and the thumb where they should be and makes sure the digits are in working order
-everything on the planet has a Sonic Hedgehog gene, which was discovered because scientists were curious about limb development, so they of course tested on chickens
-it controls how limbs are created in three dimensional space and an error with it can result in more or less digits or other mutations involving arms and hands

DNA Replication W00T

So we made DNA in class. This was...pretty difficult to say the least, as it involved a lot of cutting.
Here's the gist of it though, it involves 5 pretty cool enzymes that all read 3'-5'.
HELICASE: starts at the origin of replication and unzips the DNA.
RNA PRIMASE: lays down a few RNA nucleotides at the origin of replication.
DNA POLYMERASE III: lays down DNA nucleotides and creates a lagging and leading strand.
DNA POLYMERASE I: replaces the RNA nucleotides with DNA nucleotides
LIGASE: connects all the Okazaki fragments and finishes the process!
Now imagine this: we did all these steps with paper, cutting and taping and failing. I would say we now have a much deeper appreciation for DNA though, and we definitely know what all the enzymes do!

Survival of the Sickest Chapter 6 Summary

Hey guys, here's a little rundown of the main points of this chapter!
-junk DNA, which makes up 97% of our DNA, isn't so junk after all as we msy need to mutate it in the future, also it's largely made of jumping genes, some of which are derived from viruses, who inject DNA into individual cells
-if viruses can adapt to their environments to prolong their survival, then maybe humans evolved according to their environment too, instead of just random mutations like Darwin thought
-evolutionary pressure caused jumping genes, or transposons, that add themselves to genomes without changing location
-retroviruses are made of RNA and can transcribe themselves from RNA to DNA, and they're super dangerous, like HIV
-also the story about Lamarck coming up with the theory of acquired traits was totally wrong, and was all just gossip spread about him
I know this is kinda short, but it's just what I thought were the main points of the chapter! It's pretty informational and full of a lotta good stuff, so you may want to check it out yourself!

"From Atoms to Traits" Questions!

Bonjour!
I come to you after a 10 hour tech rehearsal to bring you the answers to these really exciting questions about the article "From Atoms to Traits" (you might even get an original drawing by me! ha not so exciting). Alrighty, I've decided to put my extraneous comments in purple, just to distinguish them from my totally serious answers.
1. Explain the significance of Mendel.
Mendel was an Austrian monk who true-bred pea plants with very obvious differences.  After several generations, one trait could be passed down undiluted, meaning that it would be the same in every parent and child.  This disproved Darwin's theory that traits of parents blended together to form the traits of their offspring.  Mendel's discoveries prompted future genetic work and helped clarify the basis of evolution. (If I remember right, there were also a lot of Punnett Squares involved, but that may have just been my 7th grade biology class).
2. Draw the structure of DNA and who discovered this structure.
Watson and Crick discovered the structure of DNA, a double-helix with a backbone made of sugar and phosphate chains and held together by adenine, cytosine, thymine, and guanine. (Can we establish that Rosalind Franklin also deserves much credit for this discovery because she did a lot of the research but then died of cancer and Watson and Crick stole it all and got the Nobel Prize.  I feel so bad for her!
Also I really apologize for how bad this drawing is)

3. Explain each of the 5 examples of variations that occur to DNA and give an example of each.
-A single base pair change, or point mutation, can determine whether or not whippet dogs are slender or stocky.
-An insertion of new letters into the sequence can determine whether pea plants are wrinkled or smooth.
-A duplication of genes is responsible for some of the enhanced digestive abilities of humans compared to chimpanzees.
-An error when duplicating a base pair can determine whether pigs have spots or not.
-A change in DNA that controls where and when genes are activated created the difference between the bushy teosinte and the modern cornstalk.
4. What is evo-devo?
Evo-devo is the study of the effects of changes in important developmental genes and how they affect evolution.
5. Make a connection between human migration and the mutation of lactose intolerance.
Normally, the lactase gene stops being effective in adulthood, when it is no longer needed.  However, descendants of populations who relied on dairy producing animals have a mutated lactase gene that functions for the entirety of their lives.  Europeans generally have this gene, while it is absent in many Asian and African populations.  This is because dairy-farming was most important in Europe. (So I'll probably never be lactose intolerant! Cool!)
Well, I know you enjoyed this enthralling look at evolution! Come back next time for some cool human-y stuff!

"Founder Mutations" One Page Response

            According to everything from Survival of the Sickest by Sharon Maolem to “Founder Mutations” by Dennis Drayna, evolution always knows what it’s doing.  Although some mutations may seem fatal or disadvantageous, they often safeguard against other deadly diseases.  In particular, founder mutations are passed on identically down a genetic line, and while having both genes for them can kill, just having one protects its recipient from a certain disease.  Although this seems troublesome, as some people will get the fatal disease from this mutation, a greater number of people will receive the benefits and be able to survive.  Mutations like these are the checks and balances of evolution; although they can be counterproductive in some cases, they have the power to protect humans from a host of problems.        

            What makes these founder mutations so special is the way they are passed on from parent to offspring.  Instead of a single small mutation existing on similar random parts of DNA, founder mutations are long strings of DNA that are damaged in the middle, or haplotypes.  Exact haplotype are passed on, getting a little shorter every generation.  According to Drayna, the length of haplotypes enables scientists to deduce the “origins of founder mutations and to track human populations.”  Younger mutations should be more similar to the original full chromosome with the mutation, while older ones would have many more differences, as more time has passed and allowed them to “shuffle.”  From the age of the mutation and the populations where it’s found, the origins of the mutation can be gleaned, including where they originated, how that population spread, and what populations they mixed with.  The movement of humans is essential to understanding the present, as seen in The Journey of Man, and that film would do well to reference founder mutations, which could provide significant support for their findings.  Founder mutations are key parts of human history and present medicine, so it is important that they are studied now in order to find cures for the diseases they cause and prevent, and learn more about human ancestors.

Journey of Man!

This video is literally all we've done the past two classes.
And while the main guy is pretty easy to make fun of, he also makes some pretty strong points about where we came from.
So we started in Africa, and maybe the oldest living example is the San Bushmen.
Next we crossed land to Australia, birthing the Aborigines, who are pretty bitter about this fact.
On that trip, we stopped in India, and started a small population there.
Next it was up from Africa through the Middle east and into central Asia, then over to Europe.
From central Asia we went through Beringia to the Americas, creating Native Americans.
This was a pretty crazy trek for humans to make, and our genetics show it!

Day 15 Blog

I think...this cold may be drawing to a close.
And also, I take back everything I said about parents day and the awkward.  Yep.
We had to MATE with our classmates.  To baby making music might I add.
To see how evolution changes the traits of populations over time, we passed on characteristics by breeding with our peers.  Mmhmm.  It was a little funny, but oh man was it uncomfortable.  (Sorry Quick, but we did TRY to mate with different people, despite our awkward.)  We used our results from our procreation to learn about Hardy Weinberg problems, which basically just FOIL genetics. What?! That's a thing. Yeah. Cool right?  The problems are a touch tricky, but I'll get the hang of them eventually.
Also, don't go with 19 friends to an island and start a new population.  Someone will get cystic fibrosis. Yep.
Hopefully next week the vlogs will be back, as I miss doing them! They're so much more fun than this stuffy writing!

Day 14 Blog

So, hairless tigers are a thing?
Apparently so, as genes can really screw them over.  By the end of this lab though, we almost wanted the tigers to die so their recessive traits could stop being passed on.  What were we doing?  Pulling beads out of a paper bag randomly to represent the genes of tigers.  Two red, hairless beads meant death.  Two furry, green beads meant guaranteed survival for them and their children.  One red, one green bead meant our frustration with the living tigers.  Well, not really, because by our 8th generation all the red genes except one had disappeared, meaning all tigers will live forever! Okay no, but they should survive. Yay live tigers!
Tata for now!

Parents' Day Blog

Okay, so you don't understand how awkward this was.
We had to choose how attractive we thought people are
WITH OUR PARENTS.
So, most of us picked the most feminine men and women, and here's why:
MEN:
The guys were pretty split 50-50 with masculine and feminine men, because they either felt intimidate by masculine men because they are competition and they need to challenge it, or they felt they could more trust the feminine men.  Guys are weird.
Girls on the other hand liked feminine men because they see them as more trustworthy and as better fathers who would help them raise a child.  Also, fun fact, girls with low self-esteem like more feminine men more because they associate masculine men with a wilder lifestyle and date "hotter" women.
WOMEN:
I think all of us chose women that looked more feminine and the reasoning is almost obvious. Of course there is the conventional media definition of beauty, but there is also the fact that more feminine women are more fertile and look more trustworthy.

So yeah. Now can we redefine "hot" as "nerdy"? Please and thank you.
Bye y'all!

Day 13 Blog

I thought I was feeling better, then BOOM sore throat comes back stronger. UGH
So, like, over the course of this lab, I'm pretty sure we're responsible for the death of little shrimp.  I feel kinda bad.  If there is a God, is this what (s)he feels like?  Okee, now we're getting a little too deep (I can't tell if I meant for that to be a pun about shrimp) for me, so let's get through this lab.
We filled petri dishes with water with a salinity of 0, .5, 1, 1.5, and 2%.  Next, we added between twenty and 40 eggs and let them sit for 24 hours for them to hatch! Oh, the miracle of life.  Well, not so much.  In the 0%, there was not even one brine shrimp, while in the other ones there were 2 in the .5%, 5 in the 1%, 13 in the 1.5%, and 21 in the 2%!  We rescued the little live shrimp and put them in a beaker with their friends to live out the rest of their (pitifully short) lives.  On day 2 (with our parents, which I'll discuss later) there were even less alive ones, with 0 in the 0% and 1%, 2 in the 2%, and 3 in the .5% and 1.5%.  I'm sure all these number don't mean that much to you, but basically they mean that brine shrimp have adapted to be more successful in different salinities of water, for us being the 2% after we calculated the viability of them.  Evolution helped these baby shrimp survive in their environments to the best they could and procreate.
Yay for the fragility of life and death!
Stay tuned for the parents' day awkward!

Day 12 Blog

So, apparently, my cold is good because we're reading this book Survival of the Sickest, and I'm feeling pretty darn sick.
So like, what we learned in this book is that fava beans kill people.  Well not all people, specifically those from around the Mediterranean.  It's not like they have a personal vendetta against Mediterranean people, it's more like they want to help them live, because malaria is generally a thing that people don't like.  Yeah, it kills you.  But people from the Mediterranean who can be killed by fava beans will generally not be killed by malaria.  Pourquoi?  Because they lack G6PD, the bouncer of the biological world.  Without this G6PD, the blood is not a very good environment for the malaria virus, who is actually quite wimpy, so it doesn't take in these people.  However, they also can't eat fava beans, one of the primary crops of the area. #worthit
Evolution: killing you so you don't die since 2 billion years ago.
I bid you adieu!

Day 11 Blog

Ugh I'm still sick...this stupid cold.
So for this class I got to embrace my inner daycare child and play with beads!  We got to make bead versions of DNA to compare our relationship to gorillas, chimpanzees, and our common ancestors.  Did you know that we share something like 98% of DNA with chimpanzees?! Yeah, me neither.  Our comparison of our beads showed that the gorilla was really closely related to the common ancestor, and not so much to the chimpanzee, who was pretty close to us.  DNA is a really interesting way to see what our evolutionary family is, in terms of who's that uncle we don't talk about and who's that third cousin twice removed that lives in the jungles and picks bugs off of his family (I'm talking to you gorillas!)
Anyways, this experiment was really cool and I really like DNA and beads (also snacktime, movies, and naps if we're going with the daycare thing)
Aloha! (it means hello AND goodbye! cool huh?)

Day 10 Blog

Hello *cough cough cough ugh I'm dying sneeze cough grr*
I took a break from vlogs because I've been sick recently so I sound and look like a dying whale.
So basically for this class we got to go to the museum (mini-not-so-cool-but-still-exciting-field-trip!)
For homework the night before we read a few chapters of Survival of the Sickest and learned about the arm bone structure that connects us to the rest of the natural world.  It's described as one bone-two bones-blobs-digits, and it can be found from everything from lizards to birds to us!  It has a profound meaning in evolution and our relationships to the natural world (very transcendentalist!).  We got to look at Tiktaalik, who is one of the earliest examples of this arm structure, as he was literally a fish with arms (and he was pretty cute too!).  He had characteristics of fish in his eyes, ribs, tail, and fin-ish appendages, but he also had the characteristics of land-dwelling creatures in his arms (who are geared for push-ups), lungs, and neck.  He was a cool fish and he is such an insight to evolution!  He opened up our evolutionary unit and was a great piece of history to look at.
Alright! Bye guys, talk to you more about evolution next time!

Evolution Quiz

So here's the quiz I have to do! My answers are below!

1. Whales weren't always the majestic sea beasts we know them as now. Originally, one of their common ancestors was that wolf-like creature from 55 million years ago.  As they got more exposure to the sea, they evolved into the second animal, similar to a seal.  They adapted more and more to the sea until they eventually became the whales we know and love today.  The more whale-like common ancestor is more closely related to the modern whale. They are an example of how land animals can transition to the ocean for reasons of food or safety.
2. E, marsupials began in North America.
3. They show convergent evolution.  They evolved separately into the same environment, so they have structures in their body that work similarly, but are made up of completely different things.
4. DNA sequencing compares the genetics of different organisms to see how similar they are. If two organisms have a more recent common ancestor, then their DNA will be more similar than with an organism whose shared common ancestor is further back down the line.  Our lab proved that chimpanzees are more closely related to humans than gorillas are because their DNA is closer to ours. Gorillas, on the other hand, are more genetically similar to a different common ancestor that is further back from humans and chimpanzees. The genetic similarities prove that we are in some way related to gorillas and chimpanzees, and therefore verify evolution.
5. Homologies are structures that are similar in many organisms because they were inherited from a common ancestor. In Your Inner Fish, Shubin elaborates on the one bone-two bone-blobs-digits structure that most animals have in their arms. It can be seen everywhere from early animals like Tiktaalik (although it was very primitive, because it was one of the first fish to venture on land) to modern birds, whales, dogs, and humans, to name a few.  This essential homology connects us with our many shared ancestors and is essential for living on land.

Day 9 Vlog

"Osmosing."
Nuff said.
http://www.youtube.com/watch?v=rbupnAoztv4

Day 8 Vlog

Have you ever had a gnawing curiosity about macromolecules? Me neither.

They are reasonably interesting though, so here's everything you need to know! 

(Rhyme only slightly intentional)
http://www.youtube.com/watch?v=okAj1qnDa0k&feature=youtu.be

Day 7 Vlog

Someone stole Jerell's iPod, and I'm on the case!
http://www.youtube.com/watch?v=qOnBxFgLpGQ

Day 6 Vlog

Hello! So if you've ever wondered what it's like to be on House, here's the inside scoop!
Okay, so not really, but it's pretty darn close (even if Hugh Laurie wasn't there).
http://www.youtube.com/watch?v=JDqb-hOIGKI

Day 4/5 Vlog

Hey there stranger! (I don't know what possessed me to type that but I'm leaving it. Maybe I'm having an internet séance). Anywho, here's my vlog for days 4 and 5 combined, since they are just one big lab

http://www.youtube.com/watch?v=dy2se5O5LkU
And pictures!

Benedict's solution (aka the coolest thing ever)

Iodine doing its thing

NaOH icky cubes!

Day 3 Vlog

Here's day 3: Waterworld! The file is too big to be uploaded here, so here's another youtube link!

http://www.youtube.com/watch?v=ffsPTE3pNAk&feature=youtu.be

And here's the pic of the water on the penny! How cool, right?

Day 2 Vlog

I finally figured out how to upload my videos here! :D Here's my day 2 recap: Chemistry for the win!

Day 1 Vlog

Here's the link to my video reviewing what we did in class (for some reason it won't upload here but it should be fine on youtube :)

http://www.youtube.com/watch?v=Wd0LmMlp65o