Saturday, December 14, 2013

Cell Cycle

Last class we learnt about cell cycle:

1. Interphase
---G1:  Normal growth
---G1 Checkpoint: enzym activates DNA replication
---S: Synthesis-- DNA replication
---G2: Cell doubles organelles
2. Mitosis
---Prophase: nuclear membrane disappears
---Pro Metaphase: spindle fiber
---Metaphase: Chromosomes line up in the middle of cell
---Anaphase: Apart
---Telophase: Two nuclei and partial cell membrane
3. Cytokinesis
Create two cells. Pinch cell membrane.

We also observed some cells at different stages:


For more detailed explanation on mitosis, I have more information in my blog from before.


Link to my Cell Tour Prezi:
http://prezi.com/z_cw0r42ucms/?utm_campaign=share&utm_medium=copy&rc=ex0share

Thursday, December 12, 2013

Why do I not have two heads?! That could have been cool!!!

All organs of organisms can be traced back to one of the three layers of a developing embryo. These three layers are called germ layers.

All animals' structures derive from the germ layers. After cell divisions, the embryo looks like tubes within a tube. The very outside layer is called ectoderm. It develops into skin and nervous system. The middle layer develops into mesoderm. It develops into tissues in between guts and skin. For example, skeleton and muscles. The very inside layer, endoderm, develops into inner structure. For example, the inner organs. 
The small patch of tissue on a developing egg that directs other cells to form a full body is called an organizer. The organizer contains a gene called "Noggin," which contains information that directs the cells to form a body. 

If one injects extra noggin into an embryo, it will develop extra back structure or an extra head.

A Hox gene provides the head-to-tail organization of an embryo. The gene that controls the head is on one end and the gene for the tail is on the other end. As a result, the embryo can develop a head on one side and a tail on the other side.

Microscope

We observed things with microscopes last class.
A lovely photo of a flea:

Cells of a plant:


My cheek cells....

Organism in a drop of salt water... and an air bubble....:



For extra credit:

Since the mother dog has yellow pigment and had black and yellow pigment offsprings,


She might be Aa or aa. Since the ratio of the puppies' phenotype 1:1, the father dog should accordingly be aa or Aa.






Thursday, December 5, 2013

BEHIND ON BLOG!!!!!!!!

I am really behind on my blog... Guess I'll just cramp a bunch of stuff into this ONE...

General Genetic Problems:
There are two ways. First is the Quick way:

Basically write out the possible combinations of the two traits and list the possibilities out in a huge square.

And then there's the Fitz's way:

Wowwww so much math!!! But I'm Asian so it's no big deal. Put the alleles that are in charge of the same traits in the same square and list all the possibilities out. And then calculate the ratios. Voila.

Genotype: The allele expression.
Phenotype: What the trait looks like.

Special Genetics:

Epistasis:
The different combinations of alleles creates different phenotypes. For example:

Incomplete Dominance:
Both alleles in heterozygous organism may be expressed in the phenotype. For example: Red rose x White rose = Pink rose.

Codominance:

Both alleles are expressed in phenotype. For example: Blood type.

Sex-Linked Genes:
Sex-linked genes that do not determine sex are usually on X chromosome. Y chromosome usually only determine sex (male). Female has XX and male has XY. Therefore, males are more likely to posses sex-linked traits.


Meiosis:
Meiosis is the making of sex cells. 

1. Cell starts off with 2n (two pairs of chromosomes)
2. Interphase: DNA replication --> 4n (four pairs of chromosomes)
3. Prophase I: Homologous chromosomes cross over to provide diversity. Homologous chromosomes --> chromosomes that control the same traits but contain different messages, one from dad and one from mom.
4. Metaphase I: Chromosomes line up in the middle of cell, big ones on top, small ones in the bottom.
5. Anaphase I: Spindle fibers split the chromosomes apart.
6. Telophase I: Forms two cells. Each cell contains 2n.
7. Metaphase II: Chromosomes in each cell line up in the middle.
8. Anaphase II: Spindle fibers split each cell into two cells.
9. Telophase II: Forms four sex cells that each contains 1n. The genes contained are randomly from mom or dad because of crossing over.

Mitosis:

MY BRAIN FREAKING BLEEDS BECAUSE OF THAT...

Diploids: 2n
Haploids: 1n

A useful video: http://www.youtube.com/watch?v=zGVBAHAsjJM


Pedigrees:

This is a pedigree. In order to identify a sex-linked trait: male offsprings have a greater chance in having sex-linked traits. In order to identify if a trait is dominant or recessive: refer to the ratio.

My PREZI on Huntington's Disease: http://prezi.com/xvcplbxsbqea/?utm_campaign=share&utm_medium=copy&rc=ex0share


Tuesday, November 19, 2013

More Genetic Stuff

We learned about Mendelian Inheritance.
First of all, the principle of segregation is: the two members of a gene pair (alleles) segregate from each other in the formation of gametes. Half the gametes carry one allele, and the other half carry the other allele.
Principle of independent assortment is: genes for different traits assort independently of one another in the formation of gametes.

If the parents have AA and aa alleles, they would give the gametes of A and a. Therefore, their progeny F1 would have the alleles of Aa. For F2, they would have the alleles of 1AA: 2Aa: 1aa. As a result, their genotype ratio would be 1:2:1, and their phenotype ratio would be 3Dom: 1rec.


Thursday, November 7, 2013

Protein Synthesis

Transcription:
1. RNA Polymerase unzips DNA and forms RNA complimentary pairs.
2. mRNA is formed. it has a tail-- Poly-A made of Adenine, which is the 3' end, and a Cap made of Guanine, which is the 5' end. The tail and the Cap protects mRNA from being disintegrated by nuclease, which are in charge of intruding virus.
RNA Processing:
1. Splicesosome cuts off introns that are build by "junk genes"(caused by transposons), and connects extrons.
2. mRNA goes through pore and goes into Cytoplasm.
Translation:
1. mRNA finds ribosome and reads from 5' to 3' end. Start codon is AUG the codes for "met"(methianine).
2. tRNAs that are attached to amino acids attach to codons and build polupeptide.
3. Once ribosome finished reading mRNA, polypeptide is released.

The amino acid sequence codes for body features. We did a lab in class and transferred the codes into body traits and "built our own aliens". This is mine:

Square-headed, hairy, plump...... Sounds like...... Mr. Quick???

Other than that, we checked the bacteria lab. 
Things didn't change that much:
Bacteria sample with plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin and arabinose: bacteria grew out some more and glowed.

Bacteria sample with plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin but without arabinose: Grew out some more but did not glow.
Bacteria sample without plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin: Did not grow out.
Bacteria sample without plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate without ampicillin: Grew out some more.

Tuesday, November 5, 2013

DNA Replication and Bacteria Lab

1. Helicase unzip DNA

2. Primase reads from 3' to 5' and creates short RNA primers

3. DNA Polymerase III form DNA complementary pairs from 3' to 5' (DNA doesn't bond with RNA primers)

4. Primase jumps backwards from 5' to 3' to the closest T or A and build RNA primers from 3' to 5'



5. DNA filled in by Polymerase III
6. DNA Polymerase I changes RNA to DNA
7. Ligase creates phosphodiester bonds between DNA fragments (Okazake fragments)


Update on the neon bacteria lab:
Bacteria sample with plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin and arabinose: bacteria grew out and glowed.

Bacteria sample with plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin but without arabinose: Grew out but did not glow.

Bacteria sample without plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate with ampicillin: Did not grow out.

Bacteria sample without plasmid DNA that allow bacteria to glow and immune to antibodies in agar plate without ampicillin: Grew out.




Thursday, October 31, 2013

Vaccine and Neon Bacteria

For the first part of the lesson, we talked about vaccines. Basically, vaccines are weakened virus. If these non-sickness-causing virus are injected into human body, the white blood cells will memorize thee virus' protein coat, and the next time when the white blood cells encounter similar virus, they would be able to recognize it and fight it off.

Usually, what virus do is to hijack cells and provide RNA and have the cell produce new virus.

For the second part, we did a lab, in which we can genetically change bacterias. Basically what we did is to have two samples of bacterias, in sample one we added a plasmid DNA that would allow the bacterias to glow and be immune to antibiotics. We didn't add anything to sample two. We prepared two agar plates for each sample. For sample one, one plate contains arabinose (I looked up online, this switches on the DNA that allow bacteria to glow) and both contains ampicillin. For sample two, one plate contains ampicillin, the other one doesn't.



Our prediction is that bacteria in sample one plate without arabinose will grow but won't glow. The other sample one plate bacteria will grow and will glow. Bacteria in sample two with apicillin won't grow. Bacteria in sample two without ampicillin will grow but won't glow.



Tuesday, October 29, 2013

Jump Into the Gene Pool

Only 3% of DNA are coded for building cells and the other 99% were once called "junk DNA"because people think they don't do anything. Recently, they are renamed as noncoding DNA because people find out that they do have their significance. McClintock found out that when organism is under harsh environment, its gene would have an intentional mutation. The genomes that switch place and cause mutations are called jumping genes. This intentional mutation is the organism's attempt to come up with a beneficial mutation to help it overcome the harsh environment. After that, natural selection kicks in and decide if this mutation would allow the organism survive and therefore evolution happens. It was found out that more than half of the noncoding DNA is made up with jumping genes, which correspond retroviruses' DNA. Scientists think that the human DNA allowed the virus genes to hitchhike. in return, the virus genes help human to evolve faster.
Here's my mind map. I also put it on my blog:
  https://sites.google.com/site/randombiocrap/home/jump-into-the-gene-pool-reading-assessment




DNA

We learned about DNA structure in class. DNA is made up with nucleotides, which are made up by a phosphate, a sugar and a nitrogen base. The tie between the phosphate and the sugar is a phosphodiester bond, and the bond between the sugar and nitrogen base is a hydrogen bond, including bonds between A-T and C-G. A and G are called Adenine and Guanine, which are Purines. T and C are called Thymine and Cytosine, which are Pyrimidines. There are 2 bonds between A and T. 3 bonds between G and C.

Sunday, October 27, 2013

Journey of Man and DNA...

For the video, "Journey of Man", that we watched in class, it said that human beings originated from Africa. In order to prove that, scientists went to all parts of the world and look for people whose DNA contain traits of the direct ancestor whose offsprings developed different traits that led to the formation of different races. They found these people, and found out that their DNA and looks resemble people of different races.

For the DNA reading questions:
1. Mendel's pea breeding proved that although some DNA information is not visible in the plants' physical traits, it still exists and might show in the plants' offsprings' physical traits.
2. Watson and Crick
3. First, point mutation. A single base pair changes. For example, if a whippet dog has a point mutation, it inactivates the "stop" sign for muscle growth, and the whippet dog will develop extra muscles.
Second, insertion. A number of bass-pair structures are inserted in the genes and make differences. For example, some bass-pair structures are inserted in the genes of pea and causes its skin to wrinkle.
Third, gene copy number. A section of genes can be copied more than once due to error and causes variations. For example, chimpanzee only has one gene for starch-digesting enzyme salivary amylase, while human has more than 10.
Fourth, duplication. sequences repeat. For example, if a certain sequence of pig's genes repeat, the pig will have dark patches on its skin.
Fifth, regulatory changes. Mutations in the DNA that controls activation can change. if this happens to corns. Two kinds of corns will emerge: bushy ones and tall ones.

4. Study that focuses on the effects of changes in important developmental genes and the roles they play in evolution.
5. If human beings migrate to a place that suits milk-producing, their milk-tolerance will arise in order to adapt to their food. It shows how culture can influence evolution.

Tuesday, October 22, 2013

One Page Response


One Page Response
            From the “Journey of Man” video and reading, I learned that the ancestor of human beings originated from Africa. They migrated over time and populated the world. The process of migration is extremely slow. Rather than migration, it is more like some of the ancestor population moved a few miles away from the others in order to have more space and food sources. After millions of years, generations of ancestors kept moving away from each other, and they eventually reached all parts of the world. How can we prove that all human beings around the world originated from Africa? By comparing the mtDNA and Y chromosomes of human beings all over the world, scientists trace the similarities and find out that all females have one ancestor and all males have one ancestor. As a result, the origin for human can be traced back to Africa. For my assigned reading, I read “Founder Mutation”. The term referred to a genetic legacy of a common ancestor that can lead its offspring to disease. If a person receives a certain founder mutation gene one side of his parents, he would not get the disease. Instead, he would be a carrier, and being a carrier of founder mutations can prevent him from getting certain kinds of disease. However, if a person receives a certain founder mutation gene from each of his parent, he will catch the disease and will probably die before reproduction. As a result, those who carry a pair of founder mutation genes will die out, and those who carry only one founder mutation gene will benefit from the gene and will pass it to their offspring and control the proportion of the founder mutation gene in a population. I think this is the reason why close relative cannot marry each other. If they do, there will be more chances that their offspring will carry a pair of founder mutation genes and die of disease. Furthermore, it will throw off the founder mutation gene proportion balance in the population.
            The founder mutation gene shortens after each generation because clean genes will be added in when reproduction takes place. Therefore, people can find out when the common ancestor lived according to the length of the founder mutation gene. Other than that, the founder mutation migration provides proof for human migration. It provided evidence that human ancestor—Homo sapiens did not interbreed with other human groups. Accordingly, we can be sure that the modern human directly evolved from Homo sapiens. This also resolves the question asked in “Journey of Man” article: if the Native Americans evolved from early human groups other than Homo sapiens. 

Sunday, October 20, 2013

CLARIFIED

I am able to correct my mistakes because i just cleared up two concepts through my study for the test:
1. p and q are not the percentage. they are FREQUENCY.
2. The reason why the percentage for heterozygous population is 2pq instead of "pq" is because the genotype can be either Aa or "aA". It can be A from father and a from mother or a from father and A from mother.

Wednesday, October 16, 2013

Hardy and Weinberg Equation

p^2+2pq+q^2=1, p+q=1, p^2=AA genotype population percentage, q^2= aa genotype population percentage, 2pq= Aa genotype population percentage. p=dominent allele frequency, q=recessive allele frequency.
The population's allele and genotype will remain constant from generation to generation when:
1. The breeding population is large
2. Mating is random
3. There is no mutation of the alleles
4. No differential migration occurs
5. There is no selection
If the above do not occur, evolution will not take place, alleles frequencies will remain unchanged.

Evolution is the sum total of genetically inherited changes in the individuals who are the members of a population's gene pool.

Saturday, October 12, 2013

Natural Selection

Following up to the brine shrimp lab, we made a graph for the data.
The percentage of surviving brine shrimp reaches its highest when the percentage of salt is 0.5%. It shows that the sample of brine shrimp that we used is best adapted to 0.5% salt water. This lab shows that brine shrimps that can adapt to the environment will survive and pass down their genes, so that the next generation will have these genes that helped them survive. In that way, species evolved to have these genes, which is the process of natural selection. 
Other factors that could have influenced the results can be temperature, season, chemical in solution, pH level, sun exposure, type and amount of brine shrimp.
We also did the "tiger lab." 
We have red beads to represent dominant alleles and green beads as recessive alleles. Red means alleles that give tiger fur and green means alleles that give tiger no fur. Tigers with fur will survive to reproduce and tiger without fur will die off. In the end, all "tigers" left had fur. They are carrying either HH or Hh genes. 
If tigers with HH genes reproduce, they will have HH offsprings. If HH and Hh reproduce, they will have HH or Hh offsprings. If hh and Hh reproduce, they will have Hh or hh offsprings. If hh and hh reproduce, they will have hh offsprings. 
Eventually, hhs die off and there comes natural selection.
The only way to have other hh is through emigration or immigration.