Class 33

Today we took the unit 5 test on cytology and previous units. We had a choice between 4 short answers or 1 essay question for the free response. I choose the essay question that had me explain the relationship between cytology, the cell cycle, DNA replication, protein synthesis and cell organelles. Then we had 30 multiple choice questions that covered topics from unit 1 to unit 5. After we finished the test we were free to leave.

Class 32

Today we learned how DNA, the Cell Cycle, Cell Organelles, Protein Synthesis, and DNA replication all work together. We first took a quiz on mitosis and meiosis and then we got packets that contained info on mitosis and meiosis. We drew a mind map on our white boards that shows the relationships between the topics covered this semester.

Class 31

     Today in class we learned about the stages of mitosis and meiosis in the cell. First there is interphase which contains G1, S, and G2 phases before starting mitosis. A prokaryote cell goes through binary fusion because it does not have a nucleus or nuclear envelope. The G1 phase is growth of the cell and the S phase is DNA replication. The G2 phase gets the cell ready for mitosis. Protein synthesis occurs before the cell goes through mitosis. The cell can also stop at checkpoints and enters G0 phase where the cell just lives its normal life and does not go through mitosis. Mitosis is the splitting of chromosomes and ends with cytokinesis which is the splitting of cells into two daughter cells. There are 5 stages of mitosis, prophase, prometaphase, metaphase, anaphase, and telephase.



We then learned about meiosis

meiosis is a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell, as in the production of gametes and plant spores.

We also got to see the stages of mitosis in microscopes and pictures 

We also practiced mitosis and meiosis with popsickle sticks 

Class 30

Today in class we dived into our next Unit on Cytology! We went over the test on genetics and made any corrections needed. Then we took out our white boards and laptops, starting on our cell tour projects where we create a visual fly through the eukaryotic animal, eukaryotic plant and prokaryote cells. We created a venn diagram and wrote a list of the different organisms that are shared between the cells and ones that are specific to the individual cell.

We then started on a lab using microscopes and studied a dog flea, cheek cells. plant leaf and a sample from a fish tank. We got to see the difference in the cells of each. 

Class 29

Test day!!

Today we took the Unit 4 test on Genetics.

The test was 30 multiple choice questions and then 2 free response questions covering the topics of monohybrid and dihybrid crosses, sex linked and autosomal, incomplete and codominance, phenotypic and genotypic ratios, pedigrees, osmosis, Hardy Weinburg problems, true-breeding, and trihybrid crosses.                              

we were free to leave once we finished the test

Class 28

Today in class we learned how to read pedigree charts to predict if the offspring or parents were infected. We were shown many different pedigrees.
We first had to determine whether it was dominant or recessive

First, if there are two parents without the trait, but their children have it, then the gene must be recessive, because if it were dominant, and the two parents both are homozygous recessive, then there is no why their children could have the trait. Their genotype must both be Aa, so that there is a possibility that one child could have the trait.
Note: if, in the second generation, there is an offspring that does not have the trait, and married someone who also doesn't have the trait and have kids that don't have it either, you still cannot be sure that the offspring is homozygous dominant, because there is a chance that they could be Aa.
If you have one parent that doesn't have the trait and one who does, and most or all of their children have the trait, then the gene must be dominant. If most of the offspring have the trait and some don't, then it is still possible that the gene could be recessive, but because MOST have it, it is more likely that it is dominant.
If you have both parents that have the trait, and their children either have the trait or not, then it is most definitely dominant. If it were recessive, then those parents could only ever have children who have the gene. And if they had children who don't have the gene as well, then both parents genotype must be Aa, and the normal children's genotype is aa.

Then we had to determine whether the pedigree was autosomal or sex linked.

 

Sex linked means of the X chromosome. Females have two X chromosomes, so as long as they have one "normal" X chromosome, they would appear normal. Males are XY, so they receive one X chromosome from their mother. If that X chromosome is the "disease" one, then the male is infected. So, a female with the "disease" will ALWAYS give her sons the disease. The pedigree chart will show this. 
A female with the disease will give ONE X chromosome to her daughters. The daughters get the other X chromosome from their fathers. If the father is normal, the daughter will be a carrier only. 
If the father has the disease too, the daughters will ALWAYS have the disease. The pedigree chart will show this also.

Class 27

    Today in class we learned about special genetics. We learned about multiple alleles, sex linked and autosomal cases, incomplete and codominance, blood types and pure and hybrid crosses.
This video helped me understand topics we learned in class.
Video on Incomplete Dominance, Sex Linked and codominance genetics

Specific combinations of genes determine traits such as color and skin pigmentation.
Incomplete dominance is when there is no longer a dominant gene

In this example, red and white flowers cross and create pink flowers.

We also learned about sex linked genes


The x chromosome carries and shows the trait but the y chromosome does not. The woman then controls what the phenotype will be.

We also learned about blood types and predicted what the blood types of the offspring would be if given the blood types of the parents or the other way around.

Your Inner Fish Chap 6 Discussion

     Shubin talks about the best-laid body plans, development from the embryo, germ layers, and the control of DNA. He explains that a scientist named Karl Ernst von Baer discovered that organs are derived from 3 developing layers in the embryo which are the ectoderm, endoderm, and mesoderm. Every animal got their organs from these three germ layers. He also talks about discoveries where the embryo splits and causes twins. I learned that the Organizer is a small piece of tissue that causes the cells in the embryo to make a body plan. All mammals, birds, amphibians and fish contain an Organizer. This links back to evolution and a common ancestor. He then gives diagrams and explanations that show that humans and flies contain Hox genes which are Organizers that are involved in the development of the body plan. DNA controls the Organizer. He finally mentions Noggin which is a gene that can grow back structures and even a second head for frogs when injected into an egg. I learned that DNA mutations and manipulation in the embryonic stages can affect the appearance and structure of an organism.

Class 26

   Today in class we were introduced dihybrid crosses and learned different ways to solve dihybrid cross problems. A dihybrid cross involves a study of inheritance patterns for organisms differing in two traits. Mendel invented the dihybrid cross to determine if different traits of pea plants, such as flower color and seed shape, were inherited independently. Our objective is to understand the principles that govern inheritance of different traits in a dihybrid cross that led Mendel to propose that alleles of different genes are assorted independently of one another during the formation of gametes. We did an exercise involving popsicle sticks were we had parents with two different traits and crossed them using steps to make phenotypes and genotype ratios. There are two ways that were shown to solve dihybrid crosses. First we learned Mr. Quicks way of crossing with a punnet square that showed the phenotype and genotypes of the offspring. Then we were shown Mr. Fitz's way that is a bit faster and uses a punnet square for each trait. This Dihybrid cross video helped me understand dihybrid crosses and is similar to Mr Fitz's way of solving the problem. We then took a short quiz and notes on dihybrid crosses.

Class 25

    Today in class we got our tests back and reviewed things we got wrong. We then started Unit 4 -Genetics. We discussed and practiced Mendelian Genetics finding the phenotype and genotype ratios of the offsprings. We learned about the effect of recessive and dominant traits on the offspring. There are two types of cells, Somatic(body cells) and Gametic(sex cells). We discussed Gametic cells that deal with Meiosis. We learned about the F1 offspring, a carrier, hybrid, pure and backcrossing. We then solved problems dealing with transmission genetics and learned how to do the punnet square to solve it
steps to solving genetic problems

step 1) Write down info
step 2) Parents genotype
step 3) Law of segregation
step 4) Punet square
step 5) fill in info
step 6) Phenotype ratio
            Genotype ratio

Unit 3 Test day

     Today in class we took the Unit 3 test about DNA. The free response covered protein synthesis in which I explained the steps in the synthesis for a eukaryote that goes through transcription, RNA processing and translation. It also had a DNA sequence which we then had to convert into mRNA, then tRNA and then code for its amino acids sequence. I then discussed the inducible operon system that starts off and needs to be turned on. I made a diagram and then explained the reason for the glow in the PGLO lab which contained arabinose. We then had 30 multiple choice questions on DNA, protein synthesis, and topics from Unit 1and 2. After we were finished with the test, we were free to leave.

Flower and Hand analysis

1. This flower has a mixture of white and purple color on its pedals. There are a number of possibilities for how the flower got its color. The colors may have been inherited by the parents and the flower got the dominant trait and the recessive white trait. A mutation might of occurred and caused the intertwine of colors. Jumping genes, also known as transposons, might have inserted themselves into the flowers genes as well.

2. A patch of tissue from the pinky side of the limb bud was taken early in development and transplanted on the opposite side, right under where the first finger will form. Then the extra set of digits will form.  

Class 23

        Today in class we reviewed Unit 3 and learned about the Operon System and Biotechnology. We first took a short quiz and then cleaned out the PGLO bacteria with bleach. We then talked about frameshift when adding or subtracting bases to change the protein. There is nonsense, no effect and missense. We then learned about repressible(on-off) and inducible(off-on) operon systems and the effect of aribonose or lactose has on the system. The operon system is a control system (controlling genes) making only useful proteins and conserving energy. In a repressible operon system, the repressor is inactive and the operator is on, so the RNA polymerase can come into the promoter, read the regulatory gene and makes tryptophan. When there is enough tryptophan, it goes into repressor and then changes it to become active. Then it goes it lock and blocks the RNA polymerase from reading the gene, shutting system off. The inducible operon system, the repressor is active and the operator is off, blocking the RNA polymerase from going through the gene. Lactose or arabinose can then come in and  sit in the protein repressor, changing its shape. Lactase or arabinase is then made and digests lactose or arabinose, unlocking operator and letting RNA polymerase through. We then related the operon system to the PGLO lab that has an inducible operon system. Biotechnology discusses restriction enzymes that cut DNA and RNA. We can isolate them and move them around.

Class 22

      Today in class we discussed the process of protein synthesis. We learned about transcription, RNA processing, and translation. Protein synthesis comprises two major parts-transcription and translation. the process involves RNA, DNA, and a set of enzymes. All types of ribonucleic acid, namely mRNA, rRNA and tRNA are required for protein synthesis. Transcription is the first part in the process of protein synthesis. It takes place in the cell nucleus, where DNA is housed in the chromosomes. From the two parallel strands, one acts as a template to produce mRNA. As an initiation step of transcription, RNA polymerase binds itself to a particular site in one of the DNA strands that will act as a template. Following its attachment to DNA template strand, the polymerase enzyme synthesizes a mRNA polymer under the direction of the template DNA. The mRNA strand continues to elongate until the polymerase reaches a 'terminator region' in the DNA template.The newly transcribed mRNA is released by the polymerase enzyme, which is then migrated to the cytoplasm to complete protein synthesis process.The second primary part of the process is translation. Contrary to transcription that occurs in nucleus, translation takes place in the cytoplasm of the cell. This part is initiated as soon as the transcribed mRNA enters the cytoplasm. The ribosomes present in the cytoplasm immediately attach to the mRNA at a specific site, called the start codon. An amino acyl tRNA also binds at the mRNA strand

As the ribosome moves along the mRNA strand, the amino acyl tRNA brings amino acid one by one. This particular stage is called elongation. At the termination phase, the ribosome reads the last codon of the mRNA strand. With this, ends the translation part and the polypeptide chain is released. Precisely speaking, in translation, the ribosomes and tRNA attach to the mRNA, which read the coded information present in the strand. Accordingly protein synthesis of a specific amino acid sequence takes place.

Overall, protein synthesis process involves transcription of DNA to mRNA, which is then translated into protein. Thus, we have seen the process of protein synthesis requires proper coordination of RNA, DNA, enzymes and ribosomes. 

We then did an activity making snorks giving physical characteristics to them

Class 21

          Today in class we took a quiz on DNA and then discussed the DNA replication process. We worked on our DNA models, learning about the process of replication in DNA and the role of enzymes in this process. We learned that Helicase separates the double helix strands of DNA to be copied by unzipping the hydrogen bonds between the bases of the two strands. Primase binds a small stretch of RNA into an existing strand of DNA called the primer. DNA polymerase III attaches to the RNA primer and works in the 5' to 3' direction and adds the complementary nucleotides to form the new strand of DNA. DNA polymerase I replaces the RNA primers on the lagging strand with DNA nucleotides. DNA ligase joins the sugar-phosphate backbones of the Okasaki fragments to create a continuous strand of DNA. we went step by step in the process of enzymes in DNA replication. We then looked at our PGLO lab and saw that only one was glowing.

class 20

       Today in class we discussed viruses, vaccines, jumping genes, "junk" DNA, RNA and other things that was read in chapter 6 of Survival of the Sickest.

We then started on the PGLO lab!

We tested the bacteria and hoped to find the prokaryote bacteria glowing after submerging it in PGLO. We knew that because of the cell membrane it would be difficult for the PGLO to enter the cell, but if we used heat shock, (cold-hot-cold) there would be a hole that would let the PGLO in. Before we could do the heat shock, we would have to label the different bacteria, transfer the bacteria to the tubes, and mix plasmid DNA in the PGLO+. We had to be careful that we did not transfer too much bacteria or mix any bacteria so that it would be sterile. Then we do the heat shock and incubate the tubes with LB nutrient broth acting as food so the bacteria can grow.

We then streak the solution onto the agar plates. Our class hypothesis was:

Class 19

     Today in class we took a quiz on the documentary, "Journey of a Man" and then discussed DNA structure, its properties and function that was in the video we watched for homework. We drew a diagram of DNA. We drew the double helix strands, labeled the nitrogen bases, pyrimidines and purines, hydrogen bonds, phosphate+sugar+nitrogen base, based pairs and the nucleotides that make up DNA. We labeled the 3',  5' ends and OH groups. We discussed the special enzymes such as helicase that helps unzip and unwind the double helix, RNA Primase that makes the primer, DNA polymerase III that elongates the leading strand and lagging strand. We then started making our own DNA diagrams, cutting and labeling strands of DNA that we would finish next class.

Inner Fish Chapter 3 Summary

     Chap. 3, "Handy Genes," was about DNA, genes, embryonic development and what parts of these genes are turned on or off to make parts of a body such as limbs in the embryonic development stages. Sequences of DNA make us who we are. Shubin's lab is separated into two parts: a section for fossils and a section devoted to DNA. While Shubin was in the Arctic, another researcher was working in his lab shooting vitamin A into skate and shark embryos. Our body knows how to develop because of the concentration of chemicals produced by the cells. All the genetic switches that control this do their thing between the third and eighth week after conception. Certain patches of cells were responsible for all limb development. Remove that patch and no limb develops. Turn the patch cells over and the limb grows backwards. Cut the patch in half and you have two limbs. Later scientists did an experiment involving flies and found a gene called hedgehog. This gene controlled which end of the fly was which. They looked for this in other creatures and found the hedgehog gene to be in many other organisms. They named the chicken version of the gene Sonic Hedgehog. It was found to be only active in the patches that control limb development. The form of Vitamin A caused the Sonic Hedgehog to activate. Every living organism with limbs has the sonic hedgehog gene. The vitamin A even caused mirror limbs to sharks and skates. Then the scientist injected mouse protein and the shark limb was affected the way it was with vitamin A injections. This means that the mouse and shark genes are similar proving the concept of common ancestor.

SOS Chap 6 summary

     Chapter 6, Survival of the Sickest was about viruses. It explained how viruses are master mutators that have the potential to create the successful genetic patterns that underlie all living cells and have helped humans evolve into complex organisms much faster than we would have on our own. Viruses are not living organisms and hijack, infect the host cell injecting DNA or RNA retroviruses. The chapter talks about vaccines that have protein coats and create white blood cells when recognizing invaders. The chapter talks about the first vaccine that gave protection against smallpox with cowpox infection. I learned that less than 3% of your DNA contains instructions for building cells, and that a third of your DNA is derived from viruses. Scientists initially believed most of the DNA was "junk DNA" because it was not directly responsible for making proteins, but it actually is "non-coding DNA" which may have provided the code for our evolution up and away from our ancestors and viruses may have infected us with that code. Humans have a total of approximately 25,000 genes. An important topic was the role of jumping genes, also known as transposons, in brain development and the immune system. These jumping genes are probably descended from viruses. The more complex an organism is, the more jumping genes it has.  Jumping genes are similar to "inherited- RNA acquired traits." These genes hump to find a mutation best fit for the environment. The author also gives a brief description of how antibodies are built. Body building follows a general path of DNA to RNA to protein. The chapter discusses retroviruses and how at least 8% of the human genome is composed of retroviruses. Retroviruses are made of RNA and use an enzyme called reverse transcriptase that transcribe itself from RNA to DNA, reversing the information flow by copying and pasting into host DNA. Our genomes have been modified by one particular retrovirus in a way that makes it easier for us to be infected by other retroviruses and allowing more rapid mutation and faster evolution. I learned variations are caused by mutation and viruses cause a change in physical traits.

From Atoms to Traits Q & A

1. Mendel conducted a breeding experiment with peas in 1850's and 1860's. The peas had obvious morphological differences and when the breeding of two plants crossed, their offspring resembled one of the two parents. Both traits would reappear in further generations. Mendel's experiments changed the general perception of that time that heritable variants from ephemeral and blendable to discreet entities passed from parents to offspring, present even though they are not always visible. Mendels findings were soon seen in the behavior of chromosomes in the cell nucleus.

2. James D Watson and Francis Crick had proposed a structure for the DNA molecule in 1953, that helped us understand hereditary and variation physically. It helped us sequence various organisms and their offspring, and look for any spontaneous changes in the long chain of DNA letters passed down from generation to generation.

3. Point mutation, insertion, gene copy number, duplication and regulatory changes are all examples of variations that occur to DNA. 

Point mutation: Or single base substation, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA. This also includes insertions or deletions of a single based pair. For example in whipped dogs, a single based pair change makes the difference between a slender silhouette and a hulking animal. The mutation inactivates the gene for a signaling molecule that regulates muscle growth is uncontrolled because there is no "stop" signal. 

Insertion: Is the addition of one or more nucleotide base pairs into a DNA sequence. For example, in pea plants, an 800 base pair sequence inserted into a gene produces wrinkled peas instead of smoothed ones. The intruding DNA element disables a gene necessary for starch synthesis, altering the peas sugar and water content. 

Gene Copy Number: Entire genes can be duplicated by copying errors during cell division, leading to differences between species and variation among the individuals of the same species. For example, the genome of chimpanzees, which have a diet consisting of mostly green plants, normally contains just a single gene for the starch-digesting enzyme salivary amylase, where as humans can carry up to 10 copies of that gene. 

Duplication: Sequences containing the same based pair copied and repeated eight or more times, known as homopolymers, are highly prone to copying errors. For example, in pigs, the gain of two additional C-G pairs in such as sequence inactivates a gene for a signal receptor in pigment cells, producing light colored coats. Copying mistakes in the individual cells can also cause the lose of bases which restores the gene's function and causes dark colored spots in the coats. 

Regulatory Changes: Mutations in the DNA that controls when and where genes are activated can produce profound trait changes by altering the formation of body parts during the development of the organism. For example, the shape difference between the bushy teosinte plant and its descendant the modern cornstalk are different because of the change in the regulatory regions of a single gene that controls patterns of cell division during stem development. 

4. Evo-devo is a subspecialty within evolutionary biology that concentrates on studying the effects of changes in important developmental genes and the role they play in evolution. It adresses the origin and evolution of embryonic development; how modifications of development and developmental processes lead to the production of novel features, such as feathers; the role of developmental plasticity in evolution; how ecology impacts development and evolutionary change; and the developmental basis of homology. 

5. In the case of some dietary adaptations, the changes enabled entire populations to migrate and take up new ways of life, such as herding and agriculture. An example of such as trait, the ability to digest milk into adulthood, is found to have risen independently in groups on different continents, attesting to the great nutritional advantage the variant provides and to the possibility of directly connecting simple DNA sequence changes to human cultural evolution. Lactose intolerant people cannot digest complex milk sugar lactose because of the lack of lactase produced. Its retention in milk dependent societies also illustrates how culture can reinforce the forces of evolution.