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.