Monthly Archives: October 2011

Lac Operon 10/24/2011

Much of the class discussions have been about/on the structures and operations that occur within the eukaryotes. Today, however, we began a discussion on the gene regulation, whether to transcribe for a protein (gene) or not, of prokaryotic organisms. Unlike eukayotes, prokaryotes have operons. Operons are multiple structural genes that are regulated by a common operator and promoters. This helps prokaryotes to be more efficient since their surface ares is not as large as eukaryotes.

We humans do possess the E.Coli bacteria but it is only present in our intestinal tract. Furthermore, the prokaryote organism E.Coli, like most bacterias, posses a repressed gene know as the lac operon. The lac operon gene is repressed because it is not constantly used but it may be needed with is why the gene has not been completely eliminated. In the presence of glucose, the lac operon is repressed because the sugar of choice are those sugars that are common to animal like glucose.

If for whatever reason glucose is not readily available and the lactose sugar is present it then binds to the repressor molecule and it released from the regulartory site on the lac operon. It is released because the shape of the repressor molecule will change its shape and no longer will be able to bind properly at the operator site. The one RNA polymerase that bacteria have can then bind at the operator site and begin its transcription of mRNA of the lac operon. This mRNA then is then joined by ribosomes and the proteins are made that E.Coli needs in order to break down the lactose into a usable sugar needed for it metabolic functions.

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Posted by on October 25, 2011 in Uncategorized


Genetic Inheritance Cont… 10/20/2011

We continued to discuss genetic inheritance but this time in greater detail. To throughly understand the concept of inheritance you must first know the difference between a genotype and phenotype. Genotype of a person is the varied genes of a certain trait that you possess along your chromosomes where as the phenotype is the expression of the gene or trait; in simpler terms, phenotype is how you look. Geneticists use punnette squares to show the probability of an offsprings to acquire a particular genotype which will essentially effect the offsprings phenotype. A punnette square can only be used to determine the probability of an offsprings acquiring ONE trait!

If you wanted to determine the acquisition of multiple traits then the best graph to use would be the dihybrid crossing graph.

Although, Gregor Mendal made genetics seem like a simple mathematical equations,9:3:3:1, governed by easy probabilistic occurrence,genetics is far from simple because traits of one characteristics of a person could rest on the same chromosome. Hence, they are not independently assorted whereas traits that are not on the same chromosome are independently assorted, or randomly given to offsprings.

When looking into inheritance, one must take into consideration the fact that some traits display incomplete or codominance characteristics. Incomplete dominance occurs when two parent organism mate and they pass to the offsprings to separate alleles and neither alleles shows complete dominance or expression over the other. In other words, there is a blending of the alleles when the phenotype of the offspring is expressed.

Codominance can also occur. When two parent come together and they pass to the offspring separate alleles that are both dominant and the offsprings expresses both proteins instead of one over the other. The most common example of codominance is blood types. Those individuals that have the AB blood type are the perfect example of an organism expressing codominance. The have the genes to produce both the A and B red blood cell antigen and not just either A or B or no antigen.

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Posted by on October 20, 2011 in Uncategorized


Class Reflection 10/18/2011

In this class, I learned about the three different types of processing proteins. There are the proteolysis, the glycosylation and the phosphorylation protein. Each protein has a different job and the glycosylation is responsible for the addition of sugar. The phospholrylation is responsible for adding a phosphate group. Lastly, the proteolysis is responsible for directing newly formed proteins to the Golgi apparatus and it is also responsible for the cleaving of polypeptides to allow the fragments to fold into different shapes.

It is possible to inject a gene into another species, which then displays the trait of the other species because of the universal genetic code. Translation, which is a cytosolic process, of RNA and DNA are the same regardless of the species, however, the only variation is that the mechanism of translation may vary. When undergoing translations, cells have a stop codon that initiate termination of protein production and the codon is usually UAG, UAA or UGA!

Genetic expression and experimentation was first done by Gregor Mendal, an Austrian Monk that went with little to no fame at his time of existence. He achieved such experimentation through the work of peas that can produce up to two generation in a one year. He was also responsible for coding, in mathematical terms, the pattern of inheritance.

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Posted by on October 19, 2011 in Uncategorized



One day Johnny was not feeling to well but he decided to go to school anyway. One his walk to school, Johnny ran into his friend Randy and they continued their 2 block walk to school and conversed along the way. When they got to school Johnny realized that they had 20 minutes until their first class was to start so he extended an invitation to Randy to go to breakfast. Randy accepted as he knew it was chicken biscuit day in the cafeteria. They went through the line and got their trays and then sat down to eat. Without a moments notice, Johnny sneezed on Randy as he was eating the last bite of his chicken biscuit. Johnny apologized and they threw away their trays and headed off to homeroom.

In the story of Pounce the Panther begins….

After Johnny’s sneeze, Pounce was transferred from Johnny to Randy and he was looking for a new place to dwell and call home. While floating carelessly through Randy’s bloodstream, Pounce noticed he spherical shaped structure and as his curiosity began to spark he made his approach to examine this new “thing.” As got closer to the structure he realized that not a lot of things were go into the structure or out of it. However, what he deduced from the things that he saw going on with this structure was that most of the same compounds were going in and most of the same molecules were coming out of it. He was fascinated so he decided to call it the membrane because he rationalized that it determined what when into the cell and what came out of it and that had to do this to maintain stability within its borders. He saw that it was a phospholipids bilayer that means it was hydrophilic and hydrophobic. He also notices that it had channels and pores that appeared to be made up of proteins. As Pounce walked around the cell to explore it more, he accidentally brushed up against the mediate endocytosis receptor. Almost immediately, the receptor began to change its shape as Pounce was the Ligand for it.

Pounce transcended down this tunnel until eventually he was within the very membrane of the cell. While inside, he realized that he was moving around the cell by fluid. He called this fluid the Cytosol. The Cytosol was with in the cytoplasm that extended throughout the entire cell and it appeared to house all the internal structures of the cell except for the nucleus. The Cytosol helps transport things around the cell and it is where reactions of the cell seem to take place. As he was transported further around the cell he noticed why the cell has it particular spherical shape. There were filaments that interlocked and connected in order to give the cell shape and it also aided in the movement of the cell around and across the human body and bloodstream.

As Pounce was moving around the cell, he saw a lot of the structures of it. He saw a structure that he called the lysosome. The lysosome was the like the sanitation worker of the cell. It picked up all the waste products like proteins, nucleotides, lipids, phospholipids, and the can remove carbohydrate, sulfate, or phosphate groups from a molecule by digesting them with the enzymes that it houses.

Pounce’s smooth ride began to get a little rougher. He was in a region in the cell that was surrounded by a ton of what he called ribosomes. He decided to call this are the Rough Endoplasmic Reticulum (RER). This region of the cell is the manufacturing site for lipids and many proteins. It is also responsible for the modification of proteins. It can viewed as network of membranes that were enclosed flattened tubules that also appear to be connect to the nucleus because it does surround the nucleus.

Ponces ride got a little smoother as he entered a separate network of flattened tubules. He thought there were the same but this area just did not have any ribosomes so he called this region the smooth endoplasmic reticulum. There were a lot with lipid manufacturing and metabolism. There always was some steroid and hormone production.

As Pounce continued on his journey of the cell he came into contact with the biggest organelle within the cell. It was very dense and dark and had lots of holes that appeared to look like pores. He wanted to explore it but he was a bit timid and scared by its size. He thought back to what his mother had said, “never be afraid to learn,” so he snapped out of his scared trance and quickly went looking around to find a way through the pores of the nucleus. THERE IT WAS, Pounces way in! Pounce saw that one of the nuclear pores were about to open to allow for an ion to pass through. He ran as fast as he could and then jumped and grabbed a hold of one corner of the ion and followed it through the passing of this nuclear pore, protein channel.  While in the nuclear pore, Pounced discovered that this holey membrane was actually TWO cellular membranes. It had both and inner and outer member that were exactly parallel to each other.  

After his arrival into the nucleus, he was surprised just how large the nuclear membrane completely enclosed the nucleus. After he got over his awe about the nuclear membrane’s size he looked around and realized that area, nucleolus, almost appeared to be manufacturing factory. Everywhere he looked, he could see that rRNA and ribosomes were being assembled.  After all of this, he concluded that this is where all of the genetic materials of the cells were housed, maintain and protected and that the nuclear membrane served to separates the cell’s genetic material from the cytoplasm and cytosol. It was hard to get into the cell now that Pounce had quenched his thirst of curiosity and now he wanted to get back out of the nucleus so that he could explore just one last structure that he failed to.  In the distance, he saw completed tRNA that was ready to be transported into the cytosol so that it could be made into a protein. He ran like an Olympic track winner until he could grab a hold of it and be transported back through the nuclear pores. YES!!! He made it and after a relatively modest time travelling through the channel, he was now back into the cytosol and off he went to the Mitochondria.


 After his arrival to the mitchondria, Pounced noticed that it was the power house of the cell. It provided the cell with ATP or the fuel that is usable by the cell fuel all the reactions of the cell and keep life living. There was an electrochemical gradient of H+ ions that he called the Proton Motive Force. It was a double membrane that had narrow folds within the outer membrane. Pounce also noticed that the mitochondria had its own ribosome, DNA and made its owns protein and that it did not appear to need the cell to replicate or grow. This got Pounce wondering back to his biology class. Maybe the mitchondria was at some point an entrirely separate organism. As a matter of fact, it was! He remembered his biology teacher going over a concept called endosymbiosis. That is when one organism lives within another organisms and one organisms transfers some if it’s DNA over the now host organism and loses gets rid of some of its original DNA and functions so that the two different organisms can combine and both organism now have a mutual relationship with each other. WOW! The mitochondrias were awesome but it was time from Pounce to head over to the Golgi apparatus.  


Lastly, the golgi apparatus is the organelle in the cell that processes and packages all of the ready proteins. It functions as the post office of the cell by stamping the proteins with its required postage (glycosylation, etc), and finally shipping the protein to where it needs to be and it is also responsible for the recycling of processing proteins to be used again. It is a structures that has stacked membranes between the RER and the cell membranes

After all of that exploring Pounce realized that he was homesick and hungry so he grabbed on to water molecule and headed out of the cell.

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Posted by on October 16, 2011 in Uncategorized


Translation/Transcription 10/13/2011

DNA transcription can be describes in a simple way. It is when cells transcribe the genetic material codes from the DNA molecule into a RNA molecule. RNA is a working copy of DNA that. The initiator factor of transcription is when a RNA Polymerase binds to a DNA molecule at the promoter site, located within the major grove, of DNA and it then unwinds the DNA molecule. RNA Polymerase does not need the aid of a Ligase or a Primer to accomplish this task. After the unwinding of the DNA molecule, the RNA Polymerase then goes into the elongation. In elongation, a single strand of DNA molecule is then transcribed into a single RNA molecule. Using the base complementary pair rule of nucleotides, Chargaff’s Rule. If a cytosine is present in DNA then the complementary pair in RNA would be guanine and vice versa. If an adenine is present in DNA, then a uracil will be present in the RNA strand according to Chargarr’s rule. Uracil takes the place of thyamine because it is not present in RNA and is only present in DNA. The newly formed strand of RNA can now be called the messenger RNA (mRNA) when the RNA Polymerase reaches a specifically coded termination point on the DNA molecules.

Before a mRNA is released from the nucleus into the cytoplasm to undergo protein synthese, it must first be proofread and edited and then submitted as the final copy, kind of like a thesis paper. This editing occurs withing the nucleus and after DNA transcription has occured. The mRNA has areas on it that are called introns and exons and essentially the nucleus only wants for the good genetic information to be presented and these are the exons. To accomplish this, there are specific enzymes involved in this process known as spliceosome and it scans the informations from the 3′ end and after all introns are removed it then does the 5′ end on the mRNA. When the splicing is complete the mRNA is now a mature mRNA and can now be released from the nucleus into the cytoplasm of the cell to deliver the message of the DNA as to what to proteins to produce.

In DNA translation, the mRNA is released from the nucleus of the cell and is then released into the cytoplasm of the cell where the translation of the mRNA is then converted into functional proteins with the help ribosomes. While the mRNA is in the cytoplasm it then comes into contact with a 30s ribosome with the matching complementary base pairing of its first three anitcodon nucleotides. Once this bonding occurs, they are then joined with a 50s ribosomal and the translation can now begin within three active sites. E (exit), P (peptidyl) site and A (aminoacyl) site. With the first codon paired in the P site, another transfer RNA (tRNA), then enters into the ribosome with the next matching anticodon and the two tRNA present in the two ribosomal subunits then bond to create a peptide bond and the ribosome shifts one codon. The tRNA that was in the P site is then moved to the E site and is released leaving behind the bonded amino acid. The next matching tRNA enters the ribosome in the A site and then creates peptide bond with the tRNA now in the P site and the ribosome shifts one codon releasing the tRNA in the P site to the E site and this process continues until the ribosome reaches the termination point or the codon with the stop message and the two subunits of ribosomes unpair and the protein is released as well as the mRNA.

This complex process occurs in all of us and it the means of a cell knowing the appropriate genetic information like which proteins to produce to help with metabolic functions and essentially gene building. We need this genetic information to live and to make us who we are!

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Posted by on October 14, 2011 in Biology


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Cell Replication 10/11/2011

When you look at someone, all you are seeing is the finished product of a very complicated and meticulous process known as DNA replication. Cells go through several stages and restriction points when they undergo cytokinesis. On of the most important and complicated processes occur in the S-Phase (synthesis) stage. DNA replication takes place in this phase.

There were three proposed models of how DNA is replicated and they are the dispersive model in which the original strand of DNA would produce two DNA molecules with sections of both old and new DNA along each new strand of DNA, the conservative model states that the original DNA molecule will remain intact but a completely new strand will generate but the most logically plausible model is the one we use today called the semi conservation model in which would produce molecules with both old and new DNA, but each molecule would be composed of one old strand and one new one.

In this semi conservation model, a DNA Helicase binds to DNA and unwinds the DNA molecule from itself. To maintain the stability of the DNA molecule, single-stranded DNA binding proteins bind to the exposed purines and pyrimidines. The double helix shape of the DNA have “gaps” of six to eight visible nucleotides that are called the DNA’s major grove region so that DNA Polymerase 3 can bind to the DNA molecule and begin the continuous replication process of the leading strand of the DNA molecule. DNA Polymerases 3 can only read from the 5’-3’direction and since DNA is antiparallel this makes replicating the lagging or the 3’-5’ end a little more complex. This 3’-5’ end forms in Okazaki fragments where a RNA primase attaches to this strand and lays down the RNA primer and then DNA Polymerase 3 comes and makes DNA in the 5’-3’ direction and then DNA Polymerase 1 comes in and converts the RNA primers into base complementary pair DNA and finally Ligase comes in to fill the gaps of each fragment and this is the continuous method is repeated until the whole lagging strand is replicated.

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Posted by on October 11, 2011 in Biology


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