Useful Materials for Chapter 13

I liked the video above because  it describes gene regulation in both prokaryotic and eukaryotic cells. The visual displays were highly beneficial to the understanding of the processes he speaks about. I particularly liked that the video references both the lac operon and the trp operon, both of which we discussed in class. The pictures were very clear, and helped me understand the topic better. Both negative and positive controls are discussed, and overall the video is thorough, clear, and concise. At only 10 minutes in length, it is certainly worth watching if anyone is having difficulty understanding some of the more general concepts regarding gene regulation.


Click here for a link to vocabulary words on prokaryotic gene regulation. It may help you remember some terms found in this chapter if you are a person who uses flashcards as a learning tool.


If you are having difficulty understanding the trp operon, which is perfectly understandable, click here to access a tutorial on the subject. It includes images, animations, and a quiz at the end to ensure that anyone can  benefit from using the tutorial. The animation is step-through as well as narrated, and may help you understand the topic if the book simply is not doing it for you.

The Role of Methylation in Gene Expression

There are several methods of controlling gene expression in eukaryotes, of which methylation is one. This is a tool in epigenetics that allows cells to "turn off" genes. Epigenetics is the control of genes by factors not related to an individual's DNA sequence. These types of tools determine what proteins are ultimately translated and function. Preserving chromosome stability, genomic imprinting, and embryonic development all involve DNA methylation, and errors in methylation have been linked to several serious human diseases. Early experiments with 5-azacytidine, which inhibits DNA methyltransferase enzymes, allowed scientists to investigate how DNA methylation impacts cell differentiation and gene expression.


DNA methyltransferase enzymes convert the cytosine bases of eukaryotic DNA to 5-methylcytosine. This cytosine is located next to a guanine nucleotide. DNA methylation's exact role in gene expression is currently unknown, although it is possible that it blocks promoters to which transcription factors would otherwise bind. Methylation of promoters has been linked to low or no transcription. There are differences in methylation levels in different tissue types as well as between normal and cancerous cells. 


Histone methylation patterns have been found to change dramatically through the cell cycle. Some studies have shown that DNA and histone methylation are connected, such as in studies that show DNA and histone  methylation working together to ensure that proper methylation patterns are passed on to daughter cells during translation. Sometimes, when DNA is methylated, deacetylation occurs in nearby histones. This allows for a stronger inhibition of transcription. Similarly, DNA that is not methylated does not attract deacetylation enzymes to nearby histone proteins. Methylation is generally a long-term process, but it can also allow for "epigenetic reprogramming".





Research is currently being conducted into the connection between methylation errors and diseases, including lupus, cancer, and muscular dystrophy. Tumor suppressor genes have been found to be silenced in cancer cells due to hypermethylation. Overall, methylation rates in cancer cells are much higher than in normal cells. In certain cancers, hypermethylation can be a marker for diagnosing cancer, as it may be detectable in early stages of the cancers.


Click here for the link to the article from which I retrieved my information. 

Octopi Respond to Environment Through RNA Editing

To start off with, the most commonly accepted plural form of the word "octopus" turns out to be "octopuses". "Octopi" and "octopedes" have also been used as plural forms, but they are more objectionable. In my blog, I will be referring to more than one octopus as octopi simply because I think it sounds better, no matter how objectionable the term may be. And also because I can.



Genetic mutations are responsible for the existence of complex creatures. The complexity of creatures can also be attributed to RNA editing, in which enzymes are altered without impacting organisms' genetic blueprints. RNA editing has allowed organisms to regulate essential functions, including the development and function of nervous systems. Octopi have provided evidence suggesting that this type of editing has allowed them to adjust to external, environmental changes in addition to internal changes. Researchers have investigated how this editing has allowed octopi to live in warm and cold bodies of water. These editing tools have helped them acclimate to different environments.


Cephalopods have been seen doing much RNA editing. Different processes can be fine-tuned in different organisms with the same genetic makeup. Since octopi are cold-blooded, temperature differences can have an impact on neural pathways. Nervous system communication is dependent on neural firings. These firings are started by sodium-ion channels and stopped by potassium-ion channels. Both of these channels slow down in cold temperatures, with the potassium-ion channels slowing significantly more than sodium-ion channels. RNA editing plays a role here, as one Antarctic octopus's editing locations allowed for an increase in the rate of the potassium channel closing. This allowed for the channels to become closer in rate. Other species of octopi, such as those living in Arctic and tropical waters, have also displayed RNA editing.


There is more than one response to the environment that requires RNA editing, and it certainly does not stop with temperature regulation. Scientists have discovered about 100 editing sites in just eight mRNAs. They are also editing the RNA that edits, allowing for greater diversity in enzymes that edit.


Click here to access the article from which I retrieved my information.

Useful Materials for Chapter 12

The video above explains the role of transcription factors in transcription. This helped me understand how transcription factors can help in gene regulation. It is a brief video with interesting animations that allow you to visualize the process. Please excuse the strange music; it seems the majority of bio videos online have some form of strange music on them.

This next video is on ribosomes and how they work in translation. I found this interesting because it shows the assembly of the ribosome, which occurs after encountering the mRNA in the cytoplasm. The video also explains the initiation factors that are involved in ribosomal activity, as I described in my previous post.

As always, I recommend Khan Academy videos if you are having difficulty understanding the concepts presented in the chapter. This video takes you back to DNA structure, then walks you through transcription and translation.

Translation: DNA to mRNA to Protein

Translation occurs using ribosomes, which are present in the cytosol of eukaryotic cells. mRNA of eukaryotic cells has to leave the nucleus and move to the cytoplasm for translation to occur. In prokaryotic cells, ribosomes are capable of attaching to the mRNA while it is still being translated from DNA.This is possible since the translation begins at the 5' end of the mRNA and transcription produces mRNA in a 5' to 3' direction, so the 5' end is created first. Since transcription and translation are done simultaneously, mRNA is more short-lived compared to that of eukaryotes. The multiple steps involved with the translation of mRNA in eukaryotic cells allow for greater ability to regulate protein production.

Ribosomes are composed of two subunits, a large one and a small one, that assemble at the mRNA and otherwise exist separately in the cytoplasm. The ribosomes contain proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). tRNA are adaptor molecules with a 3' end and an anticodon. The anticodon reads the triplet codon of the mRNA using complementary base pairing and the 3' end is attached to a particular amino acid. rRNA catalyzes the addition of amino acids to the growing protein.

There is an area of the mRNA near the 5' end that is not translated, and is known as the UTR or untranslated region. The UTR is located between the first nucleotide and the start codon of the mRNA strand. The UTR is important to translation because it provides a binding site for the ribosome. The human mRNA UTR is typically about 170 nucleotides long. Translation begins after a complex is formed on the mRNA strand. First, three initiation factor proteins bind to the smaller ribosomal subunit, after which this complex along with a tRNA that contains methionine bind to the mRNA that is being translated, close to the AUG start codon. While methionine is the first amino acid of all new proteins, it can be removed after translation. The second amino acid on the protein influences whether or not an enzyme removes the initial methionine. For example, if the amino acid alanine is the second amino acid, then the initial methionine is removed by an enzme. If the second amino acid is lysine, then the methionine is not removed.

The initiation factors are removed from the initiation complex on the mRNA when the large ribosomal subunit binds to the complex. This subunit contains three sites that the tRNA can bind to: an A site, an E site, and a P site. The mRNA codon and the aminoacyl-tRNA anticodon pair up at the A site to ensure that the correct amino acid is added to the polypeptide. The P site is where the amino acid on the 3' end of the tRNA is transferred to the polypeptide chain. The E site is where the "empty" tRNA stays before it is released into the cytoplasm. Only a tRNA containing methionine is able to bind to the ribosome's P site while the second mRNA codon lines up at the A site.

The ribosome moves along the mRNA in a 5' to 3' direction and covalently binds amino acids to one another, producing a polypeptide. This process requires GTP as an energy source and elongation factors. When the tRNA-amino acid complex binds to the A site, GTP is cleaved to form GDP and is released with certain elongation factors and is later recycled by other elongation factors. Peptidyl transferase activity binds the first and second amino acids together. This is a catayltic function of rRNA, although this process was originally thought to have been catalyzed by enzymes. Once the bond is formed, the ribosome shifts so that the now-empty tRNA molecule is in the E site. The tRNA is then released by the ribosome into the cytoplasm, where it picks up another amino acid to repeat the process. The A site is also empty for the next tRNA molecule that corresponds to the next codon. The protein-coding sequence of mRNA ends with UAA, UAG, and UGA. tRNAs do not recognize these codons and another protein, called a release factor, binds to it and causes the polypeptide to be removed from the ribosome and the ribosome disassociates.

Silencing Genes to Prevent Infection

Electron Micrograph of Ebola Virus Particles

Ebola is a virus that causes a deadly hemorrhagic fever and is spread through contact with blood and contaminated needles. About 85 percent of the reported human cases of Ebola have resulted in death. The use of vaccines has protected monkeys, but are only effective when given prior to exposure to the virus. A team of scientists, including Thomas Gesibert, was initially attempting to boost host immunity for people exposed to the virus, but later turned to muting the virus's genes. This would at least buy time for other treatments, including the vaccine, to start working.


Gene silencing, or RNA interference (RNAi) occurs naturally. Some portions of DNA are transcribed into RNA, which are then translated into proteins that keep our cells functioning. However, there are other stretches of DNA that are transcribed into siRNA, or small interfering RNA, that is not translated into proteins. Instead of being translated into protein, these RNA strands are bound to portions of other RNA strands that have complementary sequences. This prevents the RNA from being translated into proteins and offers greater control over gene expression. Geisbert and his team attempted to artificially replicate this process to work on Ebola by creating siRNA that would bind to polymerase L, a gene that is vital for replication to occur.


The researchers were able to silence the gene and prevent replication effectively in cell culture studies, but encountered a new problem when testing the approach on animals infected with Ebola. "Naked" siRNA in blood and body tissues is broken done by enzymes. When the synthetic siRNA was injected into the test animals, the researchers needed to develop a "vehicle" that the infected cells would take up so that the siRNA contained within it would not be broken down by enzymes. The initial packaging system was ineffective, but Geiser then packaged the siRNA into SNALPs, or stable nucleic acid lipid particles. Cells like dendritic cells and macrophages are targeted by Ebola and were capable of taking up the SNALPs, resulting in a successful test with siRNA-containing SNALPs when used on guinea pigs.


When testing the approach on monkeys infected with Ebola, Geiser also included siRNAs to target viral genes that are thought to inhibit the immune system. They injected the SNALPs containing the siRNAs into the monkeys 30 minutes after injecting Ebola and injected the SNALPs every day for a week as well. After seven days, all of the monkeys were virus-free. Gesier hopes to push his approach to work on people infected by Ebola up to 24 hours after infection.


To access the article that I got my information from, click here.

Useful Materials for Chapter 11

The video above reviews the process of how DNA is packaged, how it replicates, and the various proteins and enzymes involved in the process. I found this to be really interesting because it looked less cartoon-ish than biology videos tend to be. It also goes more into topics that we had not focused on in this chapter, such as DNA transcription into RNA. If you are looking for a more detailed version of what we have learned in class, I suggest looking at the lecture I have posted below. I recommend this video particularly for people who have not grasped the basics that are necessary for truly understanding DNA replication. These basics include the structure of the nucleotides in DNA and how this relates to the process of replication. It also goes into more detail about the roles of the various enzymes involved in DNA replication.

There are several parts to this lecture that can all be found on youtube.