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.

Telomerase Structure, Function, and Biogenesis

Telomerase is an enzyme, more specifically a reverse transcriptase, that adds telomeres to the ends of DNA. Telomeres is the end of a eukaryotic chromosome, consisting of a short nucleotide segment that repeats from a few dozen times to several hundred times. They basically make up for the inability of DNA polymerase to fully replicate the 3' linear chromosome ends. Telomerase consists of two parts, TERT (catalytic telomerase reverse transcriptase) and TR (telomerase RNA), and functions as a ribonucleoprotein. There have also been several accessory proteins that have been identified that function in the regulation, biogenesis, and localization of the enzyme. Understanding telomerase's molecular mechanisms is essential to developing therapies for disorders and cancers that are related to telomerase.


Idiopathic pulmonary fibrosis, or IPF, is the most common type of telomere-related disease. Mutations in hTERT and hTR genes are the cause of the defect. These mutations can lead to extra-pulmonary complications that result from telomere shortening. These complications include bone marrow failure. There is also evidence that points towards IPF being a manifestation of telomere syndromes that were autosomal dominant. With each generation, it evolved from pulmonary fibrosis to disorder that is predominantly related to bone-marrow failure. The article goes on to explain the the significance in defects of telomere for understanding the disease patterns, pathophysiology, and genetics of idiopathic pulmonary fibrosis. 


To see the articles that I got my information from click here and here.

The Value of "Junk" DNA

The genetic blueprint of human beings consists of 23 linear chromosomes that contain 3.42 billion nucleotides. The genetic blueprints of most mammals consist of similarly significant amounts of nucleotides. Some extremes in nucleotide numbers do occur in mammals, such as the red vischaca rat (8.21 billion nucleotides) and the bent-winged bat (1.69 billion nucleotides). Regardless of what kind of animal, there is a large excess of DNA that does not code for proteins. Approximately 2% of DNA codes for proteins in humans. For several decades, scientists were confounded by the purpose of such "junk" DNA, which often consisted of repeating segments that are dispersed throughout the genome.


These repeating segments come about when sections of DNA move within the genome to different positions. This process is called transposition. Biologists now believe that these transposable segments are not useless, but instead provide greater ability for the organism to evolve. They serve as areas for genetic recombination and provide new signals for genetic expression. Genomes are dynamic, with certain elements becoming extinct as new elements appear. Functional DNA can therefore be created from "junk" DNA. The term "exaptation" is used when describing how genetic entities can change their role, despite their original role if they had one at all. For example, biologist Gill Bejarano discovered a DNA fragment that was exapted as an enhancer, increasing gene transcription, when it had originally inserted itself anywhere into the genome.


DNA sequences that are nonfunctional in certain organisms could be functional in others, becoming an exon that is transcribed to messenger RNA. While non-functional DNA can be seen as "junk" DNA they actually do actually have a role in the genome. These segments are important to evolution. To access the article that I retrieved my information from, click here.