Chapter 21 Post

Buenos días! This chapter is all about genomes, proteomes, and bioinformatics! 


First of all, let's review/define exactly what these three things are:

• Genome - "the complete genetic composition of a cell or a species"
• Proteome - "the entire complement of proteins that a cell or organism can make"
• Bioinformatics - "a field of study that uses computers to study biological information"

My first useful material is this article from PubMed titled, "Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world." As you can tell from the title, it is all about bacteria and archaea genomics. Did you know the first bacterial genome was sequenced in 1995? Did you know the first archaeal genome was sequenced in 1996? Okay, maybe you did, but I didn't! I was born in '95, meaning it was first sequenced the same year as me! 16 years is a considerably long time, but in scientific terms, 16 years is nothing! These are a perfect example of "recent" advances. The article goes on to describe how analysis of hundreds of genomes has enabled scientists to form generalizations on the principles of genome organization and evolution. It mentions the importance of HGT, which stands for horizontal gene transfer. HGT "is a dominant force of prokaryotic evolution." The abstract also describes the mobilome (yes, another "ome"). The mobilome is the total of all mobile genetic elements in a genome, and includes viruses and plasmids. These are all extremely important to HGT.

My next useful material are these videos below from YouTube. The source is MindBites.com, otherwise known as "the dude in the pink shirt." I have used these videos numerous times, and I think the man always explains things in a simple and easy to interpret way. The first video is all about eukaryotic genomes. Unlike prokaryotes, eukaryotic chromosomes typically have a great amount of short repetitive sequences called repetitive DNA sequences. Repetitive sequences can be divided into two categories, moderately repetitive sequences and highly repetitive sequences. Repetitive DNA composes 59% of the genome of humans. That's a lot! Why do eukaryotes have so many of these? The reason is that much of it is derived from transposable elements.

The video above talks about the Human Genome Project. The Human Genome Project was a research effort to identify and map all human genes. In began in 1990 and was mostly finished by 2003. One of the major findings of the project was that humans only have about 35,000 or so genes while fruit flies have 13,600 and round worms have 19,098 genes. People aren't really that "high up" the animal kingdom as we once thought. 

I found another useful material describing the Human Genome Project. This article talks about the Human Genome Project Results. One of the topics mentioned, which we've described in class, is how human beings only differ from one another about 0.1%. So out of our 3.2 billion base pairs of DNA, only 10 million or so are different. The differences in base pairs are called single nucleotide polymophisms. Much more research is needed in SNPs, but the Human Genome Project has given us a great start.

Chapter 20 Post

Hola! This chapter is all about genetic technology. 


One of the really interesting topics is reproductive cloning. Reproductive cloning is defined as "the cloning of a multicellular organism." One of the most famous cloned animals was Dolly. Dolly was a lamb, the first cloned lamb. How did they create Dolly? The video below explains it in a quick, simple, yet informative manner. The first step is extracting the donor sheep's mammary cell and growing it in a tissue culture flask. Then, you have to extract another sheep's unfertilized egg and remove its nucleus. Next, the cells are fused together with electric pulses. The maternal proteins in the egg and the donor nucleus from the mammary cell initiate the development of the egg into an embryo. The embryo is then transferred into a surrogate sheep and pregnancy continues as normal. Then...bam! A lamb is born! It is genetically identical to the donor sheep. Cool, right? Unfortunately, I don't think we'll get to clone sheep in lab, but it's still interesting to learn about it. 

These guys are on the weird side and kind of wacky but they have all the right information. At least it's interesting!


Another really cool topic from this chapter was DNA fingerprinting. The video below shops how DNA fingerprinting works in forensic science. The process described in the video involves gel electrophoresis. Hmm? Wonder what that is? Just kidding! Haha hopefully by now you know this process. PCR should ring a bell too. DNA fingerprinting is done using PCR, amplifying short tandem repeat sequences (STRs). They are short DNA sequences that are repeated many times in a row. DNA appears as a series of bands on a gel. The similarities and differences of the bands show whether the DNA is the same or not. If your sample bands match one of your control bands, you know the DNA is from the same person. Science has contributed extremely to criminal justice!

The not as cool type of cloning is gene cloning. This interactive activity explains the process of gene cloning and allows you to make a clone! It explains plasmids, restriction sites, restriction enzymes, and much more! The animations are really good and I thought the activity was really informative. Have fun with gene cloning! If the above link doesn't work, go to this site and click on "view."

Chapter 18 Post

Hello! This chapter is all about the genetics of viruses and bacteria.


First of all, what are viruses? The textbook defines a virus as "a small infectious particle that consists of nucleic acid enclosed in a protein coat." What makes them interesting is that they are non-living, but still have a genome. They are considered non-living because they don't exhibit all seven properties associated with living organisms. Let's review the seven properties:

• Cells and organization - all organisms have an internal order, the simplest unit of organization being the cell
• Energy use and metabolism - all organisms need energy to sustain internal order and metabolism is collectively known as energy used in chemical reactions
• Response to environmental changes - all organisms respond to the environment to aid their survival
• Regulation and homeostasis - all organisms regulate their bodies and exhibit homeostasis, which is maintaining stable internal conditions
• Growth and development - all organisms increase size and/or number of cells and produce a defined set of characteristics
• Reproduction - all organisms must reproduce to sustain life over many generations, and offspring tend to have similar traits to their parents
• Biological evolution - populations of all organisms change over many generations, and evolution is important to promote traits that aid in survival and reproduction

Viruses are not living things for multiple reasons. First of all, viruses are not composed of cells. In addition, viruses cannot solely carry out metabolism, use energy, maintain homeostasis or reproduce. In order for a virus to "reproduce" or replicate, it must be taken up by a living cell.


However, viruses cannot just come along and infect any cell it'd like. It can only infect a cell or species in it's host range. For example, tobacco mosaic virus (TMV) can infect over 150 different species of plants. TMV is considered to have a broad host range. In contrast, some viruses can only infect a single species. Some are even more specific and can infect only a specific cell type in a species!


What's the structure of a virus, you ask? They're about 20 to 400 nanometers in diameter. That's considered relatively small, because most bacterium are 1,000 nanometers in diameter. All viruses have a protein coat called a capsid that encompasses a genome that consists of one or more molecules of nucleic acid. They're composed of protein subunits called capsomers. There are a bunch of shapes capsids can be, including helical and polyhedral. The structure of the tobacco mosaic virus (TMV) is helical, as shown below.

The structure of a virus with a helical capsid.

An additional capsid shape I mentioned was polyhedral and below is what that looks like.

The structure of a virus with a polyhedral capsid.

If you look at the virus with a polyhedral capsid (above), you can see a labeled structure called an envelope. Many viruses that infect animal cells have viral envelopes that enclose the capsid. It is comprised of a lipid bilayer that is derived from the host cell's plasma membrane and is embedded with virally encoded spike glycomers.


Spike glycomers aren't there for decoration, they help viruses bind to the surface of a host cell. Bacteriophages (viruses that infect bacteria) tend to have complex protein coats and accessory structures used for anchoring the virus onto a host cell and inserting the viral nucleic acid.


The genetic material of a virus is called a viral genome. Some viruses have nucleic acid of DNA and others have RNA. The genome can be linear or circular, depending on the virus. Some viruses have multiple copies of the genome. Genome sizes vary greatly, from a few thousand nucleotides to over a hundred thousand nucleotides in length. The extra nucleotides encode for extra genes, which in turn encrypt for many proteins involved in virus structure. 


Viruses are a great example of structure = function. Every component and detail of a virus has a specific function.


Although viruses aren't living organisms, they exhibit a "viral reproductive cycle" which is the expression of viral genes over a series of steps that result in the production of new viruses. Scientists have determined there to be five/six general steps to the viral life cycle, although each virus is unique and the steps vary among different types of viruses.


The video below describes HIV virus infection and replication. HIV stands for human immunodeficiency virus and is the virus that caused AIDS in humans. There were many videos of HIV replication on YouTube, but I found the one below to be the best.

The video talks about all of the stages of the HIV viral life cycle. These include attachment, entry, integration, synthesis, viral assembly and release. The first step is infecting a suitable host cell. There needs to be certain receptors on the cell surface for HIV to enter the host cell. The receptors interact with protein complexes in the viral envelope. Then the video shows a cool animation of entry which is difficult to describe, but you'll see it. 


In addition, the video talks about all of the key enzymes used in the process, including reverse transcriptase. Reverse transcriptase looks really complex and cool in the video! But the most awesome is integrase! It cleaves a dinucleotide from each 3' end of the DNA, creating two "sticky ends." It then transfers the DNA into the cell nucleus, integrating it. The genome the has HIV's genetic information. It looks really cool in the video! The video goes on to describe the other steps leading up to the virus exiting the cell. Also, the video talks about the effect of drugs on the HIV virus (on a molecular level). I don't know why, but I thought the sound of the inhibitors were really cool, kind of like a drum. This was an overall very helpful video because of the good information and great visuals.


Another virus that the book (and I) have mentioned is the tobacco mosaic virus, abbreviated TMV. This article from Scientific American is titled, "Tobacco Plant Transformed into Plague Vaccine Factory." TMV was the first virus to be discovered. It infects plant species and causes "mosaic-like patterns in which normal-colored patches are interspersed with light green or yellowish patches on the leaves." Tobacco mosaic virus almost never kills the plant it infects but does damage leaves, flowers, and fruit.

A plant infected with tobacco mosaic virus (TMV).

The article describes how the tobacco plant and TMV knowledge has helped scientists make vaccines. The "plague" or "black death" of the Middle Ages was one of the worst diseases in human history. To prevent any such catastrophe from occuring again, researchers used tobacco plants to make plague vaccines. Charles Arntzen and others at Arizona State University injected tobacco plants with TMV to make plague antigens. They're proteins known as F1, V and a combination of the two. The three "modified viruses" penetrated the plants and produced antigens. Arntzen and his colleagues had "a full crop of tobacco leaves filled with vaccine" in only 10 days! 


They then tested the vaccines on guinea pigs exposed to Yersinia pestis, the bacteria responsible for airborne plague. All of the guinea pigs not vaccinated died within a week, but 60% of the vaccinated guinea pigs survived (the ones who died lived longer than a week)! The V antigen was concluded to be the best because 75% of V antigen vaccinated guinea pigs survived. This vaccine could be imperative to human survival if the plague were to ever resurface.


All we've been talking about are viruses so far, but don't think I've forgotten about bacteria!


One of the topics we've discussed in class is horizontal gene transfer, something bacteria can do, but humans can't. This article from PubMed is titled, "Adaptive horizontal transfer of a bacteria gene to an invasive insect pest of coffee." Horizontal gene transfer is defined by the book as, "a process in which an organism incorporates genetic material from another organism without being the offspring of that organism. Horizontal gene transfer among animals is very rare, but possible. The HhMAN1 gene from the coffee berry borer beetle expresses horizontal gene transfer. The beetle is a pest that destroys coffee beans. HhMAN1 encrypts a mannanase (any enzyme that catalyzes the hydrolysis of mannans), "representing a class of glycosyl hydrolases that has not previously been reported in insects." So how did they get there? HhMAN1 horizontal gene transfer probably is because of intensive agricultural practices. This is validated by the fact that closely related species don't colonize coffee beans.

An illustration of Hypothenemus hampei (the coffee berry borer beetle). I would have uploaded a real picture, but trust me, they are disgusting looking! 

That's all for my chapter 18 post! Sorry for it being kind of on the long side.