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Chapter 21 Blog: Genomes, Proteomes, and Bioinformatics (Kimberley)

Page history last edited by KimberleyHausheer 13 years ago

A. Chapter Summary


          The genomes and proteomes of prokaryotes are much simpler versions of the genome and proteome of prokaryotes. They have fewer base pairs not only because they have fewer genes but also because they do not have many repetitive sequences. Prokaryote genomes consist of either circular, linear, or both circular and linear chromosomes and only have a single origin of replication. Prokaryotes also have plasmids which are relatively small pieces of circular DNA that are separated from the chromosome(s).

            Although the genome is known as the genetic material that codes for proteins the sequences that codes for proteins actually makes up only 2% of the entire genome. The rest of the genome is made up of repetitive DNA (59%), Intron DNA (24%), and unique noncoding DNA (15%).

          Transposable elements are short segments of DNA that move to different places in the genome. There are different types of transposable elements. DNA transposons are recognized by the sequence of inverted repeats on either end of the gene. Retroelements are transposable elements that move via an RNA intermediate. These are only found in eukaryotic cells and often contain genes that encode for reverse transcriptase and integrase. The function of TEs is not yet known. The selfish DNA hypothesis states that they are around because they want to be. They only cause problems when they insert themselves into the middle of an important gene which causes the gene to either not get coded or code incorrectly. Other theories are that TEs can provide a survival advantage and greater genetic variability. Transposable elements can cause gene duplications and gene deletions by causing homologous chromosomes to misalign during meiosis. Gene families are created when gene duplications occur many times and two or more homologous genes carry out the same function.

           The entire collection of proteins that a cell or organism produces is known as its proteome. Proteomes are often much larger than genomes because of alternative splicing and post-translational covalent modification. Splicing is the process where introns are taken out of the pre-mRNA. Alternative splicing is when different combinations of introns are taken out causing different mRNA sequences ultimately causing different proteins. Post-translational covalent modification include permanent and temporary modifications.

Different proteins categorized by function are metabolic enzymes, structural proteins, motor proteins, cell-signaling proteins, transport proteins, gene expression and regulatory proteins, and protective proteins.

            Bioinformatics means the use of computers, mathematical tools, and statistical techniques to record and analyze biological information. It was first developed once scientists started to realize that genes did not all work individually but instead the opposite that many genes and proteins can affect one thing. In order to look at the big picture they had to develop tools that could handle huge amounts of data and process it quickly. In the databases you can find if a sequence contain a gene, if a sequence contains a mutation that might cause a disease, where are functional sequences are located, what the amino acid sequence of the polypeptide encoded by that gene, and if there is an evolutionary relationship between two or more genetic sequences. There are many huge databases that are used around the world.


B. Useful Materials


The struggle for life of the genome's selfish architects.

This article is a review about transposable elements, their history, function, and the interactions that take place between the transposable elements and the genome. It is very similar to the information that is supplied by the book but the article goes into much more detail. Transposable elements were discovered over 50 years ago by McClintock but no one paid much attention to them. However recently in the past few decades the science community has started to increase it's interest. They play a major role in the evolution of the genome. They can also be very harmful though if they are inserted into the sequence of an important gene.

Added: 3/28/11 Source: PubMed


A Novel Unstable Duplication Upstream of HAS2 Predisposes to a Breed-Defining Skin Phenotype and a Periodic Fever Syndrome in Chinese Shar-Pei Dogs

During this experiment, researchers discovered that the gene that created the breed-defining skin phenotype also predisposes the dogs to periodic fever syndrome. They found that the genes that were the most important for determining this breed were found on chromosome 13. They discovered this by using genome-wide SNP analysis which is a part of bioinformatics, the last section of this chapter. Although it is not stated in the abstract I am assuming that they scan the entire genome for single nucleotide variance in the DNA sequence by using a computer. Chromosome 13 was also where they found the signal for the most susceptibility to the periodic fever syndrome. Next, they used dense targeted resequencing which may be similar to shotgun DNA sequencing but for a more defined area instead of the entire genome to try to find what exactly is happening. They found that due to an overlapping gene replication, which we learned about, the HAS2 gene is over expressed. HAS2 encodes the rate-limiting enzyme synthesizing hyaluronan (HA), a major component of the skin. When cracked, HA can overstimulate the immune system causing fever and inflammation which are symptoms of periodic fever syndrome. Therefore the HAS2 gene is pleiotropic, which we learned about in previous chapters, meaning that it affects more than one thing. Because of the overlapping duplication the gene is over expressed the dogs have the breed-defining wrinkly but are also more susceptible to periodic fever syndrome.

Added 3/27/11


Protein Data Bank

This is one of the databases that the book gives as an example. A database is when a large amount of data is collected, stored in a single location, and organized for rapid search and retrieval. It states that it is an archive that "contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies." It contains articles about many, many different article about different molecules, their history, function, cell processes, and how they are used today in labs. I really like this website because it is easy to use and very informational. I love the colorful pictures of all the molecules. I first found this website while I was doing the useful materials for a previous chapter.

Added 3/27/11


Human Genome Project Information

This is a website that tells everything about the human genome project. It explains the difference between proteomes and genomes. It explains how it was performed, what we learn from it, and how we use it. The Human Genome Project was a research effort to identify and map all human genes. Scientists had been discussing how to undertake this project since the mid-1980s. The Human Genome Project officially began on October 1, 1990, and was largely finished by the end of 2003. Some things we learned from it are that the average gene consists of 3000 bases, but sizes vary greatly. The total number of genes is estimated at 30,000. Almost all (99.9%) nucleotide bases are exactly the same in all people.


Comments (1)

Derek Weber said

at 1:54 am on Apr 2, 2011

Nice job.

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