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

Page history last edited by Erica Choi 12 years, 1 month ago

A. Blog

The major characteristics and variations of prokaryotic genomes is probably that it can be circular or linear, commonly circular, it's usually small and around a few million base pairs, and even though it's usually only one or two different chromosomes, these two chromosomes can be replicated multiple times. Plasmids are self-replicating usually circular DNA that can be found in bacteria. These plasmids contain genes that code for things that help them in the environment; for example the F factor carries genes for mating with other bacteria, the col-plasmid carries genes for killing other bacteria, degradative plasmids have genes that allow the bacteria to digest unusual things, virulence plasmids allow a strain of bacteria to turn pathogenic, and a resistance plasmid allows a bacteria to be resistant against toxins.


The different classes of DNA sequences in the human genome is repetitive sequences, which can be highly or moderately repetitive sequences that don't do much for the cell itself.  These sequences are kind of like parasites in the sense that they don't really serve a purpose but to be in the genome and just chill there. Unique noncoding DNA is the other portion of the genome, which is exactly that, DNA that doesn't code for anything but we do not yet know it's purpose.  Introns and other parts of genes like enhancers, and the last 2% codes for all of the other important genes like proteins from exons that eventually make things like mRNA and tRNA. Transposable elements are genes that can jump from one part of the DNA to another! They are like parasites in the sense that they are in our genome solely because they can insert themselves there.  Gene families are homologs within a certain species, and they tend to have similar transposable elements that may benefit a certain species. 


The genome of an organism is all of the genes of an organism, but the proteome of an organism is all of the proteins expressed.  Thanks to post-translational modifications and alternative splicing, there is usually more proteins produced than there are genes! So proteome>genome.  The categories of these proteins include: metabolic enzymes which can accelerate chemical reactions in the cell, structural proteins that provide shape and protection to cells, motor proteins that facilitate intracellular movements and movements of whole cells, cell-signaling proteins which allow cells to respond to environmental signs and send signals to each other, transport proteins that allow the transport of ions and molecules across membranes and throughout the body, protective proteins that help cells and organisms survive environmental stress, and lastly gene expression and regulatory proteins which are involved transcription, mRNA modification, translation, and gene regulation.


Bioinformatics is basically the collaborative knowledge of technology, math, and statistics to study biological information.  A bioinformatics database would contain information like gene sequences, gene mutation sequences, functional sequence (promotors, regulatory sites, splice sites), amino acid sequences in a gene, and evolutionary relationships between multiple sequences.  This information comes from information that has been collected for decades.  Researchers and clinicians have been collecting information and storing it in several databases from multiple laboratories. BLAST search might provide insight into a newly-discovered DNA sequence when you plug in your sequence and it does not match up with anything in the database.  This is done by matching the sequences that could code for the same protein to see if the sequence would produce the same affect as that protein would. 


B. Useful Materials

BLAST  I know we used BLAST as part of our last exam, but it was still a little unclear to me exactly how it works, and I thought that this wiki link described it pretty well. It gives a little bit of its background, and how it locates similar sequences/amino acids.  
  We learned about transposable elements and how McClinock discovered this in corn.  This virtual lecture describes this discovery further.  
Reverse Transcriptase 

This is actually an excerpt from a book about retroviruses.  In this excerpt the researchers describe how reverse transcription works, and how Temin and Mizutani's discovery of this in 1970 changed all the previous beliefs, opinions, etc. of molecular biology.  It then describes how now, we see reverse transcriptase in diseases like AIDs and how the discovery of reverse transcriptase has greatly impacted biology today. 




Comments (1)

Derek Weber said

at 2:45 am on Apr 1, 2011

Not updated.

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