On this page you are required to add two items (link to a website, video, animation, student-created slide show, student-created PowerPoint presentation) and one journal article pertaining to a topic in this chapter.  A one-paragraph summary must accompany each item describing the main idea and how it applies to the lecture topic.  Please see the PBWorks help guide for assistance embedding video and other items directly in the page.  I will also produce a how-to video on using tables to wrap text around items and other useful tips.  Please see the syllabus for organization and grading details.

This chapter was about the various aspects of genomes, proteomes, and bioinformatics.  The two types of genomes are prokaryotic and eukaryotic genomes.  Prokaryotic genomes are of interest because they can cause diseases, can be used to apply knowledge about more complex organisms, and eukaryotic cells most likely originated from them and a union with an archaeal cell.  Eukaryotic genomes are usually found in sets of linear chromosomes and extranuclear DNA found in mitochondria and chloroplasts.  Scientists want to sequence genomes because there is benefit from identifying and characterizing genes, gives more information to identify and treat human disease, improves strains of agricultural species, and establish evolutionary relationships.

A bigger genome size does not mean that the number of genes increases.  An increase in DNA usually corresponds to increasing cell size, cell complezity, and body complexity.   Eukaryotic genes have short DNA sequences that repeat a few hundred of several thousand times.  The coding region of our genome is only about 2%.   The rest includes introns/enhancers, unique noncoding DNA, and repetitive DNA such as telomeres or other sequences.  These sequences are different among individuals, leading to DNA fingerprinting uses these DNA polymorphisms to tell people apart.   

Transposable elements are DNA segments that move, or so called “jumping genes”.   Barbara McClintock discovered them in a species of corn.   These transposons have  inverted repeat, and their sequences make palindromes.  Transposase cuts the TEs at these sequences, and then relocates the TE into a different part.  RNA intermediates, which are only found in eukaryotes, contain reverse transcriptase, which uses RNA to make a complementary copy of DNA, and transposase.  These retroelements accumulate rapidly.  Alu elements are about 10% of the human genome.   It is unknown what transposable elements do- the selfish DNA hypothesis thinks of them as parasitic, while others say it may promote genetic variation. 

Gene duplications provide raw material for adding more genes into a genome by creating homologous genes- two of more genes being derived from the same ancestral gene, and is caused my misaligned chromosomal crossovers at prophase I.  One chromosome would get a gene duplication, one a gene deletion, and two would be normal.  Paralogs are two homologous genes within a single species, and a gene family are two paralogous genes that have related functions, such as the globin genes.

Proteomes are often bigger than genes (due to alternative splicing and post-translational covalent modification), and depend on the genome and gene expression.  These modifications can be reversible or irreversible, and can involve phosphorylation, methylation, and acetylation.    

Bioinformatics is the use of computers, mathematical tools and statistical techniques to record, store, and analyze biological information, and incorporates principles from a variety of subjects, not just biology.  

Useful Links:

1)  This image (submitted 3/27/11) shows the various types of reversible/irreversible post translational modifications, which can increase the size of the proteome in comparison to the genome.

2) This Youtube video (submitted 3/27/11) shows the various features of BLAST and how it is used in research.

3) This PubMed article, entitled the "Systematic documentation and analysis of human genetic variation in globin genes" talks about the different variations in those genes, as referenced to in the chapter.  14 paralogs came from a single ancestral globin gene, creating specialized globins based on differences in oxygen needs.