In the first section of this page, you will write a daily summary of that day's class.  For example in  your chapter 2 blog, your first entry should be titled 9/3/10.  You should then write a one or two paragraph summary of that day's lecture, outlining the major points.  In the second section, 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.

A.  Daily Blog

21.1: This section discusses bacterial and archaeal genomes. These are prokaryotic cells, and their genomes are usually on a circular chromosome that has a few thousand genes. The genomes of over 700 prokaryotic species have been mapped, which are usually a few million base pairs long. They are tightly coiled, and inside the bacteria are are plasmids. Plasmids are short, circular pieces of DNA that exist separately from the rest of the chromosome. They have many different functions, including resistance, degradation, killing other proteins, turning bacteria into pathogenic strain, and allowing bacteria to mate with one another. In 1995, the first genome was mapped out, using shotgun DNA sequencing, a technique that randomly sequences many DNA strands. This is a quick way to sequence the DNA, however many times strands are sequenced multiple times. 

21.2: Eukaryotic genomes are very different. They can range in nuclear genomes, size and repetitive sequences. Only 2% of the genome is actually used for coding, while the rest are either repetitive sequences, introns, and noncoding sequences. Repetitive sequences can be either moderate or high, and are not entirely understood. They can play a role in regulating gene transcription and translation, but research is still being done. 

Transposable elements move from one site on the genome to another, using transposase to aid their movement. They have inverted repeat sequences on either ends, which are recognized by transposase and cling to the new part of the genome. There are also retroelements, which are transcribed, synthesized, and then placed in the different part of the genome. Scientists are unsure as to why these elements exist, and what their overall function is to the cell.

21.3: Genomes are much smaller than proteomes because of alternative splicing. This can create many new proteins, which enlarges the size of the proteome while using the same genome. There are metabolic enzymes, which accelerate chemical reactions in the cell, structural proteins, which provide shape and protection to the cells, motor proteins, which aid in intercellular movement, cell-signaling proteins, which allow cells to respond to signals and send signals, transport proteins, which transport ions and molecules across the cellular membranes, gene expression and regulatory cells, which help in transcription, translation, modification of mRNA and gene regulation, and finally there are protective proteins, which help the cell survive through stress. Cells can also have a larger proteome than genome because of post-translational covalent modification. These can be permanent or reversible, and increase the forms of proteins in the cell.

21.4: Information stored in the bioinformatics database is analyzed and stored into computers to be available for any given scientists. This information includes gene sequencing, mutations, functional sequences, evolutionary relationships, and if the amino acids coded in the genes. This information comes from many scientists inputing data and experimental results for many years. Nucleotide sequences, amino acid sequencing, and 3D structures are all available in the database. BLAST is used to 

B.  Useful Materials

http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml

We had discussed the Human Genome Project in class, about how the entire genome of humans was mapped out and analyzed. This page describes the project and how information was gained. It also discusses results and what the next step should be in science.

http://www.dnatube.com/video/2997/Alu-repeats

This video discusses what the human genome is made up of. This includes the Alu repetitive sequence, and how repetitive sequences are helpful to the human genome.