Objectives

1. Learners will further investigate how a library is like a nucleus.
2. Learners will be taught to about junk DNA.
3. Learners will review alternative splicing and how coding sequences are used to make products in the factories.

Every town library contains a variety of books.  Some of these books are necessary for the production of the goods in the town factories.  Encyclopedias, dictionaries, and other non-fiction books are examples of these necessary and useful books.  However, a library may also contain gossip magazines, tabloids, and fiction novels.  These types of reading materials are useless to the town factories.  The information they contain is not typically necessary for the production of goods in the town.

The useful books in a library, those necessary for the production of goods, are analogous to the DNA in the nucleus of a cell that is essential for the production of proteins.  Encyclopedias and dictionaries are highly integral resources and will be virtually identical in all libraries.  Other non-fiction books are useful as well, but not every library may have exactly the same non-fiction books.  The useless gossip magazines in our library are analogous to what is commonly called "junk DNA".  (This will be covered later).

Soon, other magazines in the Town B library start to do the same thing to many of the library's useful books. This causes the encyclopedias, dictionaries, and reference books to grow larger and larger. 

Since the gossip magazines, have very little (or no) value, they are not making the encyclopedias, dictionaries, and reference books more valuable to the readers. They might eventually even cause some sections of them to become unreadable.

In the beginning the books in Town A's library were identical to the books in Town B's library. However, as the magazines kept inserting copies of themselves into the dictionary from the Town B library, the dictionary grew in size.

If this happens to many or all of the books in Town B's library, the library could become huge. Since Town A's library had all of the same books to start out with, and had no "jumping magazines", it will stay the original size.

Just like the "jumping magazines" in our library example, our DNA has mobile segments called "jumping genes" or "jumping DNA".  These mobile segments randomly insert themselves into the genome of a cell in the same way that the pages of the gossip magazine were inserted into the dictionary.  There are two types of "jumping genes":  transposons and retrotransposons.

Transposons are segments of DNA that move around to different positions in the genome of a single cell.  They can cause mutations and change the amount of DNA in the genome.  Transposons can randomly "cut and paste" their way through the genome.  A transposon segment is cut out of its location and then inserted into a new location within the genome.  Retrotransposons are a bit more complicated.  They move by a method of "copy and paste".  However, the copy is made of RNA, not DNA.  After the RNA copies are made they are transcribed back into DNA.  These DNA copies are then inserted into the genome. 

Transposons and retrotransposons have been referred to as "junk DNA" because they provide no obvious benefit to their host.   They have been called "selfish DNA" because their only function seems to be spreading through the genome, and in the case of retrotransposons continuously replicating themselves.

The genome is the complete set of chromosomes inherited from a single parent; all of the DNA of an individual. The genome size is the amount of DNA in a genomic set, also called the "C value". The "C" stands for "constant", since the size of a genome is usually constant for each species. It is measured by the number of bases in the genome of a certain species.

Figure represents genome size.

A paradox is a seemingly contradictory statement that may nevertheless be true. As we compare the C values of different organisms, we find that even though some organisms seem to be closely related, they have C values that are very different. Some of these organisms appear to have much more DNA than their close relatives. The "C value paradox" refers to the observation that there is no correlation between the amount of DNA  in an organism and the complexity of that organism.

Corn (maize) and rice seem to be very similar, after all they are both a type of grain. However, corn has a much larger genome than rice (the c-value of corn is much larger than the c-value of rice).  The corn genome is roughly six time the size of the rice genome!

Why is the corn genome so much larger than the rice genome?

The difference in the genome sizes is primarily related to the number of retrotransposons they each possess.  Corn has large amounts of retrotransposons (junk DNA) while rice has comparatively few copies.  In fact, over half of the corn genome is made up of these repeating sequences or  "jumping genes".  Obviously, retrotransposons can play a large part in determining the size of a genome.

Repeating sequences of DNA, or "junk DNA", are inherited. Some different species of animals have been found to have identical patterns within their repeating DNA. One example of these patterns of DNA have been found in the genomes of both hippopotamuses and whales, but was not found in other species. 

This discovery strongly supports the idea that the hippo is the closest living relative of the whale.  It is amazing to think that a land animal evolved into a whale, but, then again, whales are mammals.  Whales have live births, and the mothers feed their babies with milk, just like their ancestors that lived on the land.  Furthermore, hippos, like whales, are hairless, and they nurse their infants underwater and communicate by underwater sound, as do whales. 

Hippos and whales have inherited this pattern of DNA from a common ancestor.  Researchers look for large patterns in the repeated DNA that are placed into the same spots on the chromosomes of different species.  This allows researchers to determine evolutionary relationships between organisms.

In addition to books, the libraries in our towns have 3-ring binders full of loose-leaf pages (one binder per library). The majority of the pages are white, but there are some blue pages too. The white pages in the binder have coding sequences on them. These coding sequences are used to make products in the factories. The blue pages have letters on them, but no coding sequences. 

The letters on the blue pages instruct the person who photocopies pages from the binder  which white pages to photocopy. These instructions will vary depending on the time of day, street address of the business or factory, and the town the person is in. Thus, different people will copy different combinations of white pages out of the binder. Someone could photocopy all of the white pages, but others will photocopy only a portion of the binder. Different sets of white pages will code for different variations of a product.  

For instance, if a town factory made bicycles then one set of white pages may code for a red bicycle, another for a red bicycle but without wheels, and yet another for a red bicycle without a seat.  The greater the variation between two sets of white pages, the more variation there will be in the bicycles.   Also, if two sets of white pages differ by even just a single page, they will end up making slightly different products.  (Such as a slightly different color).

Different combinations of white pages give us different options for our bicycle.

The white pages in the 3-ring binder serve the same function for a town as exons do for a cell.  Exons are the coding regions of a  gene, they code for protein functions.  Exons are represented in the final mRNA so they are "expressed" in the final "product" (protein) in the same way that the white pages are represented, or expressed, in the final product that the factory will make. 

The blue pages in the binder are analogous to introns.  Introns are noncoding regions of a gene.  They are not represented in the final mRNA so they are not expressed in the protein (just as the blue pages are not represented in the factory product).

Ligase is an enzyme that can link together pieces of DNA.  The process of  bundling together pages out of the 3-ring binder in different combinations is similar to the process of ligation.  Ligation is the process of joining two pieces of DNA together.