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The Genome

We will be looking at some tools that are used for measuring DNA and RNA - collectively known as nucleic acids. There are multiple objectives of performing these measurements. These include:

• characterizing organisms
• understanding particular processes (e.g. tumor growth)
• understanding development
• understanding diseases
• inferring evolutionary history
• characterizing a sample of mixed organisms

The genome is the set of all the DNA in the organism. This usually only refers to what is in the nucleus. Most cells have other places where DNA is stored such as the mitochondria. Plant cells have chloroplasts which have DNA. These other cell organelles are not always included when people talk about the genome. Most often when scientists are interested in these other cellular parts they will reference them specifically.

The DNA is a double helix, a sort of twisted ladder where the rungs are the "base pairs". These base pairs consist of two bound nucleotides which are designated C, G, A, T. C binds only to G and A binds only to T. This is why the cell has memory - you can split the DNA apart by breaking the rungs and reassemble it because of these matches. In a diploid population, most cells have two copies of each chromosome, and so of each gene.

The basic model states that every cell in an eukaryotic organism (excepting reproductive tissues) has the same genetic material, stored in a double helix.  Nowadays we know that this is not necessarily true. For example cancer cells often have mutations that cause them to differ from normal tissue and from each other.  And there are other examples where this might not be the case such as chimeric embryos. 

We are often interested in why cells differ. When the genetic material is identical, many differences depend on what DNA is active. Gene expression studies look at which genes are active and how active. Other studies look at the mechanism of how genes are activated or inactivated - i.e. gene expression regulation.  When the genetic material may not be identical differences in the DNA itself will be of interest, particularly when looking at cancer versus normal tissue or differences between individuals.  In those cases, we might look for differences in the DNA sequence (genomic variants) or for gene duplications or deletions (copy number variations). 

Some of the fundamental problems or questions that scientists ask include:

• What is the sequence of DNA?
• Which genes are active, where, when and how are they activated?
• How do changes in DNA or gene activation affect the organism?