1. homologous chromosomes
2. chromatids
3. alleles
1. homozygous alleles
2. heterozygous alleles

We're moving into the third characteristic of life: genetics and reproduction, beginning with the definition of a gene: a nucleotide sequence in the DNA that codes for a specific protein (process: protein synthesis).

1. Chemical composition
   The genetic material (DNA and its associated proteins) does not leave the nucleus of a cell. It can be in either chromatin or chromosome form: chromatin form when the DNA and associated proteins are relaxed such that the DNA can be replicated or transcribed. In chromosome form, the genetic material is tightly coiled (and, therefore, unable to be replicated or transcribed).
1. DNA
   The DNA is the actual genetic material; (we've been through the structure.)
2. Proteins
   Proteins associated with the DNA function in its doing its genetic thing.
1. Structural
   One of the roles of proteins associated with DNA is structural, as we'll discuss under 'nucleosomes' below.
2. Enzymes
   We've discussed the functional necessity of enzymes; they are vital, as well, to the genetic processes of DNA.
2. Structure and organization
   What determines the form the genetic material takes, be it chromatin or chromosme? Nucleosomes.
1. Nucleosomes
   10.1 Nucleosome
   A nucleosome consists of 4 pairs of histone proteins and the DNA coiled around them.
1. histones form the core
   The four pairs of histones that form the nucleosome core function in coiling the DNA: some of these histone proteins have a positive charge, attracting the negative charge on the phosphorous end of the DNA. Thus, the DNA coils around the histones in a very precise way.
2. DNA coil
   In the above manner, the DNA is coiled around the 8-histone core like a spring.
2. Spacer protein (also a histone)
   A fifth type (H1, or spacer) is important in controlling the spacing between 6 nucleosomes: functioning to either relax them (chromatin form) or to condense them (chromosome form). If we compare the nucleosomes to a spring (the coiled DNA) containing groups of 8 attached proteins (histone core--as shown in the diagram), then the spacer protein is like a flexible chain attached to the spring & core, by which the they can be extended or compacted. (You can't, in this case, just extend or compact the spring directly, but only by extending or compacting the attached chain (spacer protein).)
3. Primary function of nucleosomes
   1) Important in packing and organizing the DNA (so that it won't become tangled; like a rat's nest). 2) Nucleosomes also control gene expression: (to be discussed momentarily).
3. Classes of DNA
   One way to classify the DNA is by the length of sequences (number of nucleotides), which is often related to their
1. Short repeat sequences
   About 25% of DNA in any given organism and occur in the centromere area. There is a DNA sequence (e.g. 'ACAAACT' in the fruit fly is repeated about 12 million times) that is repeated one right after the other and there is no evidence that is ever transcribed (though it may be replicated) A chromosome's centromere functions 1) to hold copies of the DNA together, and 2) in cell division: protein spindle fibers used to separate chromosomes attach to the centromere.
2. Moderate repeat sequences
   Moderate length duplicated sequences (multiple copies of the same gene.) About 10% of the DNA. Example: histone genes. Some are repeated over 100,000 times (e.g. humans have more than 300 copies of the gene that codes for rRNA.) Why have multiple copies of the same gene: to produce a lot of a histone, for example, a cell needs a lot of that histone producing gene (each gene, like a factory, can only produce at a certain rate. If one histone factory can't supply what the cell demands, there needs to be more factories (simple genetic economics 101?).
3. Long nucleotide sequences
   65% of DNA. Codes for structural proteins, (like those in muscle).

(Then Stephanie spooled some DNA, harvested from many, many intestinal E.Coli (bacterium) cells. It was mucousy, in a transparent glob. Not something you want above your lip.)

1. Coiling of DNA (DNA tightly coiled and therefore unavailable for transcription)
   The first way in which gene expression may be controlled. When tightly coiled, DNA is not available for transcription. (The nuclesomes and spacer proteins play an important role in this coiling).
2. Gene expression (DNA must be uncoiled for a gene to be expressed)
   The DNA must be uncoiled (in chromatin form) for transcription, and, ultimately, translation to occur. Genes are expressed through transcription (DNA-->mRNA) and translation: the synthesis of proteins.
3. Introns and exons
   10.2 Intons & Exons
   Introns and exons are segments on mRNA. Enzymes (small nuclear mRNA (snRNA), an enzyme, cuts the mRNA at specific sites, separating the introns from the exons. The introns are broken down into their component nucleotides, while the EXONS are spliced together and shipped out of the nucleus to where they can do their thing: translation: synthesis of proteins at the ribosomes. (mRNA with introns is nonfunctional.)
4. Transposons (or "jumping genes")
   A scientist named Barbara McClintock (1940s) suggested that genes could jump around. Studying corn, McClintock noted that jumping genes were responsible for irregular pigmentation (color). Specifically, if a gene "jumps" from one location to another on chromosome #10 in the corn, it will be expressed as a brown (or whatever color) spot on the kernel. 3 things to write down about transposons: 1 - jumping genes can move from one spot on a chromosome to another on the same chromosome, 2 - jumping genes can move from one chromosome to another, 3 - those jumping genes can move from one species to another. How? (didn't say.) (We're loaded with transposons!--they are typical of all species.)

Other ways to control gene expression: add a methyl group (CH₃) to cytosine: the added methyl group may turn off a gene (enable it to be expressed). About 5% of DNA uses this mechanism.
Similarly, acetyl groups can be added/removed, turning a gene on/off. (The adding and removing of these groups is enzyme driven.)

Basic information concerning chromosomes
10.3 Eukaryotic Chromosomes
This information will help us in the near future: when we look at mitosis and meiosis.

1. Homologous or paired chromosomes
   We have 46 chromosomes in our cells: 23 from each parent: 2 sets of 23 homologous chromosomes. Homologous chromosomes have the same gene sequence; not the same exact genes: on one homologous chromosome you may have gene "A" (say, codes for brown eyes) while the other may have gene "a" (blue eyes) which is a different. They both code for the same trait (eye color) but are different genes.
2. Chromatids
   When a chromosome is replicated it is composed of two sister chromatids. A chromatid is one of the two copies of the DNA connected at the centromere. When the chromatids separate, they are no longer referred to as chromatids, but as chromosomes. So, a chromosome is replicated into two molecules of DNA. In this state it is still referred to as a chromosome, but is now composed of two sister chromatids, which are held together at the centromere. When the chromatids separate they are no longer chromatids, but chromosomes. (Chromatids only exist as pairs.)
3. Alleles
   An allele is an alternate form of a gene. (In examples, the alleles are often labeled 'A' and 'a', or by different colors, etc.) Genes code for the same trait (example: ear-lobe attachment). Alleles code for different expressions of the same trait (e.g. ear-lobe attachment: either attached or free lobes). (I'm a free-lober.)
1. Homozygous alleles
   When alleles are the same: a-a.
2. Heterozygous alleles
   When alleles are different: A-a.