Chromosome Overview 
During mitosis and meiosis chromatin fibers coil and condense into chromosome structures. Each chromosome is made up of chromatin, a complex of proteins and DNA. The chromosomes are long pieces of DNA that are found in the center of the nucleus inside the cells. Centromeres are a constricted region on the chromosome, which determines its appearance. Centromeres can be placed along different points along the length of the chromosome classifying it as metacentric, submetacentric, acrocentric or telocentric depending on centromere location. Chromosomes are cellular structure carrying genetic material located in the nucleus of eukaryotic cells and contain DNA molecules and proteins. Somatic cells from the same species contain identical number of chromosomes, which represents the diploid number (2n). Chromosomes exist in pairs; referred to as homologous chromosomes, one homologous chromosome is inherited from the organism’s mother and one from the father. Homologous chromosomes share genetic similarities such as a locus, an identical gene site along their length. On the other hand, bacteria and viruses contain only one chromosome. A normal human cell contains 46 chromosomes in its nucleus. Sex cells contain 23 chromosomes in humans. Haploid number (n) of a chromosome is one half the diploid number. During meiosis, diploid number of chromosomes are converted to haploid number as gametes are formed. Sex determining chromosomes X and Y are not often homologous. Females carry two homologous X chromosomes while males carry one Y and one X chromosome, which are not homologous but contain homologous regions and behave homologous in meiosis. However, "the remaining chromosomes are refered to the autosomal chromosomes and they are known as chromosome pairs 1 through 22" (University of Maryland).
Chromosome Mutations 
Chromosome mutations, occur when change in the total number of chromosomes are effected by deletion or duplication of genes or chromosome segments and rearrangement of genetic material within or among chromosomes. Aneuploidy is a condition in which one or more chromosomes are present in extra copies or are deficient in number but not a complete set. To be more specific, the loss of a single chromosome from a diploid genome (diploid cell-cell containing two set of chromosomes (2n), one set inherited from each parent) is called monosomy (2n-1). The gain of one chromosome is called trisomy (2n+1). A condition with complete set of haploid chromosome is called euploidy. There are events in which organisms have more than two sets of chromosomes; triploids for example are organisms with three sets of chromosomes. Tetraploids have four sets of chromosomes.
Chromosome mutations result in serious problems such as Turner syndrome, a monosomy in which females may contain all or part of an X chromosome. Monosomy for autosomes is usually lethal in humans and other animals. Klinefelter syndrome, a trisomy genetic disorder in males caused by the presence of one or more X chromosome. The effects of trisomy are similar to those of monosomy. Down syndrome is the only autosomal trisomy in humans that has a substantial number of survivors one year after birth. Trisomy in chromosome 21 is the cause of Down syndrome and it affects 1 infant in every 800 live births.
Polyploidy, is an occurrence in which more than two sets of haploid chromosomes are present. This condition is rare in animal species but common in lizards, amphibians, fish, and very common in various plants. Polyploidy originates in two ways: (1) autopolyploidy the addition of one or more extra sets of chromosomes of the same species; (2) allopolyploidy is the combination of chromosome sets from different species. Autopolyploidy have sets of chromosomes identical to parent species. Autotriploids for example can be represented as AAA and can arise from the failure of all chromosomes to separate during meiotic division, which result in a diploid gamete. The fertilization of the gamete by a haploid gamete results in the production of a zygote with three sets of chromosomes. Autotriploids often produce genetically unbalanced gametes with odd numbers of chromosomes. Autotetraploids can be represented by AAAA and are most likely to produce balanced gametes in sexual reproduction.
Deletion and Duplication 
Deletion in chromosomes occurs when a chromosome breaks in one or more places and a portion is lost or missing. Deletions can occur either near one end or within the chromosome, which are known as intercalary deletions. Deletion loops are unpaired regions of the normal homolog which occurs when synapsis between a chromosome with intercalary deletion and a normal homolog. The size of the chromosome deletion can determine the survival of the organism and unlike large deletions, small deletions can result in survival. Duplications in chromosomes occur when a large piece of chromosome is present more than once in the genome. They can arise from unequal crossing over between synapsed chromosomes during meiosis.
Chromosome Theory of Inheritance 
In the 1902, Walter Sutton and Theordor Boveri proposed that how the chromosomes are transmitted is the same as Mendel's Theory of how genes are transmitted. Genes are located on chromosomes. Chromosomes segregate and assort independently during meiosis. The evidence comes from Morgan's experiment with fruit flies. In 1910, Thomas Hunt Morgan started his work with Drosophila melanogaster, a fruit fly. He chose fruit fly because they can be cultured easily, are very prolific, have short generation time, and have only four pair of chromosomes that can be easily identified under the microscope. They have three pair of autosomes and a pair of sex chromosomes. At that time, he already know that X and Y have to do with gender. He used normal flies with red eyes, and mutated flies with white eyes and cross breed them. He was able to conclude that gene for eye color was on the X chromosomes. Males have only 1 X, Y does not carry gene for eye color.
Cambel, Neil,Jane B Reece, et all. Biology Eigth Edition., Klug, William, Michel Cummings, et all. Esssential of Genetics Custom Edition for UCSD http://www.umm.edu/ency/article/002327.htm Image source: wikimedia-commons