Eukaryotic cilia and flagella play crucial roles in development, signaling, and motility, and their proper function is essential to many organisms, including all vertebrates. Cilia and flagella are microtubule based, membrane bound structures that protrude from the surface of the cell, and they possess a highly stereotyped, precise internal geometry. This internal structure must be correctly built and maintained for the proper functioning of these organelles, and perturbations to the structure can result in altered functionality and disease states in humans. Their extension out away from the cell body and tendency to vary in only a single dimension - their length - also make cilia and flagella ideal model organelles for the study of organelle size control. Proper size is crucial to the functioning of a cellular organelle, however, very little is understood about size control is achieved. These structures are uniquely situated to teach us more about the mechanisms cells use to regulate the size of their organelles. This dissertation seeks to further elucidate how the structure of cilia and flagella is established and maintained using the green alga Chlamydomonas. Chlamydomonas has served as an excellent model organism for the study of flagella in the past and is amenable to a wide range of genetic and biochemical experiments. Their flagella make ideal structures to use as models as they are essentially identical to those found in vertebrates, have an highly precise geometry, and mutants strains with altered internal structure and length are readily available. In this work, I first review the state of knowledge about length control of flagella in Chlamydomonas. I use Chlamydomonas mutant strains with altered flagellar length to investigate the mechanisms that result in this phenotype, and to examine how both intrinsic and extrinsic biological noise may affect these cellular structures. Finally, I identify new components of the Chlamydomonas central pair structure. Collectively, this work furthers our understanding of flagellar architecture and motility
