Metal nanoparticles, especially gold and silver, are currently among the most attractive nanomaterials due to their applications in various disciplines. The use of nanoparticles as building blocks offers an attractive bottom-up approach to produce new nanostructured materials with unique properties and applications. In this study, we have developed new and reproducible protocols to prepare gold and silver nanoparticles using various biological and chemical approaches. In particular, casein proteins were used for the synthesis of highly stable and biocompatible silver nanoparticles and spherical agglomerates. The silver particles produced by casein were tested for their pH-induced reversible agglomeration behaviour, cytotoxicity and cellular interaction by NIH/3T3 fibroblast cells. In addition, silver nanoparticles with enhanced antimicrobial activity were produced using a broad range disinfectant polyhexamethylene biguanide (PHMB) as a capping ligand. Moreover, peptide nano/ microfibers were also used for the synthesis of metal nanoparticles/ nanostructures. In order to control the assembly of nanoparticles, we have used various templates; such as egg shell membrane and cellulose fibers (unmodified and chemically modified) to produce metal nanoparticle - organic template composite materials. Heat treatment of these composite materials led to the formation of metal microwires or membranes with interesting morphologies which may have useful applications in electronics and surface enhanced Raman spectroscopy. The second part of this study deals with multilayered multifunctional polyelectrolyte capsules, which were formed by layer by layer assembly of polyelectrolytes around a sacrificial template. On removing the sacrificial template, hollow capsules containing free cargo of interest inside the cavities were obtained. It was possible to incorporate nanoparticles/ quantum dots inside the shell material to act as label during their microscopic studies. Most of all SNARF (seminaphthorhodafluor) based sensor capsules were used for real time monitoring of intracellular/ intralysosomal analyte (H+) concentration in the presence of different lysomotropic substances (Bafilomycin A1, Chloroquine, Monensin and Amiloride). The kinetics of these drugs was studied in a long term manner in living cells (MCF-7 breast cancer cells). Bafilomycin A1 caused an irreversible increase in intralysosomal pH. Chloroquine caused an increase in intralysosomal pH; however after its removal it gradually attained its baseline pH. Monensin also increased intralysosomal pH which remained high throughout its presence, but upon its removal intralysosomal pH attained baseline value very quickly. Amiloride did not show any effect on intralysosomal pH which remained constant throughout its presence in the cellular media.