Single Molecule FRET

This lecture covers the fundamentals of Biophotonics, focusing on Single Molecule FRET (Förster Resonance Energy Transfer) with Total Internal Reflection Microscopy. It explains the non-radiative energy transfer between molecules, the conditions required for energy transfer, and the selection of appropriate fluorophores. The lecture also discusses the applications of FRET in studying protein structure, protein complexes, receptor interactions, and nucleic acids. It delves into the labeling of molecules for FRET experiments, the advantages of single molecule FRET, and the techniques for surface immobilization. Additionally, it explores the principles of Total Internal Reflection Fluorescence (TIRF) microscopy and its applications in imaging cells. The lecture concludes with a discussion on TIRF instrumentation configurations and practical examples of TIRF microscopy.

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BIO-443: Fundamentals of biophotonics

This module serves as an introduction to the area of biophotonics. The approach is multidisciplinary .The course is mainly knowledge-based but students will benefit from the skills learned by carrying

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.

Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.

Super-resolution microscopy is a series of techniques in optical microscopy that allow such images to have resolutions higher than those imposed by the diffraction limit, which is due to the diffraction of light. Super-resolution imaging techniques rely on the near-field (photon-tunneling microscopy as well as those that use the Pendry Superlens and near field scanning optical microscopy) or on the far-field.

Protein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.

Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.