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Bioluminescence

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312 Terms

1

Bioluminescence

The production and emission of light by a living organism.

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Chemiluminescence

The emission of light as a result of a chemical reaction.

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Aequorea victoria

A species of jellyfish that exhibits bioluminescence.

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4

GFP (Green Fluorescent Protein)

A protein isolated from Aequorea victoria that absorbs blue light (475nm) and emits green light (510nm)

  • 238 AA peptide

  • Fluoresce originates from Ser - Tyr - Gly Tripeptide

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Photophysics

The study of the physical properties and behavior of light.

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X-ray crystallography

A technique used to determine the atomic and molecular structure of a crystal.

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Tripeptide

A peptide consisting of three amino acids.

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Post-translational modification

Chemical modifications that occur to a protein after it has been synthesized.

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EGFP (Enhanced Green Fluorescent Protein)

A variant of GFP with improved spectral properties.

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FP Spectral Variants

Variants of fluorescent proteins that exhibit different colors and characteristics.

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Red Fluorescent Proteins

Proteins isolated from corals that absorb green light and fluoresce red.

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12

FRET (Fluorescence Resonance Energy Transfer)

A process in which energy is transferred between two fluorophores.

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13

Biosensor

A device or construct that detects and measures biological molecules or processes.

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Transgenic

Referring to an organism that has had foreign DNA inserted into its genome.

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15

BRAINBOW

A technique used to label neurons with multiple distinct colors to visualize synaptic circuits.

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Genetically Encoded FRET Biosensors

Biosensors that utilize genetically encoded fluorescent proteins for FRET measurements.1. Osamu Shimomura:A scientist who discovered aequorin and GFP in 1961.

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GFP

Green Fluorescent Protein, a protein that emits green light when exposed to certain wavelengths.

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Martin Chalfie

A scientist from Columbia University who studied C. elegans nerve cells using GFP in the 1980s.

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Douglas Prasher

A scientist from Woods Hole Oceanographic Institute who sequenced the GFP gene.

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E.coli

The first organism in which GFP was used.

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Roger Tsien

A scientist from the University of California, San Diego who made modifications to GFP.

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22

Tulle Hazelrigg

A scientist from Columbia University who studied fusion proteins in Drosophila (fruit fly) and preserved the structure and function of both proteins.

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23

Protein Structure

The arrangement of amino acids in a protein molecule.

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24

Enzymes

Proteins that catalyze chemical reactions in living organisms.

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25

Defence

Proteins, such as antibodies, that protect the body against foreign substances.

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Structure

Proteins, like collagen, that provide support and shape to cells and tissues.

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Storage

Proteins, like ovalbumin, that store nutrients for later use.

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Transport

Proteins, like hemoglobin, that carry molecules and ions throughout the body.

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Movement

Proteins, like actin and myosin, that enable muscle contraction and movement.

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Regulation/Receptors

Proteins, like insulin and insulin receptors, that control and respond to signals in the body.

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Amino Acid

The building blocks of proteins.

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Hydrophobic

Amino acids with non-polar side chains that repel water.

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Polar

Amino acids with polar side chains that attract water.

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Acidic

Amino acids with negatively charged side chains.

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Basic

Amino acids with positively charged side chains.

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Hydropathy Scale

A scale that measures the hydrophobicity or hydrophilicity of amino acids.

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Peptide Bond

The bond formed between two amino acids during protein synthesis.

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Ramachandran Plot

A plot that shows the allowed regions of dihedral angles for amino acids in proteins.

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Structural Motifs

Short segments of protein 3D structure that are spatially close but not necessarily adjacent in the sequence.

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40

Tertiary Structure

The overall 3D structure of a single protein molecule.

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41

Quaternary Structure

The arrangement of multiple protein subunits in a complex.

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42

Post-Translational Modifications

Chemical modifications that occur after protein synthesis.

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43

Phosphorylation

The addition of a phosphate group to a protein, often used for regulation.

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44

Glycosylation

The addition of saccharide groups to a protein, affecting folding, stability, and regulation.

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45

Acetylation

The addition of an acetyl group to a protein, often used for regulation.

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46

Hydroxylation

The addition of a hydroxyl group to a protein, affecting regulation.

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Methylation

The addition of a methyl group to a protein, often used for regulation.

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48

Disulfide Bonds

Covalent bonds formed between two cysteine residues, contributing to protein stability.

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49

Ubiquitination

The attachment of ubiquitin molecules to a protein, marking it for degradation.

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Polymorphic

Proteins with sequence variability among individuals.

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51

Site-directed Mutagenesis

A technique used to introduce specific mutations into a protein's DNA sequence for studying structure and function.1. Extracellular fluid (ECF):The fluid surrounding cells from which they acquire molecules and ions.

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52

Diffusion

The spontaneous movement of molecules and ions down their concentration gradient.

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Active transport

The movement of molecules and ions against their concentration gradient, requiring the expenditure of energy.

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54

Electrochemical gradient/potential

The combination of the chemical gradient (difference in solute concentrations) and the electrical gradient (difference in potential/charge) across a membrane.

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Resting potential

The static membrane potential of quiescent cells.

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Action potential

The rapid rise and fall of membrane potential in a specific cell location, causing adjacent locations to similarly depolarize.

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Voltage-gated ion channels

Channels in the plasma membrane of cells that open and close in response to changes in membrane potential.

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Selectivity filter

A segment in voltage-gated ion channels that allows the selective passage of specific ions.

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Ion pore domain

A structural component of voltage-gated ion channels that forms the ion-conducting pore.

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Voltage sensor

A component of voltage-gated ion channels that detects changes in membrane potential and triggers channel opening or closing.

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Tetramerization

The process of four identical subunits coming together to form a functional channel.

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Patch clamping

A technique used to record the activity of individual ion channels.

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Ion-selective micro-electrodes

Electrodes used to measure the concentration of specific ions.

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64

X-ray crystallography

A method used to determine the three-dimensional structure of molecules, including ion channels.

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Bacterial KcsA Channel

An experimental model used to study the structure and function of potassium channels.

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Subunit structure

The organization of different segments within a potassium channel, including the selectivity filter, cavity, and internal pore.

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Ion selectivity

The ability of a channel to selectively allow the passage of certain ions while excluding others.

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Conformational change

A change in the three-dimensional structure of a molecule or protein.

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Newton's cradle

A physical demonstration of the conservation of momentum, used here to describe the oscillation of potassium ions within the selectivity filter.

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70

Vestibules

Large openings or chambers in ion channels.

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71

Coordination geometry

The arrangement of atoms and their bonding in a molecule or ion.1. Rod MacKinnon:A scientist known for his work on ion channels.

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Ion Channels

Protein structures that allow the flow of ions across cell membranes.

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Reason to purify proteins

To provide material for structural or functional studies

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Truly accurate method for determination of protein conc.

AA analysis on the hydrolysate

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Mostly used for determination of protein conc.

Bovin serum albumin (BSA)

  • Low cost, high purity, ready availability

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Ultraviolet absorption

Method for determination of protein conc, non-destructive, can be measured continuously, readily available

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Lowry method, bicimchoninic method, Bradford method

Used to determine protein conc

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Buffer composition (P. Isolation)

Ionic strength (0.1-0.2M)

PH (7-8)

Mostly Tris or phosphate

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Anti oxidant

Buffer add

  • to prevent inter-/intramolecular disulphide bridges & oxidation

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80

Enzyme inhibitors (buffer)

  • Protease inhibitors

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81

Enzyme substrate & cofactors

Buffer add

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82

EDTA

  • buffer add

  • To remove divalent metal ions

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83

PVP

  • buffer add: plant tissue

  • To absorb phenolic compounds

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84

Sodium azide

  • buffer add

  • Bacteriostatic agent

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Extrinsic membrane protein isolation

Increase ionic concentration or increase pH(9-12) of buffer

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86

Intrinsic membrane protein isolation

Add detergents (SDS, CTAB, CHAPS)

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87

Mammalian cells

  • 10um

  • Weak plasma membrane/cytoskeleton

  • Easy to disrupt

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Plant cells

  • 100um

  • Fairly rigid cell wall

  • Till susceptible to disruption by shear force

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89

Bacterial cells

  • 1-4um

  • Extremely rigid cell walls

  • Gram +/-

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90

Blender Method

Ideal for mammalian / plant tissue

bacteria/yeast with glass beads

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91

Grinding with abrasives

Ideal for bacteria/ plant cells

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92

Presses

Ideal for microbial cells

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93

Enzymatic disruption methods

  • Lysozyme: bacteria

  • Zymolyase/Yticase: yeast

  • Chitinase: fungi

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Sonication

Ideal for suspension of cultured cells/ microbial cells

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95

Stability

Denaturation fractionation (heat/pH sensitivity)

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Solubility

  • salt fractionation: ammonium sulfide (NH4)2SO4

  • Organic solvents: ethanol/ acetone/ Butanol

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Fine purification

Higher resolution chromatographic methods

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98

Charge

Ion-exchange chromatography, chromafocusing

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99

Affinity

Affinity chromatography (ligands)

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Protein sources

  • biological fluids (urea,blood plasma)

  • Intercellular components

  • Recombinant proteins

  • Membrane bound components

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