Biochemistry methods

energy transfer mechanism and microscopy technique

physical interactions and constructions between multiple proteins

way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure

chemical compound

process of separating molecules in solution by the difference in their rates of diffusion through a semipermeable membrane, such as dialysis tubing

ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation

In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule.

is an organic compound with the chemical formula (C6H11N)2C. It is a waxy white solid with a sweet odor. Its primary use is to couple amino acids during artificial peptide synthesis. The low melting point of this material allows it to be melted for easy handling. It is highly soluble in dichloromethane, tetrahydrofuran, acetonitrile and dimethylformamide, but insoluble in water.

physical phenomenon of electron resonance

buffer solution commonly used in biological research

Hydroxybenzotriazole (abbreviated HOBt) is an organic compound with the formula . It is a derivative of benzotriazole. It is a white crystalline powder, which as a commercial product contains some water (~11.7% wt as the HOBt monohydrate crystal). Anhydrous HOBt is explosive. It is mainly used to suppress the racemization and to improve the efficiency of peptide synthesis.

a chromatographic method in which molecules in solution are separated by their size, and in some cases molecular weight

technique to follow reactions by using atomic isotopes

planned process in synthetic organic chemistry

class of enzymes

technique for determining size distribution of particles

In biochemistry, ABTS ('''2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)''') is a chemical compound used to observe the reaction kinetics of specific enzymes. A common use for it is in the enzyme-linked immunosorbent assay (ELISA) to detect the binding of molecules to each other.

chemical compound

thumb|Crossed immunoelectrophoresis of 2 microlitres of normal human serum. The electrophoresis was performed in thin layers of agarose; the pictured gel is about 7x7 cm. The lower part is the first dimension gel without antibodies, where the serum was applied into the slot at the lower left. The upper part is the second dimension gel with Dako antibodies against human serum proteins. More than 50 major serum proteins can be named.

quantitative technique used to determine the thermodynamic parameters of interactions in solution

reagent commonly used in the synthesis of peptides

'''N-Ethylmaleimide (NEM''') is an organic compound that is derived from maleic acid. It is a unstable substance that reacts rapidly with thiols and is commonly used to modify cysteine residues in proteins and peptides.

thumb|400px|The BLOSUM62 matrix, the amino acids have been grouped and coloured based on Margaret Dayhoff|Margaret Dayhoff's classification scheme. Positive and zero values have been highlighted. In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based on local alignments. BLOSUM matrices were first introduced in a paper by Steven Henikoff and Jorja Henikoff. They scanned the BLOCKS database for very conserved

thumb|alt=Graphical illustration of ELISpot assay|ELISpot assay illustration The enzyme-linked immunosorbent spot (ELISpot) is a type of assay that focuses on quantitatively measuring the frequency of cytokine secretion for a single cell. The ELISpot Assay is also a form of immunostaining since it is classified as a technique that uses antibodies to detect a protein analyte, with the word analyte referring to any biological or chemical substance being identified or measured.

'''N,'-Diisopropylcarbodiimide is a carbodiimide used in peptide synthesis. As a liquid, it is easier to handle than the commonly used N,''-dicyclohexylcarbodiimide, a waxy solid. In addition, N,''-diisopropylurea, its byproduct in many chemical reactions, is soluble in most organic solvents, a property that facilitates work-up.

method for determining the concentration of a substance in an unknown sample

electrophoresis resulting in separation of molecules based on small sequence differences

Fura-2, an aminopolycarboxylic acid, is a ratiometric fluorescent dye which binds to free intracellular calcium. It was the first widely used dye for calcium imaging, and remains very popular. Fura-2 is excited at 340 nm and 380 nm of light, and the ratio of the emissions at those wavelengths is directly related to the amount of intracellular calcium. Regardless of the presence of calcium, Fura-2 emits at 510 nm of light. The use of the ratio automatically cancels out confounding variables, such as variable dye concentration and cell thickness, making Fura-2 one of the most appr

extraction technique in molecular biology

experimental technique in cell biology

Sephadex is a cross-linked dextran gel used for gel filtration. It was launched by Pharmacia in 1959, after development work by Jerker Porath and Per Flodin. The name is derived from separation Pharmacia dextran. It is normally manufactured in a bead form and most commonly used for gel filtration columns. By varying the degree of cross-linking, the fractionation properties of the gel can be altered.

thumb|400px|Examples of various lipid species.

thumbnail|Microdialysis probes manufactured by CMA Microdialysis AB, Kista, Sweden

analysing how the control of fluxes and intermediate concentrations in a metabolic pathway is distributed

measurement representing the ratio of carbon dioxide produced by the body to oxygen consumed by the body

chemical compound

Indo-1 is a popular dye that is used as a ratiometric calcium indicator similar to Fura-2. In contrast to Fura-2, Indo-1 has a dual emissions peak and a single excitation. The main emission peak in calcium-free solution is 475 nm while in the presence of calcium the emission is shifted to 400 nm. It is widely used in flow cytometry and laser scanning microscopy, due to its single excitation property. However, its use for confocal microscopy is limited due to its photo-instability caused by photobleaching. Indo-1 is also able to keep possession of its ratiometric emission, dissimilar

equation used in molecular biology

GCaMP is a genetically encoded calcium indicator (GECI) initially developed in 2001 by Junichi Nakai. It is a synthetic fusion of green fluorescent protein (GFP), calmodulin (CaM), and M13, a peptide sequence from myosin light-chain kinase. When bound to Ca2+, GCaMP fluoresces green with a peak excitation wavelength of 480 nm and a peak emission wavelength of 510 nm. It is used in biological research to measure intracellular Ca2+ levels both in vitro and in vivo using virally transfected or transgenic cell and animal lines. The genetic sequence encoding GCaMP can be inserted under th

Laboratory technique for quantitative proteomics

two groups of antibodies that are classified based on whether they bind to antigens or proteins directly or target another (primary) antibody that, in turn, is bound to an antigen or protein

A lysochrome is a soluble dye used for histochemical staining of lipids, which include triglycerides, fatty acids, and lipoproteins. Lysochromes such as Sudan IV dissolve in the lipid and show up as colored regions. The dye does not stick to any other substrates, so a quantification or qualification of lipid presence can be obtained.

biochemical technique

reaction in which antibodies bind to bacterial capsule

colorimetric method used in clinical chemistry

Stains-all is a carbocyanine dye, which stains anionic proteins, nucleic acids, anionic polysaccharides and other anionic molecules.

chemical compound

microbial, plant, or animal cells which are immobilized by attachment to solid structures

Base-labile protecting group

Titration of amino acid