Glossary
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Active Site
The region of an enzyme where a chemical reaction catalyzed by the enzyme occurs. Mutations that affect the active site of an enzyme can abolish or alter the function of the protein. Altered enzyme activity or function is a common theme in cancer. See also Enzyme, Protease.
Algorithm
In bioinformatics, an algorithm is a computer program designed to complete a task in a step-wise format, so that given an input, the program can execute a number of requests, as designed by the programmer, and give an output. An example of this would be entering a sequence of amino acids (the input), into a program that will identify the protein or proteins to which the amino acid sequence corresponds (the output) in a database. See also Bioinformatics.
Alternative Splicing
Splicing is a post-transcriptional modification that occurs in messenger RNA (mRNA), the template that is used to create a protein from a gene. Splicing refers to the enzymatic cutting of mRNA at specific recognition sites between exons (DNA segments needed to code for proteins) and introns (DNA not used to make proteins). Splicing removes the RNA that will not be used in the translation of a protein. The pieces left are joined together by the splicing machinery and introduced into the translation machinery that creates proteins. mRNA can have numerous splice recognition sites, and alternative splicing occurs when the splicing machinery excises material from different splice sites in the mRNA strand. When these alternatively spliced mRNAs are translated, the proteins produced are related, but have sequence variations. Mutations that affect protein function and stability can sometimes be attributed to mutations in splice recognition sites. See also Translation.
Amino Acid
Small molecules that contain a nitrogen-based amine group and a carbon-based carboxyl group surrounding a central carbon atom. Amino acids are the primary subunit of proteins, and in the process of protein translation are joined together in a chemical reaction, forming a peptide bond. There are many amino acids that occur in nature, but multicellular organisms utilize only 20 amino acids to create proteins. Substitution or deletion of a single amino acid can alter the function of a protein, and mutations that lead to cancer are many times attributed to changes in amino acid sequence.
Antibody
Large, Y-shaped proteins produced by the immune system that attach to pathogens and other foreign molecules, tagging them for destruction. There are five classes of antibodies, each with different characteristics and roles in the immune system. In proteomic research, antibodies engineered to react to a specific protein or peptide are an essential tool for identifying proteins, and are commonly used in several techniques. See also Microarray, Western Blot.
Aptamer
A small piece of DNA or RNA engineered to bind to a specific protein. Aptamers can be used in microarray experiments to capture a specific protein from a mixture. Aptamers can be conjugated to other molecules like fluorophores, to allow high-sensitivity detection of proteins, even in very small amounts.
See also Fluorophores, Microarray.
B
Biochemistry
The branch of biology concerned with the chemical interactions of biomolecules in an organism. Protein biochemistry studies the chemical activity of proteins as they function in physiological processes and disease. Biochemical techniques allow researchers to determine the amino acid sequence and structure of proteins in order to test their function and interactions with various biomolecules.
Bioinformatics (Computational Biology)
The branch of biology that uses modern computing techniques, mathematical algorithms, and statistical analysis to better compare and contrast biological data sets. Algorithms have been described for modeling protein structure, tracing protein evolution, predicting protein interactions and modeling molecular pathways of disease. For techniques like mass spectrometry, bioinformatics programs can define the amino acid sequence of a protein and structural relationships between protein families. Bioinformatics is important in constructing gene and protein expression profiles from techniques such as microarrays that may be indicative of disease. See also in silico, Structural Biology, Systems Biology.
Biomarker
A biomarker is any biomolecule that is associated with a particular pathological or physiological state. Protein biomarkers are often used to identify drug targets or to diagnose and monitor therapy.
Chimera
Engineered proteins created from elements of different genes. Chimeras can have subtle changes in their genetic or protein sequences, or may contain inserted pieces of other genes, so that the protein formed has elements of different genes. Fusion proteins, such as reporter proteins used in two-hybrid systems, are sometimes entire proteins, or whole elements of two proteins that are bound together. Chimeric proteins are useful in studying the function of single amino acids, protein domains, and enzyme active sites. See also Two-hybrid Systems.
Chromatography
A method of separation in which molecules are separated according to chemical characteristics or size. There are several methods of suitably separating and purifying proteins, many of which rely on liquid chromatography, by which proteins are dissolved in suitable buffers and are isolated based on interactions with solid, chemically charged matrices. See also Dialysis.
Circular Dichroism Spectroscopy
A structural biology technique that takes advantage of a physical characteristic of molecules called chirality to determine the structure of that molecule. Different secondary structures in proteins, such as alpha helices or beta sheets, will absorb left and right circularized polarized light in different ways, and differences between absorption of the two yields information on the structure of the protein.
See also Stereochemistry, Structural Biology.
Conformation
Conformation refers to protein folding and the effects of three-dimensional structure on protein function. Events that affect protein conformation are the interactions of a protein with other proteins and post-translational modifications. Environment is crucial to proper protein folding and creation of a stable conformation. The cell often destroys proteins whose conformations are not stable. See also Denaturation, Disulfide Bond, Domain, Secondary Structure, Structural Biology, Tertiary Structure.
Conservation
Protein conservation refers to an amino acid sequence of a single protein or functional domains within a protein that remains relatively unchanged in several species throughout evolution, suggesting that these sequences or domains may be vital. Bioinformatics tools that compare protein and gene sequences can show sequence homology and conservation. See also Domain, Homology, Orthology, Paralogy.
D
Denaturation
The process by which a fully folded protein is unfolded by chemicals or heat. The treatment disrupts the chemical interactions between the different amino acid residues that stabilize secondary, tertiary and quaternary structure. The act of removing the disruptive treatment can often lead to renaturation of the protein.
Dialysis
A technique by which a buffer, or solution that houses proteins, can be switched for another without disrupting protein chemistry and causing denaturation. In the technique, a protein solution is placed in membrane that will allow the flow of small molecules without the flow of the larger protein. Over time, the chemical composition of the solution in the tubing changes until it has reached the desired composition. This technique is often used for buffer exchange in chromatography, where proteins are separated based on surface chemistry. See also Biochemistry, Chromatography, Denaturation.
Disulfide Bond
A covalent bond created between sulfur atoms in two molecules of the amino acid cysteine, located at different points in the amino acid chain of a folding protein or peptide. The disulfide bond is often necessary for a protein to fold correctly and be fully functional.
Domain
The functional regions of a protein often used to classify proteins into families. Domains can be classified by protein sequence or by function. There are several different known protein domains, including DNA binding domains, protein-protein interaction domains, and phosphotyrosine binding domains.
See also Conservation, Homology, Orthology, Paralogy.
Electron Microscopy
A technique that allows researchers to define biological structures in very fine detail by studying the electron activity of proteins. An electron beam is focused with a magnet and directed onto the sample in question. The effect of the beam on the sample is magnified many fold before hitting a detector, which then transposes the image onto a computer screen. It is possible to detect proteins in a tissue sample using antibodies and electron microscopy. There are two main forms of electron microscopy, transmission electron microscopy (TEM), where electrons pass through the sample, and scanning electron microscopy (SEM), where electrons are deflected from the sample. Electron microscopy has slightly less resolution than other techniques for protein analysis.
Enzyme
Proteins that catalyze biochemical reactions in an organism. Enzymes are necessary because they provide the activation energy, for chemical reactions that otherwise would occur very slowly. Enzymes are very important in systems biology. Interactions and modifications of molecules within the cell can lead to chain reactions and changes within the cell. See also Active Site, Systems Biology.
Fluorophore
A flourophore is a molecule or part of a molecule that can absorb light at a specific wavelength and in turn, give off light at a different wavelength. Fluorophores can be bound to proteins, DNA, or RNA and are used extensively in research as a means of localizing and quantifying proteins via microscopy and biochemical techniques such as FRET. See also Antibody, Aptamer.
Fluorescence Resonance Energy Transfer (FRET)
A technique for studying how proteins interact with one another. In the technique, two different proteins are labeled with different fluorophores. If the two proteins interact, the fluorophore of one molecule will absorb light at one wavelength, and transfer it to the other fluorophore on the other molecule, where it will be emitted at a different wavelength. See also Fluorophores.
G
H
Homeostasis
The state in which a cell or biological entity is in a stable condition. Homeostasis is referred to as the normal functioning of the cell.
Homology
Homology refers to elements of a protein's amino acid sequence that when compared to other proteins, are similar. Homologous proteins share similar ancestry, and may be functionally related.
See also Conservation, Domain, Orthology, Paralogy.
Isoelectric Focusing
Isoelectric focusing is a technique for separating molecules based on the relative charge contribution of their residues, isoelectric point (pI). Proteins are placed in a matrix (a gel slab) that is created with a pH gradient, and an electrical field is applied. The proteins migrate through the matrix to the point where the pH of the gel is the same as that of the protein, the isoelectric point. After separating and identifying proteins through this method, comparison of protein expression profiles can suggest proteins that contribute to health versus disease.
in silico
A term that refers to experiments conducted through computational biology or bioinformatics methods. An example of an in silico experiment would be a comparison of an unknown protein to the sequences of known proteins in a particular database. The unknown protein, discovered and sequenced through traditional biochemistry techniques can be assigned a function or a designated part of a family based on similarities to known sequences. See also in vitro, in vivo, Conservation.
in vitro
A term that refers to experiments conducted outside animal models, using primary cells and cell lines, tubes and Petrie dishes. In vitro experiments typically precede in vivo experiments and are often used to characterize genes, proteins, and the activity of small molecules in a more defined system to better anticipate variables in animal models. See also in vivo, in silico.
in vivo
A term that refers to experiments conducted in animal models or human subjects. Typically, in vivo experiments are conducted with the information gained from in vitro experiments. Proteins, for example, can be tested for their function within the whole animal system in health versus disease. See also
in silico, in vitro.
Ligand
A small molecule that binds another larger molecule, usually called a receptor. The binding event can change the receptor's conformation or activity, triggering subsequent biochemical reactions inside a cell, or in some cases, blocking subsequent biochemical reactions. Ligands that activate receptors are called agonists. Ligands that block receptor activity are called antagonists. For cancer, major therapeutic targets would include creating ligands that can interact with receptors to block cell growth or migration, or those that can activate immune responses against tumor components. See also Conservation, Receptor, Systems Biology.
Mass Spectrometry
A technique used to identify organic compounds, including proteins, by their mass and electric charge. To utilize mass spectrometry to identify proteins, protein or peptide samples are ionized, or charged, by an ionization source. Two common sources used in proteomics are matrix-assisted laser desorption ionization (MALDI-) and electrospray ionization (ESI-). The ionization source adds protons to the amino acids in the sample. After ionization, the charged protein enters a mass analyzer, such as time-of-flight (TOF-), or quadropole ion flight, which sorts the peptides according to their mass-to-charge ratio. Finally, a detector notes the number of ions over a range of mass-to-charge ratios. The output may produce a "peptide mass fingerprint" - an amino acid sequence or a pattern of unique peptides.
Microarray
A device that measures the difference in gene expression or protein expression in biomaterials under different experimental conditions, such as healthy versus diseased tissues or cells. In the typical protein array, the capture reagent, such as a known protein or antibody, is immobilized on a microchip and treated with liquid phase reagents. Binding or interaction of elements of the liquid phase with the capture reagent is quantified by computer software. Protein microarrays measure the variations in protein levels and can be used to determine the protein expression profile in diseases like cancer. See also Aptamer, Bioinformatics, Protein Expression Profile.
Nuclear Magnetic Resonance
A procedure used to determine the property of electrons in motion around an atomic nucleus that can be perturbed with the addition of a magnetic field, and used to determine the structure of a molecule. In protein studies, NMR is used to determine structure. See also Structural Biology.
Orthology
Genes and their cognate proteins that arise in different species but are derived from a common ancestor. Orthologous proteins may not have the same function from species to species. Bioinformatics techniques can identify orthologous proteins based on gene and protein sequences and are useful for helping identify unknown proteins. See also Conformation, Conservation, Domain, Homology, Paralogy.
Paralogy
Closely related genes that arose through a genetic duplication event. Through evolution, the end result is two sequence-related genes and cognate proteins that may or may not have redundant or complementary function. Bioinformatics techniques can identify paralogous proteins based on gene and protein sequences and are useful for helping identify unknown proteins. See also Conservation, Domain, Homology, Orthology.
Peptide
Peptides are short chains of amino acids or protein fragments. They can be naturally occurring, as is the case with certain peptide hormones, or they can be created by treating proteins with enzymes known as proteases that break up the protein at specific peptide bonds. Peptides are a common input for mass spectrometry. See also Amino Acid, Protein Engineering.
Peptide Bond
A peptide bond is the covalent linkage that occurs between the carboxyl end of one amino acid and the amino group of another as a peptide or protein is being created. In the reaction, a molecule of water is released. Enzymes known as proteases break peptide bonds. See also Amino Acid.
Primary Structure
The sequence of amino acids in a protein prior to folding, that may eventually assume more complex secondary, tertiary and quaternary structure, creating a fully folded, functional protein. See also Translation.
Protein
A complex molecule made of amino acids. Proteins are found in all organisms, and are responsible for the majority of biochemical reactions that are essential for a system to function properly. Proteins are often involved in enzymatic reactions and signal transduction. In diseases, including cancer, proteins can have alterations that prevent them from either forming or working properly. See also Peptide, Peptide Bond, Proteomics.
Protein Engineering
The practice of creating artificial proteins in the laboratory. Protein engineering helps to provide an understanding of how naturally occurring proteins function so that researchers can be better able to define sites within a protein that would serve as drug targets. See also Chimera.
Protein Expression Profiling
Experimental techniques that researchers use to determine the different patterns of protein expression that are found in a cell or tissue in a given stage of health and disease. Included in these techniques are methods for analyzing quantity of proteins, as well as the presence or absence of post-translational modifications. Common techniques used to determine protein expression profiles are protein microarrays, two-dimensional electrophoresis and mass spectrometry. See also Post-Translational Modifications.
Proteomics
The field of study that seeks to understand the entire protein component of an organism. In particular, the field is concerned with the relationship between a protein's composition, structure and function, as it relates to biological activities including health and disease states. One of the products of proteomic discovery is the development of suitable biomarkers for disease diagnosis, treatment and monitoring. Proteomics encompasses general biochemistry, genetics, and bioinformatics techniques, and also relies on innovation in nanotechnology.
Post-Translational Modifications
Chemical additions to proteins that can affect their ability to fold or function properly. Examples of post-translational modifications are glycosylation, the addition of carbohydrates to a protein, or phosphorylation, the addition of a phosphate group to a protein. Without these modifications, proteins maybe incapable of carrying out their normal functions. For example, signal transduction proteins often must be phosphorylated before they can function in transmitting signals in a cell. See also Signal Transduction, Systems Biology, Protein Expression Profiling.
Proteome
The entire protein content and context of an organism. From the sequence of a genome, researchers can predict and characterize the proteins that arise from transcription of those genes. The field of proteomics aims to understand the proteome of cells, organs, tissues, and species. A better understanding of the human proteome can lead to better understanding of disease, and its prevention, diagnosis and treatment.
Protease
A protease is an enzyme that cleaves proteins at specific recognition sites determined by amino acid type or sequence, reducing a protein to shorter peptides or amino acids. Proteases are found throughout the body, and in the laboratory, are essential tools in preparing proteins for characterization via biochemical techniques.
Quaternary Structure
Quaternary structure refers to the association and arrangement of two or more proteins to create a multimeric (more than one subunit) functional unit. Multimerization is often required for the function of the protein subunits within a protein complex. An example is hemoglobin, a protein that has four subunits, two alpha helices and two beta sheets, which are essential for its role as an oxygen carrier. See also Conformation, Primary Structure, Secondary Structure, Structural Biology, Tertiary Structure.
Receptor
A receptor is a protein that interacts with other small molecules (ligands), and in turn, effects a change within a cell. Receptors can be located anywhere from the cell surface to the nucleus. Receptors are often the starting point for signal transduction cascades, which are critical for cellular functions like growth and division, and can be directly involved in gene expression. Inappropriate activation or deactivation of receptors is linked to numerous diseases such as cancer. See also Signal Transduction.
Renaturation
Renaturation is the process by which an unfolded, or denatured protein can reassume its native conformation, either by removal of the chemical reagent that denatured the protein to begin with, or by creation of a favorable environment that encourages proper folding. See also Conformation, Denaturation.
SDS-PAGE
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is a common technique for separating proteins based on size. SDS is a chemical that denatures proteins into amino acid chains, and coats them, giving them a negative charge. A mixture of proteins is added to a gel matrix and subjected to an electrical field. The negative charge permits them to migrate through the matrix, with smaller proteins migrating faster than larger proteins, enabling a researcher to visualize the proteins separated by size. See also Western Blot, Two-Dimensional Electrophoresis.
Secondary Structure
The initial intramolecular interactions that occur as a protein begins to fold. Examples of these interactions are hydrogen bonding between different amino acid residues or the disulfide bonds that form between the sulfur moieties of two individual cysteine residues. See also Conformation, Primary Structure, Quaternary Structure, Tertiary Structure.
Signal Transduction
The interaction of proteins that results in various protein modifications such as phosphorylation. These modifications can lead to a chain reaction of subsequent protein-protein interactions that end with a change in the cellular activity, either through modifications of gene expression, or changes in protein composition or localization. Signal transduction is a key component of systems biology. See also Ligand, Receptor.
Stereochemistry
The three dimensional structure of the atoms in a molecule, and how it appears in space. Because two molecules that are identical in composition may have different stereochemistries, the placement of functional groups and side chains can affect the activity of a molecule, and in terms of therapeutics, can mean the difference between an active and inactive version of a molecule or a drug. Stereochemistry is the basis of circular dichroism. See also Circular Dichroism, Structural Biology.
Structural Biology
The field of biology that studies the three-dimensional and spatial description of biomolecules. Techniques such as X-ray crystallography and NMR spectroscopy are commonly used in structural biology studies. Determining the three-dimensional, or tertiary structure of a protein is important to proteomic research. Subtle changes in structure can affect the proper function of a protein, changing its activity, and even leading to its instability and destruction by the cell. See also Bioinformatics, Conformation, NMR, X-Ray Crystallography.
Systems Biology
The field of biology that treats biological systems as entities of study rather than researching the roles of individual molecules in health and disease. Systems biology utilizes a combination of biochemistry, proteomics, genomics, metabolomics and bioinformatics to better understand the contribution of each element within a system to the whole. In proteomics and cancer, perturbations in the protein component of signal transduction systems, for example, can lead to cell and tissue changes that promote tumorigenesis, therefore understanding the entire signal transduction system can often reveal drug targets that would otherwise have been overlooked.
Tertiary Structure
The three-dimensional conformation of a protein. Proteins fold into their tertiary structure to assume the most stable energetic state, where the cell does not need to input energy to maintain the structure of the protein. Stability is also correlated with function; unstable conformations are not functional and are often destroyed by the cell. In addition, proper structure is required for the protein-protein interactions that characterize ligand-receptor interactions, enzyme-substrate interactions and the protein-protein interactions that lead to quaternary structure. See also Conformation, Primary Structure, Quaternary Structure, Secondary Structure, Structural Biology.
Translation
The biochemical process by which messenger RNA (mRNA) is used as a template by the ribosome to synthesize the respective protein. In translation, a molecule called transfer RNA (tRNA) interacts with the spliced mRNA at each codon, carrying with it the amino acid that corresponds to the codon. Amino acids are chemically linked to create the nascent peptide, which will eventually become the full-length, active protein. See also Peptide Bond, Primary Structure.
Two-Dimensional Electrophoresis
A biochemistry technique (also known as 2-D gel electrophoresis) that separates proteins based on both size and isoelectric point or pI. In the technique, proteins are first separated according to isoelectric point. The proteins are then separated by size. The protein of interest may be isolated and characterized by mass spectrometry. See also Isoelectric Focusing, SDS-PAGE.
Two Hybrid Systems
A technique used to characterize protein-protein interactions. In this technique fusion proteins or chimeras are created and introduced into cells. If the proteins interact, the cell produces a measurable marker, such as bioluminescence or drug resistance. See also Chimera.
Western Blot
A useful tool for characterizing proteins in a biological sample. In this technique, proteins are first separated by size using SDS-PAGE. The contents of the gel are transferred to a membrane, and then probed with a series of antibodies to find the protein of interest. See also Antibodies, SDS-PAGE.
X-Ray Crystallography
X-Ray Crystallography is a method for determining protein structure. X-rays are focused on a protein crystal, a repeating structure of single protein molecules. The X-rays bounce off of, or diffract the electrons in the protein. The diffraction pattern is converted to a structural diagram using computer software. See also Bioinformatics, Conformation, Structural Biology.
