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Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.

Antibody Structure

JoVE 10898

Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.

Antibodies consist of four polypeptide chains: two identical heavy chains of approximately 440 amino acids each, and two identical light chains composed of roughly 220 amino acids each. These chains are arranged in a Y-shaped structure that is held together by a combination of covalent disulfide bonds and noncovalent bonds. Furthermore, most antibodies carry sugar residues. The process of adding sugar side chains to a protein is called glycosylation. Both the light chain and heavy chain contribute to the antigen binding site at each of the tips of the Y structure. These 110-130 amino acids are highly variable to allow recognition of an almost unlimited number of antigens. This region is also called the variable region and is part of the antigen binding fragment. Each arm of the Y-shaped unit carries an identical antigen binding site. Antibodies can crosslink antigens: when one arm binds to one antigen and the other arm binds to a second, structurally identical antigen. Crosslinking is facilitated by the f

 Core: Immune System

Electrophoretic Mobility Shift Assay (EMSA)

JoVE 5694

The electrophoretic mobility shift assay (EMSA) is a biochemical procedure used to elucidate binding between proteins and nucleic acids. In this assay a radiolabeled nucleic acid and test protein are mixed. Binding is determined via gel electrophoresis which separates components based on mass, charge, and conformation.


This video shows the concepts of EMSA and a general procedure, …

 Biochemistry

16S rRNA Sequencing: A PCR-based Technique to Identify Bacterial Species

JoVE 10510

Source: Ewa Bukowska-Faniband1, Tilde Andersson1, Rolf Lood1
1 Department of Clinical Sciences Lund, Division of Infection Medicine, Biomedical Center, Lund University, 221 00 Lund, Sweden


Planet Earth is a habitat for millions of bacterial species, each of which has specific characteristics. Identification of bacterial species is…

 Microbiology

Skeletal Muscle Anatomy

JoVE 10867

Skeletal muscle is the most abundant type of muscle in the body. Tendons are the connective tissue that attaches skeletal muscle to bones. Skeletal muscles pull on tendons, which in turn pull on bones to carry out voluntary movements.

Skeletal muscles are surrounded by a layer of connective tissue called epimysium, which helps protect the muscle. Beneath the epimysium, an additional layer of connective tissue, called perimysium, surrounds and groups together subunits of skeletal muscle called fasciculi. Each fascicle is a bundle of skeletal muscle cells, or myocytes, which are often called skeletal muscle fibers due to their size and cylindrical appearance. Between the muscle fibers is an additional layer of connective tissue called endomysium. The muscle fiber membrane is called the sarcolemma. Each muscle fiber is made up of multiple rod-like chains called myofibrils, which extend across the length of the muscle fiber and contract. Myofibrils contain subunits called sarcomeres, which are made up of actin and myosin in thin and thick filaments, respectively. Actin contains myosin-binding sites that allow thin and thick filaments to connect, forming cross bridges. For a muscle to contract, accessory proteins that cover myosin-binding sites on thin filaments must be displaced to enable the formation of cross bridges. During muscle contracti

 Core: Musculoskeletal System

Ribosomes

JoVE 10692

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.

Ribosomes are composed of ribosomal RNA (rRNA) and proteins. Ribosomes are not surrounded by a membrane (i.e., despite their specific cell function, they are not an organelle). In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome production. Within the nucleolus, rRNA is combined with proteins that are imported from the cytoplasm. The assembly produces two subunits of a ribosome—the large and small subunits. These subunits then leave the nucleus through pores in the nuclear envelope. Each one large and small subunit bind to each other once mRNA binds to a site on the small subunit at the start of the translation process. This step forms a functional ribosome. Ribosomes may assemble in the cytosol—called free ribosomes—or while attached to the outside of the nuclear envelope or endoplasmic reticulum—called bound ribosomes. Generally, free ribosomes synthesize proteins used in the cytoplasm, while bound ribosomes synthesize proteins that are inserted into membranes, packaged into org

 Core: Cell Structure and Function

Internal Receptors

JoVE 11011

Many cellular signals are hydrophilic and therefore cannot pass through the plasma membrane. However, small or hydrophobic signaling molecules can cross the hydrophobic core of the plasma membrane and bind to internal, or intracellular, receptors that reside within the cell. Many mammalian steroid hormones use this mechanism of cell signaling, as does nitric oxide (NO) gas.

Similar to membrane-bound receptors, binding of a ligand to a receptor located in the cytoplasm or nucleus of a cell causes a conformational change in the receptor. Like transcription factors, the active receptor can bind to receptor-specific DNA binding sites to increase or decrease the transcription of target genes. In the case of an intracellular receptor located in the cytoplasm, the receptor-ligand complex must first cross the nuclear membrane. Many steroid hormones, including estrogen and testosterone, use intracellular receptors to induce specific effects. As an example, estrogen can diffuse across the membrane; binding of estrogen to its receptor results in dimerization of the receptors and transport of the ligand-receptor complex to the nucleus. Once in the nucleus, the complex can bind to DNA sequences called Estrogen-Response Elements (EREs). Depending on the other transcription factors and co-activators, binding of activated estrogen receptors (ERs) to EREs may cause an increa

 Core: Cell Signaling

Affinity and Avidity

JoVE 10899

Antibodies bind to toxins or substances on the surface of cells, bacteria, viruses, or fungi. The substance is called an antigen, and the precise binding site is the epitope. The strength of the antibody-epitope interaction is called affinity. When an antibody binds an antigen by multiple epitopes, the cumulative strength of the interaction is called avidity. The strength of the interaction influences the elicited immune response. By definition, everything that an antibody can bind to is called an antigen. An antigen can be from another organism, a foreign particle such as a toxin, drug or a physical intruder (e.g., splinter), or the body’s own tissue. The exact point of contact where the antibody binds is called the epitope of the antigen. The strength with which an antibody binds to an epitope is called its affinity. When the body encounters an antigen for the first time, only some of the available antibodies in the body bind the antigen by chance. The affinity of the antibody is likely low. However, the adaptive immune system earns its name by reacting adaptively to antigens that the organism encounters during its lifetime. Once an antigen has been recognized for the first time, a complex selection process leads to the production of antibodies with higher affinity against this specific antigen. Hence, the affinity of the antibody for a particul

 Core: Immune System

Protein Crystallization

JoVE 5689

Protein crystallization, obtaining a solid lattice of biomolecules, elucidates protein structure and enables the study of protein function. Crystallization involves drying purified protein under a combination of many factors, including pH, temperature, ionic strength, and protein concentration. Once crystals are obtained, the protein structure can be elucidated by x-ray diffraction and…

 Biochemistry

Operons

JoVE 10984

Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by a repressor protein. Altogether, the promoter, operator, structural genes, and terminator form the core of an operon. Operons are usually either inducible or repressible. Inducible operons, such as the bacterial lac operon, are normally “off” but will turn “on” in the presence of a small molecule called an inducer (e.g., allolactose). When glucose is absent, but lactose is present, allolactose binds and inactivates the lac operon repressor—allowing the operon to generate enzymes responsible for lactose metabolism. Repressible operons, such as the bacterial trp operon, are usually “on” but will turn “off” in the presence of a small molecule called a corepressor (e.g., tryptophan). When tryptophan—an essential amino acid—is abundant, tryptophan binds and activates the tr

 Core: Gene Expression

Receptor-mediated Endocytosis

JoVE 10708

Receptor-mediated endocytosis is a process through which bulk amounts of specific molecules can be imported into a cell after binding to cell surface receptors. The molecules bound to these receptors are taken into the cell through inward folding of the cell surface membrane, which is eventually pinched off into a vesicle within the cell. Structural proteins, such as clathrin, coat the budding vesicle and give it its round form. One well-characterized example of receptor-mediated endocytosis is the transport of low-density lipoproteins (LDL cholesterol) into the cell. LDL binds to transmembrane receptors on the cell membrane. Adapter proteins allow clathrin to attach to the inner surface of the membrane. These protein complexes bend the membrane inward, creating a clathrin-coated vesicle inside the cell. The neck of the endocytic vesicle is pinched off from the membrane by a complex of the protein dynamin and other accessory proteins. The endocytic vesicle fuses with an early endosome, and the LDL dissociates from the receptor proteins due to a lower pH environment. Empty receptor proteins are separated into transport vesicles to be re-inserted into the outer cell membrane. LDL remains in the endosome, which binds with a lysosome. The lysosome provides digestive enzymes that break up LDL into free cholesterol that can be used by the cell. There ar

 Core: Membranes and Cellular Transport

Organization of Genes

JoVE 10786

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. Genes themselves consist of protein-coding exons and non-coding introns. Introns are excised once the sequence is transcribed to mRNA, leaving only exons to code for proteins.

In eukaryotic genomes, genes are separated by large stretches of DNA that do not code for proteins. However, these intergenic regions carry important elements that regulate gene activity, for instance, the promoter where transcription starts, and enhancers and silencers that fine-tune gene expression. Sometimes these binding sites can be located far away from the associated gene. As researchers investigated the process of gene transcription in eukaryotes, they realized that the final mRNA that codes for a protein is shorter than the DNA it is derived from. This difference in length is due to a process called splicing. Once pre-mRNA has been transcribed from DNA in the nucleus, splicing immediately removes introns and joins exons together. The result is protein-coding mRNA that moves to the cytoplasm and is translated into protein. One of the largest human genes, DMD, is over two million base pairs long. This gene encodes the muscle protein dystrophin. Mutations in DMD cause muscular dystrophy, a disorder characteri

 Core: DNA Structure and Function

Metabolic Labeling

JoVE 5687

Metabolic labeling is used to probe the biochemical transformations and modifications that occur in a cell. This is accomplished by using chemical analogs that mimic the structure of natural biomolecules. Cells utilize analogs in their endogenous biochemical processes, producing compounds that are labeled. The label allows for the incorporation of detection and affinity tags, which can then be …

 Biochemistry

ELISA Assays: Indirect, Sandwich, and Competitive

JoVE 10496

Source: Whitney Swanson1,2, Frances V. Sjaastad2,3, and Thomas S. Griffith1,2,3,4
1 Department of Urology, University of Minnesota, Minneapolis, MN 55455
2 Center for Immunology, University of Minnesota, Minneapolis, MN 55455
3 Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455
4 Masonic…

 Immunology

The ELISA Method

JoVE 5061

An enzyme-linked immunosorbent assay (ELISA) is typically performed to detect the presence and/or amount of a target protein of interest within an experimental sample. Detection of the target protein is made possible by antibodies, which make the ELISA an immunoassay. Through a series of incubation and washing steps, these antibodies, which are frequently linked, or conjugated, to an enzyme,…

 Basic Methods in Cellular and Molecular Biology

Solid Phase Synthesis

JoVE 10349

Source: Vy M. Dong and Diane Le, Department of Chemistry, University of California, Irvine, CA


Merrifield's solid-phase synthesis is a Nobel Prize winning invention where a reactant molecule is bound on a solid support and undergoes successive chemical reactions to form a desired compound. When the molecules are bound to a solid…

 Organic Chemistry II

Histological Staining of Neural Tissue

JoVE 5206

In order to examine the cellular, structural and molecular layout of tissues and organs, researchers use a method known as histological staining. In this technique, a tissue of interest is preserved using chemical fixatives and sectioned, or cut into very thin slices. A variety of staining techniques are then applied to provide contrast to the visually uniform sections. In …

 Neuroscience

Histological Sample Preparation for Light Microscopy

JoVE 5039

Histology is the study of cells and tissues, which is typically aided by the use of a light microscope. The preparation of histological samples can vary greatly based on the inherent properties of the samples such as size and hardness as well as expected post-processing which includes planned staining techniques or other down-stream applications. As described in this video, specimen…

 General Laboratory Techniques

Secondary Active Transport

JoVE 10707

One example of how cells use the energy contained in electrochemical gradients is demonstrated by glucose transport into cells. The ion vital to this process is sodium (Na+), which is typically present in higher concentrations extracellularly than in the cytosol. Such a concentration difference is due, in part, to the action of an enzyme “pump” embedded in the cellular membrane that actively expels Na+ from a cell. Importantly, as this pump contributes to the high concentration of positively-charged Na+ outside a cell, it also helps to make this environment “more positive” than the intracellular region. As a result, both the chemical and electrical gradients of Na+ point towards the inside of a cell, and the electrochemical gradient is similarly directed inwards. Sodium-glucose cotransporters (SGLTs) exploit the energy stored in this electrochemical gradient. These proteins, primarily located in the membranes of intestinal or kidney cells, help in the absorption of glucose from the lumen of these organs into the bloodstream. In order to function, both an extracellular glucose molecule and two Na+ must bind to the SGLT. As Na+ migrates into a cell through the transporter, it travels with its electrochemical gradient, expelling energy that the protein uses to move glucose ins

 Core: Membranes and Cellular Transport

Sample Preparation for Analytical Characterization

JoVE 10205

Source: Laboratory of Dr. B. Jill Venton - University of Virginia


Sample preparation is the way in which a sample is treated to prepare for analysis. Careful sample preparation is critical in analytical chemistry to accurately generate either a standard or unknown sample for a chemical measurement. Errors in analytical chemistry…

 Analytical Chemistry

RNA-Seq

JoVE 5548

Among different methods to evaluate gene expression, the high-throughput sequencing of RNA, or RNA-seq. is particularly attractive, as it can be performed and analyzed without relying on prior available genomic information. During RNA-seq, RNA isolated from samples of interest is used to generate a DNA library, which is then amplified and sequenced. Ultimately, RNA-seq can …

 Genetics

Drosophila Larval IHC

JoVE 5106

Immunohistochemistry (IHC) is a technique used to visualize the presence and location of proteins within tissues. Drosophila larvae are particularly amenable to IHC because of the ease with which they can be processed for staining. Additionally, the larvae are transparent, meaning that some tissues can be visualized without the need for dissection.


In IHC, proteins are…

 Biology I

DNA Ligation Reactions

JoVE 5069

In molecular biology, ligation refers to the joining of two DNA fragments through the formation of a phosphodiester bond. An enzyme known as a ligase catalyzes the ligation reaction. In the cell, ligases repair single and double strand breaks that occur during DNA replication. In the laboratory, DNA ligase is used during molecular cloning to join DNA fragments of inserts with vectors…

 Basic Methods in Cellular and Molecular Biology

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

1Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 2A*STAR-Duke-NUS Neuroscience Research Partnership, Singapore, 3Department of Biochemistry, National University of Singapore, Singapore

JoVE 3770

 Biology

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

1Laboratory of Molecular Biology, Medical Research Council - MRC, 2European Bioinformatics Institute, EMBL Heidelberg, 3Computer and Information Science, University of Ljubljana, 4Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute

JoVE 2638

 Biology
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