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Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

Induced-fit Model

JoVE 10734

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being used up or permanently changed. They work by reducing the activation energy needed for the reactants to be converted into the products. Enzymes, which are usually proteins, work by binding to a substrate—a reactant molecule that they act upon.

Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of their active site—the region of the enzyme that binds to the substrate. According to the induced-fit model of enzyme activity, this binding changes the conformation—or shape—of both the enzyme and the substrate. This brings the substrate closer to the higher energy transition state needed for the reaction to occur, for instance, by weakening its bonds so that it can more readily react. Enzymes may also speed up a reaction by creating conditions within the active site that are more conducive for the reaction to proceed than the surrounding cellular environment. Once the products of the reaction are formed, they are released from the active site and the enzyme can be used to catalyze reactions once again.

 Core: Metabolism

Cofactors and Coenzymes

JoVE 10975

Enzymes require additional components for proper function. There are two such classes of molecules: cofactors and coenzymes. Cofactors are metallic ions and coenzymes are non-protein organic molecules. Both of these types of helper molecule can be tightly bound to the enzyme or bound only when the substrate binds.

Cofactors are present in ~30% of mature proteins. They are frequently incorporated into an enzyme as it is folded and are involved in the enzyme’s catalytic activity. Magnesium is an essential cofactor for over 300 enzymes in the human body, including DNA polymerase. In this case, the magnesium ion aids in the formation of the phosphodiester bond on the DNA backbone. Iron, copper, cobalt, and manganese are other common cofactors. Many vitamins are coenzymes, as they are nonprotein, organic helper molecules for enzymes. For example, biotin—a type of B vitamin—is important in a variety of enzymes that transfer carbon dioxide from one molecule to another.  Biotin, vitamin A and other vitamins must be ingested in our diet, as they cannot be made by human cells.

 Core: Metabolism

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids

1Department of Biocatalysis, Institute of Chemistry, Technische Universität Berlin, 2Department of Bioenergetics, Institute of Chemistry, Technische Universität Berlin, 3Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Department of Molecular Genetics, University of Groningen

JoVE 57551

 Bioengineering

Quantitative, Real-time Analysis of Base Excision Repair Activity in Cell Lysates Utilizing Lesion-specific Molecular Beacons

1Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, 2Hillman Cancer Center, University of Pittsburgh Cancer Institute, 3Department of Experimental Therapy, The Netherlands Cancer Institute, 4Department of Human Genetics, University of Pittsburgh School of Public Health

JoVE 4168

 Biology

Screening for Thermotoga Maritima Membrane-Bound Pyrophosphatase Inhibitors

1Research Program in Molecular and Integrative Biosciences, University of Helsinki, 2Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 3School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds

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JoVE 60619

 JoVE In-Press

Nanosensors to Detect Protease Activity In Vivo for Noninvasive Diagnostics

1Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, 2Parker H. Petit Institute of Bioengineering and Bioscience, 3Institute for Electronics and Nanotechnology, Georgia Tech, 4Integrated Cancer Research Center, Georgia Tech, 5The Georgia Immunoengineering Consortium, Emory University and Georgia Tech

JoVE 57937

 Bioengineering

In Vitro SUMOylation Assay to Study SUMO E3 Ligase Activity

1Institute of Microbiology and Immunology, National Yang-Ming University, 2UC Davis Cancer Center, University of California, Davis, 3Department of Biochemistry and Molecular Medicine, University of California, Davis, 4Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 5Division of Molecular and Genomic Medicine, National Health Research Institutes, 6Center for Infectious Disease and Cancer Research, Kaohsiung Medical University

JoVE 56629

 Biology

An Engineered Split-TET2 Enzyme for Chemical-inducible DNA Hydroxymethylation and Epigenetic Remodeling

1Centre for Epigenetics and Disease Prevention, Department of Molecular and Cellular Medicine, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, 2Centre for Translational Cancer Research, Department of Medical Physiology, Institute of Biosciences and Technology, College of Medicine, Texas A&M University

JoVE 56858

 Chemistry

A Fluorogenic Peptide Cleavage Assay to Screen for Proteolytic Activity: Applications for coronavirus spike protein activation

1Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, 2Department of Microbiology, College of Agricultural and Life Sciences, Cornell University, 3Virologie et Immunologie Moléculaires, Domaine de Vilvert, INRA, 4Department of Cell Biology and Molecular Genetics, University of Maryland

JoVE 58892

 Biochemistry

Fat Body Organ Culture System in Aedes Aegypti, a Vector of Zika Virus

1Department of Biology, New Mexico State University, 2Department of Molecular Genetics and Microbiology, Duke University, 3Department of Computer Sciences, New Mexico State University, 4Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 5Institute of Applied Biosciences, New Mexico State University

JoVE 55508

 Biology
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