Exploring metabolite metabolism using the Enzyme Portal

This webinar will provide a practical overview of how to use the Enzyme Portal to find enzyme-related information about metabolites. The Enzyme Portal is a freely available resource to find and explore enzyme features. It integrates relevant enzyme data for a wide range of species from various resources including UniProt, PDB, Reactome and CHEMBL. We will demonstrate how to use the Enzyme Portal to find relevant enzymes involved in a specific metabolite biosynthesis or catabolism. Who is this course for? This webinar is aimed at individuals who wish to learn more about enzymes and metabolites. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Material Type: Lecture

Novel paramagnetic substrate may allow researchers to track enzyme activity within living tissue

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview: "A team of researchers based at West Virginia University has devised an innovative way to potentially monitor enzyme activity in vivo using electron paramagnetic resonance imaging. The method could provide new insights into the molecular underpinnings of many types of disease. The team specifically focused on tracking enzymatic dephosphorylation. Abnormalities in dephosphorylation have been linked to disorders ranging from cancer to Alzheimer disease. Monitoring such malfunction in vivo can provide crucial details into disease state and progression, but direct measurement of enzyme activity within a living organism remains extremely challenging. Many imaging approaches that might be used for this purpose are hampered by concerns such as low sensitivity and penetration depth. Such limitations prompted the researchers to turn to EPRI – a method with high intrinsic sensitivity and specificity..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Transcriptional control of the cancer-promoting enzyme USP22 in lung cancer cells

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview: "In cancer cells, even seemingly small gene expression changes can have a devastating impact, but for some molecules, like the enzyme USP22, researchers don’t know how their expression is regulated. High expression of USP22 is associated with poor prognosis in many human cancers. But the gene for USP22 is rarely mutated, suggesting that the expression changes happen at the transcription step. So, researchers set out to find transcription factors, which are transcription-modulating proteins, that regulate USP22. After identifying several that modulate USP22 expression, they focused on two related factors that increased USP22 expression, AP2α, and AP2β. Overexpressing AP2α/β in cultured non-small cell lung cancer (NSCLC) cells increased the expression of USP22 and the protein it targets, Cyclin D1, while also increasing the cancer cell behaviors proliferation, migration, and invasion..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Removing proline-rich region of farnesyltransferase does not alter enzyme activity

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview: "Farnesyltransferase (FTase) is an enzyme implicated in various diseases, including cancer, hepatitis D, and progeria. One of the two subunits that make up FTase has a proline-rich region, which has been shown to affect signal transduction. Could this region be the key to FTase’s function, especially in disease? To find out, researchers recently explored how modifications altered the behavior of FTase. Phylogenetics revealed that the proline-rich region of FTase is highly conserved in mammals, with the exception of marsupials, which harbor an alanine-rich region instead. Interestingly, when the proline-rich region was removed, FTase retained the ability to bind to its normal physiological partners and did not appear to bind to itself. Indeed, the presence or absence of the proline-rich region did not affect the activity of FTase from either humans or rats. And prominent FTase inhibitors, namely lonafarnib and tipifarnib, worked just as well on either form..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Enzymology

Enzymes are biocatalyst they accelerate the chemical reaction. They are organic, all enzymes are made of protein but not all enzymes are protein. Certain biological reactions can be catalyzed by RNA called Ribozyme. Protein is a dynamic molecule; its activity depends on the three-dimensional structure. For example, the water droplet size gets flexible, if you touch. Protein folding and three-dimensional structures are vital for activity.  There is no living cell without an enzyme, in the living cell; it functions to accelerate the biological reaction. There is a misfolded protein infectious agent called Prion, which causes normal brain protein to misfold which, leads to neurodegratative disease. This module presents concise notes of enzyme basic concepts; bioinformatics tools and few examples of enzymes in everyday life.

Material Type: Activity/Lab, Lecture Notes, Module

Author: Jothibasu Karuppaiyan

Primer design for ligation/restriction cloning

In the video you can find some hints to design a primers for clone your GOI in a plasmid using restriction enzyme and ligase cloning approach

Material Type: Lecture

Author: manuele martinelli

Supplement for Standard Biochemistry Textbooks

Dr. Bolander recently retired from the University of South Carolina, where he taught biochemistry at both the graduate and undergraduate levels for decades. He accumulated considerable figures and notes and is making them available to others involved with teaching biochemistry or related courses. These notes cover material with weaker coverage in standard biochemistry textbooks. This text is supplemental rather than primary.

Material Type: Lecture Notes, Reading

Author: Dr. Franklyn F. Bolander Jr.

Integrating knowledge of proteins and small molecules with UniProtKB

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites – the metabolome – with that of genes, transcripts, and proteins (the genome, transcriptome, and metabolome). The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive, high quality and freely accessible resource of protein sequences and functional information. UniProtKB integrates, interprets and standardizes data from a range of sources including the scientific literature, tools for protein sequence analysis, other knowledge resources and databases, and automatic annotation systems, to provide a detailed overview of the available protein knowledge. This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge. Who is this course for? This webinar targets life scientists and bioinformaticians who study enzymes and small molecules, particularly those interested in linking or bridging the two domains. No prior knowledge of bioinformatics or cheminformatics is required, but an undergraduate level knowledge of biology/ biochemistry would be useful. Outcomes By the end of the webinar you will be able to: Describe how UniProt annotates enzyme and transporter function, and where the data comes from Find and retrieve information about specific enzymes, transporters and the metabolites on which they act, by searching UniProtKB using text, chemical structures, and chemical classifications Help us develop the representation of small molecule data in UniProtKB by providing valuable feedback

Material Type: Lecture

CRISPER Prokaryotic Antiviral Defense Mechanism

Barrangou and a team of researchers at Danisco first experimentally demonstrated the technique of CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats). To fight off the infecting bacteriophages, the bacterial immume systems (CRISPR-Cas9) specifically target genomic sequences. Cas9 is an enzyme that cuts DNA which is associated with the specialized stretches of CRISPR DNA. This figure clearly depicts how the bacterium protects itself from the infecting viruses (bacteriophages).

Material Type: Diagram/Illustration

Author: Theroid

Biology, The Cell, Metabolism, Enzymes

By the end of this section, you will be able to:Describe the role of enzymes in metabolic pathwaysExplain how enzymes function as molecular catalystsDiscuss enzyme regulation by various factors

Material Type: Module

Biology, The Cell, Metabolism, Enzymes

By the end of this section, you will be able to:Describe the role of enzymes in metabolic pathwaysExplain how enzymes function as molecular catalystsDiscuss enzyme regulation by various factors

Material Type: Module

Author: Tina B. Jones

Restriction enzyme

The link talks about introduction to restriction endonucleases, types, examples and other characteristics of the enzymes.

Material Type: Module

Enzyme reaction velocity and pH

Exploring the relationship between pH and enzyme activity.

Material Type: Lesson

Author: Sal Khan

Adventures in Antibody Identification: Enzymes and Dara

Only around 0.2-2.0% of the patient population will have detectable RBC antibodies -- fewer still will have multiplePatients more frequently exposed to RBC antigens are more likely to have antibodies (multiply transfused sickle cell adult patients ~47%)So you've mastered the type & screen and antibody panels... but what do you do if an antibody panel is inconclusive?Selected Cell Panels - select cells with minimal overlap of antigens; helpful for patients with a known history of an antibodyEnzyme-treated panels - destroy certain antigens and enhance expression of others; modify RBC surface by removing sialic acid residues and by denaturing or removing glycoproteinsExamples: ficin, papain, bromelin, trypsinOne-step enzyme method: enzymes utilized in place of enhancement media (instead of LISS or PEG)Two-step enzyme method: panel RBCs are treated with an enzyme first, then the antibody ID panel is done with treated cells; should compare reactivity to antibody ID panel of same cells without enzyme treatmentA special case seen in blood banking: Daratumumab ("Dara") patientsDaratumumab is a drug used in treatment of Multiple MyelomaPlasmacytoma or plasma cell cancer - plasma cells express CD 38~30k new cases, ~12.5k deaths per yearAnemia is a key symptom (with calcium levels, renal insufficiency, bone lesions)CD 38 is a cyclic ADP ribose hydrolase - with roles in calcium signalling & NAD metabolismExpressed on all cell types: notably Plasma cells and RBCsOne option for treating Multiple Myeloma is the drug Daratumumab: a monoclonal antibody IgG1K anti-CD 38; kills myeloma cells through patient's own immune responseWhat does this have to do with blood bank?CD38 is found on RBCs -- including screen and panel cells, in crossmatchesDara patients show PANAGGLUTINATION in all AHG testing - positive screen, panel, crossmatch, variable/weak positive DAT (at IgG)Multiple myeloma patients need frequent transfusions - increased chance of developing alloAbEnzyme treated panel case studyDara patient case study

Material Type: Module

Author: Ann Barrett

Enzyme Lab (online lab)

This online enzyme lab activity is written for students who are unable to attend lab in-person.

Material Type: Activity/Lab

Author: Jeff Carmichael

Enzyme Portal: Quick tour

This quick tour provides a brief introduction to Enzyme Portal - a data resource that provides access to information from several enzyme-related databases, many of which are based at EMBL-EBI. By the end of the course you will be able to: Navigate Enzyme Portal to access enzyme-related data Identify the various possibilities to search Enzyme Portal Describe what type of enzyme-related data Enzyme Portal provides

Material Type: Full Course

Got Lactose? Investigating How Enzymes Function

After studying the basics of enzyme function, students will be exposed to the history and evolution of lactose intolerance/lactase persistence. Both whole group and individual activities will ask students to interact with the concept. They will conduct a lab to understand the role of enzymes in lactose digestion and communicate their knowledge by creating a public health poster.

Material Type: Activity/Lab, Assessment, Data Set, Lesson, Lesson Plan, Student Guide

Author: Janelle Roberts

Got Lactose? Investigating How Enzymes Function

After studying the basics of enzyme function, students will be exposed to the history and evolution of lactose intolerance/lactase persistence. Both whole group and individual activities will ask students to interact with the concept. They will conduct a lab to understand the role of enzymes in lactose digestion and communicate their knowledge by creating a public health poster.

Material Type: Activity/Lab, Assessment, Data Set, Lesson, Lesson Plan, Student Guide

Author: STEMToolkit Administrator

Enzymes Help Us Digest Food

Students learn about enzyme function, enzyme specificity, and the molecular basis of lactose intolerance through experiments with the enzyme lactase and analysis and discussion questions. Students engage in the scientific practices of designing and carrying out experiments and interpreting data. This activity is aligned with the Next Generation Science Standards.

Material Type: Activity/Lab, Lesson Plan

Authors: Ingrid Waldron, Jennifer Doherty

Lessons 1: Qualitative Kinetics: Examining the effect of an enzyme on a reaction

Chemical kinetics and buffers are two topics that are extremely difficult for students to understand. Combining the two topics will allow for a staggered, repetitive approach to teaching students to understand of how these two topics in chemistry actually work. Students will both qualitatively and quantitatively track the effect and enzyme has on a reaction, calculate the reaction rate and buffer capacity. Students will use a variety of lab techniques including calculations using Beer’s Law and spectrophotometry.

Material Type: Lesson Plan

Author: Chris England