The machinery of life depends on proteins--large organic molecules composed of tens, hundreds or even thousands of amino acids bound together and folded into specifically shaped structures. How they fold into these three-dimensional structures is known as the second genetic code and is one of great challenges in science today. Join UCSD biophysicist Jose Onuchic, as he explores how physics, chemistry, biology and mathematics are all being applied to crack the protein folding mystery. Series: Atoms to X-Rays [Science] [Show ID: 5553] UCTV: UC San Diego29 min 51 sec - Jul 25, 2001www.uctv.tv

This video is courtesy of EU-IndiaGrid and shows the setup of a simple simulation using BEMuSE, software for faster folding of proteins using grid computing. (http://euindia.ictp.it/bemuse/video-tutorials/) This video shows:
* The structure of the restarts * The configuration of a simulation * The submission of the jobs

Background
The present study was designed to test the hypothesis that inactivation of virtually any component within the pathway containing the BRCA1 and BRCA2 proteins would increase the risks for lymphomas and leukemias. In people who do not have BRCA1 or BRCA2 gene mutations, the encoded proteins prevent breast/ovarian cancer. However BRCA1 and BRCA2 proteins have multiple functions including participating in a pathway that mediates repair of DNA double strand breaks by error-free methods. Inactivation of BRCA1, BRCA2 or any other critical protein within this "BRCA pathway" due to a gene mutation should inactivate this error-free repair process. DNA fragments produced by double strand breaks are then left to non-specific processes that rejoin them without regard for preserving normal gene regulation or function, so rearrangements of DNA segments are more likely. These kinds of rearrangements are typically associated with some lymphomas and leukemias.

Methods
Literature searches produced about 2500 epidemiology and basic science articles related to the BRCA pathway. These articles were reviewed and copied to a database to facilitate access. Meta-analyses of statistical information compared risks for hematologic cancers vs. mutations for the components in a model pathway containing BRCA1/2 gene products.

Results
Deleterious mutations of genes encoding proteins virtually anywhere within the BRCA pathway increased risks up to nearly 2000 fold for certain leukemias and lymphomas. Cancers with large increases in risk included mantle cell lymphoma, acute myeloid leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, and prolymphocytic leukemia. Mantle cell lymphoma is defined by a characteristic rearrangement of DNA fragments interchanged between chromosomes 11 and 14. DNA translocations or rearrangements also occur in significant percentages of the other cancers.

Conclusion
An important function of the BRCA pathway is to prevent a subgroup of human leukemias and lymphomas that may involve non-random, characteristic gene rearrangements. Here, the genetic defect in BRCA pathway deficiencies is a chromosomal misrepair syndrome that may facilitate this subgroup of somatic cancers. Inactivation of a single gene within the pathway can increase risks for multiple cancers and inactivation of a different gene in the same pathway may have similar effects. The results presented here may have clinical implications for surveillance and therapy.

Biochemistry is the study of the chemical processes and compounds, such as cellular makeup, that bring about life in organisms. This course will look at how these formed biomolecules interact and produce many of life's necessary processes. Also it will look at the most commonly used techniques in biochemistry research. Upon successful completion of this course, students will be able to: recognize and describe the structure of the following basic biomolecules: nucleic acids, amino acids, lipids, carbohydrates; diagram how these basic biomolecules are used as building blocks for more complex biomolecules; differentiate between reactions that create biomolecules; describe how these biomolecules are used in specific cellular pathways and processes; analyze how feedback from one pathway influences other pathways; explain how energy is utilized by a cell; indicate how biomolecules and pathways are regulated; describe how enzymes play a key role in catalysis; assess which biochemical technique should be used to study a given biochemical problem. (Biology 401; See also: Chemistry 109)

This is a comprehensive textbook covering life functions that are ultimately interpretable in chemical terms, as chemistry is the logic of biological phenomena.

This educational journal article addresses the implementation of bioinformatics in the classroom. The author explains how bioinformatics could play a key role for science students pursuing higher education, foster inquiry learning of content that has often been taught in a dry manner, provide the thread that ties classes together, improve biology teaching, enhance the learning of biotech issues and ethics, expose students to real-world science, and significantly help to reform biology teaching and improve learning. The article includes links to bioinformatics resources, information about how to get involved in bioinformatics, and a glossary of terms.

The endoplasmic reticulum (ER) orchestrates different cellular processes by which proteins are synthesized, correctly folded, modified and ultimately transported to their final destinations. As part of this crucial biosynthetic process, proteins that are not properly folded and consequently detrimental to normal cellular function are constantly generated. A common signature of many neurodegenerative diseases, including Alzheimer's and Parkinson's, is accumulation and deposition of misfolded proteins that arise when the ability of cells to deal with the burden of misfolded proteins is compromised. In this course, we will explore how the ER quality control machinery ensures that only properly assembled proteins exit the ER while distinguishing between nascent proteins en route to their biologically active folded state from those that are terminally misfolded.

Life as an emergent property of networks of chemical reactions involving proteins and nucleic acids. Mathematical theories of metabolism, gene regulation, signal transduction, chemotaxis, excitability, motility, mitosis, development, and immunity. Applications to directed molecular evolution, DNA computing, and metabolic and genetic engineering.

In this visualization adapted from the University of Massachusetts Medical School, discover the role that dengue viral proteins play in a human cell as the virus prepares to replicate.

This module introduces concepts on dimensionality reduction, including Principal Components Analysis (PCA) and Isomap. It also shows how to apply them to molecular motion data, and how to interpret the resulting coordinates.

The understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, ab initio simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow structure fine-tuning. Remarkably, a subset of native interactions drives the folding from the very beginning. The emerging comprehensive picture of GB1 folding perfectly matches and extends the previous experimental and theoretical studies.

Help Me Understand Genetics presents basic information about genetics in clear language and provides links to online resources.

In this interactive activity from the Exploratorium, explore the steps of protein synthesis in which the cells use genes to make proteins for critical body functions.

A look into the evolution of one family of proteins. Lecture from the Women in Bioinformatics series. Stella Veretnik, Ph.D. Computational Molecular Biology, National Laboratory for Computational Science and Engineering, University of California - San Diego

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material. 7.014 focuses on the application of the fundamental principles toward an understanding of human biology. Topics include genetics, cell biology, molecular biology, disease (infectious agents, inherited diseases and cancer), developmental biology, neurobiology and evolution.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material. 7.014 focuses on the application of these fundamental principles, toward an understanding of microorganisms as geochemical agents responsible for the evolution and renewal of the biosphere and of their role in human health and disease.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.7.014 focuses on the application of the fundamental principles toward an understanding of human biology. Topics include genetics, cell biology, molecular biology, disease (infectious agents, inherited diseases and cancer), developmental biology, neurobiology and evolution.

We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing >1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for ~40% of the mouse proteome.