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Antibiotics, Toxins, and Protein Engineering
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The lethal poison Ricin (best known as a weapon of bioterrorism), Diphtheria toxin (the causative agent of a highly contagious bacterial disease), and the widely used antibiotic tetracycline have one thing in common: They specifically target the cell’s translational apparatus and disrupt protein synthesis.
In this course, we will explore the mechanisms of action of toxins and antibiotics, their roles in everyday medicine, and the emergence and spread of drug resistance. We will also discuss the identification of new drug targets and how we can manipulate the protein synthesis machinery to provide powerful tools for protein engineering and potential new treatments for patients with devastating diseases, such as cystic fibrosis and muscular dystrophy.
This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.

Subject:
Applied Science
Biology
Engineering
Health, Medicine and Nursing
Life Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Koehrer, Caroline
Sassanfar, Mandana
Date Added:
02/01/2007
Biological Chemistry II
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CC BY-NC-SA
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This course is an advanced treatment of biochemical mechanisms that underlie biological processes. Topics include macromolecular machines such as the ribosome, the proteasome, fatty acid synthases as a paradigm for polyketide synthases and non-ribosomal polypeptide synthases, and polymerases. Emphasis will be given to the experimental methods used to unravel how these processes fit into the cellular context as well as the coordinated regulation of these processes.

Subject:
Biology
Chemistry
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Nolan, Elizabeth
Stubbe, Joanne
Date Added:
02/01/2016
Biology
Unrestricted Use
CC BY
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Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Subject:
Biology
Life Science
Material Type:
Full Course
Provider:
Rice University
Provider Set:
OpenStax College
Date Added:
08/22/2012
Biology, The Cell, Cell Structure, The Cytoskeleton
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CC BY-NC
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By the end of this section, you will be able to:Describe the cytoskeletonCompare the roles of microfilaments, intermediate filaments, and microtubulesCompare and contrast cilia and flagellaSummarize the differences among the components of prokaryotic cells, animal cells, and plant cells

Subject:
Applied Science
Biology
Life Science
Material Type:
Module
Date Added:
07/10/2017
DNA: The Human Body Recipe
Read the Fine Print
Educational Use
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As a class, students work through an example showing how DNA provides the "recipe" for making our body proteins. They see how the pattern of nucleotide bases (adenine, thymine, guanine, cytosine) forms the double helix ladder shape of DNA, and serves as the code for the steps required to make genes. They also learn some ways that engineers and scientists are applying their understanding of DNA in our world.

Subject:
Applied Science
Engineering
Genetics
Life Science
Material Type:
Activity/Lab
Lesson Plan
Teaching/Learning Strategy
Provider:
TeachEngineering
Provider Set:
TeachEngineering
Author:
Denise W. Carlson
Frank Burkholder
Jessica Todd
Malinda Schaefer Zarske
Date Added:
09/18/2014
Genetics
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CC BY-NC-SA
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This course discusses the principles of genetics with application to the study of biological function at the level of molecules, cells, and multicellular organisms, including humans. The topics include: structure and function of genes, chromosomes and genomes, biological variation resulting from recombination, mutation, and selection, population genetics, use of genetic methods to analyze protein function, gene regulation and inherited disease.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Fink, Gerald
Kaiser, Chris
Mischke, Michelle
Samson, Leona
Date Added:
09/01/2004
Introduction to Biology
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CC BY-NC-SA
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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.
7.012 focuses on the exploration of current research in cell biology, immunology, neurobiology, genomics, and molecular medicine.
Acknowledgments
The study materials, problem sets, and quiz materials used during Fall 2004 for 7.012 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course #7.012. Since the following works have evolved over a period of many years, no single source can be attributed.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Chess, Andrew
Gardel, Claudette
Lander, Eric
Weinberg, Robert
Date Added:
09/01/2004
Introductory Biology
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CC BY-NC-SA
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The MIT Biology Department core Introductory Biology courses, 7.012, 7.013, 7.014, 7.015, and 7.016 all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. The focus of 7.013 is on genomic approaches to human biology, including neuroscience, development, immunology, tissue repair and stem cells, tissue engineering, and infectious and inherited diseases, including cancer.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Amon, Angelika
Ray, Diviya
Sive, Hazel
Date Added:
02/01/2018
Introductory Biology
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CC BY-NC-SA
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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. 7.013 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.
Biological function at the molecular level is particularly emphasized in all courses 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.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Jacks, Tyler
Sinha, Diviya
Sive, Hazel
Date Added:
02/01/2013
Introductory Biology
Conditional Remix & Share Permitted
CC BY-NC-SA
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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.
Acknowledgements
The study materials, problem sets, and quiz materials used during Spring 2005 for 7.014 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course 7.014. Since the following works have evolved over a period of many years, no single source can be attributed.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Chisholm, Penny
Khodor, Julia
Mischke, Michelle
Walker, Graham
Date Added:
02/01/2005
Life Size
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In this activity on page 1 of the PDF, learners compare the relative sizes of biological objects (like DNA and bacteria) that can't be seen by the naked eye. Learners will be surprised to discover the range of sizes in the microscopic world. This activity can be followed up with a second activity, "What's in a microbe?", located on page 3 in the same resource.

Subject:
Biology
Life Science
Material Type:
Activity/Lab
Provider:
Exploratorium
Author:
Julie Yu
National Science Foundation
The Exploratorium
Date Added:
11/07/2006
The Online Macromolecular Museum
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The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM's exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.

Why devote a site to detailed visualizations of different macromolecules? In learning about the intricacies of life processes at the molecular level, it is important to understand how natural selection has fashioned the structure and chemistry of macromolecular machines to suit them for particular functions. This understanding is greatly facilitated by the visualization of 3-dimensional structure, when known. So, if static views of molecules (even in stereo) are worth a thousand words, then interactive animations of molecules should be worth much more. Indeed, we have found the types of displays represented here invaluable in gaining an appreciation for the details of key biochemical processes.

As Carl Brandon and John Tooze stated in their classic text, Introduction to Protein Structure:
"Molecular biology began some 40 years ago with the realization that structure was crucial for a proper understanding of function. Paradoxically, the dazzling achievements of molecular genetics and biochemistry led to the eclipse of structural studies. We believe the wheel has now come full circle, and those very achievements have increased the need for structural analysis at the same time that they have provided the means for it."

It is our opinion that structural analysis should extend into the classroom: as students learn about cellular mechanisms it is important that they study the chemistry of the molecular machines involved. These considerations have motivated the construction of the OMM.

The OMM is part of a collaborative effort by faculty and students interested in macromolecular structure-function relationships. The primary authors of some tutorials are students of David Marcey and he serves as author, co-author and site editor, and assumes all responsibility for content. Any criticisms, suggestions, comments, or questions should be sent to him at: marcey@callutheran.edu. All tutorials are copyrighted.

The OMM was started in 1996 for a Molecular Biology class at Kenyon College, where DM was a professor in the Biology Department (1990-1999). The OMM is now developed and housed at California Lutheran University, where DM has been a professor since 1999.

Subject:
Chemistry
Life Science
Physical Science
Material Type:
Activity/Lab
Diagram/Illustration
Homework/Assignment
Interactive
Lesson
Author:
David Marcey
Date Added:
09/28/2017
Phylogenies of the 16S rRNA gene lack concordance with core genome phylogenies
Unrestricted Use
CC BY
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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:

"The 16S rRNA gene is widely used for bacterial phylogenetics, species delineation, and microbiome research. Historically, researchers assumed that sequence variations in this gene were only due to speciation and inheritance. But there are reports of recombination events and an unreliable phylogenetic signal. To examine this directly, researchers performed four intra-genus analyses and one inter-genus analysis using pathogenic and core human microbiome genera. In all analyses, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the 16S rRNA gene averaged 50.7% concordance with the species phylogeny, one of the lowest of the core genes. Further analysis found that the single nucleotide polymorphism (SNP) count was a major factor influencing concordance. 690 ± 110 SNPs would be required to reach 80% concordance, but the average SNP count for the 16S rRNA gene was only 254..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Subject:
Biology
Life Science
Material Type:
Diagram/Illustration
Reading
Provider:
Research Square
Provider Set:
Video Bytes
Date Added:
04/14/2023