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BIOL 101(F) LEC The Cell
This course investigates cell structure and function as a consequence of evolutionary processes, and it stresses the dynamic properties of living systems. Topics include an introduction to biological molecules and enzyme action, membrane structure and function, energy exchange and design of metabolic systems, expression of genetic information, protein trafficking, cell signaling, the cell cycle, and cancer. Student-designed laboratory experiments and discussions based on primary biology literature will highlight how biological knowledge is created and understood. [ more ]
Taught by: Pei-Wen Chen, Caitlyn Bowman-Cornelius
Catalog detailsCHEM 101(F, S) LEC Concepts of Chemistry
This course broadens and deepens the foundation in chemistry of students who have had one or more years of chemistry at the high school level. Most students begin study of chemistry at Williams with this course. Familiarity with stoichiometry, basic concepts of equilibria, the model of an atom, Lewis structures and VSEPR, and gas laws is expected. Principal topics for this course include modern atomic theory, molecular structure and bonding, states of matter, chemical equilibrium (acid-base and solubility), and an introduction to atomic and molecular spectroscopies. Laboratory periods will largely focus on experiment design, data analysis, literature, scientific writing, and other skills critical to students' development as scientists. The course is of interest to students who anticipate professional study in chemistry, related sciences, or one of the health professions, as well as to those who want to explore the fundamentals of chemistry as part of their general education. This course may be taken pass/fail; however, students who are considering graduate study in science or in the health professions should elect to take this course for a grade. [ more ]
Taught by: Bob Rawle, Lee Park, Ben Augenbraun
Catalog detailsBIOL 102(S) LEC The Organism
This course focuses upon the developmental and evolutionary processes that have given rise to a wide diversity of multicellular organisms. We consider many levels of biological organization, from molecular and cellular to individuals and populations in our examination of evolutionary concepts. Topics include meiosis and sexual reproduction, developmental and evolutionary mechanisms, and speciation with representative examples from a diversity of plants and animals. Readings are drawn from a variety of sources, including the recent primary literature. Although BIOL 101 is not a prerequisite for BIOL 102, students are expected to have basic knowledge of the cell and cellular processes, including: the structure and function of the cell, nucleic acids and proteins; as well as mechanisms of transcription, translation, and the regulation of genes. [ more ]
Taught by: Robert Savage, Claire Ting
Catalog detailsCHEM 200(S) LEC Advanced Chemical Concepts
This course treats an array of topics in modern chemistry, emphasizing broad concepts that connect and weave through the various subdisciplines of the field--biochemistry, inorganic chemistry, organic chemistry, and physical chemistry. It provides the necessary background in chemical science for students who are planning advanced study or a career in chemistry, biological science, geoscience, environmental science, or a health profession. Topics include coordination complexes, thermodynamics, electrochemistry, and kinetics. Laboratory sections will give students hands-on experience involving synthesis, characterization, and reactivity studies of coordination and organic complexes; spectroscopic analyses; thermodynamics; electrochemistry; and kinetics. Students will hone their skills in the presentation of results through written reports and worksheets. [ more ]
Taught by: Enrique Peacock-López
Catalog detailsCHEM 201(F) LEC Organic Chemistry: Introductory Level
This course provides the necessary background in organic chemistry for students who are planning advanced study or a career in chemistry, the biological sciences, or the health professions. It initiates the systematic study of the common classes of organic compounds with emphasis on theories of structure and reactivity. Specific topics include basic organic structures and bonding, delocalization and conjugation, acidity & basicity, nucleophilic addition and substitution reactions, stereochemistry and molecular energetics. The theory and interpretation of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy, as well as the fundamentals of molecular modeling as applied to organic molecules are presented. The coordinated laboratory work includes organic synthesis, purification and separation techniques, as well as characterization by IR and NMR spectroscopy. [ more ]
Taught by: Kerry-Ann Green, Amanda Turek
Catalog detailsBIOL 202(F) LEC Genetics
Genetics, classically defined as the study of heredity, is today a multidisciplinary field whose principles provide critical insight and tools to most areas of biology and medicine. This course covers the experimental basis for our current understanding of the inheritance, structures, and functions of genes. It introduces approaches used by contemporary geneticists and molecular biologists to explore questions in areas of biology ranging from evolution to medicine. A primary focus of the course is on students developing familiarity with problem solving, the logic and quantitative reasoning required to understand how genetic mechanisms lead to biological patterns. The laboratory part of the course provides an experimental introduction to modern genetic analysis as well as introductions to interpreting genetic reasoning in the primary research literature. Laboratory experiments include investigating chromosome structure using microscopy, mapping a mutation to the genome by integrating multiple streams of evidence, and determining the structure of a DNA plasmid using molecular tools. [ more ]
Taught by: Luana Maroja
Catalog detailsCHEM 242(S) LEC Organic Chemistry: Intermediate Level
This course is a continuation of CHEM 156/201 and it concludes the systematic study of the common classes of organic compounds with emphasis on theories of structure and reactivity. Specific topics include radical chemistry, an introduction to mass spectrometry and ultraviolet spectroscopy, the theory and chemical reactivity of conjugated and aromatic systems, the concepts of kinetic and thermodynamic control, an extensive treatment of the chemistry of the carbonyl group, alcohols, ethers, polyfunctional compounds, the concept of selectivity, the fundamentals of organic synthesis, an introduction to carbohydrates, carboxylic acids and derivatives, acyl substitution reactions, amines, and an introduction to amino acids, peptides, and proteins. The coordinated laboratory work includes application of the techniques learned in the introductory level laboratory, along with new functional group analyses, to the separation and identification of several unknown samples. Skills in analyzing NMR, IR, and MS data are practiced and further refined. [ more ]
Taught by: Thomas Smith, B Thuronyi
Catalog detailsBIMO 321 / BIOL 321 / CHEM 321(F) LEC Biochemistry I: Structure and Function of Biological Molecules
This course introduces the foundational concepts of biochemistry with an emphasis on the structure and function of biological macromolecules. Specifically, the structure of proteins and nucleic acids are examined in detail in order to determine how their chemical properties and their biological behavior result from those structures. Other topics covered include catalysis, enzyme kinetics, mechanism and regulation; the molecular organization of biomembranes; and the flow of information from nucleic acids to proteins. In addition, the principles and applications of the methods used to characterize macromolecules in solution and the interactions between macromolecules are discussed. The laboratory provides a hands-on opportunity to study macromolecules and to learn the fundamental experimental techniques of biochemistry including electrophoresis, chromatography, and principles of enzymatic assays. [ more ]
Taught by: B Thuronyi
Catalog detailsBIMO 322 / BIOL 322 / CHEM 322(S) LEC Biochemistry II: Metabolism
This lecture course provides an in-depth presentation of the complex metabolic reactions that are central to life. Emphasis is placed on the biological flow of energy including alternative modes of energy generation (aerobic, anaerobic, photosynthetic); the regulation and integration of the metabolic pathways including compartmentalization and the transport of metabolites; and biochemical reaction mechanisms including the structures and mechanisms of coenzymes. This comprehensive study also includes the biosynthesis and catabolism of small molecules (carbohydrates, lipids, amino acids, and nucleotides). Laboratory experiments introduce the principles and procedures used to study enzymatic reactions, bioenergetics, and metabolic pathways. [ more ]
Taught by: Caitlyn Bowman-Cornelius
Catalog detailsBIMO 401(S) SEM Topics in Biochemistry and Molecular Biology
This seminar course involves critical reading, analysis, and discussion of papers from the current biochemistry and molecular biology literature. Specific topics vary from year to year but are chosen to illustrate the importance of a wide range of both biological and chemical approaches to addressing important questions in the biochemical and molecular biological fields. To facilitate discussion, students will prepare written critiques analyzing the data and conclusions of the chosen literature. [ more ]
Taught by: Katie Hart
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BIOL 301 LEC Developmental Biology
Last offered Fall 2014
Developmental biology has undergone rapid growth in recent years and is becoming a central organizing discipline that links cells and molecular biology, evolution, anatomy and medicine. We are now beginning to have a molecular understanding of fascinating questions such as how cells decide their fate, how patterns are created, how male and females are distinguished, and how organisms came to be different. We have also discovered how the misregulation of important development regulatory genes can lead to a variety of known cancers and degenerative diseases in humans. In this course we will examine these and related topics combining a rich classical literature with modern genetic and molecular analyses. [ more ]
BIOL 303(F) LEC Pharmacology
Pharmacology explores how molecules interact with biological systems to elicit a response. Roughly half of modern medicines are derived from metabolites with origins in nature, including drugs used to treat cancers and heart disease. In this course, we will consider these natural origins from plant, microbial, and animal sources, as well as how and why organisms synthesize these molecules. We will follow the path of molecules from biosynthesis in one organism to ingestion by another, to interactions with proteins in the body, to metabolism, and ultimately to excretion. Close examination of the molecular interactions between metabolites and proteins will allow us to explore how metabolite binding alters protein function and how genetic variation impacts bioactivity. In the first half of the semester, laboratory experiments will investigate caffeine metabolism using in vitro pharmacokinetic assays and protein structure analysis; these experiments lead up to a multi-week independent project in the second half of the semester. Readings for the lecture will come from the primary literature. [ more ]
Taught by: Cynthia Holland
Catalog detailsBIOL 305(S) LEC Evolution
This course offers a critical analysis of contemporary concepts in biological evolution. We focus on the relation of evolutionary mechanisms (e.g., selection, drift, and migration) to long term evolutionary patterns (e.g., evolutionary innovations, origin of major groups, and adaptation). Topics include micro-evolutionary models, natural and sexual selection, speciation, the inference of evolutionary history, evolutionary medicine among others. [ more ]
Taught by: TBA
Catalog detailsBIOL 306 LEC Cellular Regulatory Mechanisms
Last offered Spring 2015
This course explores the regulation of cellular function and gene expression from a perspective that integrates current paradigms in molecular genetics, intracellular trafficking, genomics, and synthetic biology. Selected topics include: the contribution of nuclear organization to genome regulation, mechanisms to maintain genomic integrity, transcriptional and post-transcriptional regulation, nuclear export, cell cycle and cell signaling. A central feature of the course will be discussion of articles from the primary literature, with an emphasis on the molecular bases for a variety of human pathologies such as cancer and aging. The laboratory will consist of a semester-long project that incorporates fluorescence-based approaches, quantitative PCR analysis of transcriptional patterns, bioinformatics, and protein analysis. [ more ]
BIOL 308(F) LEC Integrative Plant Biology: Fundamentals and New Frontiers
Plants are one of the most successful groups of organisms on Earth and have a profound impact on all life. Successful use of plants in addressing global problems and understanding their role in natural ecosystems depends on fundamental knowledge of the molecular mechanisms by which they grow, develop, and respond to their environment. This course will examine the molecular physiology of plants using an integrative approach that considers plants as dynamic, functional units in their environment. Major emphasis will be on understanding fundamental plant processes, such as photosynthesis, growth and development, water transport, hormone physiology, and flowering, from the molecular to the organismal level. Environmental effects on these processes will be addressed in topics including photomorphogenesis, stress physiology, mineral nutrition, and plant-microbe interactions. Discussions of original research papers will examine the mechanisms plants use to perform these processes and explore advances in the genetic engineering of plants for agricultural, environmental, and medical purposes. Laboratory activities stress modern approaches and techniques used in investigating plant physiological processes. [ more ]
Taught by: Claire Ting
Catalog detailsBIOL 310 / NSCI 310 LEC Neural Development and Plasticity
Last offered Fall 2016
Development can be seen as a tradeoff between genetically-determined processes and environmental stimuli. The tension between these two inputs is particularly apparent in the developing nervous system, where many events must be predetermined, and where plasticity, or altered outcomes in response to environmental conditions, is also essential. Plasticity is reduced as development and differentiation proceed, and the potential for regeneration after injury or disease in adults is limited; however some exceptions to this rule exist, and recent data suggest that the nervous system is not hard-wired as previously thought. In this course we will discuss the mechanisms governing nervous system development, from relatively simple nervous systems such as that of the fruitfly, to the more complicated nervous systems of humans, examining the roles played by genetically specified programs and non-genetic influences. [ more ]
BIOL 312 / NSCI 312 LEC Sensory Biology
Last offered Fall 2022
How do animals sense properties of the physical world? How do they convert physical or chemical energy to a signal within a cell that carries information? How is that information represented? What are the limits on what can be sensed? We will look for answers to these questions by investigating the molecular and cellular mechanisms of sensory transduction and how these mechanisms constrain the types of information that the nervous system encodes and processes. We will also ask how natural selection shapes the type of sensory information that animals extract from the world, and what adaptations allow some species to have "special" senses. Some of the examples we will consider are: bat echolocation (hair cells in the ear), detecting visual motion (amacrine cells in the mammalian retina), the constant reshaping of the olfactory system (chemical mapping of odors), what makes a touch stimulus noxious, and enhanced color vision (in birds, bees, and shrimp). Laboratory exercises will focus on the nematode C. elegans, an important model system, to explore and extend how we understand touch, temperature sensation, chemosensation, and light sensation. [ more ]
Taught by: Heather Williams
Catalog detailsBIOL 313 LEC Immunology
Last offered Fall 2023
The rapidly evolving field of immunology examines the complex network of interacting molecules and cells that function to recognize and respond to agents foreign to the individual. In this course, we will focus on the biochemical mechanisms that act to regulate the development and function of the immune system and how alterations in different system components can cause disease. Textbook readings will be supplemented with current literature. [ more ]
Taught by: Damian Turner
Catalog detailsBIOL 315(S) LEC Microbiology: Diversity, Cellular Physiology, and Interactions
The Covid pandemic and the alarming spread of antibiotic resistant bacteria are but two of the reasons for the resurgence of interest in the biology of viruses and microorganisms. This course will examine microbes from the perspectives of cell structure and function, genomics, and evolution. A central theme will be the adaptation of bacteria as they evolve to fill specific ecological niches, with an emphasis on microbe: host interactions that lead to pathogenesis. We will consider communication among bacteria as well as between bacteria and their environment. Topics include: microbial development, population dynamics, metagenomics, bioremediation, plant and animal defenses against infection, and bacterial strategies to subvert the immune system. We will also discuss a few viral examples, including SARS-CoV2, in the context of pathogen-host co-evolution and the immune system. In the lab, major projects will focus on the mammalian gut microbiome and the isolation and characterization of bacteria from natural environments. The lab experience will culminate in multi-week independent investigations. Readings will be comprised primarily of articles from the primary literature. [ more ]
Taught by: Lois Banta
Catalog detailsBIOL 319 / CHEM 319 / CSCI 319 / MATH 319 / PHYS 319 SEM Integrative Bioinformatics, Genomics, and Proteomics Lab
Last offered Spring 2023
What can computational biology teach us about cancer? In this lab-intensive experience for the Genomics, Proteomics, and Bioinformatics program, computational analysis and wet-lab investigations will inform each other, as students majoring in biology, chemistry, computer science, mathematics/statistics, and physics contribute their own expertise to explore how ever-growing gene and protein data-sets can provide key insights into human disease. In this course, we will take advantage of one well-studied system, the highly conserved Ras-related family of proteins, which play a central role in numerous fundamental processes within the cell. The course will integrate bioinformatics and molecular biology, using database searching, alignments and pattern matching, and phylogenetics to reconstruct the evolution of gene families by focusing on the gene duplication events and gene rearrangements that have occurred over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in the inflammatory and MAPK signal transduction pathways in human colon cancer cell lines, students will uncover regulatory mechanisms that are aberrantly altered by siRNA knockdown of putative regulatory components. This functional genomic strategy will be coupled with independent projects using phosphorylation-state specific antisera to test our hypotheses. Proteomic analysis will introduce the students to de novo structural prediction and threading algorithms, as well as data-mining approaches and Bayesian modeling of protein network dynamics in single cells. Flow cytometry and mass spectrometry may also be used to study networks of interacting proteins in colon tumor cells. [ more ]
Taught by: Lois Banta
Catalog detailsCHEM 324 LEC Enzyme Kinetics and Reaction Mechanisms
Last offered Fall 2023
Enzymes are complex biological molecules capable of catalyzing chemical reactions with very high efficiency, stereo-selectivity and specificity. The study of enzymatically-catalyzed reactions gives insight into the study of organic reaction mechanisms in general, and into the topic of catalysis especially. This course explores the methods and frameworks for determining enzymatic reaction mechanisms. These methods are based on a firm foundation of organic reaction mechanisms and chemical kinetics. We will investigate the major types of biochemical reactions, focusing on their catalytic mechanisms and how those mechanisms can be elucidated. We will lay the foundation for this mechanistic consideration with discussion of transition state theory, structure-reactivity relationships, steady state and pre-steady kinetics, use of isotopes, genetic modification, and other tools for probing enzymatic reactions. We will also examine the catalytic roles of a variety of vitamins and cofactors. [ more ]
Taught by: Amy Gehring
Catalog detailsBIOL 326 LEC Cellular Assembly and Movement
Last offered Spring 2024
This course will focus on how multi-protein complexes are assembled to control key cellular processes in eukaryotic systems: 1) protein sorting and trafficking, 2) establishment and maintenance of cell architecture, and 3) mitosis, cell migration and tissue morphogenesis that require coordination of the membrane transport and cytoskeleton. The course will highlight involvement of these processes in pathological conditions. Laboratories will use mammalian tissue culture as a model system to study cellular functions. Important techniques in cell biology will be introduced in the first half of the semester; in the second half of the term, students will conduct a multi-week independent project. Textbook readings will be supplemented with primary literature. [ more ]
Taught by: Pei-Wen Chen
Catalog detailsCHEM 326 SEM Chemical and Synthetic Biology
Last offered Spring 2024
This course surveys the rapidly evolving, interdisciplinary and interconnected fields of chemical and synthetic biology. Chemical biology uses precise molecular-level manipulations to influence living systems from the bottom up, often by introducing components that are foreign to nature. Synthetic biology takes advantage of existing molecular technology and adopts an engineering mindset to reprogram life. Students will achieve literacy through immersion in chemical and synthetic biology. We will prioritize broad exposure to these fields, their vocabulary, culture, practices and ideas, through extensive engagement with the primary literature that expert practitioners use to teach themselves. The course model is instructor-facilitated peer-to-peer instruction, emphasizing skills important for autonomous and collaborative work in real-world scientific and professional fields. Topics we will cover include synthetic genomes, metabolic engineering, chemical synthesis and manipulation of biomacromolecules, directed evolution, and reworking of the central dogma of biology. [ more ]
Taught by: B Thuronyi
Catalog detailsBIOL 330 LEC Genomes: Structure, Function, Evolution
Last offered Spring 2023
Genome sequencing technologies have opened the "book of life" to biologists. But making sense of genomes is still a work in progress. This course will examine central features of genomes, their evolution, and their contribution to human diseases such as cancer. Genome biology is a new field, and this presents the opportunity to learn science as it is being done. Biologists working today started out knowing nothing about core features of genomes, such as why most of the DNA is repetitive, or why segments of genes get removed in the RNA, or why silenced genes wake up in cancer cells. They began to find meaning by adopting dual perspectives of function and neutral evolution. Students will learn to walk these same paths and learn to evaluate for themselves what genome complexity means. In lab, students will develop hands-on and computational skills for investigating genome structural variation, then apply them in the second half of the semester in independent lab investigations. [ more ]
Taught by: David Loehlin
Catalog detailsCHEM 338 TUT Bioinorganic Chemistry: Metals in Living Systems
Last offered Spring 2021
Bioinorganic chemistry is an interdisciplinary field that examines the role of metals in living systems. Metals are key components of a wide range of processes, including oxygen transport and activation, catalytic reactions such as photosynthesis and nitrogen-fixation, and electron-transfer processes. Metals furthermore perform regulatory roles and stabilize the structures of proteins. In medical applications, they are central to many diagnostic and therapeutic tools, and some metals are highly toxic. The course begins with a review and survey of the principles of coordination chemistry: topics such as structure and bonding, spectroscopic methods, electrochemistry, kinetics and reaction mechanisms. Building on this fundamental understanding of the nature of metals, we will explore the current literature in fields of interest in small groups, presenting our findings to the class periodically. [ more ]
CHEM 342 LEC Synthetic Organic Chemistry
Last offered Spring 2024
The origins of organic chemistry are to be found in the chemistry of living things and the emphasis of this course is on the chemistry of naturally-occurring compounds. This course presents the logic and practice of chemical total synthesis while stressing the structures, properties and preparations of terpenes, polyketides and alkaloids. Modern synthetic reactions are surveyed with an emphasis on the stereochemical and mechanistic themes that underlie them. To meet the requirements for the semester's final project, each student chooses an article from the recent synthetic literature and then analyzes the logic and strategy involved in the published work in a final paper. A summary of this paper is also presented to the class in a short seminar. There will be no laboratory component in 2022. Instead, one of the three class meetings each week will focus on discussion and presentation of reactions, mechanisms, and syntheses from the chemical literature. [ more ]
Taught by: Thomas Smith
Catalog detailsCHEM 344(S) LEC Physical Organic Chemistry
The structure of a molecule is inherently linked to its reactivity, and these correlations form the basis for understanding organic reaction mechanisms. This course advances the understanding from previous organic courses through a detailed examination of the concepts that underlie these structure/reactivity relationships, including molecular strain and stability, acid/base chemistry, steric and electronic effects, and aromaticity. These concepts will also be explored in the context of specific classes of reaction mechanisms. Classical and modern experimental and theoretical tools used to elucidate reaction mechanisms will also be presented, including reaction kinetics, isotope effects, and linear free energy relationships. By studying the primary literature, we will see how these experiments have been applied to the elucidation of reaction mechanism, while also learning to design a set of experiments for study of mechanisms of contemporary interest. [ more ]
Taught by: Amanda Turek
Catalog detailsCHEM 348(S) LEC Polymer Chemistry
From synthetic to natural macromolecules, we encounter polymers everywhere and every day. This course explores the multitude of synthetic techniques available and discusses how structure defines function. Topics include polymer types, concept of molecular weight, structure-property relationships and polymer synthesis methods including condensation and chain (anionic, cationic, radical) polymerizations. Fundamentals of composition and physical properties of polymers, and methods of characterization are also covered. Examples of polymer functionalization, self-assembly, and surface modification are also discussed. [ more ]
Taught by: Sarah Goh
Catalog detailsCHEM 364 / ENVI 364 LEC Instrumental Methods of Analysis
Last offered Spring 2024
Instrumental methods of analysis provide scientists with different lenses to observe and elucidate fundamental chemical phenomena and to measure parameters and properties at the atomic, molecular, and bulk scales. This course introduces a framework for learning about a variety of instrumental techniques that typically include chromatography, mass spectrometry, thermal methods, atomic and molecular absorption and emission spectroscopy, X-ray diffraction, and optical and electron microscopies. Students complete laboratory projects and gain hands-on experience and project planning skills to study molecules and materials of interest. This practical experience is complemented by lectures that cover the theory and broader applications of these techniques. Students also explore the primary literature and highlight recent advances in instrumental methods that address today's analytical questions. The skills learned are useful in a wide variety of scientific areas and will prepare you well for research endeavors. [ more ]
Taught by: Stephanie Christau, Christopher Goh
Catalog detailsCHEM 366(F) LEC Thermodynamics and Statistical Mechanics
The thermodynamic laws provide us with our most powerful and general scientific principles for predicting the direction of spontaneous change in physical, chemical, and biological systems. This course develops the concepts of energy, entropy, free energy, temperature, heat, work, and chemical potential within the framework of classical and statistical thermodynamics. The principles developed are applied to a variety of problems: chemical reactions, phase changes, energy technology, industrial processes, and environmental science. Laboratory experiments provide quantitative and practical demonstrations of the theory of real and ideal systems studied in class. [ more ]
Taught by: Enrique Peacock-López
Catalog detailsCHEM 367(S) LEC Biophysical Chemistry
In this course, physical chemistry concepts are presented from the viewpoint of their practical application to a set of biochemical problems, which are explored side-by-side in the lecture and highly-integrated lab program. Major emphasis is placed on quantitative thermodynamic models of equilibrium processes, and students will learn how to develop and apply mathematical models to data. The main topics covered include: 1) conformations of biological macromolecules and the forces that stabilize them; 2) spectroscopic techniques for the study of structure and function; and 3) macromolecular interactions and binding. [ more ]
Taught by: Bob Rawle
Catalog detailsBIOL 406 SEM Dynamics of Internal Membrane Systems
Last offered Fall 2014
Eukaryotic cells build and maintain a diverse set of internal membrane compartments, such as the endoplasmic reticulum, the Golgi compartment, and lysosomes, which exist as parts of an interconnected and dynamic membrane system. Each of these membrane compartments has unique functions despite a high rate of exchange between the different organelles. This course will mechanistically examine how the identity of organelles is achieved via highly regulated membrane trafficking events and investigate the importance of membrane trafficking in specialized biological processes including neurotransmission, glucose homeostasis, and immune cell killing. We will read classic and current primary literature articles and discuss the essential techniques, experimental design, and models of cell biology. [ more ]
BIOL 407 / NSCI 347 SEM Neurobiology of Emotion
Last offered Spring 2024
Emotion is influenced and governed by a number of neural circuits and substrates, and emotional states can be influenced by memory, cognition, and many external stimuli. We will read and discuss articles about mammalian neuroanatomy associated with emotion as defined by classic lesion studies, pharmacology, electrophysiology, fMRI imaging, knockout and optogenetic mouse studies, for investigating neural circuit function in order to gain an understanding of the central circuits and neurotransmitter systems that are implicated in emotional processing. We will focus initially on the neural circuits involved in fear, as a model for how human and animal emotion and physiology is studied, with special sessions on emotional responses to music and art, as well as discussions about burgeoning neurobiological research into the emotion of disgust. The larger goal of the course is to give students opportunities and experience in critical evaluation and discussion of primary scientific literature, and to develop and refine strategies on how to use scientific evidence in building arguments in essays. [ more ]
Taught by: Tim Lebestky
Catalog detailsBIOL 408(S) SEM RNA Worlds
RNA is known best as the message cells use to turn genes into proteins. Yet investigations of several unusual genetic phenomena over the past few decades did not find protein-coding genes, but instead uncovered non-coding RNAs with a cornucopia of functions. Today, biologists have begun to develop a framework for how RNA's non-coding functions play central roles in immune defense and genetic conflicts, in gene regulation and cancer. We will develop our own understanding of the power of small noncoding RNA to protect the genome and direct cellular processes through reading and discussion of primary scientific literature. We will learn how this emerging perspective of RNA's non-coding functions helps to resolve genetic mysteries and has opened the door to RNA-based medications. [ more ]
Taught by: David Loehlin
Catalog detailsBIOL 410 SEM Nanomachines in Living Systems
Last offered Spring 2021
Through reading and discussing the primary literature, this course will explore how nanometer-sized biological molecules like proteins perform functions that require integration of information and transmission of force at much larger scales, microns and above. These nanoscale proteins will be considered as nanomachines that can transform a chemical energy into a mechanical one. We will focus on the cytoskeleton, which gives cells their shape, organizes the internal parts of cells and provides mechanical support for essential cellular processes like cell division and movement. An emphasis will be placed on how the biochemical properties of actin, actin-binding proteins and motors are used to generate mechanical force necessary for the respective biological function. Topics will include some controversial and emerging hypotheses in the field: sliding versus depolymerizing hypotheses for constriction of the contractile ring in cytokinesis, roles of cytoskeleton in pathogen entry and propagation, organelle dynamics, polarity establishment in cell migration, immunological synapse and neuronal function. [ more ]
BIOL 411 TUT Developmental Biology: From Patterning to Pathogenesis
Last offered Fall 2020
A small number of developmental regulators coordinate the interplay between cell proliferation and specification of cell fates during animal development. The genetic basis of many of the cancer and degenerative diseases are, in fact, due to these same developmental regulators whose expression is misregulated in the adult. Through the reading of primary literature, this course in developmental biology will examine the mechanisms of gene expression of key regulators, the biological processes they mediate in the embryo, and how they become misregulated in proliferative and degenerative diseases. [ more ]
CAOS 414 Life at Extremes: Molecular Mechanisms
Last offered NA
All organisms face variability in their environments, and the molecular and cellular responses to stresses induced by environmental change often illuminate otherwise hidden facets of normal physiology. Moreover, many organisms have evolved unique molecular mechanisms, such as novel cellular compounds or macromolecular structural modifications, which contribute to their ability to survive continuous exposure to extreme conditions, such as high temperatures or low pH. This course will examine how chaperonins, proteases, and heat- and cold-shock proteins are regulated in response to changes in the external environment. We will then consider how these and other molecular mechanisms function to stabilize DNA and proteins- and, ultimately, cells and organisms. Other extreme environments, such as hydrothermal vents on the ocean floor, snow fields, hypersaline lakes, the intertidal zone, and acid springs provide further examples of cellular and molecular responses to extreme conditions. Biotechnological applications of these molecular mechanisms in areas such as protein engineering will also be considered. Class discussions will focus upon readings from the primary literature. [ more ]
Taught by: Claire Ting
Catalog detailsBIOL 418 SEM Signal Transduction to Cancer
Last offered Spring 2020
Division of normal cells is a highly regulated process based on input from both intrinsic and extrinsic signals. The cell's response to its environment affects all aspects of cell behavior: proliferation, death, differentiation and migration. The goal of the course is to understand the molecular mechanisms of signal transduction that guide normal cell behavior and how disruptions in this process can lead to cancer. We will focus on the Hedgehog-Gli signaling pathway that is activated in 30% of all known cancers. Genetic studies will serve as an introduction to the components of the pathway, followed by an examination of the molecular mechanisms of signal reception, transduction of intracellular information, scaffolding and transcriptional targets. The final section of the course will investigate how high throughput screens, medicinal chemistry studies and mouse models are used to identify small molecular inhibitors of pathway components. We will consider the effectiveness of these inhibitors in pharmacological studies, clinical trials and potential cancer treatments. [ more ]
BIOL 419(S) SEM Secrets of Enzymes: Fidelity, Promiscuity, and Disease
Living organisms have spent the past 4 billion years evolving proteins and enzymes that perform basic cellular functions to support life. Over time, duplications and mutations of these enzymes have led to novel reactions, pathways, and chemistries. To gain an appreciation for these molecular catalysts, we will start by considering how enzymes are synthesized and how errors are introduced and naturally corrected. The course will focus on how enzymes such as CRISPR/Cas9 act as 'molecular scissors' to cut DNA and how these enzymes are used to correct errors. We will explore the implications of this field in active areas of biomedical, agricultural, and ecological research. Discussions and writing assignments will focus on reading and critiquing the scientific literature. [ more ]
Taught by: Cynthia Holland
Catalog detailsBIOL 426 TUT Frontiers in Muscle Physiology: Controversies
Last offered Fall 2013
While an active muscle produces force, contraction of muscle is far from the only function of this intriguing organ system. Muscle plays a major role in metabolic regulation of organisms, acts as a glucose storage facility, regulates blood pressure in mammals, and produces numerous hormones. The mechanism for contractile activity varies not only among different organisms, but also among different muscles within the same organism. Controversies, disagreements, and arguments pervade the muscle biology literature perhaps because of the integrative nature of the science. In this tutorial course, we will utilize molecular, physiological, comparative, and evolutionary aspects of muscle biology to address current controversies of this dynamic tissue. Some questions that will be addressed include: 1) Lactic acid generated by skeletal muscle is / is not involved with fatigue at high exercise intensity, 2) Satellite cells are / are not obligatory for skeletal muscle hypertrophy, 3) Do mammals possess the same "stretch activation" of skeletal muscle as seen in insect flight muscle?, 4) Are smooth and skeletal muscles from the same lineage of cells, or do they represent convergent evolution on the tissue level? After an initial group meeting, students meet weekly with a tutorial partner and the instructor for an hour each week. Every other week at this tutorial meeting, students present a written and oral critical analysis of the assigned research articles. Students not making a presentation question and critique the work of their colleague. [ more ]
BIOL 430 TUT Genome Sciences: At the Cutting Edge
Last offered Spring 2020
Research in genomics has integrated and revolutionized the field of biology, including areas of medicine, plant biology, microbiology, and evolutionary biology. Moreover, recent developments in "metagenomics" (genomic studies of entire communities of microorganisms in natural environments, such as the mammalian gut and the deep sea) and "metatranscriptomics" (studies of genome wide changes in expression and mRNA levels in natural communities of organisms) have generated unprecedented knowledge about the genomic potential of a community and the in situ biological activity of different ecological niches. In this course we will explore how research in these and related areas, including proteomics, have advanced our fundamental understanding of (1) organisms in the three domains of life, and their interactions and evolutionary relationships; (2) biological systems and environments, such as the human body, extreme environments, and the oceans; (3) strategies for solving global challenges in medicine, agriculture, energy resources, and environmental sciences. During the course, students will meet each week for one hour with a tutorial partner and the instructor. Every other week, students will present a written and oral critical analysis of the assigned research articles. On alternate weeks, students will question/critique the work of their colleague. [ more ]
BIOL 436 SEM Metabolites as Messengers
Last offered Fall 2023
Beyond the genome, transcriptome, and proteome is the metabolome, the suite of small-molecule metabolites present in a biological sample. These molecules are not simply the products of the proteome nor a collection of cellular fuels and wastes. In this seminar, we will investigate metabolites as signals that influence cellular processes. Biochemistry and molecular biology textbooks often emphasize the proteins that mediate cellular communication. Of course, specialized metabolites like neurotransmitters and certain hormones are well known to regulate information flow between cells. But what about molecules that participate in the metabolic processes of almost every cell--how can these intermediary metabolites be used as signals? How do they communicate acutely and with specificity? What role do they play in sensing (or promoting) environmental change? And how can metabolites be regulated to override their typical fates in metabolic pathways and serve as signals? We'll examine these questions and more at the levels of inter-organellar, intercellular, and inter-organismal metabolic communication by reading the primary scientific literature together. Familiarity with typical mechanisms of cellular communication and/or physiology (BIOL 205) is recommended but not required. [ more ]
Taught by: Caitlyn Bowman-Cornelius
Catalog detailsBIOL 440(S) TUT Cell Signaling and Tissue Engineering: A Potential Fountain of Youth?
It is a long quest of mankind to have a healthy and long life but it is inevitable that our bodies lose function due to injury, disease or as we grow old. At the heart of tissue engineering is the idea that we can restore tissue function by replacing with or rebuild the right structure. To artificially generate tissues, organs or even organisms, one fundamental question must be addressed: How do our different organs, composed of cells with the identical genetic information, develop into such functionally different organs? Through the lens of tissue engineering, we will explore the mechanism by which cells sense the surrounding physical and chemical cues, and respond by changing their gene expression and consequent behaviors. We will devote most of our discussion to the scientific rationale and challenges of tissue engineering. Topics to be covered include 3D organoids in regenerative medicine, disease modeling, biobanking and drug discovery, computational modeling of stem cell dynamics, tissue growth and pattern formation, mechanotransduction, biomaterial fabrication, immunomodulation and cultured meat. Bioengineering of bone and cartilage, cardiovascular and nervous systems, etc. will be presented as case studies to illustrate details of certain aspects of tissue engineering in the broader context of the overall strategic approach used to solve a clinical problem. We will also consider the role of social factors like legislative regulation, health care philosophy, ethics and economics in the process of moving concept into the clinic and market. [ more ]
Taught by: Pei-Wen Chen
Catalog details
Students can check with the program chair to see if other courses not listed here might count as electives.
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