BIOC (BIOC)

BIOC 307. Introduction to Biochemistry: From Molecules To Medical Science. 4 Units.

Overview of the macromolecules and small molecules key to all living systems. Topics include: protein structure and function; enzyme mechanisms, kinetics and regulation; membrane structure and function; bioenergetics; hormone action; intermediary metabolism, including pathways and regulation of carbohydrate, lipid, amino acid, and nucleotide biosynthesis and breakdown. The material is presented to build links to human biology and human disease. One semester of biology is recommended. Offered as BIOC 307, BIOC 407, and BIOL 407. Prereq: CHEM 223 and CHEM 224.

BIOC 308. Molecular Biology. 4 Units.

An examination of the flow of genetic information from DNA to RNA to protein. Topics include: nucleic acid structure; mechanisms and control of DNA, RNA, and protein biosynthesis; recombinant DNA; and mRNA processing and modification. Where possible, eukaryotic and prokaryotic systems are compared. Special topics include yeast as a model organism, molecular biology of cancer, and molecular biology of the cell cycle. Current literature is discussed briefly as an introduction to techniques of genetic engineering. Recommended preparation: BIOC 307. Offered as BIOC 308, BIOL 308, BIOC 408, and BIOL 408. Prereq: CHEM 223, BIOL 214, and BIOL 215.

BIOC 312. Proteins and Enzymes. 3 Units.

Aspects of protein and nucleic acid function and interactions are discussed, including binding properties, protein-nucleic acid interactions, kinetics and mechanism of proteins and enzymes, and macromolecular machines. Recommended Preparation: CHEM 301. Offered as BIOC 312 and BIOC 412. Prereq: BIOC 307.

BIOC 315. Nuclear Receptors in Health and Disease. 3 Units.

This course focuses on hormone-gene interactions mediated by the ligand-inducible transcription factors termed nuclear hormone receptors. The class will address the mechanisms of action, regulatory features, and biological activities of several nuclear receptors. The usage of nuclear receptors as therapeutic targets in disease states such as cancer, inflammation, and diabetes will also be discussed. The course aims to teach students to critically evaluate primary literature relevant to nuclear hormone receptors biology, and to reinforce presentation/discussion skills. Grades for undergraduates will be based on midterm, final exam; grades for graduates will be based on midterm, final exam, and presentation of a recently published research article related to the role of nuclear receptors in health and disease. Offered as PHRM 315, BIOC 315, PHRM 415 and BIOC 415.

BIOC 334. Structural Biology. 3 Units.

Introduces basic chemical properties of proteins and discusses the physical forces that determine protein structure. Topics include: the elucidation of protein structure by NMR and by X-ray crystallographic methods; the acquisition of protein structures from data bases; and simple modeling experiments based on protein structures. Offered as BIOC 334, BIOL 334, BIOC 434, and BIOL 434. Prereq: BIOC 307.

BIOC 354. Biochemistry and Biology of RNA. 3 Units.

Systematic overview of RNA biochemistry and biology. Course provides solid foundation for understanding processes of post-transcriptional regulation of gene expression. Topics include: RNA structure, RNA types, RNA-protein interactions, eukaryotic RNA metabolism including mRNA processing, ribosome biogenesis, tRNA metabolism, miRNA processing and function, bacterial RNA metabolism, transcriptomics. BIOC 454 requires an additional research proposal. Recommended preparation for BIOC 354: Undergraduate Biology (1 semester minimum), equivalents of CHEM 301, BIOC 307 or BIOC 308, CHEM 223, CHEM 224. Offered as BIOC 354 and BIOC 454. Prereq: CHEM 223, CHEM 224.

BIOC 373. Biochemistry SAGES Seminar. 3 Units.

Discussion of current topics in biochemical research using readings from the scientific literature. The goals are for the student: 1) to discuss and critically analyze selections from the biochemical literature; 2) to gain a broader understanding of important topics not formally covered in the didactic courses; and 3) to learn to write in the style of journals in the field of biochemistry. Counts as SAGES Departmental Seminar. Prereq: BIOC 307 and BIOC 308. Restricted to majors in Biochemistry.

BIOC 391. Research Project. 1 - 9 Units.

(Credit as arranged.) Offered on a pass/fail basis only. Maximum 9 hours total credit.

BIOC 393. Senior Capstone Experience. 3 Units.

Students will complete their Capstone Projects, begun in BIOC 391. Pertinent research activities will depend on the nature of the student's project. The student will meet regularly with their Capstone adviser, at least twice monthly, to provide progress reports, discuss the project, and for critique and guidance. By the end of this course, the student will have completed their SAGES Senior Capstone research project, written a project report in the form of a manuscript, and presented their project reports orally in the department and at the Senior Capstone Fair, or its equivalent. Counts as SAGES Senior Capstone. Prereq: BIOC 307 and BIOC 308.

BIOC 405. Principles of Biochemistry: An Introduction to the Molecules of Life. 3 Units.

This summer course provides an introduction to the macromolecules and small molecules that are the foundation of living systems. The focus is on mammalian biochemistry, with links to human biology and human disease. Topics include: protein structure and function; enzyme mechanisms, kinetics and regulation; membranes; hormone action; bioenergetics; intermediary metabolism, including pathways and regulation of carbohydrate, lipid, amino acid, and nucleotide biosynthesis and breakdown. One semester of biology is recommended. Suitable for students interested in careers in the health professions. This course is not open to undergraduate Biochemistry majors or Biochemistry graduate students. Prereq: CHEM 223 and CHEM 224.

BIOC 407. Introduction to Biochemistry: From Molecules To Medical Science. 4 Units.

Overview of the macromolecules and small molecules key to all living systems. Topics include: protein structure and function; enzyme mechanisms, kinetics and regulation; membrane structure and function; bioenergetics; hormone action; intermediary metabolism, including pathways and regulation of carbohydrate, lipid, amino acid, and nucleotide biosynthesis and breakdown. The material is presented to build links to human biology and human disease. One semester of biology is recommended. Offered as BIOC 307, BIOC 407, and BIOL 407. Prereq: CHEM 223 and CHEM 224.

BIOC 408. Molecular Biology. 4 Units.

An examination of the flow of genetic information from DNA to RNA to protein. Topics include: nucleic acid structure; mechanisms and control of DNA, RNA, and protein biosynthesis; recombinant DNA; and mRNA processing and modification. Where possible, eukaryotic and prokaryotic systems are compared. Special topics include yeast as a model organism, molecular biology of cancer, and molecular biology of the cell cycle. Current literature is discussed briefly as an introduction to techniques of genetic engineering. Recommended preparation: BIOC 307. Offered as BIOC 308, BIOL 308, BIOC 408, and BIOL 408.

BIOC 412. Proteins and Enzymes. 3 Units.

Aspects of protein and nucleic acid function and interactions are discussed, including binding properties, protein-nucleic acid interactions, kinetics and mechanism of proteins and enzymes, and macromolecular machines. Recommended Preparation: CHEM 301. Offered as BIOC 312 and BIOC 412.

BIOC 415. Nuclear Receptors in Health and Disease. 3 Units.

This course focuses on hormone-gene interactions mediated by the ligand-inducible transcription factors termed nuclear hormone receptors. The class will address the mechanisms of action, regulatory features, and biological activities of several nuclear receptors. The usage of nuclear receptors as therapeutic targets in disease states such as cancer, inflammation, and diabetes will also be discussed. The course aims to teach students to critically evaluate primary literature relevant to nuclear hormone receptors biology, and to reinforce presentation/discussion skills. Grades for undergraduates will be based on midterm, final exam; grades for graduates will be based on midterm, final exam, and presentation of a recently published research article related to the role of nuclear receptors in health and disease. Offered as PHRM 315, BIOC 315, PHRM 415 and BIOC 415.

BIOC 420. Current Topics in Cancer. 3 Units.

The concept of cancer hallmarks has provided a useful guiding principle in our understanding of the complexity of cancer. The hallmarks include sustaining proliferative signaling, evading growth suppressors, enabling replicative immortality, activating invasion and metastasis, inducing angiogenesis, resisting cell death, deregulating cellular energetics, avoiding immune destruction, tumor-promoting inflammation, and genome instability and mutation. The objectives of this course are to (1) examine the principles of some of these hallmarks, and (2) explore potential therapies developed based on these hallmarks of cancer. This is a student-driven and discussion-based graduate course. Students should have had some background on the related subjects and have read scientific papers in their prior coursework. Students will be called on to present and discuss experimental design, data and conclusions from assigned publications. There will be no exams or comprehensive papers but students will submit a one-page critique (strengths and weaknesses) of one of the assigned papers prior to each class meeting. The course will end with a full-day student-run symposium on topics to be decided jointly by students and the course director. Grades will be based on class participation, written critiques, and symposium presentations. Offered as BIOC 420, MBIO 420, PATH 422, and PHRM 420. Prereq: CBIO 453 and CBIO 455.

BIOC 430. Advanced Methods in Structural Biology. 1 - 6 Units.

The course is designed for graduate students who will be focusing on one or more methods of structural biology in their thesis project. This course is divided into 3-6 sections (depending on demand). The topics offered will include X-ray crystallography, nuclear magnetic resonance spectroscopy, optical spectroscopy, mass spectrometry, cryo-electron microscopy, and computational and design methods. Students can select one or more modules. Modules will be scheduled so that students can take all the offered modules in one semester. Each section is given in 5 weeks and is worth 1 credit. Each section covers one area of structural biology at an advanced level such that the student is prepared for graduate level research in that topic. Offered as BIOC 430, CHEM 430, PHOL 430, and PHRM 430.

BIOC 432. Current Topics in Vision Research. 3 Units.

Vision research is an exciting and multidisciplinary area that draws on the disciplines of biochemistry, genetics, molecular biology, structural biology, neuroscience, and pathology. This graduate level course will provide the student with broad exposure to the most recent and relevant research currently being conducted in the field. Topics will cover a variety of diseases and fundamental biological processes occurring in the eye. Regions of the eye that will be discussed include the cornea, lens, and retina. Vision disorders discussed include age-related macular degeneration, retinal ciliopathies, and diabetic retinopathy. Instructors in the course are experts in their field and are members of the multidisciplinary visual sciences research community here at Case Western Reserve University. Students will be exposed to the experimental approaches and instrumentation currently being used in the laboratory and in clinical settings. Topics will be covered by traditional lectures, demonstrations in the laboratory and the clinic, and journal club presentations. Students will be graded on their performance in journal club presentations (40%), research proposal (40%), and class participation (20%). Offered as NEUR 432, PATH 432, PHRM 432 and BIOC 432.

BIOC 434. Structural Biology. 3 Units.

Introduces basic chemical properties of proteins and discusses the physical forces that determine protein structure. Topics include: the elucidation of protein structure by NMR and by X-ray crystallographic methods; the acquisition of protein structures from data bases; and simple modeling experiments based on protein structures. Offered as BIOC 334, BIOL 334, BIOC 434, and BIOL 434.

BIOC 452. Nutritional Biochemistry and Metabolism. 3 Units.

Mechanisms of regulation of pathways of intermediary metabolism; amplification of biochemical signals; substrate cycling and use of radioactive and stable isotopes to measure metabolic rates. Recommended preparation: BIOC 307 or equivalent. Offered as BIOC 452 and NTRN 452.

BIOC 454. Biochemistry and Biology of RNA. 3 Units.

Systematic overview of RNA biochemistry and biology. Course provides solid foundation for understanding processes of post-transcriptional regulation of gene expression. Topics include: RNA structure, RNA types, RNA-protein interactions, eukaryotic RNA metabolism including mRNA processing, ribosome biogenesis, tRNA metabolism, miRNA processing and function, bacterial RNA metabolism, transcriptomics. BIOC 454 requires an additional research proposal. Recommended preparation for BIOC 354: Undergraduate Biology (1 semester minimum), equivalents of CHEM 301, BIOC 307 or BIOC 308, CHEM 223, CHEM 224. Offered as BIOC 354 and BIOC 454.

BIOC 460. Introduction to Microarrays. 3 Units.

Microarray technology is an exciting new technique that is used to analyze gene expression in a wide variety of organisms. The goal of this course is to give participants a hands-on introduction to this technology. The course is intended for individuals who are preparing to use this technique, including students, fellows, and other investigators. This is a hands-on computer-based course, which will enable participants to conduct meaningful analyses of microarray data. Participants will gain an understanding of the principles underlying microarray technologies, including: theory of sample preparation, sample processing on microarrays, familiarity with the use of Affymetrix Microarray Suite software and generation of data sets. Transferring data among software packages to manipulate data will also be discussed. Importation of data into other software (GeneSpring and DecisionSite) will enable participants to mine the data for higher-order patterns. Participants will learn about the rationale behind the choice of normalization and data filtering strategies, distance metrics, use of appropriate clustering choices such as K-means, Hierarchical, and Self Organizing Maps. Offered as BIOC 460, PATH 460 and CNCR 460. Prereq: CBIO 455.

BIOC 475. Protein Biophysics. 3 Units.

This course focuses on in-depth understanding of the molecular biophysics of proteins. Structural, thermodynamic and kinetic aspects of protein function and structure-function relationships will be considered at the advanced conceptual level. The application of these theoretical frameworks will be illustrated with examples from the literature and integration of biophysical knowledge with description at the cellular and systems level. The format consists of lectures, problem sets, and student presentations. A special emphasis will be placed on discussion of original publications. Offered as BIOC 475, CHEM 475, PHOL 475, PHRM 475, and NEUR 475.

BIOC 519. Molecular Biology of RNA. 3 Units.

Selected topics regarding editing, enzymatic function, splicing, and structure of RNA. Offered as BIOC 519, CLBY 519, and MBIO 519.

BIOC 528. Contemporary Approaches to Drug Discovery. 3 Units.

This course is designed to teach the students how lead compounds are discovered, optimized, and processed through clinical trials for FDA approval. Topics will include: medicinal chemistry, parallel synthesis, drug delivery and devices, drug administration and pharmacokinetics, and clinical trials. A special emphasis will be placed on describing how structural biology is used for in silico screening and lead optimization. This component will include hands-on experience in using sophisticated drug discovery software to conduct in silico screening and the development of drug libraries. Each student will conduct a course project involving in silico screening and lead optimization against known drug targets, followed by the drafting of an inventory disclosure. Another important aspect of this course will be inclusion of guest lectures by industrial leaders who describe examples of success stories of drug development. Offered as BIOC 528, PHOL 528, PHRM 528, and SYBB 528.

BIOC 599. RNA Structure and Function. 3 Units.

This course will cover fundamental aspects of modern RNA biology with emphasis on the interplay of three dimensional structure of nucleic acids and their function. The main focus of the course is on the recent discoveries that indicate a prominent role of RNA as a major regulator of cellular function. Topics discussed will include an introduction to RNA structure, folding and dynamics, RNA/RNA and RNA-protein interactions, and role of RNA in catalysis of biological reactions in ribosome and the role of other catalytic RNAs in tRNA biogenesis, pre-mRNA splicing, and viral replication. The course also covers the recently discovered RNA regulatory switches, large noncoding regulatory RNAs, and the role of RNA in human diseases and novel, RNA-based therapeutics. Offered as BIOC 599, CLBY 599, and MBIO 599.

BIOC 601. Biochemical Research. 1 - 18 Units.

Credit as arranged.

BIOC 611. Biochemistry Seminar I. 1 Unit.

Student presentations of topics from the current scientific literature unrelated to the student's research project. Participants are required to present a seminar.

BIOC 612. Biochemistry Seminar II. 1 Unit.

Discussion of current research.

BIOC 641. Proposition I. 2 Units.

Design of research proposal.

BIOC 651. Thesis M.S.. 1 - 6 Units.

(Credit as arranged.)

BIOC 701. Dissertation Ph.D.. 1 - 9 Units.

(Credit as arranged.) Prereq: Predoctoral research consent or advanced to Ph.D. candidacy milestone.