Is climate change real? Yes, it is! And technologies to reduce Greenhouse Gas (GHG) emissions are being developed. One type of technology that is imperative in the short run is biofuels; however, biofuels must meet specifications for gasoline, diesel, and jet fuel, or catastrophic damage could occur. This course will examine the chemistry of technologies of bio-based sources for power generation and transportation fuels. We'll consider various biomasses that can be utilized for fuel generation, understand the processes necessary for biomass processing, explore biorefining, and analyze how biofuels can be used in current fuel infrastructure.

This class analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis is placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. The course examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular/cellular/tissue/organ-level functions. Chemical and quantitative views of the interplay of multiple pathways as biological networks are emphasized. Student work will culminate in the preparation of a unique grant application in an area of biological networks.

This course focuses on the interaction of chemical engineering, biochemistry, and microbiology. Mathematical representations of microbial systems are featured among lecture topics. Kinetics of growth, death, and metabolism are also covered. Continuous fermentation, agitation, mass transfer, and scale-up in fermentation systems, and enzyme technology round out the subject material.

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)

Six case studies, case study keys, and instructor notes were developed for this grant project. A brief description of the studies is as follows:

Blood Clotting- This case study discusses the causes, symptoms, and possible treatments for blood clots. I chose this study because the story is about my brother who was misdiagnosed with a clot and almost died. I felt it was a study that included the importance of proper diagnosis in a medical situation.

Immunization-This case study includes a brief history of immunization, how vaccines work, what type of vaccines are available, what chemicals can be found in vaccines, and why people may choose not to be vaccinated. This study was written before the COVID-19 pandemic, but more information can be added to it concerning a possible vaccination for the COVID-19 virus.

The Stereochemistry of Ephedrine- This case study centers around the drug ephedrine. The study discusses how ephedrine binds to adrenergic receptors. Ephedrine is a chiral molecule which means it has stereoisomers. This study focuses on stereochemistry and guides students on how stereoisomers bind to specific receptors. The way an isomer binds to a receptor affects how a drug interacts with our body.

Understanding Solutions- This case study connects the concepts of concentration and molarity in chemistry terms to terms used in a medical field. Students will study the concepts of osmolarity, molarity, hyper and hypotonic solutions, and salt solutions. The study involves the story of a young nurse learning to understand the important terms and solutions in a medical situation.

Red Blood Cell Alloimmunization- This case study discusses the differences of blood types and blood type groups (ABO and Rh). The study focuses on the possibility of complications due to allergic reactions to red blood cell antigens (alloimmunization). Alloimmunization is especially harmful for patients needing blood transfusions or women and fetuses during pregnancy.

Radioactivity- This case study discusses thyroid hormones and how problems with these hormones can be treated with radiation. Students learn about the function of the thyroid and causes of hypo and hyperthyroidism. Students also learn about radioactive treatment, half lives of radiation, and types of radiation.

We are happy to welcome you to our second Open Educational Resource (OER) textbook, Biochemistry Free For All. Biochemistry is a relatively young science, but its rate of growth has been truly impressive. The rapid pace of discoveries, which shows no sign of slowing, is reflected in the steady increase in the size of biochemistry textbooks. Growing faster than the size of biochemistry books have been the skyrocketing costs of higher education and the even faster rising costs of college textbooks. These unfortunate realities have created a situation where the costs of going to college are beyond the means of increasing numbers of students.

Table of Contents
Basic Biology
Basic Chemistry
Water and Buffers
Amino Acids
Protein Structure
Structure and Function of Nucleic Acids
Structure and Function of Carbohydrates
Structure and Function of Lipids
Membranes: Basic Concepts
Membranes: Transport
Membranes: Other Considerations
Catalysis: Basic Principles
Catalysis: Control of Activity
Catalysis: Mechanisms
Blood Clotting
Energy: Basics
Electron Transport and Oxidative Phosphorylation
Photophosphorylation
Metabolism of Sugars
Metabolism of Polysaccharides
Citric Acid Cycle
Metabolism of Fats and Fatty Acids
Metabolism of Other Lipids
Metabolis of Amino Acids and the Urea Cycle
Metabolism of Nucleotides
Genes and Genomes
DNA Replication
DNA Repair
Transcription
RNA Processing
Translation
Regulation of Gene Expression
Cell Signaling
Basic Techniques
Point by Point: In the Beginning
Point by Point: Structure and Function
Point by Point: Membranes
Point by Point: Catalysis
Point by Point: Energy
Point by Point: Metabolism
Point by Point: Information Processing
Point by Point: Techniques

We are happy to welcome you to our second Open Educational Resource (OER) textbook, Biochemistry Free For All. Biochemistry is a relatively young science, but its rate of growth has been truly impressive. The rapid pace of discoveries, which shows no sign of slowing, is reflected in the steady increase in the size of biochemistry textbooks. Growing faster than the size of biochemistry books have been the skyrocketing costs of higher education and the even faster rising costs of college textbooks. These unfortunate realities have created a situation where the costs of going to college are beyond the means of increasing numbers of students.

" The course, which spans two thirds of a semester, provides students with a research-inspired laboratory experience that introduces standard biochemical techniques in the context of investigating a current and exciting research topic, acquired resistance to the cancer drug Gleevec. Techniques include protein expression, purification, and gel analysis, PCR, site-directed mutagenesis, kinase activity assays, and protein structure viewing. This class is part of the new laboratory curriculum in the MIT Department of Chemistry. Undergraduate Research-Inspired Experimental Chemistry Alternatives (URIECA) introduces students to cutting edge research topics in a modular format. Acknowledgments Development of this course was funded through an HHMI Professors grant to Professor Catherine L. Drennan."

Exploration of the biological importance of inorganic complexes. Topics include: biochemistry and transition metal chemistry review, characterization methods, metal ion transport and cellular storage, biological electron transfer, the nitrogen cycle, oxygen transport and transfer, oxygen processing, and enzymes and proteins.

More advanced treatment of biochemical mechanisms that underlie biological processes. Emphasis on experimental methods used to unravel these processes, and how these processes fit into the cellular context and coordinate regulation of these processes. Topics include macromolecular machines for energy and force transduction, regulation of biosynthetic and degradative pathways, and structure and function of nucleic acids.

Biology 2e is designed to cover the scope and sequence requirements of a typical two-semester biology course for science majors. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology includes rich features that engage students in scientific inquiry, highlight careers in the biological sciences, and offer everyday applications. The book also includes various types of practice and homework questions that help students understand—and apply—key concepts. The 2nd edition has been revised to incorporate clearer, more current, and more dynamic explanations, while maintaining the same organization as the first edition. Art and illustrations have been substantially improved, and the textbook features additional assessments and related resources.

By the end of this section, you will be able to do the following:

Identify and describe the properties of life
Describe the levels of organization among living things
Recognize and interpret a phylogenetic tree
List examples of different subdisciplines in biology

Examination of the biological importance of organic molecules. Topics include: bioorganic mechanisms, chirality and its role in bioactivity, lipids, carbohydrates, animo acids, peptides, and porteins, nucleic acids, enzymes, coenzymes, and coupled reactions, lipid metabolism, carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism.

Table of Contents:
Chapter 1: Foundations of Biochemistry
Chapter 2: Protein Structure
Chapter 3: Investigating Proteins
Chapter 4: DNA, RNA and the Human Genome
Chapter 5: Investigating DNA
Chapter 6: Enzyme Principles and Biotechnological Applications
Chapter 7: Catalytic Mechanisms of Enzymes
Chapter 8: Protein Regulation and Degradation
Chapter 9: DNA Replication
Chapter 10: Transcription and RNA Processing
Chapter 11: Translation
Chapter 12: DNA Damage and Repair
Chapter 13: Transcriptional Control and Epigenetics

Cell Biology, Genetics, and Biochemistry for Pre-Clinical Students (2021) is an undergraduate medical-level resource for foundational knowledge across the disciplines of genetics, cell biology and biochemistry. This USMLE-aligned text is designed for a first-year undergraduate medical course that is delivered typically before students start to explore systems physiology and pathophysiology. The text is meant to provide the essential information from these content areas in a concise format that would allow learner preparation to engage in an active classroom. Clinical correlates and additional application of content is intended to be provided in the classroom experience. The text assumes that the students will have completed medical school prerequisites (including the MCAT) in which they will have been introduced to the most fundamental concepts of biology and chemistry that are essential to understand the content presented here. This resource should be assistive to the learner later in medical school and for exam preparation given the material is presented in a succinct manner, with a focus on high-yield concepts.

The 276-page text was created specifically for use by pre-clinical students at Virginia Tech Carilion School of Medicine and was based on faculty experience and peer review to guide development and hone important topics.

Available Formats
978-1-949373-42-4 (PDF)
978-1-949373-43-1 (ePub) [coming soon]
978-1-949373-41-7 (Pressbooks) https://pressbooks.lib.vt.edu/cellbio
Also available via LibreTexts: https://med.libretexts.org/@go/page/37584

How to Adopt this Book
Instructors reviewing, adopting, or adapting parts or the whole of the text are requested to register their interest at: https://bit.ly/interest-preclinical.

Instructors and subject matter experts interested in and sharing their original course materials relevant to pre-clinical education are requested to join the instructor portal at https://www.oercommons.org/groups/pre-clinical-resources/10133.

Features of this Book
1. Detailed learning objectives are provided at the beginning of each subsection
2. High resolution, color contrasting figures illustrate concepts, relationships, and processes throughout
3. Summary tables display detailed information
4. End of chapter lists provide additional sources of information
5. Accessibility features including structured heads and alternative-text provide access for readers accessing the work via a screen-reader

Table of Contents
1. Biochemistry basics
2. Basic laboratory measurements
3. Fed and fasted state
4. Fuel for now
5. Fuel for later
6. Lipoprotein metabolism and cholesterol synthesis
7. Pentose phosphate pathway (PPP), purine and pyrimidine metabolism
8. Amino acid metabolism and heritable disorders of degradation
9. Disorders of monosaccharide metabolism and other metabolic conditions
10. Genes, genomes, and DNA
11. Transcription and translation
12. Gene regulation and the cell cycle
13. Human genetics
14. Linkage studies, pedigrees, and population genetics
15. Cellular signaling
16. Plasma membrane
17. Cytoplasmic membranes
18. Cytoskeleton
19. Extracellular matrix

Suggested Citation
LeClair, Renée J., (2021). Cell Biology, Genetics, and Biochemistry for Pre-Clinical Students, Blacksburg, VA: Virginia Tech Publishing. https://doi.org/10.21061/cellbio. Licensed with CC BY NC-SA 4.0.

About the Author
Renée J. LeClair is an Associate Professor in the Department of Basic Science Education at the Virginia Tech Carilion School of Medicine, where her role is to engage activities that support the departmental mission of developing an integrated medical experience using evidence-based delivery grounded in the science of learning. She received a Ph.D. at Rice University and completed a postdoctoral fellowship at the Maine Medical Center Research Institute in vascular biology. She became involved in medical education, curricular renovation, and implementation of innovative teaching methods during her first faculty appointment, at the University of New England, College of Osteopathic Medicine. In 2013, she moved to a new medical school, University of South Carolina, School of Medicine, Greenville. The opportunities afforded by joining a new program and serving as the Chair of the Curriculum committee provided a blank slate for creative curricular development and close involvement with the accreditation process. During her tenure she developed and directed a team-taught student-centered undergraduate medical course that integrated the scientific and clinical sciences to assess all six-core competencies of medical education.

Accessibility Note
The University Libraries at Virginia Tech and Virginia Tech Publishing are committed to making its publications accessible in accordance with the Americans with Disabilities Act of 1990. The HTML (Pressbooks) and ePub versions of this book utilize header structures and include alternative text which allow for machine-readability.

Please report any errors at https://bit.ly/feedback-preclinical

Cell Biology, Genetics, and Biochemistry for Pre-Clinical Students is an undergraduate medical-level resource for foundational knowledge across the disciplines of genetics, cell biology and biochemistry. This USMLE-aligned text is designed for a course in first-year undergraduate medical course that is delivered typically before students start to explore systems physiology and pathophysiology. The text is meant to provide the essential information from these content areas in a concise format that would allow learner preparation to engage in an active classroom. Clinical correlates and additional application of content is intended to be provided in the classroom experience. The text assumes that the students will have completed medical school prerequisites (including the MCAT) in which they will have been introduced to the most fundamental concepts of biology and chemistry that are essential to understand the content presented here. This resource should be assistive to the learner later in medical school and for exam preparation given the material is presented in a succinct manner, with a focus on high-yield concepts.

The 276-page text was created specifically for use by pre-clinical students at Virginia Tech Carilion School of Medicine and was based on faculty experience and peer review to guide development and hone important topics.

Instructors reviewing, adopting, or adapting parts or the whole of the text are requested to register their interest at: https://bit.ly/interest-preclinical.

Instructors and subject matter experts interested in and sharing their original course materials relevant to pre-clinical education are requested to join the instructor portal at https://www.oercommons.org/groups/pre-clinical-resources/10133.

Table of Contents
1. Biochemistry basics
2. Basic laboratory measurements
3. Fed and fasted state
4. Fuel for now
5. Fuel for later
6. Lipoprotein metabolism and cholesterol synthesis
7. Pentose phosphate pathway (PPP), purine and pyrimidine metabolism
8. Amino acid metabolism and heritable disorders of degradation
9. Disorders of monosaccharide metabolism and other metabolic conditions
10. Genes, genomes, and DNA
11. Transcription and translation
12. Gene regulation and the cell cycle
13. Human genetics
14. Linkage studies, pedigrees, and population genetics
15. Cellular signaling
16. Plasma membrane
17. Cytoplasmic membranes
18. Cytoskeleton
19. Extracellular matrix

View the animation to see how one type of immune cell-the helper T cell-interprets a message presented at the surface of the cell membrane. The message is an antigen, a protein fragment taken from an invading microbe. A series of events unfolds that results in the production of many clones of the helper T cell. These identical T cells can serve as a brigade forming an essential communication network to activate B cells, which make antibodies that will specifically attack the activating antigen.

Introduction to the use of computers to automate data analysis or model hypotheses in the field of biology, and its application for molecular and cellular biology, biochemistry, neuroscience and evolution.