The intestines occupy the caudal part of the body. They contact the reproductive organs and the gizzard. The small intestine is long and relatively uniform in shape and size. There is no demarcation between the jejunum and the ileum.

In this class we will learn about how the process of DNA replication is regulated throughout the cell cycle and what happens when DNA replication goes awry. How does the cell know when and where to begin replicating its DNA? How does a cell prevent its DNA from being replicated more than once? How does damaged DNA cause the cell to arrest DNA replication until that damage has been repaired? And how is the duplication of the genome coordinated with other essential processes? We will examine both classical and current papers from the scientific literature to provide answers to these questions and to gain insights into how biologists have approached such problems. 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.

So named as they were initially found in the Bursa of Fabricius, B cells produce antibodies and are associated with humoral immunity (T cells are part of the cell-mediated immune response), and are an integral part of the adaptive immune system. They represent 20-30% of circulating lymphocytes.

Introduction to Microscopy Lab
Measurement Lab
History of Life Lab
Phylogeny Lab
Prokaryotes Lab I
Prokaryotes Lab II
Supergroups Excavata and Amoebozoa
Supergroup SAR
Supergroup Archaeplastida I – red algae, green algae, charophytes, seedless plants
Supergroup Archaeplastida II – seed plants
Supergroup Opisthokonta – Fungi
Supergroup Opisthokonta – Basal Animals and Deuterostomes
Supergroup Opisthokonta – Protostomes

BIOL 242 – Human Anatomy and Physiology II

Human Anatomy and Physiology (A&P) 242 is the second class in a two quarter sequence in which human anatomy and physiology are studied using a body systems approach with emphasis on the interrelationships between form and function at the gross and microscopic levels of organization. You can think of this course as “An Owner’s Guide to the Human Body”. My goal is to help you learn how your body works so that you can explain concepts to others and apply knowledge to novel situations (e.g. make informed decisions regarding your own health and those whom you care about). You’ll also learn how to evaluate scientific research that forms the basis of our understanding of human anatomy and physiology and gain an appreciation for what remains to be discovered. To accomplish these goals requires significant effort from both of us. Although you will need to commit information to memory, I will ask you to focus on learning for understanding and your assessments will reflect this emphasis.

ANP 242 topics include: nervous system structure and physiology; special senses; endocrine system, reproductive system; digestive system; metabolism; urinary system; fluid and electrolyte balance; and, unifying themes of homeostasis, health and disease.

You will also gain experience problem solving, interpreting data, communicating verbally and in writing with others, developing information literacy skills, using technology and exploring how your knowledge of anatomy and physiology can be applied to real world health challenges. This course is designed to build the core knowledge and skills needed to succeed in a world that demands flexibility and continuous learning and to prepare you for advanced study of anatomy, physiology and clinically-related subjects.

Lab 1: Overview & The Microscope
Lab 2: Cytology
Lab 3: Histology
Lab 4: The Integumentary System
Lab 5: The Axial Skeleton
Lab 6: The Appendicular Skeleton
Lab 7: Joints
Lab 8: The Axial Muscles
Lab 9: The Appendicular Muscles
Lab 10: Nervous Tissue
Lab 11: The Central Nervous System (Brain)
Lab 12: Cranial and Spinal Nerves
Lab 13: The Somatic Nervous System (Special Senses)
Lab 14: The Endocrine System
Lab 15: Blood
Lab 16: The Heart
Lab 17: Blood Vessels and Circulation
Lab 18: The Lymphatic System
Lab 19: The Respiratory System
Lab 20: The Digestive System
Lab 21: The Urinary System
Lab 22: The Reproductive System (Male)
Lab 23: The Reproductive System (Female)

A grasp of the logic and practice of science is essential to understand the rest of the world around us. To that end, the CMB4e iText (like earlier editions) remains focused on experimental support for what we know about cell and molecular biology, and on showing students the relationship of cell structure and function. Rather than trying to be a comprehensive reference book, CMB4e selectively details investigative questions, methods and experiments that lead to our understanding of cell biology. This focus is nowhere more obvious than in the chapter learning objectives and in external links to supplementary material. The Basic CMB3e version of the iText includes links to external web-sources as well as the author’s short, just-in-time YouTube VOPs (with edited, optional closed captions), all embedded in or near relevant text. Each video is identified with a descriptive title and video play and QR bar codes.

Basophils are derived from the same stem cell line as mast cells and while they are similar to mast cells, they are not identical (they are thought by some to be immature mast cells). They are the least common of all the leukocytes, are a similar size to neutrophils and eosinophils and are characterised by the large number of basophilic staining granules in their cytoplasm. They are present in the circulation but rarely found in tissue.

Mature B cells that undergo stimulation by an antigen undergo class switching, and differentiate into either plasma or memory cells. In the paracortex region of the lymph node binding to MHC II in the presence of IL-4 produced by the CD4+ T cells (TH2 type) causes the B cells to differentiate; most will become plasma cells, however a small number will become memory cells. Follicular dendritic cells present in the germinal centers of peripheral lymphoid organs can absorb intact antigen onto their surface to present to B cells to stimulate differentiation.

" Where do new drugs and treatments come from? This class will take you from the test tubes and mice of the laboratory to the treatment of patients with deadly blood disorders. Students will learn how to think as a scientist through discussion of primary research papers describing the discoveries of several novel treatments. Topics such as gene therapy, the potential of drugs based on RNA interference and the reprogramming of somatic cells into stem cells for regenerative medicine will be discussed. 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."

Systematic error, or 'bias' is of particular importance in any epidemiological investigation, and should be avoided wherever possible. Biases will reduce the validity of any results obtained, whether it be by overestimating or underestimating the frequency of disease in a population or the association between an exposure and disease. The forms of bias covered here can only be minimised through careful study design and execution - they cannot be accounted for in the analysis. Although confounding is considered by many authors as a form of bias, it can be accounted for during analysis, and so is covered separately.

Bile formation is an osmotic secretory process that is driven by the active concentration of bile salts in the bile canaliculi. Bile acids are produced from cholesterol and prior to being excreted from hepatocytes are bound to specific amino acids allowing them to exist as bile salts. One side of the bile salt molecule is negatively charged (hydrophilic) whilst the other is hydrophobic allowing bile salts to form micelles once a certain bile salt concentration has been reached.

Antibodies, antigens, antigen-antibody reactions, cells and tissues of lymphoreticular and hematopoietic systems, and individual and collective components of cell-mediated and humoral immune response.

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)

Course Description: Biochemistry 551 is an integrated lecture, lab and seminar course that covers biochemistry-centered theory and techniques. The course is designed for upper-level undergraduate students majoring in Biochemistry. Students learn how to apply a broad range of biochemical, genetic, and physical techniques to modern biochemical research. Students also learn how to analyze and interpret the primary scientific literature, develop an understanding of the communication of data, and connect biochemical techniques to basic research.

Lectures introduce concepts and theory that are subsequently explored in detail in experiments. The virtual labs are designed to provide experience with techniques that are used in modern biochemical research through interactive online activities. The curriculum incorporates a research project beginning with the PCR amplification and cloning of the HCAII gene, which codes for the enzyme human carbonic anhydrase II (HCAII). As the semester progresses, students explore how to overexpress, purify and assay wild type and mutant HCAII protein. Experiments covered include PCR, spectrophotometry, gel electrophoresis, protein overexpression and purification, enzyme assays and fluorescence spectroscopy. Several times during the semester, at-home lab experiments are incorporated to provide hands-on experience to supplement student understanding of the virtual labs.

This lab manual contains detailed descriptions of each online laboratory exercise in this course. Please see the course Canvas site for other course information, such as: a syllabus, schedule, assignment guidelines, and lecture and seminar materials.

Table of Contents:

Lab 1: Structural analysis of HCAII using PyMOL
Lab 2: PCR Amplification of HCAII and pETblue2
Lab 3: Lab-at-home: Introduction to Biotechnology Methods
Lab 4: Gibson assembly of HCAII into pETblue2 vector and transformation of E. coli with the reactions
Lab 5: Screening for pETblue2-HCAII clones
Lab 6: Mutant Exploration
Lab 7: Protein Expression and Purification in E. coli
Lab 8: Analysis of His-tagged HCAII Expression and Purification
Lab 9: Determination of Protein Stability using Chemical Denaturation and Intrinsic Fluorescence
Lab 10: Investigation of wild type and mutant HCAII enzyme activity
Lab 11: Forster Resonance Energy Transfer (FRET) to detect ligand-binding to HCAII

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.