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1.II:. Intro to Biochemistry - Biology

1.II:. Intro to Biochemistry - Biology



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A. What is biochemistry and who needs it?

Literally "Biochemistry" is the chemistry of life. This is synonymous with "Molecular Biology", but traditionally biochemistry has dealt more with the study of proteins and smaller biomolecules and molecular biology has dealt more with gene expression and associated molecules. Davis, "Biochemistry and Molecular Biology". Because biomolecules are the underlying basis for all aspects of the physiology and behavior of living systems, anyone who chooses to work in a biologically-related field has a need for an understanding of biochemistry.

B. Molecules in an E. coli cell

Compound% weightave. MW#/cell# of kindscomment
(H_2O)7018(4 imes 10^{10})1
Ions (Na,K,SO4, etc.)140(2.6 imes 10^8)20 majorexampleNa+ ~0.050 M
Carbohydrates3150(2 imes 10^8)250
Amino Acids0.4120(3 imes 10^7)20 main ~120 total
Nucleotides0.4300(1.2 imes 10^7)5 main ~100 total
Lipids2750(2.5 imes 10^7)50
Proteins1540,000(1 imes 10^6)4,28835 -85,000 in humans!
RNA6(10^6)(2 imes 10^4)~2,00035 -85,000 in humans
DNA1(2.5 imes 10^9)(1, (4))146 @ 5 imes 10^10 (human)

Introduction to Biochemistry and Molecular Biology

PREREQUISITE FOR HEALTH SCIENCES PROGRAMS.
PREPARATION FOR THE MCAT.
UF ONLINE DEGREE COURSEWORK.

Course Description

BCH 4024 (Special Programs – Online)
BCH 4024 surveys the structure, function, and metabolism of amino acids, proteins, carbohydrates, lipids, and nucleic acids. It introduces concepts in cell structure, replication and growth, and metabolic regulation. Lecture notes are available as downloadable PDF files and video recordings of each lecture can be streamed directly from the UF E-Learning website. Please refer to the above PDF file for specific information on online testing, as well as available tutoring and exam review.

Semesters Offered

Offered each semester and runs along the same timeframe as the regular UF semesters.

Prerequisites

CHM 2210 Organic Chemistry 1 and CHM 2211 Organic Chemistry 2 (or their equivalents at other universities).

Non-Degree Transcript

All courses taken as a non-degree seeking student are credit-bearing. Your official transcript will list coursework, course number, course title and grade received. The earned hours, hours carried and GPA will read as zero on your official transcript as those fields are only completed for UF degree-seeking students.

If you are planning on transferring UF non-degree coursework to another institution for credit, it’s advised that you first verify with the other institution that the credit will be accepted.

Eligibility

Eligible students are those enrolled in a Distance Learning Degree Program at the University of Florida and those students with Nondegree Enrollment Status. See information below if you would like to apply.

Application Deadline

Since the application process can take up to one month to process, both applications must be submitted by the deadline listed below for your enrollment in that specific semester.

– Spring 2021: December 1, 2020
– Summer C 2021: April 15, 2021
– Fall 2021: August 1, 2021

Please note, applications submitted after the deadline will need to apply for the next semester’s enrollment.


Reviews

Reviewed by Jeffry Nichols, Associate Professor, Worcester State University on 6/1/21

The material covered is fairly similar to other biochemistry textbooks, but does lack some of the details of a more comprehensive biochemistry text (i.e. Lehninger's text). This isn't a negative, just an observation. The order in which the. read more

Reviewed by Jeffry Nichols, Associate Professor, Worcester State University on 6/1/21

Comprehensiveness rating: 3 see less

The material covered is fairly similar to other biochemistry textbooks, but does lack some of the details of a more comprehensive biochemistry text (i.e. Lehninger's text). This isn't a negative, just an observation. The order in which the concepts are presented is different, but again still fairly complete.

Content Accuracy rating: 4

From what I could tell, the information is accurate. Examples appear to be unbiased and give good everyday correlations to biochemistry ideas.

Relevance/Longevity rating: 3

The material for the basics and background for biochemistry are unlikely to change, so in that sense they are relevant. The way in which the material is presented, i.e. the formatting, does make it difficult to follow at times. The tables and figures are not always near the relevant text and often there are figures/tables that appear before the section in the text. Again, this could be a formatting issue.

The text is easy to follow, avoids jargon for the most part (until it needs defining). As mentioned above, references to tables/figures are hard to follow and some tables/figures seem "stuck in" at random points. This hurts the clarity of the text while reading.

Each chapter sticks to a familiar layout and walks the student through the various topics in a coherent manner.

Overall the text could be broken up, but again, possibly due to formatting, many of the links do not work, interrupting the flow, On all the end of chapter sections, I couldn't get any of the links to work, with a message about "to be developed" or "coming soon". This is unfortunate as these links could be great for further exploration and follow up assignments.

Organization/Structure/Flow rating: 3

Yes, the organization is pretty good, although I think the introduction of electron transport and electrochemistry should come after an understanding of WHERE these molecules are coming from, i.e. metabolism, breakdown of sugars, fats, amino acids, etc. This doesn't make it "bad", just no my personal preference. And as mentioned previously, the plethora of tables/figures can be overwhelming when they don't always line up with the discussion of them in the text.

Couldn't get the links to work--although it appears many of the links are "printed" after the end of entire book. So the material might be there, but as it is currently put together, it would be difficult for instructors or students to use these links effectively.

Grammatical Errors rating: 4

From what I can tell, the grammar is fine throughout the text.

Cultural Relevance rating: 4

Again, from what I read, I didn't notice any insensitive or offensive parts. Examples were clear and highlighted the biochemical aspects without a need address social or other issues. (which could actually be good depending on the nature of the class and student's interest in how science touch many aspects of our lives)

I have hope for this book, but I couldn't readily tell if this book is being maintained or updated on a regular basis, or if it is just a framework for others to build upon. The organization isn't ideal, and there are problems with links and such, but the overall material and coverage looks pretty good.

Reviewed by Joyce Easter, Professor, Virginia Wesleyan University on 5/31/21

The foundational concepts, as identified and defined by ASBMB, within Energy &amp Metabolism, Structure &amp Function, Information Storage &amp Transfer, homeostasis, and evolution are all covered sufficiently for an undergraduate survey course. read more

Reviewed by Joyce Easter, Professor, Virginia Wesleyan University on 5/31/21

Comprehensiveness rating: 4 see less

The foundational concepts, as identified and defined by ASBMB, within Energy & Metabolism, Structure & Function, Information Storage & Transfer, homeostasis, and evolution are all covered sufficiently for an undergraduate survey course in biochemistry. Overall there is a good balance between breadth and depth, but there are a couple topics that are oversimplified or lacking some key points. For example, the chapter on enzyme mechanisms has several good examples of enzymes and their mechanisms, but no overall concepts or general themes observed in enzyme mechanisms. The glossary contains more than 2400 entries, many of which are illustrated and/or have a link to an additional online resource. However, the “Find Term” button to hyperlink to the term in the text is not functional in the downloaded PDF version of the text.

Content Accuracy rating: 4

The majority of the content is accurate, but a few descriptions lack some detail that would make the explanation clearer and more complete.

Relevance/Longevity rating: 5

This is a fairly recent edition of the text that has been updated to include our current understanding the biochemical processes and systems as we understand them today.

The writing is appropriate for an undergraduate audience and has a sufficient number of graphics to complement the text. Terms are clearly defined when introduced, but the comprehensive glossary is a good resource for those students who may need further reinforcement.

Terminology used and the organization of the text is consistent throughout, but there is less consistency for the images and graphics due to the variety of sources and artists used for the visual content. Labeling within graphics is also not consistent throughout and some of the figures have blurry text.

The text is organized with the biological macromolecules introduced first then more complex structures, processes and pathways. The chapters could be easily assigned in a different order to align with an instructor’s preferred course order.

Organization/Structure/Flow rating: 5

Each chapter is organized logically with the introduction of the ideas necessary for comprehension presented in an appropriate order. Chapters are arranged to introduce similar and related topics in a logical sequence, as well as content coming earlier in the text than where it is applied in later chapter.

This book is essentially a PDF file of over 3600 pages. When the file is downloaded onto a student's computer, the hyperlinks in the table of contents do not link to bookmarks in the file, which means that this book is harder to navigate offline. If you want to read the text as you would a hard copy, then finding the chapter by page number and reading through the chapter is simple enough, but if you want the benefit of an electronic textbook, this text is more limited than other electronic books in that regard. The hyperlinks to the online resources (videos, images, etc) will take students to the appropriate web resource.

Grammatical Errors rating: 5

As a revised edition that has been used for several years by many students, it is free of grammatical errors.

Cultural Relevance rating: 3

Although the examples provided are not culturally insensitive or offensive, the examples are not inclusive of a variety of races, ethnicities and backgrounds.

Reviewed by Quan Wang, Research Associate, Indiana University - Bloomington on 5/18/21

The authors have provided a thorough coverage of core concepts with key information of a first-semester college course in biochemistry. Descriptions are kept brief and to the point. With over 30 years of classroom experience and their three. read more

Reviewed by Quan Wang, Research Associate, Indiana University - Bloomington on 5/18/21

Comprehensiveness rating: 5 see less

The authors have provided a thorough coverage of core concepts with key information of a first-semester college course in biochemistry. Descriptions are kept brief and to the point. With over 30 years of classroom experience and their three popular textbooks, the authors tour the readers with intensive pictures and keep them always on track, even when explaining the complex pathways of glycolysis and the Krebs citric acid cycle—two of the major stages leading from food to energy. One highlight of the book is the “metabolic melodies”—clever poems and songs composed by the authors to help students in memorizing material.

Content Accuracy rating: 5

The authors organized the information of the book with the Foundational Concepts defined by the American Society for Biochemistry and Molecular Biology (ASBMB). The content is accurate and unbiased.

Relevance/Longevity rating: 5

This book current version (1.3) is published in 2018 and thoroughly up to date, reflecting the subject as it is taught in the classroom today. For example, 3-D structures of the proteins were once conventionally thought to have relatively fixed based on the crystal structure. However, with the recent progress of the Cryogenic electron microscopy (cryo-EM) techniques, people found that many proteins have intrinsically disordered region that allows them to flexibly interact to a wider variety of partners. This book is suitable for one semester biochemistry introduction class.

The seven “point by point” parts are the summaries of the chapter and section in the same theme that can be used as the study guides for students.

The text is internally consistent in terms of terminology and framework.

The book accompanies 26 teaching PowerPoint files for different topics as well as links to Youtube lectures given by Professor Kevin Ahern.

Organization/Structure/Flow rating: 5

It is amazing that biochemistry deals chiefly with just six bonding elements (out of the more than 100 in the periodic table of elements). The book started with water that is by far the most abundant component of every cell with simple chemical bonds. Then the authors expanded these themes and the nature of chemical bonds to twenty amino acids that form the building blocks of proteins, which are the basis of all living tissues. And the instructions for building proteins are in the genes that comprise DNA and its related molecule, RNA. As you proceed through the course, complexity mounts in intriguing ways, but there are always surprising links to an astonishing array of questions.

Beside the written content, the E-book also provides access to videotaped lectures, interactive learning modules and rotatable 3-D molecules. The book is best used (currently) on iBooks (available for Macs and iPads), which allows readers to click on figures to enlarge them, watch video lectures relevant to each topic, listen to the selected songs, and link out to the internet to find more information simply by clicking on any term. Other formats, such as PDF and Kindle, allow access to all of the hyperlinks, but not all of the multimedia. If you are using the PDF version, you can download the Metabolic Melody songs at http:www.davincipress.com.

Grammatical Errors rating: 5

With extensive use of this book in the authors’ classroom and proofread by hundreds of students since the book was first published in 2016, no grammatical error was found in current version (1.3).

Cultural Relevance rating: 5

This book is about the chemical reactions in the cells and real world examples were carefully chosen to avoid being culturally insensitive or offensive.

The associated PPT slides and related Youtube lectures given by Professor Kevin Ahern are generous resources for both the teachers and students using this book. In 2019, Prof. Kevin Ahern, the lead author of this book has released an online course "Biochemistry and Molecular Biology: How Life Works" at the Great courses website with below link: https://www.thegreatcourses.com/fb9572?ai=180339&cmp=Social_Facebook_Advertising_2019BioChemistry&fbclid=IwAR0AOo9CUYm0ZsXKSCfG9ct5NmoFSSZZ245C50aWbNDY56tSnrGDuv8Rw64

Reviewed by Justin P'Pool, Visiting Assistant Professor of Chemistry, Franklin College on 4/22/21

This is a comprehensive text which can be used for a one-semester introduction to biochemistry, or for a two-semester sequence. The glossary is thorough and illustrated read more

Reviewed by Justin P'Pool, Visiting Assistant Professor of Chemistry, Franklin College on 4/22/21

Comprehensiveness rating: 5 see less

This is a comprehensive text which can be used for a one-semester introduction to biochemistry, or for a two-semester sequence. The glossary is thorough and illustrated

Content Accuracy rating: 5

The content is accurate and free from error.

Relevance/Longevity rating: 5

Published in 2018, the content of the book is up to date. The focus of this text is on an introduction to material in which the basics will likely not change. This leaves room for the material to be updated easily.

The text is easy to read and abbreviations and terminology are explained.

The text is internally consistent.

The chapters consist of many topics under smaller headings, making each chapter customizable with regard to reading assignments. The “Point by Point” sections will also be extremely helpful for students for quick review.

Organization/Structure/Flow rating: 5

The flow of the book is a logical progression, but not laid out in such a way that customizing material order will be difficult.

All images are clear and undistorted. However, as a pdf the navigation is a little more difficult due to the navigation links not working. Students will not have this problem if used on an iPad or similar device.

Grammatical Errors rating: 5

The book is free of grammatical errors

Cultural Relevance rating: 5

This is not only a comprehensive book, the available power points are well crafted. The many topics in the text have summary sections that enable students to quickly review, as well as catchy songs that many will find helpful as a memorization resource. The combination of materials makes this an excellent open-access resource that I will be using in my class.


Outline

Unit 1: Cells, Water, and Buffers

  • Lesson 1: Introduction to Biochemistry and Biochemical Research Literature
  • Lesson 2: Cells: The Bio of Biochemistry
  • Lesson 3: Water
  • Lesson 4: pH and Buffers
  • Lesson 1: Energy Reactions
  • Lesson 2: Thermodynamics
  • Lesson 3: Cellular Phosphorylations and Electron Transport
  • Lesson 4: Energy Efficiency
  • Lesson 5: Metabolic Controls

Unit 3: Structure and Function

  • Lesson 1: Proteins
  • Lesson 2: Nucleic Acids
  • Lesson 3: Carbohydrates
  • Lesson 4: Lipids
  • Lesson 5: Membranes and Transport
  • Lesson 6: Vitamins and Cofactors
  • Lesson 1: Activation Energy
  • Lesson 2: Enzyme Catalysis
  • Lesson 3: Enzyme Kinetics
  • Lesson 4: Enzyme Inhibition
  • Lesson 5: Control of Enzymes

Unit 5: Flow of Genetic Information

  • Lesson 1: DNA Replication
  • Lesson 2: DNA Repair
  • Lesson 3: Transcription
  • Lesson 4: Regulation of Transcription
  • Lesson 5: RNA Processing
  • Lesson 6: Translation
  • Lesson 1: Overview of Metabolic Concepts
  • Lesson 2: Glycolysis, Fermentation, and Gluconeogenesis
  • Lesson 3: Citric Acid and Glyoxylate Cycles
  • Lesson 4: Acetyl-CoA and Cholesterol Metabolism
  • Lesson 5: Ketone Bodies
  • Lesson 6: Fatty Acid Oxidation and Synthesis
  • Lesson 1: Carbohydrate Storage and Breakdown
  • Lesson 2: Pentose Phosphate Pathway
  • Lesson 3: Calvin Cycle
  • Lesson 4: Urea Cycle
  • Lesson 5: Nitrogen Fixation
  • Lesson 6: Amino Acid Metabolism and Catabolism
  • Lesson 7: Nucleotide Metabolism and de novo Biosynthesis
  • Lesson 1: Cell Signaling
  • Lesson 2: Ligand-gated Ion Channel Receptors
  • Lesson 3: Nuclear Hormone Receptors
  • Lesson 4: G-protein Coupled Receptors (GPCRs)
  • Lesson 5: Receptor Tyrosine Kinases (RTKs)

Unit 9: Biochemical Techniques

  • Lesson 1: Cell Disruption and Fractionation
  • Lesson 2: Chromatography
  • Lesson 3: Electrophoresis
  • Lesson 4: Blotting
  • Lesson 5: DNA Techniques

Unit 10: Synthesis of Concepts in Biochemistry


Graduate Course Offerings UP

For the most up to date list of course offerings by semester, please visit the MSU schedule of courses page: www.schedule.msu.edu

Course: BMB 801 "Molecular Biology" UP Description: Organization of genes. Regulation of gene expression, replication, and recombination. Semester(s) offered: Fall of every year Credits: 3 Recommended background: BMB 462, CEM 383 Most Recent Syllabus: Fall 2019 (PDF) Previous: Fall 2017 (PDF) Course: BMB 802 "Metabolic Regulation and Signal Transduction" UP Description: Molecular basis for metabolic regulation. Molecular signalling mechanisms and mechanisms for allosteric and covalent protein modifications. Semester(s) offered: Spring of every year Credits: 3 Recommended background: BMB 801 Most Recent Syllabus: Spring 2021 (PDF) Previous: Spring 2020 (PDF) Course: BMB 803 "Protein Structure and Function" UP Description: Protein structure and relationship of function to structure. Applications of kinetic methods to elucidation of enzyme mechanisms and regulation. (NOTE: This course is to serve students in non-BMB programs who desire a course in protein structure, but who do not require training in enzyme mechanisms. NOT open to Biochemistry majors or students who already have credit in BMB 805.) Semester(s) offered: Spring of every year (1st ten weeks of the semester) Credits: Total Credits: 2 Lecture/Recitation/Discussion Hours: 2 Recommended Background: BMB 462 and CEM 383 Most Recent Syllabus: Spring 2020 (PDF) Previous: Spring 2019 (PDF) Course: BMB 805 "Protein Structure, Design, and Mechanism" UP Description: Protein architecture, dynamics, folding, stability, and evolution. Conformational changes, ligand binding, and kinetics. Elucidation of enzyme mechanisms. Semester(s) offered: Spring of every year Credits: 3 Recommended background: BMB 462 and CEM 383 Most Recent Syllabus: Spring 2020 (PDF) Previous: Spring 2019 (PDF) Course: BMB 816 "Integrative Toxicology: Mechanisms, Pathology and Regulation" (Interdepartmental with PHM) UP Description: Biochemical, molecular, and physiological mechanisms of toxicology. Functional and pathological responses of major organ systems to chemical insult. Mechanisms of mutagenesis, carcinogenesis, and reproductive toxicology. Concepts in risk and safety assessment. Semester(s) offered: Fall of odd years Credits: 3 Prerequisite: PHM 819 Most Recent Syllabus: Fall 2019 (PDF) Course: BMB 825 "Cell Structure and Function" (Interdepartmental with MMG and PSL) UP Description: Molecular basis of structure and function. Cell properties: reproduction, dynamic organization, integration, programmed and integrative information transfer. Original investigations in all five kingsdoms. Semester(s) offered: Spring of every year Credits: 3 Recommended background: BMB 401 or BMB 461. Most Recent Syllabus: Spring 2020
Previous: Spring 2018 (PDF) Course: BMB 829 "Methods of Macromolecular Analysis and Synthesis" UP Description: Techniques of isolation and characterization of macromolecules. Computer use in structure-function analysis of macromolecules. Semester(s) offered: Fall of every year Credits: 2 Recommended background: BMB 462 or concurrently. Most Recent Syllabus: Fall 2019 Previous: Fall 2017 (PDF) Course: BMB 855 "Special Problems" UP Description: Laboratory or library research on special problems in biochemistry. Semester(s) offered: Fall, Spring, and Summer of every year. Credits: 1-4 Restrictions: Approval of department. A student may earn a maximum of 8 credits in all enrollments for this course. Course: BMB 856 "Plant Molecular and Omic Biology" (Interdepartmental with PLB, CSS. Administered by PLB.) UP Description: Recent advances in genetics and molecular biology of higher plants. Semester(s) offered: Spring 2021, and then every Spring semester after that Credits: 3 Recommended background: ZOL 341 Most Recent Syllabus: Spring 2021 (PDF) Schedule: Fall 2018 (PDF) --> Previous: Fall 2019 (PDF) Course: BMB 864 "Plant Biochemistry" (Interdepartmental with PLB) UP Description: Biochemistry unique to photosynthetic organisms. Photosynthetic and respiratory electron transport, nitrogen fixation, carbon dioxide fixation, lipid metabolism, carbon partitioning, cell walls, sulfur and nitrogen metabolism and specialized metabolism including isoprenoids, phenylpropanoids and alkaloids. Semester(s) offered: Fall 2017 and then TBD after that Credits: 3 Recommended background: (BMB 401 or BMB 462) and prior undergraduate course in plant physiology. Most Recent Syllabus: Fall 2017 (PDF)
Previous: Fall 2016 (PDF) Course: BMB 866 "Molecular Plant Physiology" (Interdepartmental with PLB) UP Description: PLB 866 is designed for first year graduate students in the molecular plant sciences program but is open to anyone wanting a comprehensive treatment of molecular plant physiology. This is a core course in the MPS program and it is assumed that the student will have taken PLB 856. Topics in that course will not be repeated in this course. The main topics will be molecular (including biochemical) aspects of plant physiology including cell biology, photosynthesis, cell wall metabolism, lipid metabolism and other topics. A quantitative understanding of plant processes will be emphasized through a series of homework exercises. Semester(s) offered: Fall 2020, and then every Fall semester after that Credits: 3 Recommended background: Enrolled in a graduate program in plant molecular science. An advanced undergraduate course in biochemistry or plant physiology. Most Recent Syllabus: Spring 2019 (PDF) Course: BMB 888 "Laboratory Rotation" UP Description: Participation in research laboratories to learn experimental techniques and approaches, broaden research experience, and assess research interests prior to selecting a thesis or dissertation advisor. Semester(s) offered: Fall, Spring, and Summer of every year Credits: 1-4 Restrictions: Open only to graduate students in Biochemistry. A student may earn a maximum of 12 credits in all enrollments for this course. Course: BMB 899 "Master's Thesis Research" UP Description: Master's thesis research. Semester(s) offered: Fall, Spring, and Summer of every year Credits: 1-12 Restrictions: Open only to master's students in Biochemistry. A student may earn a maximum of 36 credits in all enrollments for this course.

Course: BMB 960 "Selected Topics in Biochemistry I" UP Description: Selected topics in Biochemistry with substantial student presentations Semester(s) offered: Fall and Spring of every year Credits: 1-3 Restrictions: Open to graduate students in the Department of Biochemistry and Molecular Biology or approval of department. A student may earn a maximum of 7 credits in all enrollments for this course. Course: BMB 960 Sect 301 "Plant Biotechnology Research Forum" UP Semester(s) offered: Fall (First 8 weeks of the semester)
Credits: 1 Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor Description:

This is an advanced seminar focusing on reading of the literature and student presentations on topics related to plant biotechnology. Topic areas in general address modern problems in human health and environmental sustainability. Specifically, areas in the past have included the boosting of lipid productivity in oleaginous microalga, synthetic biology and microbial biosynthesis from industrial perspective, abiotic stress tolerance as agronomic trait and its quantification, electronically controlled microorganisms, the organization, function and evolution of plant metabolism and synthetic biology and the future of space exploration. The course is part of the training program in plant biotechnology 'Plants for Health and Sustainability' (https://plantmetabolism.natsci.msu.edu/), though students not participating in the training program are also very welcome to take the course. Confirmed speakers for the associated Annual Symposium on Plant Biotechnology for Health and Sustainability are representatives from the industry, research foundations, national labs and academia.

Goals for the course include increasing competence in reading scientific literature and oral presentation skills, and to prepare students for engagement in the affiliated Plant Biotechnology Symposium (https://plantmetabolism.natsci.msu.edu/posts/save-the-dates-2019-annual-symposium/. IMPORTANT: Attendance of the Symposium taking place October 31 to November 2 will be a required portion of the course.

During each class, two students will give presentations based on 2-3 published works. The topics and papers will be selected based upon the topics contributed by, and relevant for the background of the speakers, and thus will vary each year. The course will meet once each week for 6-8 weeks. The actual day/time/location of the course is Wednesdays 3:00-4:30 pm, in MPS2060. While the instructors will provide the students with suggested topics and papers, students are encouraged to go beyond the suggested publications.

If you are not a declared Biochemistry graduate student, you will need to submit the online override request form (http://bmb.natsci.msu.edu/undergraduate/override-request-special-permissions-form/) and then contact the instructors (Drs Björn Hamberger, [email protected], Greg Bonito, [email protected], Rob Last, [email protected]) for permission to enroll. Enrollment will be limited to 14 students.

The class meeting after the Annual Symposium on Plant Biotechnology for Health and Sustainability, will be used to evaluate the course and the symposium. We hope that each student will participate actively in the symposium.

Format: During each class meeting two students will deliver 25+5 presentations and discussion, based upon the assigned topics. We suggest that you read the papers that we listed to get you started. Please feel free to include other papers, book chapters or online resources in your reading and for the preparation of the presentation.

The suggested overall format is: 5' of introduction, suitable for students familiar with molecular techniques but approachable for students with a variety of backgrounds. 15' of discussion of key experiments, making sure to highlight both basic biological insight and applications when appropriate. 5' of conclusions including ideas for future experimental and engineering approaches, insights and ideas for your research that the work gave you or anything else that might be of interest to the class members. 5&rsquo of open discussion, moderated by the speaker

Grading will be based upon class participation (30%) and the research presentation (70%).
Course materials will be made available to enrolled students at D2L.msu.edu.

Syllabus: Fall 2019 (PDF) Previous: Fall 2018 (PDF) Course: BMB 960 001/GEN 800 001 "Genetic Applications for Improving Food Security" UP Semester(s) offered: Fall 2017 Credits: 1 Description: As the world population is projected to reach 9 billion people by the year 2050, issues of food security are increasingly pressing. In this course, students will be introduced to ways in which genetics and genomics tools are used to enhance crop and livestock production in a changing world. We plan to investigate how -omics and other &ldquobig data&rdquo studies in particular can provide solutions to relevant issues such as climate change, antibiotic resistance, animal welfare concerns, and human malnutrition. Throughout the semester, students will be asked to present scientific papers related to these topics, prepare questions, and moderate class discussion. In addition, a component of this seminar will be focused on improving students&rsquo science communication skills to the general public and understanding how genetic research has manifested in science policy. Syllabus: Fall 2017 (PDF) Course: BMB 960 "Photosynthesis" UP Semester(s) offered: Spring of every year (May vary in the future. Please visit the schedule of courses page for updates: www.schedule.msu.edu) Credits: 3 Restrictions: Approval of the Instructor (Limited to 12 students) Description: The course will focus on the mechanisms and measurements of photosynthetic energy capture, CO2 fixation and production of energy-rich molecules, as well as the limitations and possible improvements to these processes for food and fuel. The course is designed to meet the needs of MSU graduate students with projects related to photosynthesis and integrate knowledge across a range of disciplines, ranging from chemistry and biophysics of light capture, metabolisms, bioenergy and cell biology, through synthetic biology and gene discovery. Each set of lectures will start with background and move to higher-level discussion based on literature and applications (e.g. scientific measurements, data analyses, etc.). Course evaluation will be by research-related presentations and a final poster session that demonstrates the integration of new knowledge of photosynthesis in on-going research projects. NOTE: To reserve a spot in this course, you will first need to contact Dr. David Kramer at [email protected] and you'll also need to complete the BMB Course Override link. Syllabus: Spring 2020 Previous: Spring 2017 (PDF) Course: BMB 960 "Intersection of Mitochondrial Science and Medicine " UP Semester(s) offered: Spring 2018 Credits: 1 Description: BMB and the MSU Center for Mitochondrial Science and Medicine will offer a graduate level seminar course (BMB 960) in Spring Semester 2018 on the topic of &ldquoIntersection of Mitochondrial Science and Medicine,&rdquo with the objective of exploring mitochondrial biochemistry in the context of the current field of mitochondrial medicine, including clinical correlations. The course will feature a combination of faculty and student presentations and consider topics such as: impact of nuclear and mitochondrial DNA mutagenesis and variability on organismal function, regulation of respiration and mitochondrial transcription by cell signaling, role of mitochondria in memory and neurodegenerative disease and the general field of mitochondrial health, oxidative stress and stress response, toxicity and disease. Syllabus: Spring 2018 (PDF) Course: BMB 961 "Selected Topics in Biochemistry II" UP Semester(s) offered: Fall and Spring of every year Credits: 1-3 Restrictions: Open to graduate students in the Department of Biochemistry and Molecular Biology or approval of department. Description: Selected topics in Biochemistry with faculty lectures, laboratory, or other instruction Course: BMB 961 "Genomics and Proteomics and Complex Genetic Systems" UP Semester(s) offered: Fall of even years Credits: 2 Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor Prerequisites: BMB 801 or instructor approved equivalent Description: Coming Soon NOTE: If you are NOT a Biochemistry major, you must contact Dr. John Lapres ([email protected]) for approval. (NOTE: Please fill out this override request form and then contact the instructor: https://bmb.natsci.msu.edu/undergraduate/override-request-special-permissions-form/). Syllabus: Fall 2016 (PDF) Course: BMB 961 "Metals in Biology" UP Semester(s) offered: Varies - please check the schedule of courses page for updates: www.schedule.msu.edu Credits: 2 Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor Description: Sec 004-Topic: "Metals in Biology" is intended for graduate students with backgrounds in biochemistry, molecular/cellular biology, microbiology, and/or chemistry. (May be cross-listed with the MMG and CMB departments.) In this course we will discuss the roles of metals in biological systems, including metalloenzymes, metallocenter biosynthesis, metal transport, metal toxicity, and metaloregulation. Discussions will focus on the catalytic mechanisms as well as they way in which the different protein environments 'tune' their active site. Student presentations will be an important emphasis in this class. Syllabus: Spring 2021
Schedule: Spring 2021 Previous: Spring 2020 Course: BMB 961 "Concepts in Protein Structure & Modeling" (formally "Protein Structure Analysis and Modeling") UP Semester(s) offered: Usually offered in Spring (check www. schedule.msu.edu for updates) Credits: 2 Prerequisites: Biochemistry 803 or detailed knowledge of protein and nucleic acid sequences and structures some use of computers and permission of the instructors. Description: This is a hands-on, project-oriented course dealing with several aspects of protein structure analysis and modeling. We will go through UNIX basics and some of the most commonly used graphics software packages for visualizing and manipulating macromolecule structures. Then we will look at the databases of three-dimensional structures of proteins which are determined by X-ray Crystallography and NMR and how one can assess the quality of these structures. This will be followed by identifying and aligning homologous protein sequences and structures analyzing superimposed crystal structures and ligand binding determinants, and designing mutations. Then we will cover the various methods for protein structure prediction such as homology modeling and fold recognition followed by methods for RNA structure prediction. We will be using well tested and documented tools which are available online and other programs which are installed on our UNIX workstations. Lectures will cover the theory and demonstrate the computer methods used lab hours will provide hands-on experience. NOTE: For more information and permission to enroll, please contact Kaillathe (Pappan) Padmanabhan ([email protected]). Please also submit an override request at https://bmb.natsci.msu.edu/undergraduate/override-request-special-permissions-form/ Syllabus: Spring 2017 (PDF) Course: BMB 961 sec 301 "Gaps, Missteps, and Errors in Statistical Data Analysis" UP Semester(s) offered: Fall every year Credits: 1 Restrictions: Restricted to Biochemistry Graduate Students or Approval of the Instructor. If you are not a declared Biochemistry graduate student, please contact the course instructor, Dr. Arjun Krishnan ([email protected]), and then submit the online override request form found here: https://bmb.natsci.msu.edu/undergraduate/override-request-special-permissions-form/. Prerequisites: This is *not* an introductory course in statistics or programming. We will assume: 1) Familiarity with basic statistics & probability. 2) Ability to do basic data wrangling, analyses, & visualization using R or Python.
&bull Strongly recommended MSU courses: CMSE 201 and CMSE 890 Sec 301-or-304 and Sec 302.
Description: Please fill out the course survey to: a) express your interest, b) find out if this course is right for you, and c) provide early input: https://bit.ly/bmb961_nov18_survey
This is an advanced short (1-credit) course designed to:
1) Discuss common misunderstandings & typical errors in the practice of statistical data analysis.
2) Provide a mental toolkit for critical thinking and enquiry of analytical methods and results.

Classes will involve lectures, discussions, hands-on exercises, and homework about concepts critical to the day-to-day use and consumption of quantitative/computational techniques.

Topics
Underpowered statistics &bull Pseudoreplication &bull P-hacking & multiple hypothesis correction &bull Difference in significance & significant differences &bull Base rates & permutation tests &bull Regression to the mean &bull Descriptive statistics & spurious correlations &bull Estimation of error and uncertainty &bull (Others under consideration Subject to small changes) Course Flyer: /sites/_bmb/assets/File/syllabi/BMB961-301_Nov18_Flyer.pdf Syllabus: Coming Soon Course: BMB 961 "Drug Discovery and Medicinal Chemistry" UP Semester(s) offered: Please check the schedule of courses page for current information (www.schedule.msu.edu) Credits: 2 Restrictions: Open to doctoral students in the Departments of Biochemistry, Chemistry, Pharmacology and Toxicology or approval of department. Description: Fundamentals of pharmaceutical drug discovery including basic chemistry, drug-design principles, high throughput screening, computational modeling, and drug metabolic pathways. If you are unable to enroll on your own, or are an undergraduate student, you will need to submit the BMB online course override form found in the 'Undergraduate' tab drop down menu on the BMB Dept website homepage: www.bmb.natsci.msu.edu and then contact Dr. KinSing ([email protected]) for approval to enroll.

Syllabus: Academic Year 2020-2021 NOTE: Course is taught in conjunction with PHM 809. Course: BMB 978 Seminar in Biochemistry UP Semester: Fall of every year, Spring of every year Credits: Total Credits: 1 Reenrollment Information: A student may earn a maximum of 8 credits in all enrollments for this course. Restrictions: Open only to graduate students in the Department of Biochemistry and Molecular Biology. Description: BMB Colloquium seminars on biochemistry research mainly with visiting scientists. Seminars are held each Thursday from 11:00 AM - 12:00 PM in room 101, Biochemistry.


Undergraduate Courses

Course Coordinator – Fall/Spring: Lauren Douma, Ph.D. Course Coordinator – Summer: William L. Zeile, Ph.D.
Room: R3-252 ARB Room: R3-206A
Phone: 352-294-8693 Phone: 352-294-4974
E-mail: [email protected] E-mail: [email protected]

Course Description: BCH 4024 surveys the structure, function, and metabolism of amino acids, proteins, carbohydrates, lipids, and nucleic acids. It introduces concepts in cell structure, replication and growth, and metabolic regulation.

Prerequisites: Organic Chemistry (CHM 2210 and 2211, CHM 2215 and 2216, or their equivalents at other universities) or consent of course coordinator. In certain cases, with permission, CHM 2211 or CHM 2216 may be taken concurrently. CHM 2200 is NOT an acceptable prerequisite for BCH 4024.

BCH 4024, Spring 2021
M-T-W-F (4th and 6th periods)
Room N2-200 (2nd floor Stetson Medical Sciences Bldg Auditorium)

BCH 4024, Fall 2020
M-T-W-F (4th and 6th periods)
Room N2-200 (2nd floor Stetson Medical Sciences Bldg Auditorium)

BCH 4024, Summer A/C 2021
BCH 4024, Summer A/C 2021, Calendar
Days: M-T-W-F
Time: 2nd period, 9:30am – 10:45am
Location: Medical Sciences Building (MSB) Room N2-200

BCH4905 (sec SC4L) Science for Life Research Seminar Course

1 credit
R, 8th period (Fall)

This research seminar course will introduce students to the many research opportunities available to them in bench, field and computer laboratories across all STEM and Health disciplines on campus. Each week, three faculty members will discuss their research focus, how and why they study the systems they do, and the broader impacts of their work. These brief presentations are designed to offer students a deeper awareness and understanding of the breadth of interdisciplinary research ongoing at UF (and globally), and to inspire, encourage, and facilitate student interest in exploring the many opportunities to engage in research at this world-class research university.

Students majoring in STEM fields will find this course to be engaging and valuable. However, non-STEM majors with a strong background in high school science and a passion for research will also benefit from the multi-disciplinary research and guidance offered by the presenters in this course. All students will have the opportunity to enhance their scientific literacy, active listening, and critical thinking skills.

Course Coordinator: Mary Jo Koroly, Ph.D. [email protected]

Research Experience-Based Courses

BCH 4905 Biochemistry Senior Research
1-7 credits Offered each semester (sections for both IDS students and undergraduate students in general)


Biochemistry Careers


This is an image of a biochemist working in a laboratory.

In order to be a competent biochemist, one must be interested in biology or chemistry research and learn proper laboratory skills and safety procedures. It is also important to have an aptitude for mathematics and statistics, and be able to analyze the data generated from experiments. The ability to think outside the box and brainstorm new ideas is important for designing experiments. Biochemists must also keep up with the scientific literature by reading recent publications in scientific journals and attending conferences. Although it takes a lot of hard work, training, and study, biochemists are able to uncover new information about the chemistry of living things and contribute to advancing scientific knowledge.


Undergraduate Courses

The structure and function of biological molecules, enzymology, metabolism and bioenergetics, and recombinant DNA technology.

The structure and function of biological molecules, enzymology, metabolism and bioenergetics, and recombinant DNA technology.

Seminars, readings, and discussions of topics related to biochemistry, biotechnology, and molecular biology. Scientific writing will be emphasized, and visits to laboratories may be scheduled.

Seminars, readings, and discussions of topics related to biochemistry, biotechnology, and molecular biology. Scientific writing will be emphasized, and visits to laboratories may be scheduled.

Selected topics in biochemistry, molecular biology, genetics, and biotechnology involved in modern medicine. Includes cloning, stem cells, endocrinology, human genetics, gene testing, and human population genetics. Bioethical issues will also be discussed. Both formal lectures and discussion…

A focus on the remarkable impact that genome sequencing projects is having on virtually all aspects of biochemistry, as well as on medicine and biotechnology. An introduction to a broad range of 'omic' topics, including functional genomics, microarrays, proteomics, physiological genomics, and…

A focus on the remarkable impact that genome sequencing projects is having on virtually all aspects of biochemistry, as well as on medicine and biotechnology. An introduction to a broad range of 'omic' topics, including functional genomics, microarrays, proteomics, physiological genomics, and…

A comprehensive treatment of biochemistry and molecular biology stressing structures of biological molecules, including proteins, nucleic acids, carbohydrates, and lipids, enzymology and selected aspects of metabolism and bioenergetics.

A comprehensive treatment of biochemistry and molecular biology stressing aspects of metabolism, metabolic regulation, bioenergetics, and recombinant DNA methodologies.

Basic techniques in biochemistry and molecular biology, including enzyme assays and purification, nucleic acid purification and characterization, chromatography, spectroscopy, and other modern methods.

The principles of physical chemistry applied to biological molecules and systems, including current approaches in structural biology.

Integrated treatment of human biochemistry and selected topics on the biochemical basis of human disease. Examples will be given of inheritable and acquired disorders.

Various topics in human biochemistry and pathophysiology.

Examination of the mechanistic basis of inherited and acquired human disorders at the molecular level. Background into the cellular pathways involved in each disease will be presented as well as discussion of recent advances in research and therapeutics.

Examination of the mechanistic basis of inherited and acquired human disorders at the molecular level. Background into the cellular pathways involved in each disease will be presented as well as discussion of recent advances in research and therapeutics.

Instrumental aspects of NMR spectroscopy including pulsed Fourier transform techniques, proton and carbon-13 techniques used in the analysis of organic compounds, polypeptides and other small molecules. The focus is on the operation of NMR spectrometers presently available in the University of…

Principles and instrumental aspects of NMR spectroscopy, including pulsed Fourier transform techniques, proton and carbon-13 techniques used in the analysis of organic compounds, polypeptides and other small molecules. Students also learn to operate NMR spectrometers in the Chemistry Department…

Applied aspects of biochemistry and molecular biology in various fields, with emphasis on the use of recombinant DNA methods and protein engineering.

Molecular and biochemical regulation of plant metabolic pathways activated in response to environmental cues, environmental stress, and interaction with pathogenic and symbiotic organisms. Cell wall formation (primary wall, wood), secondary metabolism (lignin, flavonoids, phenolics), wounding,…

The objective of these courses is to train students in the basic techniques used in biochemistry and molecular biology, and the application of the scientific method. Students typically become part of a dynamic research environment and gain experience in both the experimental approach and the…

The objective of these courses is to train students in the basic techniques used in biochemistry and molecular biology, and the application of the scientific method. Students typically become part of a dynamic research environment and gain experience in both the experimental approach and the…

The objective of these courses is for students to conduct research projects in a team of undergraduate researchers, their faculty mentors, and other scientists such as graduate students, postdoctoral associates, and faculty collaborators. Students will develop research skills, including…

The objective of these courses is to train students in the basic techniques used in biochemistry and molecular biology, and the application of the scientific method. Students typically become part of a dynamic research environment and gain experience in both the experimental approach and the…

The objective of these courses is to train students in the basic techniques used in biochemistry and molecular biology, and the application of the scientific method. Students typically become part of a dynamic research environment and gain experience in both the experimental approach and the…


Introduction to Biochemistry

A question pack on biochemistry in the context of anatomy and physiology. Content courtesy of the Open Learning Initiative.

An ion can be best described as which of the following:

A collection of electrons

An atom with an altered number of electrons

Rank the order of length scales from smallest to largest:

insulin (a protein ̦which is a molecule)

Refer to a periodic table. Which of the atoms in tryotophan is the most electronegative?

Refer to a periodic table. What is the molecular mass of tryptophan in amu (also called Daltons)?

Refer to a periodic table. Estimate the mass of glucose C 6 _6 6 ​ H 12 _ <12>1 2 ​ O 6 _6 6 ​ using the information in the periodic table

Tryptophan is an essential amino acid which is used in proteins and in amino acid derived hormones. The structure is important, but for now we will focus on the atoms involved. The molecular formula is

Which of the following atoms are present in tryptophan?

A molecule would best be described as:

A stable bond between atoms of at least 2 different elements.

A stable bond between 2 atoms of the same element

A charged molecule made up of more than one atom

the first 2 responses are correct.

All three responses are correct.

Identify the type of bond:

DNA is a negatively charged molecule that binds with calcium (Ca2+) and magnesium (Mg2+)

Identify the type of bond:

Within a protein, amino acids are linked by the bonding of carbon (C) to nitrogen (N)

Which of the following is a correct statement?

Only covalent bonds lead to molecules that are stable in air.

Covalent bonds only occur between atoms of similar electronegativies while ionic bonds only occur between atoms of differing electronegativities.

Ionic bonds do not share valence electrons while covalent bonds do.

Only ionic bonds lead to molecules that are stable in air.

The partial negative charge at one end of a water molecule is attracted to the partial positive charge of another water molecule. This attraction is called:


10 Questions for Incredible Learning

Inorganic substances, such as water, mineral salts, molecular oxygen and carbon dioxide, are small molecules made up of few atoms. Organic substances, in general, such as glucose, fatty acids and proteins, are much more complex molecules made of sequences of carbons bound in carbon chains. The capacity of carbon to form chains is one of the main chemical facts that allowed for the emergence of life on the planet.

3. What are the most important inorganic molecular substances for living organisms?

The most important inorganic substances for living organisms are water, mineral salts, carbon dioxide and molecular oxygen. (There are several other inorganic substances without which cells would die.)

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Mineral Salts

4. What are mineral salts? Where can mineral salts be found in living organisms?

Mineral salts are simple, inorganic substances made up of metallic chemical elements, such as iron, sodium, potassium, calcium and magnesium, or of non-metallic elements, such as chlorine and phosphorus.

They can be found in their non-solubilized form as a part of structures in an organism, like the calcium in bones. They can also be found solubilized in water as ions: such as, the sodium and potassium cations within cells.

Functions of Organic Molecules

ਅ. What are the most important organic molecules for living organisms?

There are many types of organic molecules that are important for living organisms. Especially important are amino acids and proteins, carbohydrates (including glucose), lipids and nucleic acids (DNA and RNA). 

6. What are the main functions of organic molecules in living organisms?

Organic molecules, such as proteins, lipids and carbohydrates, perform several functions in living organisms. Noteworthy functions are structural functions (as part of the material that composes, surrounds and maintains organs, membranes, cell organelles, etc.), energetic functions (chemical reactions of energetic metabolism), control and informative functions (genetic code control, inter and intracellular signaling, endocrine integration) and enzymatic functions of proteins (facilitation of chemical reactions). 

7. What are some examples of the structural function of organic molecules?

Organic molecules are carrying out a structural function when they form a part of cell membranes, cytoskeletons, organ and blood vessel walls, bones, cartilage and, in plants, of conducting and supporting tissues. 

8. What are some examples of the energetic function of organic molecules?

Since they are complex molecules, which contain many chemical bonds, organic molecules store a large amount of energy.

Glucose, for example, is the main energy source for the formation of ATP (adenosine triphosphate), a molecule that is necessary for several metabolic reactions. ATP is also an organic molecule and is the energy source for many biochemical reactions. Fat, proteins and some types of organic polymers, such as starch and glycogen, which are polymers of glucose, are energy reservoirs for organisms. 

9. What are some examples of the control and informative function of organic molecules?

Based on genetic information, organic molecules control all functions of cells. The nucleic acids, DNA and RNA, are organic molecules that direct protein synthesis, and in turn, proteins are the main molecules responsible for the diversity of cellular biological tasks. In membranes and within the cell, some organic molecules act as information receptors and signalers. Proteins and lipids have an important role in the communication between cells and tissues, acting as hormones, which are substances that transmit information at a distance throughout an organism.

Biopolymers

10. What are biopolymers?

Polymers are macromolecules made up by the union of several smaller identical molecules, which are then called monomers. Biopolymers are polymers present in living organisms. Cellulose, starch, and glycogen, for example, are polymers of glucose.

Now that you have finished studying the Introduction to Biochemistry, these are your options: