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Biochemistry Labs - Biology

Biochemistry Labs - Biology



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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. This class is part of the new laboratory curriculum in the MIT Department of Chemistry.


Research Labs

Research in my laboratory is focused on double-stranded RNA (dsRNA)—its biological functions and the proteins that bind it to mediate these functions.

Neurons in the brain form complex neural circuits by connecting to each other through highly specialized junctions called synapses. A molecular logic underlies the formation, establishment and properties of each of these synapses and is likely driven by synaptic cell adhesion molecules. In the lab we aim to understand the protein complexes formed at these junctions and how they assemble and arrange in respect to each other in the synaptic cleft with the overall aim to understand the extracellular architecture of the synapse.

We are broadly interested in understanding atomic-sale mechanisms of how membrane proteins function under normal and diseased states.

We work with the powerful, exciting and relatively new tools of precise genome engineering, using the ZFN, TALEN and CRISPR-Cas platforms.

We are a basic research lab working on regulation of gene expression and functions of viral and cellular non-coding RNAs

Research in our group is focused on understanding the biochemical, cellular and organismal changes in metabolism that enable disease. To do this, we integrate modern techniques in mammalian genetics and mass spectrometry to study metabolic transformations in molecular detail.

We create and apply molecular tools to control and understand human health and disease. We strive to quickly share our discoveries, combining contemporary methods of directed evolution and protein engineering with classic principles of pharmacology and biochemistry.

We use yeast to study a highly conserved complex called FACT, which reorganizes nucleosomes and therefore alters the fundamental structure of chromatin.

Our lab explores how physiological signals regulate stem cell differentiation. One major focus of the lab is to study the molecular mechanisms regulating adipogenesis. To do this, we use a combination of animal models and cell culture techniques. We are particularly interested in understanding how the primary cilium, an antenna-like signaling organelle, senses and organizes signal transduction pathways to regulate stem cell fate.

In the most general sense, we aim to understand how proteins function in important biological processes by determining their structures at atomic resolution and by using complementary biochemical and biological experiments.

We use a multi-organismal approach to identify mechanisms cells use to achieve organelle homeostasis, and understand how failure to maintain organelle integrity contributes to aging and the development of age-associated diseases.

I am interested in creating accurate and compelling visualizations of molecular and cellular processes that will support research, learning and scientific communication. Molecular animations are a powerful tool for communicating important concepts to students and to members of the public. By empowering researchers to visualize what had previously been an abstract idea, these visualizations can also engender new ideas and modes of thinking.

The Kay Lab is dedicated to finding ways to combat HIV infection and other life threatening diseases. Our research sheds light on the mechanisms of enveloped viral entry and its inhibition. Through a collaboration with a local pharmaceutical company, Navigen, we hope to translate our research into the development of effective human therapeutics.

My passion is teaching metabolism from an intuitive perspective, with a strong emphasis on nutrition. My current research focuses on the outcomes of educational interventions on student performance and satisfaction.

Our research focuses on how dividing cells ensure that each resulting daughter cell inherits a copy of every chromosome. We take an interdisciplinary approach that combines protein biochemistry, yeast genetics, cell biology, and biophysical approaches to understand the macromolecular machines that carry out this process.

We use a combination of animal models and cell culture techniques to understand the microenvironmental influences on tumor cell behaviour in vivo.

My laboratory is currently exploring three areas. While distinct, these programs are all centered upon cellular metabolic homeostasis—the concept that cells must constantly monitor their nutrient, metabolic and hormonal environments and adjust their behavior accordingly.

Our lab uses yeast and mammalian cells to study how mitochondrial fission, fusion and transport regulate mitochondrial function, and inheritance during cell division.

The Shen lab uses genetics, biochemistry, and structural biology to study the mechanisms underlying protein homeostasis. We focus on using cryo-EM to visualize dynamics among multi-component protein complexes.

In my laboratory, we develop and apply diverse cellular, genetic, chemical, and biophysical tools to uncover general metabolic principles and adaptations governing the unique biology of P. falciparum parasites during infection of human red blood cells.

We study the molecular and structural biology of retroviruses, with particular emphasis on the Human Immunodeficiency Virus (HIV). Major projects in the laboratory include studies of: 1) Enveloped virus assembly, 2) ESCRT pathway functions and regulation in cell division and cancer, and 3) HIV replication and restriction. Our approaches include structural studies of viral complexes, identification and biochemical analyses of the interactions between viral components and their cellular partners, and genetic analyses of viral and cellular protein functions.

University of Utah School of Medicine Department of Biochemistry

15 N Medical Drive East, Rm 4100 - Salt Lake City, Utah 84112-5650
801-581-2117


I. Required Biology Courses

  1. Both terms of the introductory biology sequence (Barnard courses cannot be used for Intro Bio):
      - Introductory Biology I: Biochemistry, Genetics and Molecular Biology - Introductory Biology II: Cell Biology, Developmental & Physiology
  2. Both of these Biology-Chemistry courses:
    • UN3501/GU4501 - Biochemistry or UN3300 (Biochemistry)
    • UN3512/GU4512 - Molecular Biology

Secondary Divisional Affiliates

The following faculty have a secondary affiliation with the Biochemistry, Biophysics and Structural Biology division.

Stephen Brohawn
Assistant Professor of Neurobiology
Molecular basis of sensory transduction and cellular electrical signaling

G. Steven Martin
Professor Emeritus of Cell and Developmental Biology
Cell biology tumor virology

Michael Rape
Howard Hughes Medical Institute Investigator and Professor of Cell and Developmental Biology
Protein ubiquitination, degradation and the control of cell division and differentiation

Randy Schekman
Howard Hughes Medical Institute Investigator and Professor of Cell and Developmental Biology
Organelle assembly protein transport


CONCEPTS AND SKILLS FOR THE FUTURE BMB LAB

No matter how sophisticated the instrumentation, how new the techniques, or how adept the instructor's pedagogy, a teaching lab without organized and thoughtful content is meaningless. We often turn to our scientific societies to gain advice on what principles and concepts students should learn.

The American Chemical Society divides recommendations for biochemistry lab into two categories [ 19 ].

error and statistical analysis of experimental data

isolation and characterization of biological materials

DNA cloning and sequencing

plasmid isolation and mapping

peptide isolation and sequencing

computer graphics and structure calculations

The American Society for Biochemistry and Molecular Biology (ASBMB) has prepared a recommended curriculum for the undergraduate biochemistry degree, but it does not specify techniques or content [ 20 ]. The Education and Professional Development Committee of ASBMB is currently working on a new BMB curriculum that will include suggested lab skills.

analytical methods in chemistry (NMR, MS, etc.)

basic techniques for analyzing, cloning, and sequencing DNA

experimental techniques for the study and analysis of enzyme kinetics

techniques for studying macromolecular structure including purification and characterization and use of the computer for structural information

the main techniques used in cell biology

The Biosciences Industry Skill Standards Project (BISSP) sponsored by the United States Department of Education has recently generated an extensive list of skills expected of a bioscience technician [ 22 ].

The goal of all BMB lab instructors is to offer practical, hands-on experiences that introduce their students to the most contemporary instrumentation and principles the institution can afford. It is also important that students learn and practice all the steps necessary to design an appropriate experimental plan to solve a problem. Here I will attempt to present ideas on how these goals may be accomplished.

Table I shows “general” lab skills, procedures, and methods. This listing defines broadly those concepts that are used routinely and regularly in a lab setting for work on all types of biomolecules and for all types of measurements. This list is not all inclusive as instructors will be able to add a few of their own. The manner in which these general skills are presented by the instructor and practiced by the students will be dependent on many factors including the time and facilities available for the lab, the size of the class, the past experiences of the students, and the specific interests of the instructor. Perhaps it is helpful to provide some ideas on the mode of presentation and the relative amount of time spent on the general skills. In a typical BMB lab of 3–4 h per week, one-half of the first period may be spent discussing the first five skills listed in Table I (safety through computer). The remainder of the first period could be used for students practicing the next group of skills (solutions, pipetting, pH, buffers). Perhaps these skills could be learned with an experiment where students measure protein and/or nucleic acid solutions. I believe it is much more instructive to have students practice with “real samples” rather than just going through the motions of pipetting. Students at the BMB lab level will have already become adept at some of these general skills by work in earlier labs in Introductory Biology and Chemistry, Organic Chemistry, and others. Therefore it is important for instructors who know of the students' past experiences to make judgments about how much time should be devoted for each technique. It is expected that most students, after completing the BMB lab, would be proficient in the application of all of the general concepts in Table I. One exception to this may be the topic of radioisotopes where instructors need to make their own decision on the relative importance of this concept.

The importance of teaching skills in communication (writing and reporting results in Table I) is secondary only to the topic of lab safety. New scientific knowledge that is not communicated is of no value to anyone. Learning communication skills needs to begin with introductory labs (Chemistry and Biology) and continue through all future courses, lab and classroom [ 23 ]. Coordination and consistency among all lab instructors in a department are of vital importance so students do not learn different communication techniques at each level. Specific skills that students must master in the BMB lab include maintaining a lab notebook (journal), writing up a lab experiment, writing a journal-style article, critical analysis of other writing (other student's and journal articles), giving an oral presentation on experimental results, and the preparation and presentation of a poster [ 1 , 12 , 16 , 18 ]. Students should practice presentations at their local institution and then gain experience at regional and national meetings.

Table II presents “selective” methods that serve a more specific purpose in the BMB lab as they may not be applicable for all types of biomolecules and measurements. It is obviously impossible for students to be introduced, in a one- or even two-term lab, to all of the selective lab methods. Instructors usually pick and choose those methods based on what facilities are available and what they believe their students should practice. The methods listed in Table II have been placed in order of relative importance on the bases of the author's prejudice and many years of experience. Methods that I would consider the most essential for BMB students include spectroscopy (UV/visible), chromatography (HPLC, affinity, gel filtration, ion-exchange, column), computational (enzyme kinetics/inhibition, ligand binding, databases), electrophoresis (all types), and biotechnology (recombinant DNA, plasmids, PCR, and restriction enzymes). Students should be encouraged to learn other skills and concepts in a future research experience.

Many of the methods listed in Table II require expensive instrumentation. Such equipment may not be present at smaller institutions, and even students at larger institutions may not have access to it because it is reserved for research. Instructors at these institutions must provide alternate opportunities to expose their students to the latest techniques and instrumentation. This may be done by visiting facilities at nearby research institutions, government labs, or industrial labs. Additionally, students could be encouraged to increase their understanding of the selective techniques by participating in a summer research project at an academic, industrial, or government laboratory. Students may also become acquainted with modern BMB principles and instrumentation by review of the University of Virginia Lab3D Project [ 24 ] and the Virtual Biochemistry Lab sponsored by the Nobel Foundation [ 25 ].

Science work is being done increasingly in groups, and students need to gain experience working in teams to gain confidence and to learn how to play the roles of team members. In addition to being adept with their hands, they also need to understand and practice the ethical characteristics of fairness, honesty, cooperation, and responsibility. This includes an understanding of fair and proper use of scientific data and the literature and a consideration of intellectual property, patents, and copyrights [ 26 ].

In these heady days when academic research and industrial science seem to be driven by instant results for the advancement of the principal investigator and for the profit motive, it is important that we and our students not lose site of the real goals of research and development: to better the lives of the peoples of the world.


  • Edwin Antony, Ph.D.
  • Yuna Ayala, Ph.D.
  • Angel Baldan, Ph.D.
  • Tomasz Heyduk, Ph.D.
  • Michelle Pherson, Ph.D.
  • Nicola Pozzi, Ph.D.
  • Tracey Baird
  • Enrico Di Cera, M.D.
  • Joel Eissenberg, Ph.D.
  • Zachary Montague
  • Angela Spencer

Abdul Waheed, Ph.D., Emeritus Research Professor of Biochemistry, gifted $1 million to the Department of&hellip

Congratulations to Kaush Amunugama, Ph.D. Student in Dave Ford's lab, on receiving an ASBMB 2021 Graduate/Postdoctoral&hellip

Congratulations to David Ford, Ph.D., Professor of Biochemistry and Director of the Center for Cardiovascular&hellip

Congratulations to Sergey Korolev, Ph.D., whose application was the first to be funded through the&hellip

A recently published commentary by David Ford, Professor of Biochemistry, was highlighted in ASBMBToday. The&hellip


Biochemistry, Biophysics & Structural Biology

Biochemistry and Biophysics are the foundation of all cellular processes and systems. Biochemical processes account for the functions of cellular building blocks, from nucleic acids and proteins to lipids and metabolites, and the formation of complex networks that make a cell or system work. Biophysics explains the complexity of life with the simplicity of physical laws and math.

The mission of our collaborative unit ‘Biochemistry & Biophysics’ is to train the next generation of scientists and to uncover how life works at the molecular level. Our scientists study macromolecular complexes and their specificity, protein design and evolution, and molecular networks. We illuminate how the cytoskeleton determines cell shape, how cells transduce signals, how membranes fuse, how chromatin organizes the genome, how metabolism is coordinated, how viruses hijack cells, how the immune response works, and how cells form patterns and communicate with each other.

We are experts in bioengineering, structural biology, computation and modeling, optics and microscopy, and microfluidics. Some examples of the approaches being used, and in some cases developed, at Princeton include X-ray crystallography, electron microscopy, mass spectrometry, NMR spectroscopy, super-resolution optical microscopy, single-molecule methods, and computational modeling. These tools are being applied to biological problems ranging from protein folding and design, to signal transduction, to intracellular trafficking.

A long-standing tradition and strength of our University is that biologists, chemists and physicists work closely together in an interdisciplinary setting. It is also common to see computational biologists working together with wet-lab biologists to address problems that neither could tackle alone with spectacular results. This is facilitated by the intimate connection between the Department of Molecular Biology with the Departments of Chemistry, Physics and Chemical and Biological Engineering, as well at the Lewis-Sigler Institute for Integrative Genomics.


The Department of Biochemistry

At the University of Nebraska's Department of Biochemistry, we are developing the world’s next great scientists and researchers.

They come here to learn from and with our distinguished faculty — internationally recognized researchers who work at science’s cutting edge, maintaining externally funded laboratories that investigate an array of exciting questions. They come here because we offer both a strong undergraduate major and a thriving graduate program.

And they come here because many of our significant discoveries are made by undergraduate, graduate, and postdoctoral researchers working closely with our faculty.

We are Nebraska's premier biochemistry program, largely because we have created an engaging environment that positions our students to succeed.

We feature award-winning professional advisers, and incomparable mentorship opportunities. We get students out of the book, and into the lab.

Our faculty treat students as future colleagues, working hand-in-hand on high-impact research projects addressing real-world problems related to areas such as metabolism and metabolic engineering, structural and chemical basis of protein function, molecular mechanisms of disease, plant and microbial biochemistry and biotechnology.

Our graduates go on to excel in their careers — both academic and in private industry — focusing their talents on medicine, law, pharmaceutical, bio-technology, agriculture, dental and many other fields.

We are asking exciting questions. Help us answer them.

We are one of only four Big Ten universities accredited by the American Society for Biochemistry and Molecular Biology.

Seniors who pass the accreditation exam are recognized by the professional society as earning a certified degree!


Biochemistry & Molecular Biology

Housed within the Division of Biochemistry, Biophysics, & Structural Biology, the Biochemistry and Molecular Biology (BMB) emphasis is dedicated to the mechanistic understanding, at the molecular level, of essential processes for the life of the cell. To this end, the BMB emphasis uses rigorous and reductionist approaches to describe living systems in chemical and physical terms. Unique to BMB is the combination of powerful molecular biological methodologies (e.g. cloning, gene splicing and gene expression), with biochemical and biophysical assays, as well as structural biology strategies (e.g. X-ray crystallography, 2-D NMR, cryo-electron microscopy) for dissecting structure and function of macromolecules. Berkeley hosts unique, state-of-the-art facilities to carry out research using these methodologies.

The ability to understand complex biological processes by characterizing the activity of the molecular machinery governing processes such as DNA replication, transcription, transposition, recombination, protein synthesis, protein degradation and RNA processing, have greatly advanced our understanding of the living cell. Furthermore, these approaches and new knowledge are playing a major role in unraveling many complex biological processes at the organismal level, such as development, differentiation, mutagenesis, gene regulation, pathogenesis, oncogenesis, and aging.

Through the major, you will learn not only how the molecules of life work in the healthy cells and organisms, but also how disruption of their function leads to disease. Furthermore, the identification and characterization of the molecular culprits for human illness is an essential step towards treatment by pharmacological agents that target these molecules to alter their activity. An exciting and invigorating aspect of these types of studies is that they can be done by individual students, armed with keen interest and curiosity.

Upper Division Requirements

MCB C110L: Biochemistry & Molecular Biology Lab (Fa, Sp 4 un)

OR MCB 170L: Molecular & Cell Biology Laboratory (Su only 4 un)

MCB C110L: Biochemistry & Molecular Biology Lab (Fa, Sp 4 un)

OR MCB 170L: Molecular & Cell Biology Laboratory (Su only 4 un)

Alternative Lower Division Chem Sequence for track 2:

Students planning major in the MCB: Biological Chemistry track are required to take the following chem sequence:

Chem 1A/1AL, Chem 1B, Chem 12A, and Chem 12B

Please note the Chem 12A/B replaces Chem 3A/3AL, 3B/3BL.

The Chem 3 series provides less rigorous preparation for the upper division chemistry courses required for this track. Once students decide to pursue the Biological Chemistry track, they should adhere to the alternative sequence requirements (e.g., complete Chem 12B, not Chem 3B).

Petitioning to Substitute MCB C110L with Research Units

Students may petition to substitute the lab course with equivalent knowledge and units obtained through independent research experience (such as 199 or H196 research), as determined by the Head Faculty Advisor of their major emphasis. Careful consideration and discussion with your faculty advisor are important when making the decision whether to use independent research to substitute the lab, as MCB labs expose students to many biological approaches not always encountered during these research projects. For more information on the approval process see Petition to Substitute MCB Lab Course.

Sample 4-yr Plans

These are just examples, for more sample schedules including spring start and transfer see guide.berkeley.edu or meet with an advisor to explore your options. It is recommended by MCB advisors and faculty to take the upper division lab as early as you can if you are interested in research and/or honors research.

Approved Electives List for BMB

Molecular and Cell Biology

  • 100B Biochemistry: Pathways, Mechanisms, & Regulations (Sp 4 units) Track 2 Only
  • C103 Bacterial Pathogenesis (Sp, 3 units)
  • C112 General Microbiology (F, Su 4 units)
  • C114 Introduction to Comparative Virology (Sp, 4 units)
  • C116 Microbial Diversity (F, 3 units)
  • 130 Cell and Systems Biology (Sp, 4 units) (If track 2: only can use if take 140 for core BMB)
  • 132 Biology of Human Cancer (F, 4 units)
  • C134 Chromosome Biology / Cytogenetics (Sp, 3 units)
  • 135A Molecular Endocrinology (F 3 units)
  • 136 Physiology (F, Sp 4 units)
  • 137L Physical Biology of the Cell (Sp, 3 units)
  • 141 Developmental Biology (Sp, 3 units)
  • C148 Microbial Genomics & Genetics (Sp, 4 units) (If track 1: only can use if take 140 for core BMB)
  • 149 The Human Genome (F, 3 units)
  • 150 Molecular Immunology (F, Sp, 4 units)
  • 153 Molecular Therapeutics (F, 4 units)
  • 160 Cellular and Molecular Neurobiology (F, 4 units)
  • 161 Circuit, Systems and Behavioral Neuroscience (Sp, 4 units)
  • 165 Neurobiology of Disease (Sp, 3 units)
  • 166 Biophysical Neurobiology (F, 3 units)
  • 113 Advanced Mechanistic Organic Chemistry (F 3 units)
  • 115 Organic Chemistry - Advanced Lab Methods (Sp 4 units)
  • 130B Biophysical Chemistry (Sp 3 units) (Track 1 only)

Environmental Science, Policy & Management

Mathematics

Nutritional Sciences & Toxicology

  • 112 Introduction to Statistical & Thermal Physics (F, Sp 4 units)
  • 177 Principles of Molecular Biophysics (Sp 3 units)

Plant & Microbial Biology

  • C112 General Microbiology (F 4 units)
  • C114 Comparative Virology (Sp 4 units)
  • C116 Microbial Diversity (F 3 units)
  • C134 Chromosome Biology / Cytogenetics (Sp 3 units)
  • 135 Physiology & Biochemistry of Plants (F 3 units)
  • 150 Plant and Microbial Biology (F 3 units)
  • 160 Plant Molecular Genetics (Sp 3 units)

Public Health

  • 141 Intro to Bio-Statistics (Su 5 units)
  • 142 Introduction to Probability & Statistics in Biology & Public Health (F, Sp 4 units) - Note: For students who have completed Math 10A/B, or Stat 2 or 20, this course is not accepted to meet the elective requirement.

Approved Electives but NOT Regularly Offered

  • BioEng C141 Stats for Bioinformatics
  • Math 127 Mathematical & Computational Methods in Molecular Biology
  • MCB 143 Evolution of Genomes, Cells & Development (F, 3 units)
  • Physics 132 Contemporary Physics
  • Stat C141 Stats for Bioinformatics

Series: Laboratory Techniques in Biochemistry and Molecular Biology

The books in this well established series LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY cover all aspects of laboratory work in biochemistry and molecular biology. Each volume provides sufficient information for laboratory workers to apply a new technique without having seen it in practice or having any prior knowledge of it. The series is published in hardbound and paperback versions. In those cases where a volume consists of more than one part, a hardbound edition combines the parts for reference purposes.

As topical as its subject, the Laboratory Techniques series provides an up-to-date and comprehensive coverage of biochemical and molecular biological research techniques, and is specifically designed for use by researchers and laboratory technicians. Each book in the series provides a clear, concise, and easy-to-follow layout, which is ideal for use as a reference source, on-the-bench, or as a student tutorial.


Additional Requirements

Minimum Grade Requirement

  • All courses required and used toward any biology major requirements must be taken for a letter grade and completed with a C- or better.
  • The minimum grade requirement applies to all lower-division, upper-division, required courses taken in other departments, as well as courses transferred and used toward major requirements.
  • Exceptions will be made for those required courses that have a P/NP only grading option (e.g., BISP 199).
  • The minimum major GPA requirement is 2.0.

Please note: The degree audit may not automatically reject D grades for the major. If your degree audit appears to apply a course in which you have earned a D to a requirement for the major, please contact a biology advisor.

Upper-Division Unit Requirement

To receive a Bachelor of Science from UC San Diego, all students must complete 48 or more units of upper-division course work within the major.

Please note: The degree audit may not display an accurate number of upper division biology electives required for the major in order to meet the 48 upper division unit requirement.

If your do not have at least 48 upper division units within your major requirements, you will need to take additional upper division biology coursework in order to satisfy this requirement.  If you have questions, please contact a biology advisor.

Biology Residency Requirement

To receive a Bachelor of Science in Biological Sciences from UC San Diego, all students must complete at least twenty units of upper-division coursework in the Division of Biological Sciences with a grade of C- or better. This coursework must directly apply to the student’s Biology major requirements, and must be taken while officially enrolled at UC San Diego. Courses completed outside of the UC San Diego Division of Biological Sciences will not be counted toward the residency requirement.  


Watch the video: Biochemistry Lab Equipment - extended version (August 2022).