The document describes a workshop on using interactive teaching software tools called STAR biology tools to teach concepts in biology. The workshop covers the educational goals of the tools which are to teach difficult concepts like protein structure and experimental design using interactive 3D viewers. It discusses the design process which involves collaboration between MIT faculty and educational experts. The tools and curriculum materials are made freely available online. The workshop agenda covers introducing the protein structure viewer StarBiochem, demonstrating its educational applications for classrooms and labs, and designing new curriculum activities using the software.
Benjamin Merritt is a biology student at Rochester Institute of Technology expected to graduate in May 2016 with a 3.76 GPA. He has extensive research experience including projects at RIT and The Scripps Research Institute focused on plant biology, chemistry, and pharmacology. He has authored two publications and presented his work at several conferences. Merritt maintains an active role in professional organizations and has received multiple honors and awards for his academic and research accomplishments.
Dr. Bharat Bhusan Patnaik has extensive experience in research and academia. He has a PhD in biotechnology and expertise in areas such as biochemistry, molecular biology, immunology, and bioinformatics. He has worked with mammalian, aquatic, and insect models. Dr. Patnaik also has management experience overseeing instrumentation and laboratories. He has received several fellowships and awards for his work.
This document introduces a companion website for a biochemistry textbook. It provides the following key information:
1. The website accompanies the third edition of a biochemistry textbook by Mathews, van Holde, and Ahern.
2. The website contains outlines, concepts, terminology, and quizzing for each textbook chapter to help students learn biochemistry.
3. The same material on the website is also available on a CD-ROM included with the textbook for offline use.
4. The website provides links between concepts covered and related external websites for expanded information.
International Mother Language Day has been observed every year since February 2000 to promote linguistic and cultural diversity and multilingualism. The date represents the day in 1952 when students demonstrating for recognition of their language, Bangla, as one of the two national languages of the then Pakistan, were shot and killed by police in Dhaka, the capital of what is now Bangladesh.
21st february is the mother language day of bangladeshMaruf Hasan
Bangladesh observes Mother Language Day on February 21st to honor the students who were killed while protesting for Bangla to be declared an official language of Pakistan. The day is known as Shohid Dibosh in Bangladesh and commemorates the language movement that led to Bangla gaining official status. In 1999, UNESCO declared February 21st to be International Mother Language Day to promote linguistic and cultural diversity worldwide.
The document discusses the development of atomic models and the structure of atoms. It describes early models like the plum pudding model and Rutherford's solar system model. Modern atomic structure consists of protons and neutrons in the nucleus and electrons in shells or orbits around the nucleus. The key properties of subatomic particles like protons, neutrons and electrons are given. Proton number is defined as the number of protons in an atom and nucleon number as the sum of protons and neutrons. Examples are provided to show how to determine the number of protons, neutrons and electrons from the periodic table.
Benjamin Merritt is a biology student at Rochester Institute of Technology expected to graduate in May 2016 with a 3.76 GPA. He has extensive research experience including projects at RIT and The Scripps Research Institute focused on plant biology, chemistry, and pharmacology. He has authored two publications and presented his work at several conferences. Merritt maintains an active role in professional organizations and has received multiple honors and awards for his academic and research accomplishments.
Dr. Bharat Bhusan Patnaik has extensive experience in research and academia. He has a PhD in biotechnology and expertise in areas such as biochemistry, molecular biology, immunology, and bioinformatics. He has worked with mammalian, aquatic, and insect models. Dr. Patnaik also has management experience overseeing instrumentation and laboratories. He has received several fellowships and awards for his work.
This document introduces a companion website for a biochemistry textbook. It provides the following key information:
1. The website accompanies the third edition of a biochemistry textbook by Mathews, van Holde, and Ahern.
2. The website contains outlines, concepts, terminology, and quizzing for each textbook chapter to help students learn biochemistry.
3. The same material on the website is also available on a CD-ROM included with the textbook for offline use.
4. The website provides links between concepts covered and related external websites for expanded information.
International Mother Language Day has been observed every year since February 2000 to promote linguistic and cultural diversity and multilingualism. The date represents the day in 1952 when students demonstrating for recognition of their language, Bangla, as one of the two national languages of the then Pakistan, were shot and killed by police in Dhaka, the capital of what is now Bangladesh.
21st february is the mother language day of bangladeshMaruf Hasan
Bangladesh observes Mother Language Day on February 21st to honor the students who were killed while protesting for Bangla to be declared an official language of Pakistan. The day is known as Shohid Dibosh in Bangladesh and commemorates the language movement that led to Bangla gaining official status. In 1999, UNESCO declared February 21st to be International Mother Language Day to promote linguistic and cultural diversity worldwide.
The document discusses the development of atomic models and the structure of atoms. It describes early models like the plum pudding model and Rutherford's solar system model. Modern atomic structure consists of protons and neutrons in the nucleus and electrons in shells or orbits around the nucleus. The key properties of subatomic particles like protons, neutrons and electrons are given. Proton number is defined as the number of protons in an atom and nucleon number as the sum of protons and neutrons. Examples are provided to show how to determine the number of protons, neutrons and electrons from the periodic table.
This document provides information about a primer course on molecular biology taught at UC Berkeley. The course aims to introduce students to common laboratory techniques in molecular biology, such as PCR, cloning, cell culture and transfection. It will help students develop a strong foundation in molecular biology and facilitate their transition into research laboratories. The course involves lectures, activities and assignments, including a final presentation. It is graded on a pass/no pass basis based on attendance, participation, homework, a research paper, and the final project.
The document outlines plans for a proposed 3-year biotechnology program at Carlmont High School. It discusses goals of preparing students for higher education and careers in biotechnology. It proposes targeting honor students and implementing the program through existing science classrooms. Key components would include biotechnology curriculum, industry partnerships, and pathways for students to continue in the field after high school through programs at local colleges and universities. Financial support would come from school and district funds as well as industry and private donations.
Prahlad Rao is a fourth year graduate student at the University of Illinois at Chicago studying systems biology approaches to understand Mycobacterium tuberculosis using proteomics. His research focuses on investigating the pathogen's response to stress through global protein turnover analysis. He has extensive experience in proteomics techniques and managing a proteomics facility. Rao has a background in biotechnology and has taught at the university level.
A Primer on Molecular Biology, Spring 2016 SyllabusBillal Ahmed
This document provides information about a primer course on molecular biology taught at UC Berkeley in Spring 2016. The course aims to introduce students to basic laboratory techniques in molecular biology, such as PCR, cloning, cell culture and transfection. It will prepare them for research experiences in university laboratories. The course involves lectures, activities, homework assignments, a research paper, and a final student presentation project. Taking the course will benefit students who wish to pursue research and provide a foundation for advanced science courses.
Science Prof Online provides free online science education resources including virtual science classrooms, PowerPoints, articles and images. The site offers educational materials like practice questions, lectures, videos and course materials. PowerPoints are available in different formats for ease of use and printing. Prokaryotic cells, which include bacteria, differ from eukaryotic cells in that they lack a nucleus and membrane-bound organelles. They have variations in cell wall structure that determine if they are gram-positive or gram-negative. Prokaryotes also have distinctive cell shapes, surface appendages and arrangements that provide clues to their identification.
The document discusses developing curriculum to support careers in biomanufacturing and the bioeconomy. It proposes hands-on workshops for teachers and students to learn biomanufacturing concepts and techniques. These include transforming bacteria, purifying proteins through various types of chromatography, and analyzing purified proteins through electrophoresis. The goal is to promote STEM education and careers in the growing biomanufacturing industry.
This course, Applied Clinical Biochemistry- II, is designed to impart in-depth knowledge about the techniques and methods used in clinical biochemistry. The curriculum focuses on automation in clinical biochemistry, methods of estimation and assessment, enzyme principles and estimation, gastric analysis, renal function tests, qualitative tests, and chemical examination. The students will engage in practical applications of these concepts through hands-on experimentation.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
31_Program Elective course - II (Invitro fertilization).pdfVamsi kumar
The elective course on "In vitro Fertilization" is designed to equip students with a comprehensive understanding of the IVF process, from the history and evolution of the practice to the advanced techniques and procedures used in today's IVF labs. The course delves into the roles of endocrinology in IVF, the future trends of IVF, and the ethical and legal challenges faced in the field. It's a hands-on course that combines theoretical knowledge with real-world case studies to help students apply their learning in a practical context.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
The document summarizes STAR (Software Tools for Academics & Researchers), an MIT program that develops interactive educational software for use in and outside classrooms. It describes software tools like StarBiochem for visualizing proteins and StarGenetics for simulating genetics experiments. The goals are to expose students to research processes and bridge the divide between labs and classrooms using technology. The software is available free online and sees worldwide usage, including in introductory biology and genetics courses at universities and for high school students.
Software Tools for Academics & Researchers : Deeper Learning through bridging the divide between the research laboratory and the classroom using interactive technology.
From the Stem Cell workshop at the Bio-Link Summer Fellows Forum 2011
presenters: Edie Kaeuper, Carin Zimmerman, Golnar Afshar, Samantha Croft, & Bill Woodruff
This document outlines the course structure for BIO101 Essentials of Biology Lab, a one-semester course for non-science majors. The course introduces concepts in cells and metabolism, biodiversity, genetics, evolution, health and disease, and ecology. It enables students to apply biological principles to everyday life. The course involves both lectures and laboratory work. Students will be evaluated through tests, assignments, lab work, and a final exam assessing their understanding of core biological concepts and ability to apply scientific thinking.
The Clinical Visit course for Medical Lab Technology students is designed to offer a comprehensive understanding of clinical laboratories. The course is organized into three units, providing knowledge about the healthcare system, regulations, clinical lab techniques, roles of lab technologists, and the significance of lab reports. Each unit is enriched with case studies to support practical, experiential learning and foster critical thinking. The course aims to prepare students to effectively function in a clinical lab setting, promoting professional development and competency in medical lab technology.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
The document describes 19 webpages related to biology standards on various topics including cell biology, genetics, development, DNA, and genetic alteration. Each entry provides the standard, website URL, and a brief 1-2 sentence annotation summarizing what is covered on the site. The sites provide resources such as animations, lessons, activities, and virtual labs covering topics like cell structures and functions, mitosis, meiosis, mutation, development from zygote, gene expression, DNA extraction, and bacterial transformation.
This course on the 'Fundamentals of Histology' equips students with comprehensive knowledge of diseases associated with various body systems, including digestive, circulatory, respiratory, urinary, reproductive, nervous, endocrine systems, and sense organs. It fosters understanding of disease etiology, clinical manifestations, and histological changes, alongside offering practical exposure through slide preparations and microscopic study.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
16_Program Elective course - I (Good lab practies).pdfVamsi kumar
This course "Good Laboratory Practices" will guide the students through the basics of good lab practices, ensuring safety and risk management, delve deeper into quality control and assurance, and finally explore the implementation of these practices in specialized areas like clinical, diagnostic, and research labs. The syllabus will provide a deep understanding of laboratory standard operating procedures, quality improvement cycles, the role of proficiency testing, and the ethical considerations involved in lab practices. Through a series of case studies, students will also be exposed to practical, real-world scenarios where they can apply their theoretical knowledge.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
Zhonghua Wang has over 10 years of experience in biochemistry research and development. He holds a Ph.D. in Chemistry and Biochemistry from Florida International University and has worked in roles developing immunoassay reagents and purifying proteins. Currently he is a senior engineer at Mindray North America focusing on cell culture, protein purification, and assay development.
The document compares biochemistry programs in Pakistan and the USA. It outlines the history and activities of the Pakistan Society for Biochemistry and Molecular Biology, including conferences and publications. It also provides details on biochemistry degree programs and course offerings at universities in Pakistan and the USA, noting specialized areas of study like neurochemistry, clinical biochemistry, and biotechnology. Top biochemistry schools and programs in the USA are highlighted.
This document is a resume for Aditya Mandapati, who has a Master's degree in Molecular Biology and a Bachelor's degree in Cell Biology and Genetics. He has over 2 years of experience in molecular biology techniques and cell culture work. His research experience includes investigating protein function in mammalian cells and studying immune cell mechanisms. He is skilled in various molecular biology and protein biochemistry techniques and is seeking a position applying his expertise.
This document provides information about a primer course on molecular biology taught at UC Berkeley. The course aims to introduce students to common laboratory techniques in molecular biology, such as PCR, cloning, cell culture and transfection. It will help students develop a strong foundation in molecular biology and facilitate their transition into research laboratories. The course involves lectures, activities and assignments, including a final presentation. It is graded on a pass/no pass basis based on attendance, participation, homework, a research paper, and the final project.
The document outlines plans for a proposed 3-year biotechnology program at Carlmont High School. It discusses goals of preparing students for higher education and careers in biotechnology. It proposes targeting honor students and implementing the program through existing science classrooms. Key components would include biotechnology curriculum, industry partnerships, and pathways for students to continue in the field after high school through programs at local colleges and universities. Financial support would come from school and district funds as well as industry and private donations.
Prahlad Rao is a fourth year graduate student at the University of Illinois at Chicago studying systems biology approaches to understand Mycobacterium tuberculosis using proteomics. His research focuses on investigating the pathogen's response to stress through global protein turnover analysis. He has extensive experience in proteomics techniques and managing a proteomics facility. Rao has a background in biotechnology and has taught at the university level.
A Primer on Molecular Biology, Spring 2016 SyllabusBillal Ahmed
This document provides information about a primer course on molecular biology taught at UC Berkeley in Spring 2016. The course aims to introduce students to basic laboratory techniques in molecular biology, such as PCR, cloning, cell culture and transfection. It will prepare them for research experiences in university laboratories. The course involves lectures, activities, homework assignments, a research paper, and a final student presentation project. Taking the course will benefit students who wish to pursue research and provide a foundation for advanced science courses.
Science Prof Online provides free online science education resources including virtual science classrooms, PowerPoints, articles and images. The site offers educational materials like practice questions, lectures, videos and course materials. PowerPoints are available in different formats for ease of use and printing. Prokaryotic cells, which include bacteria, differ from eukaryotic cells in that they lack a nucleus and membrane-bound organelles. They have variations in cell wall structure that determine if they are gram-positive or gram-negative. Prokaryotes also have distinctive cell shapes, surface appendages and arrangements that provide clues to their identification.
The document discusses developing curriculum to support careers in biomanufacturing and the bioeconomy. It proposes hands-on workshops for teachers and students to learn biomanufacturing concepts and techniques. These include transforming bacteria, purifying proteins through various types of chromatography, and analyzing purified proteins through electrophoresis. The goal is to promote STEM education and careers in the growing biomanufacturing industry.
This course, Applied Clinical Biochemistry- II, is designed to impart in-depth knowledge about the techniques and methods used in clinical biochemistry. The curriculum focuses on automation in clinical biochemistry, methods of estimation and assessment, enzyme principles and estimation, gastric analysis, renal function tests, qualitative tests, and chemical examination. The students will engage in practical applications of these concepts through hands-on experimentation.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
31_Program Elective course - II (Invitro fertilization).pdfVamsi kumar
The elective course on "In vitro Fertilization" is designed to equip students with a comprehensive understanding of the IVF process, from the history and evolution of the practice to the advanced techniques and procedures used in today's IVF labs. The course delves into the roles of endocrinology in IVF, the future trends of IVF, and the ethical and legal challenges faced in the field. It's a hands-on course that combines theoretical knowledge with real-world case studies to help students apply their learning in a practical context.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
The document summarizes STAR (Software Tools for Academics & Researchers), an MIT program that develops interactive educational software for use in and outside classrooms. It describes software tools like StarBiochem for visualizing proteins and StarGenetics for simulating genetics experiments. The goals are to expose students to research processes and bridge the divide between labs and classrooms using technology. The software is available free online and sees worldwide usage, including in introductory biology and genetics courses at universities and for high school students.
Software Tools for Academics & Researchers : Deeper Learning through bridging the divide between the research laboratory and the classroom using interactive technology.
From the Stem Cell workshop at the Bio-Link Summer Fellows Forum 2011
presenters: Edie Kaeuper, Carin Zimmerman, Golnar Afshar, Samantha Croft, & Bill Woodruff
This document outlines the course structure for BIO101 Essentials of Biology Lab, a one-semester course for non-science majors. The course introduces concepts in cells and metabolism, biodiversity, genetics, evolution, health and disease, and ecology. It enables students to apply biological principles to everyday life. The course involves both lectures and laboratory work. Students will be evaluated through tests, assignments, lab work, and a final exam assessing their understanding of core biological concepts and ability to apply scientific thinking.
The Clinical Visit course for Medical Lab Technology students is designed to offer a comprehensive understanding of clinical laboratories. The course is organized into three units, providing knowledge about the healthcare system, regulations, clinical lab techniques, roles of lab technologists, and the significance of lab reports. Each unit is enriched with case studies to support practical, experiential learning and foster critical thinking. The course aims to prepare students to effectively function in a clinical lab setting, promoting professional development and competency in medical lab technology.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
The document describes 19 webpages related to biology standards on various topics including cell biology, genetics, development, DNA, and genetic alteration. Each entry provides the standard, website URL, and a brief 1-2 sentence annotation summarizing what is covered on the site. The sites provide resources such as animations, lessons, activities, and virtual labs covering topics like cell structures and functions, mitosis, meiosis, mutation, development from zygote, gene expression, DNA extraction, and bacterial transformation.
This course on the 'Fundamentals of Histology' equips students with comprehensive knowledge of diseases associated with various body systems, including digestive, circulatory, respiratory, urinary, reproductive, nervous, endocrine systems, and sense organs. It fosters understanding of disease etiology, clinical manifestations, and histological changes, alongside offering practical exposure through slide preparations and microscopic study.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
16_Program Elective course - I (Good lab practies).pdfVamsi kumar
This course "Good Laboratory Practices" will guide the students through the basics of good lab practices, ensuring safety and risk management, delve deeper into quality control and assurance, and finally explore the implementation of these practices in specialized areas like clinical, diagnostic, and research labs. The syllabus will provide a deep understanding of laboratory standard operating procedures, quality improvement cycles, the role of proficiency testing, and the ethical considerations involved in lab practices. Through a series of case studies, students will also be exposed to practical, real-world scenarios where they can apply their theoretical knowledge.
Created by: Mr. Attuluri Vamsi Kumar, Assistant Professor, Department of MLT, UIAHS, Chandigarh University, Mohali, Punjab. For more details website: https://www.mltmaster.com
Zhonghua Wang has over 10 years of experience in biochemistry research and development. He holds a Ph.D. in Chemistry and Biochemistry from Florida International University and has worked in roles developing immunoassay reagents and purifying proteins. Currently he is a senior engineer at Mindray North America focusing on cell culture, protein purification, and assay development.
The document compares biochemistry programs in Pakistan and the USA. It outlines the history and activities of the Pakistan Society for Biochemistry and Molecular Biology, including conferences and publications. It also provides details on biochemistry degree programs and course offerings at universities in Pakistan and the USA, noting specialized areas of study like neurochemistry, clinical biochemistry, and biotechnology. Top biochemistry schools and programs in the USA are highlighted.
This document is a resume for Aditya Mandapati, who has a Master's degree in Molecular Biology and a Bachelor's degree in Cell Biology and Genetics. He has over 2 years of experience in molecular biology techniques and cell culture work. His research experience includes investigating protein function in mammalian cells and studying immune cell mechanisms. He is skilled in various molecular biology and protein biochemistry techniques and is seeking a position applying his expertise.
Similar to Howard university presentation ver3 (20)
1. Lourdes Alemán, Ph.D.
Stacie Bumgarner, Ph.D.
April 8-9th, 2010
Howard University STAR Workshop
Office of Educational Innovation and Technology (OEIT)
Biology Department
4. 10% of what they hear
30% of what they see
60% of what they hear & see
80% of what they hear, see, & do
100% of what they hear, see, do, smell, feel, taste…& purchase on credit
By Ronald A. Berk
Professors are from Mars. Students are from Snickers.
Students learn…
8. Who we are
MIT Biology Department
Office of Educational Innovation & Technology (OEIT)
What we are doing
Designing interactive teaching software tools
to be used IN & OUTSIDE class
9. Software Tools for Academics &
Researchers (STAR) biology tools
1 Educational goals
2 Design process
3 Access & outreach
10. Educational goals
Challenge
Teaching protein structure in a traditional classroom setting
StarBiochem: protein 3D viewer
Challenge
Teaching experimental design & data interpretation outside of
a genetics lab
StarGenetics: virtual genetics lab
11. Design process
Collaboration between MIT faculty & OEIT
StarBiochem Professor Graham Walker
Introductory Biology Series
StarGenetics Professor Chris Kaiser
Genetics
Graduate Student Bridge Program
13. Create curriculum modules.
Conduct workshops.
Collaborate with wide range of educational institutions.
Assess how software tools impact different populations of
students.
Access & outreach
17. Proteins perform many important
biological functions
hemoglobin
carry oxygen
in the blood
F1 ATPase
generate energy
antibody
protect against
infections
aquaporin
water transport
microtubules
cell division
Protein Data Bank website
18. The function of a protein is
determined by its structure
structure function
20. Traditional methods for teaching
about protein structure and function
Cartoons
Can introduce misconceptions
2-D representations
Limits student exploration
Protein Structure & Function (2007)
21. Using 3-D protein viewers for teaching
about protein structure & function
Research PyMol, KING, Rasmol, Chimera,
First Glance in Jmol, Webmol
Educational Protein Explorer, BioMolecular
Explorer, other guided tutorials
22. Limitations of existing 3-D proteins viewers for
teaching about proteins structure & function
Research
Educational
uses crystallography jargon
not user-friendly
ability to scale-up not known
windows functionality only
tutorials with limited views/manipulations
24. StarBiochem is a protein 3-D viewer designed
for educational purposes
Website: http://web.mit.edu/star/biochem/
Platform independent.
Interface is designed with students in mind.
Parallels how proteins are taught in introductory biology.
Can upload >54,000 Protein Data Bank structures.
27. How mutations in DNA can result in disease
sickle cell anemia: hemoglobin
28. Hemoglobin
Highly expressed in red blood cells
Responsible for oxygen transport
Contains four protein subunits -> each one binds to a O2 molecule
Protein Data Bank website
29. Hemoglobin
heme
heme
Protein Data Bank website
Highly expressed in red blood cells
Responsible for oxygen transport
Contains four protein subunits -> each one binds to a O2 molecule
30. severe bone pain & necrosis
stroke
enlarged heart
bloodstream infections and pneumonia
www.commercialappeal.com
Sickle cell anemia
31. A mutation in hemoglobin
causes sickle cell anemia
University of Utah Learn Genetics website
32. How does a mutation in the hemoglobin
gene causes the protein to become sticky?
normal hemoglobin vs.sickle hemoglobin
(2HBS)(1A3N)
33. Structure of sickle hemoglobin:
DNA sequence
A -> T
protein
hemoglobin becomes sticky
amino acid sequence
Glu6 -> Val6
disease
sickle cell anemia
38. Current StarBiochem educational
applications
• Undergraduate setting
Introductory Biology (MIT)
Introductory Biology Lab (Brandeis)
• High school setting
MIT Museum/Environmental Health Sciences Outreach Program (MIT)
Outreach HS program (Broad Institute)
HS fieldtrips (Biology Department, MIT)
39. Introductory Biology Courses (7.01 series)
StarBiochem modules core topics
StarBiochem case study: MIT
biochemistry molecular
biology
recombinant
DNA technology
signalingimmunology
cancer biology
neurobiology genetics
PAH amyloid GFP BCR-Abl Herceptin DNA pol Ras Hemoglobin
PFK
crystallin
Diviya Sinha
40. StarBiochem case study: Brandeis University
Introductory Biology Lab Course (Bio118)
crystallin protein cataracts
• explore the structure of crystallin using StarBiochem
• design mutation in crystallin based on structure
• test mutant crystallin for in vitro cataract formation
Melissa Kosinski-Collins
43. StarBiochem in-class activities
Short
Example: snapshot of a structure or a concept
use StarBiochem live
create video using StarBiochem
create images of a particular structural snapshot
44. StarBiochem in-class activities
Short
Example: snapshot of a structure or a concept
use StarBiochem live
create video using StarBiochem (ex: hemoglobin)
create images of a particular structural snapshot
46. StarBiochem in-class activities
Intermediate
Example: interactive building protein activity
Protein 1 Protein 2
cell membrane protein cytoplasmic protein
1 Students are asked to consider what would be necessary to build
proteins: location & function.
2 Students answers are compared with actual protein structures in
StarBiochem.
48. Protein structure lecture using StarBiochem
Introductory Biology
The live demos using StarBiochem helped me gain a
better understanding of the relationship between a
protein's structure and its function.
The live demos on the potassium channel protein in
StarBiochem helped me understand how this channel
allows for the passage of potassium ions ONLY.
The live demos using StarBiochem helped me
understand the four levels of protein structure:
primary, secondary, tertiary & quaternary.
The live demos using StarBiochem helped me
understand what protein structures look like in 3D.
I enjoyed today’s lecture on protein structure.
Howard University (2009)
51. Review available curriculum modules online (exercises).
Modify current modules or develop your own.
Students download software from web.
Each module contains full step-by-step instructions for
students to use software.
Outside-class activities
53. Goal
Assess effectiveness of the software in illustrating a concept
Assess implementation of StarBiochem activity
Assessment & testing
54. Example: open-ended exam question
Introductory Biology (MIT)
Aquaporin exercise (homework)
•basics of protein structure
•aquaporin specificity for passage of water only
Aquaporin question (exam)
•assess both protein structure basics and aquaporin structure -> function
relationships
•could not be completed without doing the aquaporin exercise
Assessment of software’s ability to
illustrate concept
55. Assessment of software’s curriculum
implementation
Use simple sample survey provided
1 Survey Monkey (http://www.surveymonkey.com/)
• best for remote assessment
• data is automatically analyzed
• basic membership (free), Pro membership ($300/year)
2 Paper survey
• best for direct assessment
• manual data manipulation
• free
71. Lab activity: pre-assignment
Reading
“Mapping the Cancer Genome”
by Francis S. Collins and Anna D. Barker
Scientific American Magazine, March 2007: 50-5
Questions
• usefulness of the genomic cancer atlas for studying & treating
cancer.
• hallmarks of cancer cells such as abnormalities in self-control and
repair mechanisms.
• complexity of assembly a genomic cancer atlas.
76. DNA glycosylase proteins help repair
DNA damage caused by oxidation
DNA glycosylases
1
2
1a
1b
2a
2b
77. How does DNA glycosylase fix
DNA oxidation damage?
DNA glycosylase:
human 8-oxoguanine glycosylase (hOGG1)
78. Structure of DNA glycosylase:
structure
human DNA glycosylase &
DNA substrate
mechanism
rotating DNA bases outside of
double helix to check for mutations
85. Lab activity: post-assignment
Questions
• understand how the genomic cancer atlas can be used to uncover
potential new roles of hOGG1 in cancer.
• understand how new cancer treatments can be design based on
hOGG1.
88. Goal
Empower you to build your own StarBiochem exercises by
illustrating the design and building process.
89. Designing & writing StarBiochem
curriculum activities
1 Design & building process
What is the goal of the activity?
What type of activity accomplishes goal?
How to select a structure that accomplishes goal?
How to structure the activity?
2 Interactive exercise creating a StarBiochem activity
90. Designing & writing StarBiochem
curriculum activities
1 Design & building process
What is the goal of the activity?
What type of activity accomplishes goal?
How to select a structure that accomplishes goal?
How to structure the activity?
2 Interactive exercise creating a StarBiochem activity
91. What is the goal of the activity?
structure -> function
structure -> function -> disease
structure -> medical therapies
protein regulation
evolution of protein structure
92. What type of activity accomplishes goal?
1 Course
• Introductory Biology
• Biochemistry
• Cell/Molecular Biology
• Pharmacology
• Etc.
2 Course curriculum
• format
• duration of activity
93. What type of activity accomplishes goal?
Example 1
Structure -> function
Course Introductory Biology
Curriculum central concept of the course
Activity
StarBiochem protein structure lecture + StarBiochem exercise
(homework/lab activity)
94. What type of activity accomplishes goal?
Example 2
Structure -> medical therapies
Course Cell Biology
Curriculum minor point within a lecture
Activity
StarBiochem video or in class-demo illustrating structure –>
targeted therapies
95. How to select a structure that accomplishes goal?
1 Goal
Is the structure suitable for illustrating goal?
2 Course/format of activity
Is the structure accessible to your students?
Is the activity format suitable for explaining the structure?
96. Schneider, T.L. and Linton, B. (2008) Introduction to Protein Structure
through Genetics Diseases. Journal of Chemical Education 85: 663-665
How to select a structure that accomplishes goal?
97. Schneider, T.L. and Linton, B. (2008) Introduction to Protein Structure
through Genetics Diseases. Journal of Chemical Education 85: 663-665
How to select a structure that accomplishes goal?
98. Researching & finding the appropriate structure
Protein Data Bank http://www.pdb.org/pdb/home/home.do
Search:
• keyword
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How to select a structure that accomplishes goal?
99. Researching & finding the appropriate structure
Hemoglobin: exercise with a well defined activity
structure -> function -> disease
Glu6 -> Val6 in hemoglobin leads to sickle cell anemia
DNA glycosylase: exercise with less well defined activity
structure -> function
illustrate how DNA glycosylase repairs DNA
How to select a structure that accomplishes goal?
100. How to structure the activity?
1 Format/duration
Short activity straight to the the point
ex: DNA glycosylase video
Long activity framework for building complexity
ex: DNA glycosylase exercise
101. How to structure the activity?
1 Format/duration
Short activity straight to the the point
ex: DNA glycosylase video
Long activity framework for building complexity
ex: DNA glycosylase exercise
102. How to structure the activity?
1 Format/duration
Short activity straight to the the point
ex: DNA glycosylase video
Long activity framework for building complexity
ex: DNA glycosylase exercise
103. How to structure the activity?
References
Structure: 1EBM
Bruner, S. et al. (2000) Structural basis for recognition and repair of the
endogenous mutagen 8-oxoguanine in DNA. Nature 403: 859-866.
Structures: 1YQK, 1YQR
Banerjee, A. et al. (2005) Structure of a repair enzyme interrogating
undamaged DNA elucidates recognition of damaged DNA. Nature
434: 612-618.
104. How to structure the activity?
Structure: 1EBM
Bruner, S. et al. (2000) Structural basis for recognition and repair of the
endogenous mutagen 8-oxoguanine in DNA. Nature 403: 859-866.
How hOGG1 repairs oxidized guanines:
1.Extrusion of oxoG from the double helix
1.Recognition of oxoG by Gly 42
105. How hOGG1 repairs oxidized guanines:
1.Extrusion of oxoG from the double helix
1.Recognition of oxoG by Gly 42
“The structure of the hOGG1-DNA complex
provides a clear solution to the long-standing
puzzle of how the cellular repair machinery
recognizes oxoG in DNA amidst the vast excess
of guanine, a close structural relative. The oxoG
residue is fully extruded from the DNA helix and
inserted into an extrahelical active-site pocket
on the enzyme, consistent with structure-based
predictions made for other members of the HhH-
GPD superfamily.”
106. “The most characteristic feature of oxoG - its
8-oxo-carbonyl function - is completely devoid of
any interacting partner. Instead, the enzyme
recognizes the urea system in oxoG by virtue of its
N7-H, which donates a hydrogen bond to the main
chain carbonyl of Gly 42… Indeed, of all the
contacts made to the oxoG base, that involving Gly
42 is the only one that would clearly be different
with oxoG versus guanine; thus, the responsibility
for discriminating oxoG from guanine appears to
be borne by a single hydrogen bond.”
How hOGG1 repairs oxidized guanines:
1.Extrusion of oxoG from the double helix
1.Recognition of oxoG by Gly 42
107. How to structure the activity?
Structures: 1YQK, 1YQR
Banerjee, A. et al. (2005) Structure of a repair enzyme interrogating
undamaged DNA elucidates recognition of damaged DNA. Nature
434: 612-618.
How hOGG1 distinguishes oxidized guanines from
undamaged guanines:
1.oxoG:hOGG1 interaction differs from the
G:hOGG1 interaction
108. How hOGG1 distinguishes oxidized guanines from
undamaged guanines:
1.oxoG:hOGG1 interaction differs from the G:hOGG1 interaction
“Whereas the oxoG nucleobase inserts itself
deeply into the lesion recognition pocket on the
enzyme (Figs 2, left, and 3a), G is rejected by the
lesion recognition pocket and instead lies
against the protein surface at an exo-site some
5A ° outside the pocket (Figs 2, right panel, and
3b). The G base does interact with two active-
site residues, Phe 319 and His 270, but the
contacts are completely different from those
made with oxoG.”
109. How hOGG1 distinguishes oxidized guanines from
undamaged guanines:
1.oxoG:hOGG1 interaction differs from the G:hOGG1 interaction
“…a hydrogen bond is apparent between the
carbonyl oxygen of Gly 42 and N7 H of oxoG.
This attractive interaction would be replaced in
the case of G by a strongly repulsive interaction
with the N7 lone pair, if G and Gly 42 assumed
the same positions as in the oxoG complex.”
110. How to structure the activity?
Long activity: framework for building complexity
Begin with: simple questions
Allow students to become familiar with protein structure basics
End with: complex questions
Allow students to understand the goal of the activity
111. How to structure the activity?
Long activity: framework for building complexity
Begin with: simple questions
Allow students to become familiar with protein structure basics
DNA Glycosylase Exercise: questions 1-5
End with: goal of the exercise
structure -> function
DNA Glycosylase Exercise: questions 6-8
112. DNA Glycosylase Exercise: simple questions
Question 1: overall structure
explore different 3-D models for representing atoms
Question 2: amino acid structure
explore difference between amino acid backbone and side chain
Question 3,4: secondary structure
explore how individual amino acids fold to form secondary structures
Question 5: tertiary structure
explore relationship between a protein’s environment & its tertiary
structure
113. DNA Glycosylase Exercise: complex questions
Question 6: hOGG1 repairs DNA by extruding oxidized bases from
double helix
location of oxoG with respect to the double helix
Question 7: hOGG1 recognizes oxidized bases by contacting the
damaged base directly and recognizing a specific modification
comparison of secondary structures where amino acids that interact
with oxoG are likely to be located
Question 8: hOGG1’s specificity for oxidized guanines lies in the
inability of guanine to bind to the active site of hOGG1
comparison of the oxoG:hOGG1 interaction with that of the G:hOGG1
interaction
114. Designing & writing StarBiochem
curriculum activities
1 Design & building process
What is the goal of the activity?
What type of activity accomplishes goal?
How to select a structure that accomplishes goal?
How to structure the activity?
2 Interactive exercise creating a StarBiochem activity
115. Designing & writing StarBiochem
curriculum activities
1 Design & building process
What is the goal of the activity?
What type of activity accomplishes goal?
How to select a structure that accomplishes goal?
How to structure the activity?
2 Interactive exercise creating a StarBiochem activity
116. Interactive exercise: creating a
StarBiochem activity
- Goal of the activity you would like to implement
- Type of activity (length, structure, specifics)
1. Work alone
2. Discuss with a partner
3. Share ideas with the group
118. Acknowledgements
Star Team
Sara Bonner
Rocklyn Clarke
Ivan Ceraj
Justin Riley
Chuck Shubert
Biology Department
Chris Kaiser
Graham Walker
Diviya Sinha
OEIT
Vikay Kumar
Molly Ruggles
Collaborators
Stacie Bumgarner
Melissa Kosinski-Collins
Megan Rokop
Kathy Vandiver
Lourdes Aleman laleman@mit.edu
Collaborating Institutions
Brandeis University
Broad Institute Outreach Program
Howard University
MIT Museum
Suffolk University
Tufts University
Outside Funding
Davis Educational Foundation
HHMI MIT’s Institutional Grant
119. “The ‘trip’ through the potassium channel protein was AMAZING.
I'll explain to Grandma. Refreshing! :)”
“I'm not a bio major but found the interphase fun, easy, and
educational. I plan to recommend it to my high school bio
teacher.”
“I have found an appreciation for biochemistry almost entirely
due to this program.”
“Great Job! Thank you! The StarBiochem program is truly
innovative and gives a new perspective on the 2-D images
provided by books and overheads.”
StarBiochem feedback
120. StarGenetics
•test new version (Yeast)
•add visualizers
-C. elegans
-bacteria
•curriculum modules
•tutorials
•videos:
-illustrate use cases
•assessment
•human pedigrees
•association studies
•population genetics
Other genetic tools StarCellBio
•test new version
•curriculum modules
•videos:
-illustrate use cases
StarBiochem
Future directions for
STAR biology software
Some exciting educational tools that we have been developing to increase student’s understanding of biological concepts. In particular, I am here to tell you about StarBiochem.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
Be specific about the last statement
Why is it that understanding protein structure is an important educational goal in biology classrooms?
Proteins are the cells work horses, performing most of the cell’s function. Here are five different proteins that have important functions. Hemoglobin carries oxygen from the lungs to the rest of the body. F1 ATPase produces the energy necessary that allows you to breath, walk, think, etc. Antibodies protect us from current and future infections. Microtubules form the skeleton of the cell and are responsible for properly dividing the DNA content of the cell into two identical halves during cell division. Aquaporins are the proteins that allow the passage of H2O in and out of cells.
What is apparent from these examples is that proteins come in many sizes and shapes. Some are globular, others look like long hollow cylinders and others have very unique shapes.
This diversity in 3D structures has a functional consequence, because the structure of a protein determines its function. In other words, the structure of a protein is directly linked to the specific function that a protein is responsible for. Therefore to understand how a particular protein performs an specific function we turn to its structure.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
Neither of these is actually an optimal tool for teaching about protein structure. Cartoons, can introduce huge misconceptions, given that the real structure of proteins is overly simplified and typically proteins are represented by a globular blob, even though proteins are extremely varied in their 3D mensional structure. 2D snapshots of protein structures offer a more realistic representations of proteins, but they limited in that they only offer a single view of the structure and cannot be manipulated.
StarBiochem resolves limitations of both educational and research based 3D viewers.
StarBiochem is designed so that hundreds of students access it without crashing!
Interface represents each level of protein structure.
Now, I will like to turn your attention to the second teaching point that we will be exploring today and for this hands on activity we will be using sickle cell anemia as a case study.
Sickle cell anemia is disease of the blood that is genetically inherited. It has pretty severe symptoms and medical consequences. Patients with sickle cell anemia have severe bone pain. Sickle cell anemia can lead to stroke and other cardiovascular complications such as an enlarged heart and severe infections.
The reason sickle cell anemia leads to such severe medical problems is because of a mutation in hemoglobin. Hemoglobin is a protein found in red blood cells that is responsible for binding oxygen in the lungs and distributing it throughout the body. In normal red blood cells hemoglobin is freely floating. Normal red blood cells are shaped are compact and flexible allowing them to squeeze through small capillaries. In patients with sickle cell anemia, hemoglobin is sticky and likes to form long, inflexible chains with other hemoglobin molecules. This long inflexible hemoglobin chains, distore the shape of red blood cells, causing them to become elongated and unflexible. This causes sickle red blood cells to become stuck in small capillaries. This is the reason why patients with this disease often have strokes, enlarged hearts and infections.
What makes hemoglobin sticky in patients with sickle cell anemia? To understand this issue, we now turn to the structure of sickle hemoglobin in StarBiochem.
I hope that this small hands-on activity allows you to appreciate how the altered structure sickle hemoglobin, in particular the lysine amino acid at position 6, alters the function of this protein, making it sticky and causing this severe disease.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
Hypothesis driven lab project
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
StarBiochem has been used in both undergraduate and high school settings inside and outside of MIT.
We are interest in collecting both direct and indirect assessment tools. This is an example
In this particular example, StarBiochem viewer was used as a chore part of a lecture of protein structure fort the introductory biology course at Howard University.
Put a lot of energy into developing these and
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
10, 000 is the number of unintended changes (mutations) that occur to a single cell’s DNA each day.
Note: a human body has approximately 10-50 trillion cells.
Activity Question:
How many mutations per cell would you have after 3 days?
DNA mutations can be cause by different types of agents:
External manmade substances/agents : industrial chemicals, X-rays used for medical purposes (dentist, hospital, etc), chemicals found in cigarettes, etc.
- External substances found in the environment: natural chemicals, certain types of viruses (ex: Human Papillomavirus which can cause cervical cancer in women), UV rays, natural radiation present in the soil and in the atmosphere, etc.
Internal body processes: respiration (breathing) and DNA replication mistakes.
Different agents cause different types of DNA changes. For example, respiration, radadiation and smoking cause a type of damage call DNA oxidation. DNA oxidation is caused by the inappropriate attachment of a reactive oxygen atom (‘radical’) to one of the DNA bases.
Activity Question:
Which of these type of DNA mutations causing agents can be avoided?
DNA mutations can be cause by different types of agents:
External manmade substances/agents : industrial chemicals, X-rays used for medical purposes (dentist, hospital, etc), chemicals found in cigarettes, etc.
- External substances found in the environment: natural chemicals, certain types of viruses (ex: Human Papillomavirus which can cause cervical cancer in women), UV rays, natural radiation present in the soil and in the atmosphere, etc.
Internal body processes: respiration (breathing) and DNA replication mistakes.
Different agents cause different types of DNA changes. For example, respiration, radadiation and smoking cause a type of damage call DNA oxidation. DNA oxidation is caused by the inappropriate attachment of a reactive oxygen atom (‘radical’) to one of the DNA bases.
Activity Question:
Which of these type of DNA mutations causing agents can be avoided?
Now, I will like to turn your attention to the second teaching point that we will be exploring today and for this hands on activity we will be using sickle cell anemia as a case study.
Attachment of an active (radical) oxygen molecule can occur to any of the four DNA bases (A,T, C & G), but the most commonly modified base due to oxidation is guanine (G). Among, the four DNA bases, guanine is most susceptible to oxidation.
During the first round of DNA replication, the strand containing the oxidated guanine (G=O) is misread and instead of pairing with ‘C’, the modified guanine pairs with ‘A’, resulting in double helix 1.
At the end of the first round of DNA replication, we have one double helix with a G=0 to A pair (1) and a double helix with a G to C pair (2). Let’s follow what happens when each of these double helixes is replicated.
During the next round of DNA replication, each strand of double helix 1 and 2 serves as a template. Double helix 2 will yield two helices (2a and 2b), each one with a G to C pair. For double helix 1, the strand with the oxidated G (G=O) will again be misspaired to an ‘A’, resulting in double helix 1b. The template strand with an A at that position will be paired to a T, resulting in double helix 1a. Therefore, the result of an oxidated G is the conversion of a G to C pair into a T to A pair.
DNA glycosylase prevents this conversion of a G to C pair into an T to A pair by fixing the oxidated G (G=O) before DNA replication.
What makes hemoglobin sticky in patients with sickle cell anemia? To understand this issue, we now turn to the structure of sickle hemoglobin in StarBiochem.
I hope that this small hands-on activity allows you to appreciate how the structure of this protein in its relationship to DNA allows us to visualize how this protein works to recognize damaged DNA bases.
Let’s say that you are a cancer doctor and that you have 10 people who all have been diagnosed with lung cancer. You treat them with a strong medication against lung cancer: some patients will respond well to the treatment and some will not (in some cases the treatment is even toxic). In the past we had no way of knowing which patients responded to what type of treatments. Today we can look at the genes in the individual’s cancer cells to see which patients will respond to this particular therapy and therefore only give the therapy to those who will respond to it.
Let’s say that you are a cancer doctor and that you have 10 people who all have been diagnosed with lung cancer. You treat them with a strong medication against lung cancer: some patients will respond well to the treatment and some will not (in some cases the treatment is even toxic). In the past we had no way of knowing which patients responded to what type of treatments. Today we can look at the genes in the individual’s cancer cells to see which patients will respond to this particular therapy and therefore only give the therapy to those who will respond to it.
We are currently learning how an individual genes informs us about which treatments are effective and which are not.
Let’s say you are a doctor and you are having difficult convincing your patient to stop smoking. If you were to find out that this person had low hOGG1 levels, then you can try to convince them to stop smoking because not only are they are risk for smoking but on top of that they have an added risk of developing cancer because of their hOGG1 levels are low.
Therefore, faculty and teachers face the challenge of communicating and explaining these 3D relationships in traditional classrooms, where 2D mediums are prevalent.
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As we continue to learn from faculty and student user experience with both software tools, we are moving forward with additional changes and improvements with our current suite of programs and looking forward to addressing new challenges outside of biochemistry and genetics.