What knowledge have you connected with past knowledge?

"Main Entry: knowl•edge Pronunciation: \ˈnä-lij\ Function: noun
Etymology: Middle English knowlege, from knowlechen to acknowledge, irregular from knowen
Date: 14th century 1 obsolete : COGNIZANCE 2 a (1) : the fact or condition of knowing something with familiarity gained through experience or association (2) : acquaintance with or understanding of a science, art, or technique b (1) : the fact or condition of being aware of something (2) : the range of one's information or understanding c : the circumstance or condition of apprehending truth or fact through reasoning : COGNITION d : the fact or condition of having information or of being learned . ERUDITION strongly implies the acquiring of profound, recondite, or bookish learning . SCHOLARSHIP implies the possession of learning characteristic of the advanced scholar in a specialized field of study or investigation  3 archaic : SEXUAL INTERCOURSE 4 a : the sum of what is known : the body of truth, information, and principles acquired by humankind b archaic : a branch of learning synonyms KNOWLEDGE, LEARNING, ERUDITION, SCHOLARSHIP mean what is or can be known by an individual or by humankind. KNOWLEDGE applies to facts or ideas acquired by study, investigation, observation, or experience . LEARNING applies to knowledge acquired especially through formal, often advanced, schooling"
Excerpt  from  http://www.merriam-webster.com/dictionary/knowledge


Basically, the aforementioned question is very broad and wide sweeping when referring to knowledge.

The scope of this blog entry will be based on the General Biochemistry Spring 2010 course (BCHM658) at the University of New Hampshire at Manchester.  Science is married with technology this semester so there will be new terminology for biochemistry as well as the technology.

We will be developing an Electronic Lab Portfolio within the Blackboard Academic Suite.  A new concept in a laboratory class for myself.  There was initially a sharp learning curve with the set up of the portfolio with each content page representing a separate laboratory experiment.  Within each content page there will be a entry for a pre-lab assignment, lab data/results and an abstract referred to as personal artifacts.  It is like having a file folder on your own personal computer for organization that you can allow access to the instructor.

This Biochemistry Connections Blog is being utilized, per the syllabus for the course, to make "connections with material learned in this course with past courses or other knowledge you have outside the course."  The objective is to track "this progressive learning via use of online technology."
Before this assignment, the most I knew about a blog was the movie Julie & Julia which followed a woman blogging about her experiences completing chef Julia Child's recipes.  To learn more about the story of this technology go to http://www.blogger.com/about.

The final major piece of technology to be utilized will be a Biochemistry Technique Wiki web site.  For more information and to create your own web site go to http://www.wikispaces.com/.  Here I do have past experience and knowledge.  First with the Organic Chemistry class from Fall 2009, where we created a wiki site.  Finally, with a web site I created for a haunted house attraction that I helped run for five years.  This vehicle of presentation, wiki space, will allow for a large amount of research on a biochemistry technique to be organized and available to "report on these original findings to a larger non-scientific community using technology."

When I signed up for biochemistry, I did not expect to put my BS in Applied Computer Science, I earned in 2001, to such extent.  Although, it does feel good to apply knowledge in a field I left for the Nursing field to better use then just checking my email. 

Some days I feel like I am on top of all the things I have to do for biochemistry as represented by the hawk.  Other days I feel like I am buried with all this technology needed to complete assignments or "dead meat" as represented by the chipmunk   I felt this picture represented those feelings in spades.  I took this photograph at Detroit Zoo in Michigan in 2005.




Works Cited

Campbell, M. K. (2008). Biochemistry (6th Edition). Belmont: Brooks/Cole, Cengage Learning.

Merriam-Webster. (2010). Merriam-Webster's Collegiate Dictionary, Eleventh Edition. Retrieved February 2010, from Merriam-Webster Inc Web Site: http://www.merriam-webster.com/dictionary/knowledge

Structural Genomics - A New Discipline in Biomedical Research

If you have an interest in protein structures, protein analysis or anything else you can think of involving proteins, then listed below is the site for you.  This biochemistry web site is easily navigated.  As part of the Protein Structure Initiate (PSI), it also makes available a detailed list of Structural Genomic Research Centers' (SG Sites) web links available to investigate.  I present to you,  for your enjoyment and research needs:

Midwest Center for Structural Genomics (MCSG)

"The MCSG is a component of the NIH-funded Protein Structure Initiative. Based at Argonne, the MCSG uses beamlines at the Advanced Photon Source (APS), the premier hard X-ray research facility in the United States. The APS is supported by the Office of Basic Energy Sciences within the DOE Office of Science (SC). The beamlines used by the MCSG are supported by NIH and SC’s Office of Biological and Environmental Research."  (press release July 17, 2009)

 
Protein Structure Initiative (PSI)
"Enabling High-Throughput Stuctural Biology and Structural Genomics"The Protein Structure Initiative (PSI) is a federal, university and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure."

 

Keeping the world informed and alerted on "advances in structural biology and structural genomics."  The Structural Genomics Knowledgebase is a great resource to investigate "how protein sequences, three-dimensional structures and models relate to biological function."   Allowing for the busy student to "stay up to date with the latest protocols, materials and technologies".

 

PSI Presents:  The Structures of Life

• Preface: Why Structure?
• Chapter 1: Proteins are the Body's Worker Molecules
• Chapter 2: X-ray Crystallography: Art Marries Science
• Chapter 3: The World of NMR: Magnets, Radio Waves, and Detective Work
• Chapter 4: Structure-based Drug Design: From the Computer to the Clinic
• Chapter 5: Beyond Drug Design

One of the most interesting pieces of information found on this biochemistry website is that MCSG Technologies are available for use by the general public.  The MCSG consortium is "organized around seven highly integrated core-technology units."

1. Target Selection
2. Gene Cloning and Protein Expression
3. Protein Production
4. Crystal Production
5. Structure Determination and Refinement
6. Model Validation and Fold Function Analysis
7. Dissemination of Data

      Breaking News in Structural Genomics      

1129 solved 3D Structures (1175 PDB deposits)
893 unique structures 28 new folds 

  

Works Cited

Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science. (2010). Argonne National Laboratory Newsroom. Retrieved February 26, 2010, from Argonne's Midwest Center for Structural Genomics: http://www.anl.gov/Media_Center/News/2009/news090727.html

Goodsell, D. S. (2010, March). PSI-Nature Structural Genomics Knowledgebase. Retrieved February 26, 2010, from CBS Domain Protein TA0289 (ISSN 1758-1338): http://kb.psi-structuralgenomics.org/KB/archives.jsp?pageshow=11

 
National Institute of General Medical Sciences.  (2010, February)  Protein Structure Initiative. Retrieved February 26, 2010, from One of the National Institute of Health  NIGMS Web site : http://kb.psi-structuralgenomics.org/KB/

National Institutes of Health, Bethesda, MD.  (Revised 2007).   The Structures of Life:  Preface:  Why Structure?  National Institute of General Medical Sciences.  Retrieved March 11, 2010, from
http://publications.nigms.nih.gov/structlife/preface.html

W. Minor Lab. (2010). Midwest Center for Structural Genomics. Retrieved February 26, 2010, from MCSG is supported by the NIH as part of the Protein Structure Initiative:  http://www.mcsg.anl.gov/

CBS (cystathionin beta-synthase) Domain Protein TA0289 - A New Family

A modular protein mystery

Bioinformatics is "the collection, classification, storage, and analysis of biochemicals and biological information using computers especially as applied to molecular genetics and genomics."  (Merriam-Webster,2010 ) Research in bioinformatics shows many proteins are modular which means it can mix and match modules to form new proteins with new functions.
 All image credit is given to both David Goodsell and the PSI Structural Genomics Knowledgebase
Researchers at Protein Structure Initiative (PSI) Midwest Center for Structural Genomics (MCSG) http://www.mcsg.anl.gov/ are in the business to developing "integrated methods for highly cost-effective determination of protein structures through X-ray crystallography."  MCSG discovered this "new structure of a protein" and "made the first steps towards uncovering the function of this unusual new family of proteins" called CBS  Domain Protein TA0289.

MCSG uncovered several proteins that contained the CBS amino acid sequence. (w. Minor Lab, 2010)  These domains were "connected to a short unannotated sequence with four cysteine amino acids."  The "CBS module can add a regulatory function to a protein, changing activity of the protein based on the levels of ATP in the cell."  Along with affecting function, "CBS modules also play structural roles, by forming protein-protein interaction sites in oligomeric complexes."

  

The structure, after purification, revealed a reddish-purple color which led to a better understanding of TA0289's function. The color is a result of the metal-binding site being occupied by iron ions. If TA0289 could transport electrons then it could perform valuable functions within the cell. This discovery shows that "CBS domain links the two chains into a stable dimer, so its role may be primarily structural." 

"Why TA0289 needs to be a dimer is still a mystery."

 
Works Cited

Merriam-Webster. (2010). Merriam-Webster's Collegiate Dictionary, Eleventh Edition. Retrieved February 26, 2010, from Merriam-Webster Inc Web Site: http://www.merriam-webster.com/dictionary/bioinformatics

Proudfoot, M. S. (2008, January 4). Biochemical and Sturctural Characterization of a Novel Family of Cystationine Beta-Synthase Domain Fused to a Zn Ribbon-Like Domain. Retrieved February 26, 2010, from ScienceDirect - Journal of Molecular Biology Volumer 375, Issue 1: http://dx.doi.org/10.1016/j.jmb.2007.10.060


Goodsell, D. S. (2010, March). PSI-Nature Structural Genomics Knowledgebase. Retrieved February 26, 2010, from CBS Domain Protein TA0289 (ISSN 1758-1338): http://kb.psistructuralgenomics.org/KB/archives.jsp?pageshow=11


Rutgers and UCSD. (2010, March 2). RCSB Protein Data Bank (PDB). Retrieved February 26, 2010, from An Information Portal to Biological Macromolecular Structures: http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=2BDCA0C9&tabtoshow=Current


W. Minor Lab. (2010). Midwest Center for Structural Genomics. Retrieved February 26, 2010, from MCSG: http://www.mcsg.anl.gov/

What is biochemistry, and how does it differ from the fields of genetics, biology, chemistry, and molecular biology?

"From so simple a beginning, endless forms most beautiful and most wonderful have been and are being, evolved." - Charles Darwin

"Trying to understand the chemical processes of living organisms but having trouble metabolizing the complex concepts?"- Biochemistry DeMYSTiFied

To understand how biochemistry differs from the fields of genetics, biology, chemistry and molecular biology, one must first understand what is biochemistry.  An explanation of biochemistry was gathered from three different sources.

original photography by J. Russell (07-09-07)

1. "Biochemistry is the chemistry of living organisms.  Biochemists study the chemical reactions that occur at the molecular level of organism.  Biochemistry really reaches out and combines aspects of all the fields of chemistry."  Carbon is the building blocks of life on earth, so organic chemistry plays a large role in biochemistry.  If it is alive and kicking, there will be a biochemists who shall study it. (Moore,2008)

2.  "Biochemistry is the process of life.  A knowledge of biochemistry is essential to all students of the life sciences, including biology, genetics, health, nutrition and pathology."  A background in the study of chemistry is essential to understand how biomolecules follow basic chemical processes. (Walker, 2008)

3.  "Biochemistry describes the molecular nature of life processes.  Biochemistry is a multidisciplinary science answering the questions about "the molecular nature of life processes." (Campbell, 2008)

To see how biochemistry is different from the other fields of study, it is important to know what is studied in the aforementioned sciences.  Genetics is a branch of "biology that deals with the heredity and variation of organisms".  Biology is "a branch of knowledge that deals with living organisms and vital processes."  Chemistry is "a science that deals with the composition, structure, and properties of substances and with the transformations that they undergo."  Molecular biology is "a branch of biology dealing with the ultimate physiochemical organization of living matter and especially with the molecular basis of inheritance and protein synthesis." (Merriam-Webster, 2010)

Now, to put these disciplines into some order, based on their differences in the fields of study.  Chemistry is the base of knowledge for the other life science studies.  It deals with the basic building blocks (chemicals) that compose other larger substances and their properties.  To understand how something functions, it is important to first understand the structure.  Biology studies how living organisms' structure determines how they function.  Genetics and molecular biology are branches of the larger subject of biology interested in inheritance.  Genetics studies how organisms gain their specific structures (genes).  Molecular biology attempts to organize the physiochemical structures of living organisms.  Ultimately, biochemistry integrates all the concepts in the other sciences into the study of biomolecule structures and how their makeup, in all living organism, define their chemical processes.  Chemical processes which ties all the life sciences together and brings this discussion full circle back to the base science of chemistry.

Works Cited

Campbell, M. K. (2008).  Biochemistry (6th Edition).  Belmont: Brooks/Cole,  Cengage Learning.

Merriam-Webster. (2010).  Merriam-Webster's Collegiate Dictionary, Eleventh Edition.  Retrieved February 2010, from Merriam-Webster Inc Web Site: http://www.merriam-webster.com

Moore, J. E. (2008).  Biochemistry for Dummies. Hoboken:  Wiley Publishing Inc.

Walker, S. P. (2008).  Biochemistry Demystified - A Self-Teaching Guide.  New York: The McGraw-Hill Companies.