Enzymes, Chemical Bonds and Energy

Reflecting back on the course, what are three major themes you would identify that connect that various topics discussed in this course - how are they connected to more than one topic, and how do they connect with what you knew before this course?  What knowledge have you gained with regards to these three themes you have identified?

The three major themes I will be proposing, that connect various topics discussed in biochemistry this semester are enzymes, chemical bonds and energy. Starting with the six basic types of enzymes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and synthetases (ligases). Those basic types of enzymes are the muscle behind metabolism of food sources to create adenosine triphosphate ATP.  ATP is the key player to be utilized as energy by cellular processes.  Enzymes can make chemical bonds to store energy or break chemical bonds to releases energy. These three themes are intertwined.

Development of restriction enzymes allows DNA sequences to be cut at known base sequences to allow researchers to analyze specific sequence of interest. DNA contains the genetic code (genes) that can pass on the information to RNA to create proteins. And enzymes are primarily composed of …. Proteins. 

(Original photo by J Russell)

Here is where the hands on aspect of the class made the biggest impact for me this semester.  The extraction of our own DNA in the laboratory experiment "369 - Human PCR Tool Box."  The polymerase chain reaction was also my topic for my biochemistry wiki site.  All the reading and research had an impact but the hands on processing of the sample of eye brow hairs and watching the tracking dye move across the electrophoresis gel made DNA something accessible.  The viewing of the processed gel and finding bands to be analyzed to determine VNTR, ALU and regions of mitochondrial DNA was the best experience this semester.  We utilized enzymes to break chemical bonds in the DNA and used the energy inherent in all cells to draw the fragments across the electrophoresis gel.

Structure determines Function – knowledge connected to the past

What knowledge have you connected with past knowledge?

(Original Photo by J Russell)

One piece of knowledge that is always good to go back to is the basic concept of structure determines function.  I learned this vital piece of information in the beginning of my of study of biology and it still holds true for biochemistry today. Just as the mantra that carbon can only form four bonds from organic chemistry which comes back at the same time.  Welcome to chapter sixteen which introduces a seemingly harmless topic of carbohydrates.  Now who can hate carbohydrates?  They provide the all important sugar (glucose) for our body to produce energy which is essential to live. Well here is the catch, not all carbohydrates (CHO) are created equal. The configuration, spacial arrangement, (structure) of the CHO has a direct impact on the function. Why is that important to know?  Carbohydrates play a role in the processes that take palce at surface of cells and in immune recognition. So it would be important to know the structure of the CHO when designing drugs for interaction. The reemergence of stereochemistry involving concepts such as highest chiral C, carbon connected to four different groups, and alpha (opposite side) versus beta (same side) linkage were much easier to comprehend the second time around.  Learning it for a second time and applying it to a new concept of metabolism seems allowed me to better understand and apply the concepts of organic chemistry. 

Connection between Glucose and Energy

The question was purposed on how would your explain the connection between glucose entering the body and energy created by the body to a friend, using your new biochemistry knowledge? 
Original picture by J. Russell 2010

Glucose enters the body. I start explaining the process and my friends leave the room.  Just kidding.  It is a story involving the major component of most of our snack foods, my friend's and I enjoy.  Glucose is a major source of energy for the body. It can be used for energy to running cell processes by the metabolizing of the glucose. The breakdown or catabolism of glucose converts this source of energy to adenosine triphosphate or ATP.  Pause for dramatic effect.  Oh, but it is not done so in one easy step. The high point is glucose is no slacker when it comes to producing the body's energy currency source.  It yields 36 ATP molecules which is an average of 6 ATP per carbon atom.  Not a bad rate of exchange. This conversion from food source to energy source is accomplished by the powerhouse of the cell called the mitochondria. The process that links catabolism to ATP consists of intermediate steps of the citric acid cycle (TCA), electron transport chain and oxidative phosphorylation. Now if my friends, if they have not left the room, want the basic details of what those consist of here it comes.  TCA packs a punch to break down that glucose and put it to work with eight reactions utilizing eight different enzymes: citrate synthase, aconitase, isocitrate dehydrogenase, succinyl-CoA synthetaase, sucinate dehydrogenase, fumarase, and malate dehydrogenase. Painting with broad strokes, the catabolism of glucose produces acetyl-CoA that is then input into the TCA which through the cascade of eight reactions then produces oxaloacetate (oxidation of acetyl group), two NADH molecules, a GTP molecule, a FADH₂ molecule and two CO₂. Oxidative phosphorylation utilizes the electron transport chain to convert the TCA products.  Pause again to let my friends refocus for the big finale.  The electron transport chain consists of four protein complexes: complex I oxidation of NADH, complex II oxidation of FADH₂, complex III oxidation of COQ and complex IV oxidation of cytochrome C.  Interestingly, the product of the electron transfer chain is energy and water.  But wait my friends say, "You said the energy currency of the body was ATP.  Now you are rewritting the ending."  Wait for it.  This free energy is utilized by ATP synthase to produce ATP from ADP and inorganic phosphate within the mitochondrial matrix.  Remember the powerhouse of the cell I interject.  Finally, the ATP is released by the mitochondria to the cell to be used as energy for body processes.  Pass the chips and dip my friends say.  They need to fuel up on some ATP.    Now we are talking lactate and starch, but that is a story for another day.

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.