URC Poster Summary - Primary Tumors and Brain Metastasis

During the Undergraduate Research Conference Poster Session, I was taken back by my fellow classmates and their professionalism while presenting their research topics. Both Michael and Marcus did excellent jobs and both should be very proud of themselves for the job they did.

I chose to summarize, Marcus's poster on Primary Tumors and Brain Metastasis because I found the information to be extensive yet well organized. I believe if a passer-by was to read this poster not having any pre-existing knowledge about tumors or metastasis he would walk away having a good handle on what tumors are, their signs and symptoms, how they are diagnosed, and what can be done to treat them. The poster even accomplishes this without being entirely covered in text.

A tumor is an abnormal mass of cells while metastasis is the process by which cancer spreads from the place to distant locations in the body. Not all tumors will undergo metastasis and are referred to as benign. Tumors which do continue to grow and spread to other parts of the body via metastasis are referred to as malignant. Signs of such tumors could include seizure, headaches, anemia, lymphademiopathy, and hemoptysis, much of which depends where the tumor is located.

If you were to notice similar signs a doctor would order lab test such as blood tests for tumor marker, and a complete blood count (CBC). In addition to this he would order urine test for protein cytology. If any of these test were to suggest a tumor was present treatments are available but are not 100% effective.

Marcus used a variety of sources to compile his research; however he relied heavily on peer review journal articles. Some source obtained via pubmed, and other by obtaining the actual journal text.

Three major Themes

I hope you have enjoyed the discussions in my blog to this point, unfortunately this is my last blog entry. That being said we covered a lot of material this semester and if I had to pick 3 themes that wove there way through the material, I would pick:


1) The unique properties of water

2) Oxidation reactions

3) Reduction reactions


The unique properties of water are not only essential to biochemistry, but are essential to all of life. Chapter 2 of the text introduces us to the unique properties of water which included waters ability to act as a solvent, form hydrogen bonds, and act as an acid or base. These concepts were important to learn as they continued to appear throughout the semester.

Hydrogen bonding became a major instrument of the three dimensional structures of proteins. It was also a major theme of general chemistry as well as organic as it was a major predictor of a molecules tendency to react with other molecules.

Oxidation reactions involve the loss of electrons via a reducing agent. These reactions where discussed in chapter 17 of the text in the glycolysis cycle, specifically reaction 6. In this reaction the -CHO group of glyceraldehyde-3-phosphate is oxidized to a carboxyl group.

Reduction reaction comes hand in hand with oxidation reaction but, reduction reaction involves the gain of electrons. These reactions are happening at the same time as the oxidation reactions and can also be found in rxn 6 of the glycolysis cycle. NAD+ gets reduced to NADH.

Both reaction are key components of general chemistry and are involve in reaction such as the oxidation of copper to copper ion and the reduction of silver.

How would I explain the connection between glucose entering the body and energy created by the body to a friend using my new biochemistry knowledge?

If I was forced to explain the connection of glucose entering the body and energy being created by the body to my friends, I better either have a lot of time, or have a picture to show them. To help simplify this process I may mention the phrase “THROUGH A SERIES OF REACTIONS” often.

To get the ball rolling I would start by explaining that glucose is a carbohydrate in its simplest form called a monosaccharide. From there I would explain that for 1 molecule of glucose we will produce a net gain of approximately 36 ATP molecules each of which can be used by the body when energy is needed. To reach a glucose molecule's potential of 36 ATP the body must use 3 processes. (GlycolysisCitric Acid Cycle, and the Electron Transport Chain)

In glycolysis 1 glucose molecule will go through a series of 10 reactions which will produce 4 ATP molecules via substrate level phosphorylation, and 2NADH2 molecules. In this process glucose subsequently gets converted into 2 pyruvate molecules. To accomplish this task the body had to invest 2 ATP molecules to facilitate the reactions.

An addition 2 ATP will be by the cell to shuttle electrons from 2 NADH2 molecules produced in the cytosol.

In the Citric Acid Cycle each pyruvate molecule will go through a series of reactions and become 2 molecules of Acetyl CoA. Together the molecules will produce 6NADH2, 2 FADH, 2 GTP.

Finally in the Electron transport chain we begin to harness our energy. Each of the 10 NADH2 with produce approximately 3 ATP, totaling 30 ATP. Both FADH2’s will produces approximately 2 ATP, totaling 4 ATP.

10 NADH2 x 3 = 30
2 FADH2 x 2 = 4
2 ATP = 2
___________________
36 ATP

What knowlegde have I connected with past knowledge

As the semester continues to progress and discussion shifts from biochemical concepts to biochemical pathways, I find myself drawing many connections with the information I learned in Anatomy and Physiology. Having taken A&P I am finding it easier to retain the information presented in biochemistry because I am able to think about the material in relation to a biological system of the body.

In chapter 17 of the text we discussed glycolysis cycle, as it relates to the production of ATP. The glycolysis cycle was also discussed in GENERALITIES while taking Anatomy and Physiology, but at the time I often wondered how I was going to retain all that knowledge. What’s fun about taking A&P is that after studying glycolysis you can talk to friends and sound very intelligent on the topic. Now that I am in biochemistry and a conversation about glycolysis involves ten different reactions, numerous enzymes, and words like isomerization, I am told to get new friends.

Find an interesting biochemistry website and put its link in this entry, and describe briefly what is found there.

While doing research for this blog entry I was reminded what a power tool the internet can be. It was my goal to find an interesting biochemical website I could share with my fellow students and instructors alike. I aimed to find a website my classmate and I could use as a reference to nail down biochemical concepts especially biochemical pathways as I have found them to be extremely complex.

http://dwb4.unl.edu/Chem/CHEM869P/CHEM869PLinks/www.gwu.edu/~mpb/index.html

The name of this website is Metabolic Pathways of Biochemistry. This website is geared to students and teachers . This website’s primary focus is pathways utilized by the human body. I found this website to be organized, and easy to navigate. Once you find the pathway you are looking for and click on it, one will see an illustration of the pathway with labels in both 3D and 2D forms. Each pathway also has a step by step explanation of the process.

Although I am not yet familiar with all of the pathways listed at this website I feel like it is a valuable resource to have when trying to nail down a topic. Often times if I can explain what is going on in a graph with out looking at the description I retain the knowledge a lot better.

What knowledge have you connected with past knowledge?

In a pervious blog I mentioned that biology and chemistry are taught to students early in their scientific careers because it allows for a broad knowledge base. Having taken both biology and chemistry I often recognize concepts relevant to biochemistry.

Chapter 6 of our text “Protein and Enzymes” discusses the principles of thermodynamics which is a core topic in General Chemistry classes. I can remember learning these principles and found it challenging to grasp the concepts while in Gen. Chem. Today concepts such as activation energy, exergonic and endergonic reaction, and reaction rates are easily absorbed as I have a base knowledge. Biochemistry also allows us to connect these concepts to life processes. This allows me to conceptualize the information making it easier to get the big picture rather than a concept.

Chapter 8 of our text “Lipids and Membranes” directly correlates information I have discussed in detail while in anatomy and physiology. The phrase “structure depicts function” was repeated over and over again while in A&P, and is a concept I will continue to keep in mind while in biochemistry. The structure of the phospholipid bilayer membrane determines its function and ability to isolate the cell while allow certain molecules to pass through. The membrane of the cell performs many tasks, because of this many reaction take place to accomplish these task. While in A&P pathways were identified and discussed. In biochemistry we will build upon the base knowledge we have obtained to dig a little deeper.

As a science student I relate many of the classes to layers of an onion. Biology and chemistry we learn major concepts, and with each additional class we seem to pull another layer of the onion off, getting more and more detailed as we continue.

Find a protein using PDB explorer - decribe your protein, including what disease state or other real-world application it has.

For this exercise we were instructed to search PDBlite.org, which is a website designed to search for, and download macromolecules. There were no restrictions limiting our search criteria for these macromolecules. I decided to narrow my search to molecules relating to human alcohol dehydrogenase. Forty one related results matched my search. From this list I chose to explore the structure of Human Zinc-binding alcohol dehydrogenase 1 (ZADH1) pdb id # 2VNA.

With the above information I searched the National Center for Biotechnology Information for my molecule. From here I was able to identify my molecule derived from humans, and had tertiary structure as it only had a single unit/subunit. Shown above is a 3D image of the molecule which clearly shows the secondary structures: alpha helix and beta pleated sheets. Little information was given about the real world application of this molecule but it is assumed that it has a role with the binding of zinc to alcohol dehydrogenase. It is also assumed by the name of this molecule that alcohol dehydrogenase is an enzyme.


Having access to this tool allows researches to search known molecules by name, related topics, and even primary structure sequencing. Researchers now have the ability to compare unknown proteins or amino acids against researchers around the world. Another huge tool for researchers is the ability to search for molecules with a similar sequence against an existing molecule with a known function and make assumption on what function the unknown protein might have.