Reflecting back on the course, what are the three major themes you would identify that connect the various topics discussed in this course – how are t

As discussed earlier in this blog, the subject of Biochemistry is the study of the chemical processes in living organisms. This knowledge along with other science disciplines gives us the tools we need to fully understand the biological processes and their purposes. This course focused on the three major themes of the structure, the function and the connection between biomolecules.

With each biomolecule we studied we began with the structure of each one individually. If there is one thing that I know that I will always remember from Dr. K’s lectures, it is that “structure determines function”. She said this many times in organic chemistry and she repeated it in biochemistry. So clearly, an understanding of structure is necessary for the understanding of function. Proteins were discussed in detail because proteins make up many of the biomolecules that are important in many of the biological processes. The structure of a protein is very important in the way that it will react with other molecules. In fact it is the way that these molecules react with each other that give us the chemical reactions necessary for life. We also discussed carbohydrates and sugars. The structure of these molecules is different and the different structures are important in how they will provide energy for the cell.

Function was also discussed in detail. We studied how enzymes catalyze reactions and how the structure of an enzyme determines what it will catalyze. We studied how DNA holds genetic code, replicates and translates. The function of DNA is important in relaying information necessary for life to proceed. Lipids were discussed as well. These molecules have an important function of providing energy and storing it in a way that allows the organism to be still mobile and productive.

Finally we studied the connection between all of these biomolecules. The metabolic processes took all of these biomolecules and showed how they proceed through many chemical reactions to provide energy and store energy necessary for life. When we were discussing ATP Synthase in oxidative phosphorylation it was stressed that F0 and F1 were both necessary for ATP production to be successful. Like F0 and F1 it is necessary for all of these biomolecules to be present and react with one another for life to continue. It is when one of these processes is not functioning properly or its structure has been modified that we develop disease or death of an organism. It is true that all systems affect one another from the top of your head all the way to your toes.

Biochemistry showed us what these biomolecules look like, how they behave and how they work together to provide the necessary reactions for life. This understanding and knowledge will be valuable when we continue our journeys into the scientific world that we are all heading for.

Answers to presentation questions

Thank you all for your nice comments regarding my oral presentation. I am going to try to answer the questions that you asked.

1. Do acids play a role in the predisposition of getting cavities? Will all that consume acids get cavities or is this related to genes or a combination of both?
The process of getting decay is also related to the amount of time that the tooth is exposed to the acids. If someone consumes one soda a day with there lunch (over a 15-20 minute period) compared to someone else that consumes the same one soda a day but, leaves it at their desk and sips it every 20 minutes or so. The person sipping the soda will have far more decay than the person that drinks it down in 15 minutes. This is because the sipper is constantly bathing the teeth in acids throughout the day.
As far as being predisposed to decay, it is true that some individuals or cultures have lower decay rates. This is due to the hardness of the enamel as well as diet. As I mentioned in my presentation, communities with higher levels of fluoride have harder enamel and are then less likely to develop decay.

2. Should people without city water supplement their fluoride?
As a child with un-erupted teeth, fluoride supplement is recommended to help harden the now forming permanent teeth. Once the tooth is erupted into the mouth the only way that fluoride is beneficial is through topical use, such as: fluoride treatments at the dentist or through use of fluoride toothpaste or mouth rinses. If you are not on city water it is very important to have your water tested for natural fluoride before any supplement is given to a child. Too much fluoride can result in discoloring of the teeth ranging from white spots to brown spots depending on how much fluoride is given.

3. How long does it take for tooth to decay?
It will vary for all individuals. It depends on hardness of enamel, level of pH and the amount of time the tooth is exposed.

4. Where can I get xylitol?
My best suggestion is to ask your dentist for a toothpaste that contains xylitol. Keep reading the ingredients, in time you will find over the counter toothpastes containing xylitol.

5. What type of bacteria occurs in cases that require root canals?
When a tooth is in need of a root canal it is because the center of the tooth, where the nerve and blood supply of the tooth are, have been infected with bacteria. This is often due to a large amount of decay. Since this is inside the tooth, there is not very much oxygen available and the bacteria involved are likely anaerobic.

I hope that I have answered everyone’s questions.

How would you explain the connection between glucose entering the body and energy created by the body to a friend, using your new biochemistry knowled

For many this would need to be simplified for a better understanding. I would begin with; foods containing carbohydrates (sugars) are broken down and converted to energy by our bodies. Carbohydrates enter the body through foods that we eat and are broken down into smaller microscopic pieces that we call glucose. These glucose molecules are broken down even further in a process called glycolysis. Glycolysis has ten steps. Each of these steps changes the molecule slightly or breaks it apart until the glucose molecule is finally converted to two pyruvate molecules. In this process energy is used and energy is made. It has a 1:2 ratio of energy used to energy made.

After the glucose has been converted to pyruvate it can then enter one of two different processes depending on the oxygen available. If oxygen is not present the pyruvate will take the path of anaerobic glycolysis. In this process it is converted to lactate. The lactate is stored in the muscles and can be recycled in the liver back to pyruvate or even glucose to be used for energy synthesis. If oxygen is present the pyruvate will enter the citric acid cycle. This process is cyclic and is a high energy producer. In this process there is a 1:32 ratio of energy used to energy produced.

These processes are all very intricate and efficient. They are continuous and all proceed at the same time. There are many enzymes used to help this process continue at a very rapid rate. By breaking down food and making energy at the same time we are able to maintain a constant state of equilibrium and continue to function and be productive on a daily basis.

What knowledge have you connected with past knowledge?

Since the last knowledge connection question we have discussed the structure of DNA, transcription and translation. In biology we discussed the processes of transcription and translation as well as the structure of DNA. We discussed DNA further in chemistry. In biochemistry the discussion was more in depth. We discussed the interactions of other proteins with the DNA and in more detail the super structures. Transcription and translation put more emphasis on transcription factors, enzymes and initiation factors. Before this class it seemed like we knew about these subjects from other courses. After taking it we realize that we have only scratched the surface.

Now we are beginning to discuss catabolism and anabolism. These subjects were discussed in biology as well. We memorized the Citric Acid Cycle without fully understanding the chemical process. In chemistry we learned about oxidation reactions and redox reactions. In this course we are putting the two together. Making the connection helps to understand why a reductive process requires energy and an oxidative process releases energy. Further discussion in biochemistry focused on the reactions that occur between each of the ten steps of glycolysis. This showed in more detail how one sugar molecule proceeds through the cycle to become two pyruvate molecules ready to advance to other pathways depending on the conditions. As with transcription and translation this discussion reminds us of the magnitude of importance that these small steps have on everyday functions. It also gives us the understanding of how small irregularities can have a huge impact on the overall processes.

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

http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.swf

This is an interesting site that has an animated version of DNA replication. It is another way to show the replication process and explain the various processes that occur. After the animation there is a quiz to see if you were paying attention. These kinds of sites help to give you a visual of the process and make it a little easier to understand and remember. Good luck on the quiz.

http://biology.clc.uc.edu/courses/bio104/lipids.htm

Lipids: Fats, Oils, Waxes, etc.

By: J. Stein Carter (1996)

This site is a good resource for lipids. Everything you wanted to know about lipids. The chemical structures along with some information regarding each kind lipids.

http://themedicalbiochemistrypage.org/home.html

The Medical Biochemistry Page, by: Michael W. King PhD; copyright 1996

This is a very large site with links to many biochemistry topics. There are also links to diseases and disorders as well as treatments of disease. If there is a particular biochemical reaction or process you are interested in, you can search for that and then follow links to find disorders caused by abnormalities or malfunctions of this process. This is a site that can be helpful if you are looking for specific information regarding a particular disease. It can also be helpful if you are looking for a broad overview of the impact that minute disruptions in the molecular processes can have on life.

What knowledge have you connected with past knowledge?

There have been many examples of connections between what we are learning in biochemistry and what we have learned in other disciplines. In general chemistry we learned about the rate equation and in biochemistry we can apply it to reactions that occur within the cell. In organic chemistry we learned about functional groups and in biochemistry we are able to recognize those functional groups in amino acids and the importance of how structure determines function. In biology we studied the organelles of a cell and in biochemistry we examine the chemical reactions that occur within the organelles. In physics we studied kinetics and in biochemistry we are able to relate kinetics to reactions that occur within the cell.

In biochemistry we recently discussed the functions of enzymes and the enzyme deficient disease that comes to mind is Lactose Intolerance. The intolerance is caused from an over abundance of lactose (milk products) and a deficiency in lactase enzyme to bind with the substrate to catalyze the breakdown of the milk. People who are lactose intolerant are not able to produce the necessary lactase to keep up with the abundance of substrate. In these cases the rate of the reaction is zero order because the concentration of the substrate is so high that the enzyme is completely saturated with reactant molecules. (Campbell, p. 147) Without the catalyst the lactose remains in the intestine and ferments. This causes a production of gas that is painful and uncomfortable. In biochemistry we learned that enzymes can bind, catalyze and are released to bind again with another substrate. This may explain why some adults continue to drink milk without any ill effects. Studies have shown that adult mammals normally have a 90 to 95 percent reduction in birth lactase levels. (Swagerty, 2002) This suggests that lactase deficiencies are normal and that people who are able to tolerate large amounts of milk products are abnormal. As an infant or young child it is necessary to have large quantities of milk products making it necessary for the body to produce large amounts of enzyme to digest them. Once the body has matured the need for milk products is decreased and the need for enzyme to digest it decreases as well. In people that continue to intake large amounts of milk products, there is likely a message that is sent to continue to produce the enzyme. Since the body is likely to have a significant reduction in enzyme production it is required to reuse the enzymes over and over to keep up with the demand for a catalyst.



Reference:
• Campbell, Mark K., Farrell, Shawn O. (2008), Biochemistry, sixth edition
• National Digestive Disease Information Clearinghouse (June 2009), retrieved 2/25/2010 from: http://digestive.niddk.nih.gov/ddiseases/pubs/lactoseintolerance/
• Swagerty, Daniel L. JR., M.D., M.P.H., Walling, Anne D. M.D., and Klein, Robert M. PH.D. (May 2002), American Academy of Family Physicians, retrieved 2/25/2010 from: http://www.aafp.org/afp/2002/0501/p1845.html

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

1K8Q - Dog Gastric Lipase






Used for fat digestion in dogs. This is a very stable protein despite the high acidic conditions that occur with in the stomach. This is a quaternary structure with 2 subunits. It is a globular protein.

Reference:
• National Center for Biotechnology Information (Oct. 2009), retrieved 2/14/2010 form: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=18937