Three Major Themes

It seems that biochemistry class with Dr. K. is coming to an end. As I look back and think about some of the fascinating topics we have discussed it is very difficult to choose three. There are many things that I have learned before, not in such detail of course, in previous science courses. If I were to to choose three important topics that I have learned the most about and have connected most with past knowledge I would say protein structure, transcription/translation, and glycolysis. These topics were discussion in great detail during biochemistry lectures because they are some of the most important parts about biochemistry.
Proteins structure started our class off with a bang. We learned the basic principles and then got into great detail concerning this class of biological molecules that play such an important role in science today. I connect this topic with past knowledge that I learned in general bio when I first started my secondary education. Proteins were a great starting point because once these were discussed we were able to just into transcription and translation to see how they were created.
Transcription and translation were taught one after the other because they go together like pretzels and cream cheese (if you haven't tried it I strongly suggest it!). We had just learned about protein and their structure but we need to know how it all falls together. What a better topic to teach us than these processes. We learned the differences in prokaryotic and eukaryotic transcription and translation and we learned the importance of both of these processes.
One of the best parts about learning these processes was that they were also covered in great detail during our genetics class this semester. It was helpful to have both courses teach these processes because it created a stronger background for future sciences courses that I plan to take. There is so much going on during these processes that I am thankful that I took both genetics and biochemistry at the same time.
The third theme that I connect to other topics in this course is movement of these biomolecules known as proteins that we created during transcription and translation. Processes that were discussed range from the electron transport chain to glycolysis and gluconeogenesis. There are many different ways our bodies create energy and use the proteins we learned so much about. I was able to use a lot of what was taught in earlier classes this semester to help understand processes like glycolysis, metabolism of fatty acids, the electron transport chain, and gluconeogenesis.
I was able to connect all three of these themes with past knowledge that I learned in biology, general chemistry, anatomy and physiology, and even in recent studies such as genetics. I am glad to have studied these topics in such detail because I can explain their importance to others around me and I was always have this knowledge to further my education.

Explaining the connection between glucose entering the body and energy created by the body.

So you want to know how glucose can enter our bodies and then somehow we have all this energy to chase after our children? Well here is my attempt to simplify it for a normal human being that doesn't spend their free time folding and bending protein molecules online or watching videos of the metabolism of triacylglycerols. ;)
Glucose is a simple sugar also called a monosaccharide. It is very important, not just to the human body, but to many things such as plants and even bacteria. Glucose is a major form of energy for these things. Humans find a source of glucose in carbohydrates. These carbohydrates enter the body in forms of delicious (mmm moms homemade stuffing), and some not so delicious (yuk, shredded wheat), foods. Once the glucose enters the body it goes through an anaerobic process called glycolysis. Anaerobic simply means "without air" and in this process it means that it is done with out the presence of oxygen.
During glycolysis many changes are made to glucose in the form of chemical reactions. Parts are removed, some things are added, and completely new molecules are created! There are 10 steps to glycolysis and the end result are 2 molecules of pyruvate for every one molecule of glucose.
Pyruvate is important because this molecule can take 3 different pathways. In our case we want it to take the aerobic pathway called the citric acid cycle. During this cycle our body takes these molecules of pyruvate and through this pathway it is able to create 32 molecules of ATP (energy storage molecule) and have only used 1 ATP molecule.
These processes that I have mentioned are happening all the time and even simultaneously. If for every one molecule of glucose that enters our body we get 32 molecules of ATP that is an awful lot of energy our bodies can use to do many other the other amazing and complicated processes that we continue to learn more and more about through new technologies and scientific discoveries every day.

What Knowledge Have You Connected #2

Biochemistry is a field that is constantly changing and adapting due to new discoveries and technologies. It is a science that utilizes many of the other science fields to explain the complicated topics that biochemistry focuses on. Recently we have discussed, in detail, the processes of transcription and translation. Having a background of biology and chemistry is key to being able to understand what eukaryotic and prokaryotic DNA is capable of. Their importance to, not only biochemists but also geneticists and other scientists, reinforce how important these topics are to students and is why they are discussed in such detail in a biochemistry course. I can remember studying Okazaki fragments and polymerases in high school and thinking to myself how complicated the process of DNA replication seemed at that time. I now look back and am thankful for the background information I attained, no matter how simplified it was, because it has been extremely useful to me. Not just in aiding the learning of this more complicated version of it but also in realizing the importance of DNA and a cells ability to create and recreate.

Interesting Biochemistry Website Link and Brief Description

Below is a link to a great biochemistry website that allows you to "play" with proteins. The game is to fold, bend, and wiggle the amino acid ribbons into the correct three dimensional shape. The player has to take into account opposite charges attracting each other, angles of rotation, and hydrophobic and hydrophilic parts of the amino acid molecules. The closer you can get to the actual shape of the protein the more points you receive.
The game can be downloaded to your computer and you can play with the other 100,000 people that have downloaded the game. The original idea was to get more than just scientist into putting proteins in their correct shapes. People can work with different complex proteins from their homes and their structure ideas can be seen by the creators of the game.
The website where you can download this game is: http://fold.it/portal/
I strongly suggest you check out this game. It has a great theory behind it and is worth taking some time out and playing around with.

What Knowledge Have You Connected with Past Knowledge?

There is much information that my biochemistry class has discussed since the beginning of the semester that pertain to, and gather results and background information, from classes that I have previously taken. Some of these classes include, but are not limited to, General Biology 1 & 2, General Chemistry, Organic Chemistry, and Genetics. These classes served as an excellent background for this course. Recent covered material in biochemistry had to do with enzymes as inhibitors and activators. I was first introduced to enzymes back in general chemistry during my first year away at school. More general chemistry background was connected to our discussion of water, its properties, and how important it is in biochemistry. Material I am currently discussing in genetics is connected with biochemistry through DNA and proteins. The processes and functions of proteins that genetics covers are discussed in biochemistry as well as amino acid structure and much more.
So far I am interested in what I have learned and I am thankful that I have the background information from previous science classes to encourage and support the new material that is being introduced.

PDB Explorer Protein: Discription, Disease, and Real World Application.

The protein that I found interesting is called the Human Papillomavirus E2 Protein Type 16. Its pdb ID is IDTO. Many people have heard of HPV and the infection that it can cause. It is one of the most common sexually transmitted infections we know about today (cdc.gov). HPV Type 16 belongs to the papillomavirus E2 protein family and is located on the E2 gene.
This E2 gene is chain A and its function deals with nucleotide and DNA binding. Its processes are DNA replication and transcription. The E1-E2 protein complex binds to the the origin of DNA replication which allows it to regulate the replication by either activating or repressing transcription depending on its position.
Works cited:
www.cdc.gov/hpv/WhatIsHPV.html
http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocaids

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

Biochemistry is a description of life processes. All life processes use the same types of biomolecules that are studied throughout the field of biochemistry. Biochemistry studies these biological organisms through methods of chemistry. A firm background is key to understanding the connections that biochemistry has with the fields of genetics, general and molecular biology, and chemistry.
Biochemistry differs from the fields mentioned above because it describes life processes by its multidisciplinary nature. It utilizes the results and information described by genetics, general and molecular biology, and chemistry to answer questions about the molecular level of life processes. The information learned in the field of biochemistry has a great importance in the medical field and the future of health and disease.
Works cited:
Campbell, M. and Farrell, S. Biochemistry. 6th Edition. California: Brooks/ Cole, 2008.