Biochemistry

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

Biochemistry is the study of all of the chemical processes present in living organisms.(encyclopedia.com) The only way that biochemistry differs from all of the fields listed above is that it is a combination of all of them not a derivation. Each of the above stated fields contribute their own piece to what makes up biochemistry. Biomolecules, proteins, carbohydrates, lipids, nucleic acids, and the genetic code are all included in the study of biochemistry and each of those is extensively covered in one or more of the above fields.

Genetics is the study of the effect of genetic differences on organisms. Biochemistry is clearly a huge component of biology that studies the basic building blocks; Cells are the basic unit of life, new species and inherited traits are the product of evolution, genes are the basic unit of heredity, living organisms consume and transform energy, and an organism will regulate its internal environment to maintain a stable and constant condition.

Subdisciplines of biology are recognized on the basis of the level at which organisms are studied and the methods used to study them: biochemistry examines the basic chemistry of life and molecular biology studies the complex interactions of systems of biological molecules. Individuals need to have a familiar background in chemistry, biology, genetics and molecular biology to fully comprehend what is indeed happening in the various chemical reactions within an organism.(Biochemistry, Campbell & Farrell)

Image source: biochemistrybu.com

My Protein

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

IBX2 is a crystallized myelin protein related to the disease mulitiple sclerosis. In multiple sclerosis, the immune system launches an attack against the myelin sheath surrounding nerve cells, causing them to misfire. According to the Multiple Sclerosis Foundation, up to 500,000 people in the United States have been diagnosed with the condition, which causes varying symptoms depending on the location and extent of the scarring of the myelin sheath. Common symptoms include fatigue, weakness, vertigo, numbness and vision problems.This protein - alphaB-crystallin - is not normally found in the brain, but develops in response to the injuries inflicted on nerve cells by multiple sclerosis. The nerve-cell injuries can cause people to suffer loss of motor control and even paralysis.



This protein shows to have tertiary structure due to it's three dimensional structure. Also containing alpha helices and beta pleated sheets.

image source: ncbi.nlm.nih.gov

Connections

What knowledge have you connected with past knowledge?

I'm not a biology major and I haven't taken as many of the courses that my classmates have, but I have made connections nonetheless. The most that I can relate to, so far in this course, is Anatomy and Physiology. All of the connections topic presentations remind me a lot of the information and material that was covered in A&P. A topic that is relevent in my life and fresh in my mind is the myelination of nerve cells and its relation to multiple sclerosis.

In A&P we focused on how the main purpose of a myelin layer (or sheath) is to increase the speed at which impulses propagate along the myelinated fiber. Just in the most recent chapters covered in this class we discussed sphingolipids with respect to myelin , sphingomyelin. Demyelination is the loss of the myelin sheath insulating the nerves, and is the hallmark of some neurodegenerative autoimmune diseases, including multiple sclerosis.

My aunt recently passed away and she had MS so this disease has played a major role in my life. In the past few chapters learning about lipids and membranes more exclusively and connecting that with everything that I have learnt previously in A&P has only helped me to make more connections about this particular disease that was not already obvious to me. The more I absorb from every class the more all of this "connects" within my mind, no pun intended. It is easy to get a generic two sentence definition of a disease from "webmd", but the more I become familiar with the biology and chemistry involved in the causes for diseases present with in living organisms the more I realize how truly complex these processes are.

Biochem Website

Find an interesting biochemistry website and put its link in this entry, and describe briefly what is found there.
http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm


All of the interactive animations on this website visually demonstrate various biochemical processes and there are also tabs that provide ways to learn and become familiar with other biochemical concepts such as pH and buffers, redox reactions, thermodynamics, logarithms, and elementary kinetics. The animations show processes like DNA replication, cloning, the Cori Cycle, the central dogma of biochemistry, catalysis, cell structure, enzyme inhibition and so many more. You all should definitely check out this site because I think it will be extremely beneficial when studying!

Brief Description of all the tabs:
Concept reviews: is a refresher on critical chemistry concepts
Interactive animations: help review/learn particular biochemical processes
Structure Tutorials: designed to help students learn biochemical structures ( also interactive)
Cutting edge: shows articles that relate to how biochemistry is used to solve real-world problems
Web links: more links to help fully understand biochemistry
Quizzes: (divided by course material) just to help refresh and become more familiar with study topics

Here is an example of one of the interactive tutorials, DNA Replication:
http://www.wiley.com/legacy/college/boyer/0470003790/animations/images/cib_logo.gif

You NEED to visit Wiley.com :)

Knowledge

What knowledge have you connected with past knowledge?
Choosing to discuss three topics that I have become more familiar with and connected with my past knowledge, I would choose glycolysis, the citric acid cycle, and the function of enzymes. I am very much interested in nutrition and how the body metabolizes the different substances that are taken in. Simply from a diet standpoint, I've learnt how the size of proteins makes them harder to digest(over fats and carbohydrates) and how too much of anything is converted to fat, which is not what I wanted to read.
Through researching my biochemical connection topic I learnt so much about how the body stores and utilizes fat. A lot of that research involved the citric acid cycle and how it is a metabolic pathway involved in the chemical conversion of fats, carbs, and proteins into useable energy for the body. The roles of the citric acid cycle and glycolysis are huge within our bodies and as much as I took away from anatomy and physiology I took so much more out of this class. Enzymes are also a major topic that is discussed in most every science course I have taken here. My knowledge had been expended greatly and I feel more confident now advancing in my education as it is going to only get more involved from this point on as I learn more.

Glucose

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

Well fortunately, I could draw heavily upon both my knowledge gained by taking a year of A & P and also from the text book that we used in the class, the Fundamentals of Anatomy & Physiology 2008, written by Martini and Nath. I would have to choose the friend to whom I chose to explain this process too carefully, but nevertheless, here is how it would go.

Glucose is a six carbon sugar, C6H12O6 and is the preferred energy source for most cells and in most circumstances is the only energy source available for one’s neurons, due to the blood brain barrier existing in mammals. When we take in food, our bodies convert this food into smaller molecular subunits. This process is known as catabolism and is the backbone of our existence so to speak. Well once we get the food broken down, the cells of our body typically receive the byproduct of the catabolic or digestive process in the form of glucose from the blood.

The cells in turn actively transports these critical molecules into the cell membrane and ultimately to the mitochondria, where the sugar is further catabolized. The molecules of sugar are broken down into many other intermediate products, until these products are broken down to acetyl CO enzyme a, thus the cycle, same starting and ending product. Ultimately ATP synthase is to be driven by an H+ ion gradient and the cycle goes on in our own bodies each and every day. It is just fascinating, Are you still awake?

Reflection

Reflecting back on the course, what are three major themes you would identify that connect the 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 semester is not quite half way to its completion, so it is impossible to fully reflect or to fully evaluate the impact that Biochemistry will have on me. I can however say that I cannot imagine attending PA school (Knock of Wood) without this course. Every class, my understanding of processes and systems I thought I understood come into focus and become clearer. Looking forward from here, I see this class and the experience gained by it making Organic Chemistry much more manageable.

The scope of this class is perfect when considering it as an introduction to the organic concepts needed to succeed in a legendarily hard class. Meanwhile, the introduction organizing and creating the various media sites that we have been working on may one day come in handy. The world is changing rapidly and technology is steadily creeping into our lives and not by osmosis either, this is full scale active transport.

From the Iphone that I carry, allowing me access to the internet from just about anywhere in the world, to texting and keeping up with the events of my life, as well as the lives of my family and friends (Note: IF you have 4 Iphones, you can pop popcorn with them, LOOK that up on UTUBE when you get the chance!!!) to the laptop computer that I am writing this blog entry with; our lives are changing and the experience given by the technology related portion of this class with help to keep me relevant in the days and years to come.