Three Major Themes

The three themes that I can identify from this course are molecules, structures and function. The first several chapters we focused on had to do with the building blocks of life. What and how the simple pieces fit into the larger structures. For example we studied amino acids which are important for DNA/RNA structure. We then focused on structures and how they are built affects what role they will play in the cell, their function. For example DNA/RNA contains information based on what sequences they contain, they ultimately participate in the control of the functioning of the entire cell. And lastly, function. We studied several important cellular metabolic processes that carry out life sustaining reactions. For example an enzyme is coded for in DNA/RNA and once expressed has a role in glycolysis which provides energy for the cell. The themes from the material in this course are connected to each other because they build on each other. Each piece of information is important to gain the big picture of what is going on in the cell.

I have studied much of the material that we covered in this class in previous science courses. However, I have gained the big picture in this class. I now have a perspective of how reactions happen in the cell and why. Before this course gene regulation, metabolism and cellular respiration were disjointed pieces of information in my mind but now they flow and I can see how they are connected. 

Explanation To a Friend

When you eat carbohydrates they go into you digestive system and are ultimately broken down into simple sugars, the most important being glucose. Glucose is sent off to individual cells which take the glucose into their innards, the cytosol. In the cell every one molecule of glucose is transformed into two molecules of pyruvate by an energy creating process called glycolysis. The pyruvates are handed off to these things inside the cell called mitochondria which convert glucose into Acetyl CoA.

Inside the mitochondria Acetyl CoA is put through a process called the citric acid cycle where even more energy is created. During both glycolysis and the citric acid cycle hydrogen atoms are primarily handed off to a molecule called nicotinamide adenine dinucleotide (NAD+) to form NADH. There is another molecule with the same function abbreviated FAD+ that gets changed to FADH₂ when hydrogen is added. The NADH and FADH₂ are responsible for handing those hydrogen atoms off to the electron transport chain.

The hydrogen atoms, aka: protons are pumped across a membrane in the mitochondria by the reactions of the electron transport chain and are allowed to travel back across the membrane though an enzyme called ATP Synthase. These protons passing through stimulate ATP Synthase to create energy. The currency of energy in the cell is in the form of molecules called ATP when we say energy is created it means ATP is made by adding a phosphate to ADP and conversely when we say energy is used it means ATP is changed back into ADP by removal of a phosphate. The whole process from glycolysis to the electron transport chain creates about 38 ATP for the cell to use as energy.

More connections with past knowledge

It’s interesting to be in lecture and realize that not only have I learned the material before but now we will be analyzing it in a new light. The integrative biochemistry perspective has made so many connections for me. I’m glad to have taken this class at the end of my undergrad because it is serving me well as a reminder of all the other science/lab classes I have taken. There are some areas that I’m realizing I need to delve further into and this class has opened doors for the possibilities of research.

There was one moment in class that I specifically remember when one of these bridges between knowledge being made was when we were talking about glycolysis and gluconeogenesis. I made this connection with endocrinology about the autonomic nervous system’s fight or flight response. I realized that these two metabolic pathways, while they generally occur unnoticed, are more influenced by an individual’s environment than simply by what the body is in need of at a given time.

Interesting Lens

http://www.squidoo.com/ChemistryOfDailyLife

I found a lens created by a PhD researcher “The Chemistry of Daily Life” which covers everyday biochemical topics. Her articles are easy to read, very informative and they just make you want to keep reading –bad science jokes included! The best part of this lens is that complex topics are explained simply but none of the science behind them is lost. The author encourages comments through the guestbook.

The topics covered are:

• Soap
• Veggies and color
• Pressure cooker dynamics
• Invisible ink recipe
• Onions make you cry
• Cholesterol
• Cigarettes
• Why is the sky blue
• Coffee
• Decaffeination
• The chemistry of love
• Lactose intolerance

Connections with past knowledge

A professor once told me that all science is science, that the lines between the disciplines frequently blur and the things which keep those from different disciplines from effectively communicating is either terminology or pretentiousness. While I have not encountered said pretentiousness I have seen the lines blur between scientific disciplines. I am finding that I have been exposed to a good majority of the material we are covering in this course at one point or another. I’ll be sitting in class listening and realize these connections to other classes I’ve taken. Some of the topics we discuss in class I have already covered in more detail in other classes. However, in biochemistry we discuss topics I have touched on but have not gone in depth with. Other classes from my education where the material overlaps are: environmental evolution, microbiology, soils, mycology, botany, chemistry, organic chemistry, biology, neurobiology, and neruoendocrinology. 

Green Fluorescent Protein (GFP)

PBD# 1GFL

GFP is found in Aequorea victoria, a jellyfish in the North Pacific. This protein is comprised of a “β-can,” which means it has a cylinder shape made up of 11 strands of β-sheet with an internal αhelix and short α-helices on the ends of the cylinder. This protein has biochemical significance because it emits light when shown light. When GFP is exposed to blue light (395 nm) it emits a green light (509 nm). Researchers have been able to create transgenic organisms that express GFP in whatever part of the organism being observed. GFP is conveniently able to fold by itself with no additional steps to make it fluoresce. Just attach this protein to what you want to observe and shine UV light on it, thus eliminating the need for staining processes. Since its discovery, GFP has been engineered to emit different colors. The resulting mutants of GFP can now fluoresce in blue and yellow. This protein has also been put to use as biosensors, glowing when detecting the presence of specific ions or pH changes.

Picture of GFP:

Applications of GFP have also spread into animal breeding for pets and art. The artist Eduardo Kac has created a transgenic bunny which he has titled “Alba.” Alba is an albino rabbit that glows green when exposed to blue light (488 nm). Breeders of pets are also exploring the applications of GFP to the point where now you can purchase fluorescent fish and plants. However, there is significant controversy regarding the safety and morality of genetically engineered pets.

Alba the fluorescent bunny:

What is Biochemistry?

Biochemistry is a study of the structure and function of organic molecules found in living systems and how these molecules react and are regulated within cells to form the mechanisms of all biological processes. While biochemistry spans a range of topics, the main focus is the biological basis of disease in humans, animals and plants. Because biochemistry is a broad based science there are many subspecialties which include, but are not limited to: neurochemistry, bioorganic chemistry, clinical/physical biochemistry, molecular genetics, biochemical pharmacology and immunochemistry. The molecules analyzed in biochemistry include: proteins, nucleic acids, lipids, vitamins and hormones/neurotransmitters. An example of biochemistry being put to work is seen in biopharmaceutical companies where protein drugs are exuded by genetically modified cells and subsequently purified from the resulting solution.


There are some subtle differences between the field of biochemistry and the fields of genetics, biology, chemistry and molecular biology but it is very important to note there are many instances where these sciences cross over. It is sometimes difficult to distinguish where a given topic may be categorized within this list.


What I believe are the main differences between these sciences:

• Biology includes studies of organisms that are not always mediated by organic chemical reactions  
• One of focus of chemistry is chemical reactions between elements not found in organic systems.
• While genetics is a study that is mainly focused on biological inheritance, biochemistry delves into other topics that may or may not include genetic materials.
• Molecular biology is a study that mainly focuses on the interactions within a cell while biochemistry goes beyond the membrane.