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?

As this course comes to a close if I had to choose three themes that connect the topics discussed in this class I would have to choose amino acids, enzymes and energy production. More specifically amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. As we have seen in this class amino acids, which are defined by a unique sequence of amine residues, play an essential role in our daily lives. They are most commonly thought of as being the building blocks of proteins. Specifically amino acids join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribosome. The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes. As is evidenced amino acids clearly play an integral role in not only biochemistry but genetics as well.


With regards to enzymes if there is anything that this class has taught us is that there is an infinite number of enzymes. Further, there can be any number of enzymes that catalyze a particular reaction with many reactions having one specific enzyme dedicated to it. For example the eighth step of glycolysis requires phosphoglycerate mutase in order for the reaction to occur. Further, by definition enzymes are proteins which speed up a chemical reaction by lowering the energy needed for the reaction to occur. Lastly, considering that enzymes are proteins and proteins are made up of chains of amino acids it is easy to see how they connect.

Finally, the production of energy has also been an important theme in this course as well. Most notably we spent several weeks examining mechanisms such as glycolysis, the citric acid cycle and the electron transport chain. All of these mechanisms are metabolic pathways that lead to the production of ATP which is the body’s primary energy source. Further, all of these cycles rely heavily upon the use of enzymes. If it wasn’t for enzymes the reactions in these pathways, which are endergonic meaning they are not thermodynamically favorably, would not occur on their own. Thus, enzymes which as I already noted are made of proteins, are truly necessary to ensure that the body is capable of producing energy.

Lastly, while the themes related to amino acids, enzymes and energy production were not altogether new to me this class certainly went into them in much greater detail than any of my previous classes. I was able to fill in a lot of gaps from previous classes regarding things such as the way enzymes bind using the induced model to gaining a greater understanding of how the steps on glycolysis work together to yield ATP. Finally what I appreciated most about this class was how it helped me to put all of these themes and concepts in perspective. In past classes enzymes or translation for example have always been taught one by one, almost as if they were being compartmentalized. Taking this class was refreshing as it allowed me to see how all of these processes work together.

How would you explain the connection between glucose entering the body and energy created by the body to a friend?

Glucose is the molecule our bodies use the most often to fuel our energy needs. The reason for this being that for many people a large portion of their diet is made up of carbohydrates. Glucose just happens to be a carbohydrate. More specifically glucose is a monosaccharide or simple sugar. Unfortunately, the carbohydrates that we eat are usually not simple sugars, but long chains of sugars known as polysaccharides. Thankfully we have something called salivary amylase or saliva in our mouths. Thus the minute we put food in our mouths the amylase begins the process of breaking down the food, both mechanically and chemically. Once a carbohydrate for example is broken down into glucose, glucose can then enter the metabolic pathway known as glycolysis.


Glycolysis occurs in the cytoplasm of cells in all living organisms, not just in humans. It is an anaerobic process that converts one molecule of glucose into two molecules of pyruvate. Although it would be wonderful if glycolysis was an instantaneous reaction it actually takes some time as the conversion of glucose to pyruvate requires ten separate steps which modify the glucose. These ten steps include several phosphorlyations, wherein a phosphate is added, as well as several isomerizations ,where the arrangement of the atom is merely altered. In spite of having to wait on these ten steps glycolysis is certainly worthwhile as it produces two molecules of ATP which can be used as energy for the body. It also yields two molecules of pyruvate which can then be sent on to other pathways such as the citric acid cycle, which in conjunction with the electron transport chain, can produce thirty two molecules of ATP. This ATP will certainly help our body to maintain normal functioning.

What knowledge have you connected with past knowledge?

Just when I thought I was safe from concepts such as redox reactions and glycolysis I once again find myself revisiting these concepts only in greater detail. Had you asked me a few weeks ago to explain redox reactions I would have likely said “Leo the Lion Goes Grrrrr”. I know it is a rather childish pneumonic, but it was engrained in me by my tenth grade honors chemistry teacher as a way to remember that loss of electrons is oxidation and gain in electrons is reduction, hence the Leo and the Grr. Howeverm after taking this class I like to think that I am slightly more enlightened and would be able to explain redox reactions as coupled reactions that are essential to metabolic pathways.


Another concept that has spurred old memories from a past class is that of chirality. When I think of chirality my thoughts immediately drift back to organic chemistry. Chirality was one of the few things in organic chemistry that made sense to me. I was thus pleased when it was introduced again in biochemistry. I will even admit to slightly enjoying deciding whether a particular glycosidic linkage was D or L or alpha or beta. It is funny as back in organic I remember thinking it was difficult at first and now it is one of the easier parts of biochemistry.

Lastly, the topic of glycolysis is something that has been touched on in most of my previous science courses and yet it is still challenging. My introduction to glycolysis was in 9th grade biology when I had to memorize the ten reactions in their most basic form. Ever since then my knowledge and understanding of glycolysis has been steadily increasing. It may just be that I am finally getting it after so many lectures upon the topic. I also think that the different ways it has been presented in classes such as biology or anatomy and physiology versus biochemistry has really helped me to garner an understanding. For example, anatomy focuses on where in the body glycolsyis takes place and how glycolysis is paired with other processes to meet the body’s energy needs. Alternately, biochemistry focuses on understanding the intricate mixing of the substrates, enzymes and products that play a part in glycolysis. Thus far this class has really helped my understanding of glycolysis and moved it far beyond a mere process that yields two molecules of ATP per molecule of glucose.

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

http://spdbv.vital-it.ch/TheMolecularLevel/Biochem/Text/Topics.html


The above link references an interesting website I discovered that has a plethora of information regarding biochemistry. The site was put together by Gale Rhodes a now retired Emeritus Professor of Chemistry from the University of Southern Maine. The site is organized using a simple chart. The first column names a topic, the second column lists the essential skills one should have after learning about the topic, the third column gives one strategies for learning the information and the last column offers links to exercises that use visuals or graphics to explain the topic. For example one topic is that of protein structure and function. If one looks at the essential skills there is a list of the things one should know and be able to understand after having studied protein structure and function. In essence this is a study guide to better help you narrow down what it is that you need to focus on. The next column offers learning strategies that entail both review and memorization. That is Professor Rhodes tells you what information you should revisit from prior classes as well as what current information needs to be committed to memory. The memorization aspect is minimal and required only so that one is able read a biochemistry article without having to stop and look up every other word. This column also has suggested problems which are helpful when one is studying for a quiz or exam. The last column uses visual examples to help enhance learning. In the case of protein structure and function the first exercise actually walks you through using a model kit. It is a simple exercise but really helps to reinforce protein structure. More in-depth exercises call for the use of the Swiss-PdbViewer. There are links for individual proteins followed by instructions on how to locate and identify everything from hydrogen bonding to beta pleated sheets. Overall I really like the website. I think it is organized well and appeals to many different types of learners. Whether you like to do problems in order to understand a concept, or whether you need a visual representation to understand, this website has it all.

What knowledge have you connected with past knowledge?

Thus far this course has proved to be quite interesting. I have seen many connections with topics I have learned about in past classes including general chemistry, biology and even a smattering of psychology. I almost feel as though this class is letting me in on all the secrets that other classes have kept from me. Perhaps the best example of this is in to regards enzymes and their structure. More specifically, past courses have always espoused the four types of structural components ranging from primary to quaternary structure. What struck me as odd was that up until this semester I was not aware that secondary structure encompassed more than alpha helices and beta pleated sheets. I was unaware of the existence of beta bulges or supersecondary structures such as motifs. Additionally, I have always been taught that the enzyme substrate complex is a model much akin to a lock and a key. It wasn’t until this class that I was introduced to the induced fit model wherein the binding of a substrate to an enzyme at the active site initiates a change in the active site such that there is tight bonding. I find the induced fit model much more interesting and plausible.

Further, since the beginning of the semester this class has made me stop and assess what is in everything from the food that I eat, to the medicine that I take. In one particular instance I took some Sudafed for a head cold and was surprised that the warning on the side of the box said not to take with monoamine oxidase inhibitors (MAOIs). I was slightly intrigued as my introductory psychology class had taught me that MAOIs were used to treat depression. I didn’t see the connection between cold medicines like Sudafed and MAOIs until I took this course. In this course I learned that MAOIs allow for greater levels of tryptophan and tyrosine which are the precursors of several important neurotransmitters including epinephrine, serotonin and dopamine. It is these neurotransmitters which help one to moderate mood and act as antidepressants. The drawback however to MAOIs is that the increased presence of tryptophan and tyrosine in the blood can interact with certain foods or medicine such as Sudafed to induce dangerously high blood pressure that is aptly described as hypertensive crisis. Hypertensive crisis symptoms include high blood pressure, severe headache, anxiety and even shortness of breath. Needless to say I was shocked to discover that taking a medicine as common as Sudafed along with an MAOI could have such extreme ramifications.

As is evident, this course has undoubtedly given me some new insights into everything from enzyme structure and function to fatal drug interactions. While this course is almost half over I look forward to uncovering more connections between course materials and my past learning experiences.

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

The protein that I chose to look at was Lactose-Liganded Congerin I. This particular protein is part of the galectin family and is found in the skin mucous of the conger eel. Proteins from the galectin family perform several different biological activities. Congerin I is known for its activity against marine bacteria and starfish embryos. As such it is also plays an important role in conger eels’ biological defense mechanism against parasites. The structure of Congerin I is shown to the left. As is evident the protein is a homodimer and as such it possesses secondary structure. Lastly this secondary structure has a bounty of both alpha helices and beta pleated sheets.

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

Biochemistry can be defined as the application of chemistry to the study of biological processes at both the molecular and cellular levels. As both a life and chemical science, biochemistry explores the chemistry of living organisms, paying particular attention to the molecular basis for the changes that occur in living cells. Using methods from disciplines including physics, chemistry, molecular biology, immunology and genetics, biochemistry looks at the structure and behavior of the complex molecules found in biological material and the ways these molecules interact to form cells, tissues and entire organisms. For example biochemists seek to understand brain functioning, cellular communication within and between cells and organs, and lastly the chemical basis of inheritance and disease. Biochemists explore how molecules such as proteins, lipids and nucleic acids function in the aforementioned processes with emphasis placed on regulating chemical reactions within cells. Accordingly, biochemistry differs from fields like chemistry, biology, genetics and molecular biology in that it truly encompasses various aspects of each of these disciplines. That is chemistry, for example, focuses solely on the properties, composition, and activities of various elementary forms of matter; while biology is the study of life and living organisms. Further subdivisions in the field of biology include genetics which is the study of heredity and variation in living organisms, and molecular biology which looks at life at the molecular level with a focus on interactions between the various systems of a cell, including the interactions between DNA, RNA and protein synthesis, as well as learning how these interactions are regulated. As is evident biochemistry differs from discipline such as chemistry or genetics in that it can’t stand alone. Biochemistry relies on these other science disciplines to aid in its own research and studies.