Major Themes in Biochemistry

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?

Three major themes in this course that I would identify as themes that connect the various topics discussed in this course would be:

Molecules as Building Blocks, Activity vs Inactivity, and Major Macromolecules as Energy Sources

 Molecules as Building Blocks: This theme was made evident in Biochem through the various lecture topics which all addressed at least one of the four classes of small molecules (amino acids, carbs, lipids, and nucleosides or nucleotides) as the building block to one or more important biomolecular structures. 


Activity vs Inactivity: This theme was made evident in Biochemistry lecture topics which explored stereoisomers of different biomolecular structures and their optically active forms vs their inactive forms. Stereoisomers are compounds with the same kinds and numbers of atoms, but with different molecular arrangements. Typically, most of the biomolecular structures that we discussed are only found in one of the possible stereoisomers. The naming systems which we learned (L/D forms and Alpha/Beta forms) help to distinguish whether or not a compound is in its active form or not and also whether or not there needs to be any conformational changes made to the structure before it can play its role in whatever process it may be involved in.


Macromolecules as Energy Sources: This theme was prominent throughout all of our lectures in Biochem and can possibly even be seen as an umbrella theme under which many of the others fall. The different cycles and mechanisms which we explored as part of the cycle of cellular respiration all play a role in the breakdown of Carbs, Protein, and Fat so that those macromolecules can be utilized for energy sources. What I found especially interesting about this theme in biochemistry was discovering how many ways these macromolecules can be used and the functions they serve in the body. For example, proteins are not just the building blocks of muscle tissue but can be found as part of DNA structure, hormones, enzymes, and as the material for many other essential structures and substances. Carbohydrates make up different parts of nucleotides and are also present in some components of ALL cell membranes. Lipids too are an essential component of membranes, and they also help to transport some vitamins (lipid soluble ones A,D,E,K) and are important energy stores in both plans and animals. 

Glucose and Energy

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? The foods that we eat are mixed with acid and enzymes on the way from our mouth into the stomach and finally the intestines, where the majority of the breakdown takes place. By 'breakdown', what I am referencing is the process by which the energy you ingest in the form of whatever food it is that you eat is subjected to these acids and enzymes which break the food up into molecules of sugars, called glucose. This glucose is absorbed by the stomach and small intestines and then released into the bloodstream, where it can be utilized as an immediate source of energy, or it can be stored back in our bodies to be used at a later time. The hormone insulin plays a key role in regulating the amount of glucose in the bloodstream at any given time. Insulin that is released from the pancreas travels through the bloodstream to the body's cell and orders that the glucose be let inside. Inside the cell, the cellular respiration set of metabolic reactions takes place and the glucose can either be utilized or stored. For example, if a large meal is eaten, and the body doesn't need that much glucose right away, insulin will act to help the body store the glucose so that it can be converted into energy later. The method by which insulin helps to store glucose involves larger packages of glucose, called glycogen. These glycogen packages are stored in both the liver and the muscles. One more important note about insulin is that in addition to helping us store the glucose from the meal, it can also help store the fat and the protein too. As discussed in class, although glucose is the preferred energy source, the body will also resort to fat stores and even protein if it is in a state where it requires the extra energy.

L-Carnitine

Thus far in Biochemistry, some new knowledge that I have connected with past knowledge is about the ammonium compound carnitine, which is biosynthesized from the amino acids lysine and methionine. Before learning about Carnitine in biochemistry, my only knowledge about it was from having seen it marketed as a workout supplement by itself, most often labeled as L-Carnitine.

In living cells, Carnitine is required for the transport of fatty acids from the cytosol into the mitochondria during the breakdown of lipids for the generation of metabolic energy. The reason that I have most often seen it labeled as L-Carnitine is because, as we learned in class, many amino acids (and other products of metabolism) have two forms that are mirror images of each other and are considered the L and D forms of the substance, based on chemical structure. the L form is the biologically active form of Carnitine, whereas the D-form is the enantiomer and is not a marketed product because it is biologically inactive.

Even if you are not considered an athlete, there is medical evidence that suggests that the body's production of carnitine slows just with age. As a result, many nutritionists have begun suggesting that their older clients increase dietary sources of carnitine, which are mainly derived from the muscle, kidney, and liver content of animal products but some plant sources can also be found in avocado, alfafa, and wheat germ.

BIOCHEMISTRY WEBSITE

http://www.wiley.com/college/boyer/0470003790/animations/translation/translation.htm

This is the perfect interactive website tool to replicate the synthesis of proteins. Although this particular slide is on the proteins involved in just the transcription and translation processes, there are a wide variety of animations available to watch but simply returning one webpage closer to wiley.com and then there will be a list of all animations available.      

       In addition to this website, there are numerous other interactive biochemistry webpages which I came across by typing in the key word animation. Being somewhat of a visual learner, I find these to be extremely helpful!

KNOWLEDGE CONNECTED WITH PAST KNOWLEDGE

I have had a great deal of previous learning experience dealing with both enzymes and hormones and proteins which function as enzymes. Now that we are involved in discussing this topic, I have found the lecture material to be a reminder of the importance of the many different functions that a protein can have in the body. Our discussion on subunits and the folding of a protein structure is both a connection with past knowledge I have as well as one of what I find to be the most interesting aspects of our biochemistry class so far. I can recall having been introduced to this material but the identification of which amino acids are part of which structures, as well as the action of enzymes on protein structure to either catalyze a reaction or alter it in some way, are new aspects of protein identification to me. I truly do find protein structure and synthesis to be an interesting topic to cover and one that is relative to our everyday lives on many levels!

PROTEIN USING PDB EXPLORER

 

Alcohol Dehydrogenase, or aldehyde reductase, is found in a wide variety of species (even those which don’t consume alcohol!) because the primary purpose of a dehydrogenase enzyme is to utilize a mechanism to convert alcohol into aldehydes or ketones. ADH can not only oxidize ethanol to acetaldehyde (as most college students can relate to) but they can also oxidize secondary, cyclic secondary, or hemi-acetal  alcohols.

                Each of the subunits on ADH has two different domains; an NAD binding domain which is shown in purple and green, and also an alcohol (substrate) binding domain which is shown in blue and yellow. These two subunits with their respective domains makes ADH active as a dimer in humans.

                Another note about structure is that ADH uses two molecules to act as tools and help it perform a reaction on ethanol when ingested. A zinc atom is used to hold and position the alcohol group on ethanol. The other tool utilized is a large NAD cofactor which is the work-horse and actually performs the reaction. The mechanism to describe how this works can be found here:

http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/mech.htm

Works Cited:

Alcohol Dehydrogenase.  20 May, 1999. Retrieved from    http://www.users.csbsju.edu/~hjakubow/classes/rasmolchime/99ch331proj/alcoholdehydro/index.htm. Feb 27, 2011.

Goodsell, D. (2001, December). Alcohol Dehydrogenase. Retrieved from http://www.rcsb.org/pdb/101/motm.do?momID=13

Blog #1

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


Biochemistry is the study of the chemistry of our biological systems, specifically focusing on the enzyme reactions that take place and the chemistry of the protein structures explored. Biochemistry differs from the field of genetics, biology, chemistry, and molecular biology but can also be related to all of these fields of study because of the subject matter that it explores. A more in-depth explanation of the focuses of these studies is as follows.
Genetics: At times, microbiology can be considered a specialization within the field of genetics. The field of genetics deals with anything that has to do with genes and genetic DNA, and can include alteration of genetic material to further investigate or understand specific genes.
Biology: Biology is a field which deals with the study of life and living organisms, including their structure, function, growth and development, evolution, and distribution. This field of study is closely related to biochemistry but explores a wider realm of organisms within specific systems in both plants and animals.
Microbiology: Microbiology can be considered a part of the Genetics field because it can be defined similarly to the above definition for Biology but micro implies that the scientists in this field deal with microscopic living organisms.
Chemistry: The field of chemistry involves using chemical experiments and techniques to manipulate certain biological systems. Chemistry can pertain to both inorganic or organic (carbon-containing) compounds and explores their reactions with biological systems. Organic chemistry is indeed its own specific field that focuses on only carbon-containing compounds.