Chemistry at UW - Parkside

A post from biochemistry student Emily Meyer!

Have you ever wondered how antibodies are made? A method that we have learned so far, in this semester of CHEM 324, is polyclonal antibody production. First, antibodies are Y-shaped proteins, also called immunoglobins, that are composed of heavy and light chains of immunoglobin molecules. They possess an antigen binding site (Fab : see photo below!) and a constant recognition site (Fc). The structure of antibodies is correlated with its function; this is an important point that is made throughout biochemistry. The paratope is the binding site of an antibody that binds to the binding site on the antigen, which is the epitope.

Polyclonal antibody production starts when the unknown antigen is injected into an animal such as a mouse, goat, or bunny. An antibody is produced in B-cells, which are antibody factories that reside in the immune system like in the spleen or lymph nodes. The B-cells of the animal respond to the antigen and make antibodies against it. The blood of these animals is collected, centrifuged to a serum, and purified to isolate the antibodies that respond to the specific antigen (Sanderson et al., 2019). These antibodies may have different specificities, meaning that there is a larger variety of antibodies to bind to different epitopes of the antigen.

Polyclonal antibodies have a wide range of uses for us as well as cons. First, they are used for enhancing antigen quality or purifying antigens in a process called immunoaffinity purification. And most importantly, polyclonal antibodies are used to create recombinant antibodies (made in vitro instead of in animals) to treat cancer cells. The extensive variation of polyclonal antibodies allows for many points of binding to malignant tumor cells and can be a form of cancer therapy. On the other hand, polyclonal antibody production presents some flaws. This includes a limit on how many antibodies can be collected from the animal host based on their lifespan. Also, the binding ability that antibodies have for antigens can be altered over a period of time and generate varying antibody qauntities between each collection (Cheriyedath, 2023).

Sources:
Cheriyedath, S. (2023, July 19). What are polyclonal antibodies (pAbs)?. News-Medical.net. https://www.news-medical.net/life-sciences/Polyclonal-Antibodies.aspx #:~:text=Apart%20from%20these%20applications%2C%20pAbs,cells%20compared%20to%20monoclonal%20antibodies.
Sanderson, T., Wild, G., Cull, A. M., Marston, J., & Zardin, G. (2019). 19 - Immunohistochemical and immunofluorescent techniques. In Bancroft’s theory and practice of histological techniques. (8th ed. pp. 337–394). Elsevier.
Photo:
https://www.facebook.com/biomedmemes/photos/this-is-probably-the-worst-meme-well-make-all-year-and-its-only-one-week-into-ja/391381217972067/

CHEM 215 extra credit from Jenna Nielsen!
Something fun in organic chemistry was how to get a correct IUPAC name for a molecule! To name these molecules you have to follow these steps in order. First, find what type of functional group the molecule is. Step two, find the parent chain and get the number of carbons the longest chain consists of. Third, if there is a branch make sure you name it accordingly to the position. Lastly, take all of the substituents and put them in one word. Here is an example:
The IUPAC name for the following molecule is 2-methylpentane.

CHEM 215 extra credit from Brennan!
Intermolecular forces come in three varieties and include the following, Dipole-Dipole, London Dispersion forces, and Hydrogen Bonding. Intermolecular forces are what bond atoms together forming the basis of our existence. These bonds determine the transition between the three states of matter through the melting, boiling, and freezing points. Dipole-Dipole interactions are bonds that behave like magnets with two poles where opposites attract and likes repulse. In this case, the strength of the bond is proportional to the distance between the molecules. Hydrogen bonds are the strongest of the three and are caused when Hydrogen bonds with an atom with several lone pairs and is highly electronegative. Examples of these include oxygen, nitrogen, and fluorine. In this case, the hydrogen interacts with a lone pair connected to one of the aforementioned molecules. Lastly, LDFs form as a result of the distribution of electrons through the molecules resulting in temporary induced Dipoles that allow for the creation of a bond. LDFs allow for the intermolecular bonding of non-polar molecules. LDFs are responsible for the widely fluctuating physical properties of non-polar molecules across various temperatures and pressures.
Sources
https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/11%3A_Liquids_and_Intermolecular_Forces/11.02%3A_Intermolecular_Forces
Image Sources
chemistrylearner.com/chemical-bonds/hydrogen-bond
chemistrylearner.com/chemical-bonds/london-dispersion-forces
chemistrylearner.com/chemical-bonds/dipole-dipole-forces

CHEM 215 Extra Credit from Jasmine Williams!😊 In our biochemistry lab this semester we talked about many different types of proteins and enzymes, but before we talk about French fries, let’s talk about the things that make fries, potatoes. A potato is made up of 80% water, 15% carbohydrates (carbohydrates play an important role in the human body because they act as an energy source, help control blood glucose and insulin metabolism, participate in cholesterol and triglyceride metabolism, and help with fermentation), and 4% proteins. The primary carbohydrate source in fries is starch, a polysaccharide made up of connected glucose molecules. In order for us to figure out how much fat is infused in fries after the frying process, we tested old French fries to determine the percentage of fat that is contained in each fry. In order to accomplish that we extracted the fat from the French fries using dichloromethane (CH2Cl2) and the isolated fat was tested for unsaturation using a Br2/CH2Cl2 solution. We also tested relative unsaturation levels of some other fats using Br2/CH2Cl2.
https://prezi.com/opd88ng2vsln/the-biochemistry-of-french-fries/

CHEM 215 extra credit!
This first image shows the structure of a phospholipid bilayer, which is the main component of cell membranes. A phospholipid bilayer consists of two layers of phospholipids, which are lipids that have a phosphate group attached to the glycerol backbone instead of one fatty acid. The phosphate group is hydrophilic (water-loving), while the fatty acid tails are hydrophobic (water-fearing). In a phospholipid bilayer, the hydrophilic heads face the aqueous environment on both sides of the membrane, while the hydrophobic tails face each other in the interior of the membrane. This arrangement creates a selective barrier that allows only certain molecules to pass through the membrane.

Lipids are a diverse group of biomolecules that are essential for many structures and functions. They are insoluble in water but soluble in organic solvents. Lipids are found in all living things, and they play a role in many important biological processes, such as: energy storage, cell signaling, membrane formation, hormone production, vitamin absorption, and protection from the environment.

Lipids can be classified into four main groups: triglycerides, phospholipids, steroids, and waxes.

Triglycerides are the most common type of lipid. They are composed of three fatty acids that are linked together by a glycerol molecule. Triglycerides are a major source of energy for the body, and they are also found in cell membranes.

Phospholipids are another important type of lipid. They are composed of two fatty acids, a glycerol molecule, and a phosphate group. Phospholipids are found in cell membranes, and they also play a role in cell signaling.

Steroids are a group of lipids that have a characteristic four-ring structure. Steroids are found in many different parts of the body, including the skin, bones, and liver. They are also important for the production of hormones, such as testosterone and estrogen.

Waxes are a group of lipids that are composed of long chains of fatty acids that are linked together by ester bonds. Waxes are found in the skin, hair, and feathers of animals. They also protect plants from the environment.

Lipids are an essential part of a healthy diet. They provide energy, help to absorb fat-soluble vitamins, and protect organs and tissues. However, it is important to consume the right types of lipids in the right amounts. Too much saturated and trans-fat can increase the risk of heart disease, so it is important to choose unsaturated fats instead.

In organic chemistry lab this semester we made luminol in two steps from 3-nitrophthalic acid. Mix with some strong base, hydrogen peroxide, and a catalyst and viola - brilliant blue chemiluminescence!

CHEM 323 extra credit from LaSadiez West. 😂
The Diels-Alder chemical reaction dealt with a diene and a dienophile conjugating to form an unsaturated six-membered ring.
Ashenhurst, J. (2023, January 17). The diels-alder reaction. Master Organic Chemistry. Retrieved April 27, 2023, from https://www.masterorganicchemistry.com/2017/08/30/the-diels-alder-reaction/