Lesson 2
Types of Molecular Interactions
As we mentioned in the first lesson, understanding molecular interactions is key to understanding how and why different biological processes work. Molecular interactions occur between different molecules (intermolecular) and within a single molecule (intramolecular). Interactions within molecules contribute to the
shape and structure of the molecule. Interactions between molecules largely
dictate the function of the molecule.
The difficulty a lot of the time in studying molecular interactions is that there are many, many different interactions with different strengths occurring at the same time and these interactions also change over time. Not only are we interested in what molecules interact, but how they interact and how strongly - which is dictated by the type of interaction that forms.
Think about the case of membrane proteins (proteins residing in a membrane as pictured below in teal). Q1: Interactions between which molecules do you think we might be interested in understanding? If these interactions that you identified were weak, what might be the consequence? If these interactions that you identified were strong, what might be the consequence?
[1]
You have probably learned about electrostatic or ion-ion interactions - those interactions between a positive and a negative charge. There are three additional general types of molecular interactions not involving fully charged molecules that are also important to understand biological molecules. From strongest to weakest these are hydrogen bonds, dipolar interactions, and dispersion forces.
Watch this video of Dr. McCord from the University of Texas explaining these three types of interactions.
Now that you have been introduced to these types of molecular interactions, read this excellent description of the types of molecular interactions by Dr. Loren Williams, a Professor at Georgia Tech which goes into greater detail.
Read sections A through G1, skipping C1 and F (those focus on interactions in proteins which we will get to in Module 2).
We haven't yet learned about the structure of proteins, but as an introduction, proteins are made up of molecules called amino acids which each have the same backbone structure and unique "side chain" structures (see figure below - the backbone atoms are toward the top and the side chain toward the bottom of each amino acid).
Q2: Using just the information you learned in this lesson and the structures of the amino acids shown below, can you predict amino acid "side chains" that would interact with each other and what types of interactions they would form? Pick at least four pairs including those that correspond to each of the molecular interactions we have covered.
Q3: Which amino acids do you think would rather face water? (First determine what interactions water forms with itself and how the atoms are oriented to form those interactions- are there side chains with those atoms?)
Q4: Can you draw the orientation of water molecules around a lysine NH3+ group?
[2]
Assignment (Q5): Most drugs (such as antibiotics or antidepressants) target proteins. What intermolecular interactions do you think are important in designing drugs to target proteins? Find a journal article abstract by searching in PubMed (see Searching in PubMed) that relates to this topic, and do your best to summarize it for the group in two to three sentences.
An abstract is the first section of a scientific paper. Usually around 250 words, it should introduce why the research was performed (the motivation) and
summarize the main findings of the paper. If the authors did a good job in writing the abstract, the main findings and overall importance of the research should be understood from just reading the abstract. While many scientific papers are accessed through subscriptions (provided by your university), abstracts are freely available. The majority of the time you will read an abstract first to determine if the paper will contain what you are searching for, and determine if you should continue reading the rest of the paper.
There will be words you don't understand and that is ok! (Again, google is your friend). This exercise will give you good practice in literature searching and start giving you practice with reading scientific literature. Remember, each time you read a paper you will learn more and get more out of it!
[1] "File:Cell membrane detailed diagram 3.svg" by derivative work: Dhatfield (talk) Cell_membrane_detailed_diagram.svg: LadyofHats Mariana Ruiz is licensed under CC BY-SA 3.0
[2] "File:Amino Acids002.svg" by Pk0001 is licensed under CC BY-SA 4.0